BVBRC_Strains_Metadata.csv

,Genome ID,Genome Name,gram,Organism Name,NCBI Taxon ID,Genome Status,Strain,Serovar,Biovar,Pathovar,MLST,Other Typing,Culture Collection,Type Strain,Completion Date,Publication,BioProject Accession,BioSample Accession,Assembly Accession,SRA Accession,GenBank Accessions,RefSeq Accessions,Sequencing Centers,Sequencing Status,Sequencing Platform,Sequencing Depth,Assembly Method,Chromosomes,Plasmids,Contigs,Genome Length,GC Content,PATRIC CDS,RefSeq CDS,Isolation Source,Isolation Source,Isolation Comments,Collection Date,Isolation Country,Geographic Location,Latitude,Longitude,Altitude,Depth,Other Environmental,Host Name,Host Gender,Host Age,Host Health,Body Sample Site,Body Sample Subsite,Other Clinical,AntiMicrobial Resistance,AntiMicrobial Resistance Evidence,Gram Stain,Cell Shape,Motility,Sporulation,Temperature Range,Optimal Temperature,Salinity,Oxygen Requirement,Habitat,Disease,Comments,Additional Metadata,Coarse Consistency,Fine Consistency,Checkm Completeness,Checkm Contamination,Genome Quality Flags,Genome Quality,Date Inserted,Date Modified
1683,139.96,Borreliella burgdorferi strain B331,negative,,139,Complete,B331,,,,,,,,2017-10-04T00:00:00Z,,PRJNA342676,SAMN05763278,GCA_002442595.1,,"CP017201,CP017202,CP017203,CP017204,CP017205,CP017206,CP017207,CP017208,CP017209,CP017210,CP017211,CP017212",,New York Medical College,,Illumina; PacBio,150x,HGAP assembly v. 3,1,18,19,1410009,28.3,1494,1385,Skin,Skin,,Jul-96,USA,USA:New York,,,,,,"Human, Homo sapiens",,,Lyme disease,,,host_health_state:NY,,,,,,,,,,,,,Whole genome sequencing of clinical isolates of Borrelia burgdorferi,collected_by:NYMC,99.9,99.8,23.1,0.2,Low CheckM completeness score,Poor,2017-11-23T02:51:34.555Z,2017-11-23T02:51:34.555Z
1700,140.36,Borrelia hermsii strain ML1,negative,,140,Complete,ML1,,,,,,,,2021-11-15T00:00:00Z,,PRJNA767670,SAMN21924093,GCA_020865525.1,,CP086371,,University of California Irvine,,Illumina HiSeq,1150.0x,CLC NGS Cell v. 21.04,1,,1,922239,29.824265,858,828,Blood,blood,,2018,USA,"USA:Mono County, CA",,,,,,Homo sapiens,,,tick-borne relapsing fever,,,,,,,,,,,,,,,,Genome sequence of a strain of the relapsing fever agent Borrelia hermsii ML1 from the eastern Sierra Nevada mountains of California,collected_by:Alan Barbour;lab_host:Mus musculus,96.7,96.3,,,,Good,2021-12-24T22:46:37.709Z,2021-12-24T22:46:37.709Z
1717,142.3,Borrelia turicatae strain BTE5EL,negative,,142,Complete,BTE5EL,,,,,,,,2016-05-19T00:00:00Z,,PRJNA318287,SAMN04695901,GCA_003568645.1,,"CP015629,CP015630,CP015631,CP015632,CP015633,CP015634,CP015635,CP015636",,Centers for Disease Control and Prevention,,PacBio,270X,"HGAP3, SMRTAnalysis v. 2.3.0",1,7,8,1305758,29.353218,1284,1185,None,,,2015,USA,USA: Texas,,,,,,"Human, Homo sapiens",,,Tick borne relapsing fever,,,,,,,,,,,,,,,,Chromosome and linear plasmid sequence,,99.7,99.3,30.3,39,High CheckM contamination score;Low CheckM completeness score,Poor,2018-10-03T13:36:11.750Z,2018-10-03T13:36:11.750Z
2019,160.25,Treponema pallidum strain UW-148B2,negative,,160,Complete,UW-148B2,,,,,,,,2019-10-13T00:00:00Z,,PRJNA534087,SAMN11476982,GCA_009017475.1,,CP045004,,University of Washington,,Illumina MiSeq,275.1x,SPAdes v. v3.13.0,1,,1,1139560,52.78594,1030,1015,None,rabbit,,2009,USA,USA: Washington,,,,,,"Human, Homo sapiens",,,syphilis,,,,,,,,,,,,,,,,WGS of two Treponema pallidum isolates from a single patient,collected_by:Christina Marra,,,,,,Good,2019-10-27T23:57:23.050Z,2019-10-27T23:57:23.050Z
2079,161.9,Treponema pallidum subsp. pallidum strain SMUTp_09,negative,,161,Complete,SMUTp_09,,,,,,,,2020-11-05T00:00:00Z,,PRJNA562373,SAMN12638761,GCA_015239395.1,,CP051889,,Southern Medical University,,Illumina MiSeq,641.0x,Bwa-men v. 0.7.15-r1140,1,,1,1139569,52.54348,1074,,Skin,Chancre,,11-Apr-18,China,China: Guangzhou,,,,,,"Human, Homo sapiens",,,Syphilis,,,,,,,,,,,,,,,,"Treponema pallidum subsp. pallidum (TPA) is the infectious agent of syphilis. This study presents six TPA genomes of Chinese isolates, four of them obtained directly from the clinical material (strain SMUTp_04, SMUTp_07, SMUTp_08, and SMUTp_09) and two obtained from a multiplication in rabbits(strain SMUTp_01 and SMUTp_02).",collected_by:Dermatology hospital of Southern Medical University,94.8,94.5,,,,Good,2020-11-30T12:59:45.073Z,2020-11-30T12:59:45.073Z
2168,168.12,Treponema pallidum subsp. pertenue strain CDC-1,negative,,168,Complete,CDC-1,,,,,,,,2018-12-18T00:00:00Z,,PRJNA416916,SAMN07967415,GCA_003952805.1,,CP024750,,"Masaryk University, Faculty of Medicine",,Illumina MiSeq,460.0x,IDBA_UD v. 1.1.1,1,,1,1139578,52.785446,1036,1064,Wound,papillomatous lesion,isolated from a 5-year old patient with yaws infection in Ghana in 1980,Nov-80,Ghana,Ghana: Densuso,,,,,,"Human, Homo sapiens",male,5 years,yaws,,,host_disease_outcome:yaws,,,,,,,,,,,,,Complete genome sequencing of Treponema pallidum subsp. pertenue strain CDC-1. Strain CDC-1 was isolated from a 5-year old patient with yaws infection in Ghana in 1980.,,99.6,99.5,,,,Good,2019-01-31T15:52:47.267Z,2019-01-31T15:52:47.267Z
2184,173.21,Leptospira interrogans strain FMAS_AW1,negative,,173,Complete,FMAS_AW1,,,,,,,,2019-05-07T00:00:00Z,,PRJNA528695,SAMN11289421,GCA_005222625.1,,"CP039283,CP039284,CP039285,CP039286",,Rajarata University of Sri lanka,,PacBio RSII,30x,Canu 1.8 v. 1.0,2,2,4,5071735,35.18082,5290,4491,Blood,blood,,6/22/17,Sri Lanka,Sri Lanka: Awissawella,,,,,,"Human, Homo sapiens",female,38 yrs,Leptospirosis,,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",99.6,98.8,,,,Good,2019-07-13T18:40:47.488Z,2019-07-13T18:40:47.488Z
2191,174.8,Leptospira borgpetersenii strain FMAS_AP4,negative,,174,Complete,FMAS_AP4,,,,MLST.Leptospira_spp_3.132,,,,2021-05-18T00:00:00Z,,PRJNA528695,SAMN11919586,GCA_018403825.1,,"CP072626,CP072627",,Rajarata University of Sri lanka,,PacBio Sequel System,1229x,Canu v. 2.1,2,,2,3916982,40.090992,4181,3325,Blood,blood,,12/19/17,Sri Lanka,Sri Lanka:Anuradhapura,,,,,,Homo sapiens,male,21 yrs,Leptospirosis,,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",99.8,99.6,,,,Good,2021-06-03T03:57:41.656Z,2021-06-03T03:57:41.656Z
2697,195.3313,Campylobacter coli strain R19.1157,negative,,195,Complete,R19.1157,,,,,,,,2021-06-15T00:00:00Z,,PRJNA637789,SAMN15156991,GCA_018885245.1,,CP076513,,"Centers for Disease Control, Taiwan",,Illumina MiSeq; Oxford Nanopore,100x,unicycler v. v0.4.8,1,,1,1811840,31.349678,1926,1863,Stool,stool,,2019,Taiwan,Taiwan,,,,,,Homo sapiens,,,not collected,,,,,,,,,,,,,,,,"Whole genome sequence data uploaded by Centers for Disease Control, Taiwan",collected_by:Taiwan CDC,100,99.9,,,,Good,2021-06-26T05:51:35.753Z,2021-06-26T05:51:35.753Z
2839,199.901,Campylobacter concisus strain P2CDO4,negative,,199,Complete,P2CDO4,,,,,,,,2018-04-18T00:00:00Z,29636463,PRJNA388128,SAMN07160232,GCA_003048375.1,,"CP021642,CP021643",,University of New South Wales,,PacBio,41.6x,Canu v. 1.3,1,1,2,2095236,39.234722,2099,2077,Mouth,Oral,isolated from patients with IBD and healthy controls,2-Jan-09,Australia,Australia,,,,,,"Human, Homo sapiens",,,Crohn's disease,,,,,,,,,,,,,,,,"This project examined the genomes of C. concisus strains isolated from patients with IBD and healthy controls. We found a secreted superantigen homologue, the Csep1 protein, which was encoded by C. concisus chromosome and a novel plasmid pICON. The prevalence of Csep1 proteins and their polymorphisms were shown to be associated with active IBD. Additionally, the novel plasmid pICON was only found in C. concisus strains isolated from relapsed CD patients with previous ileocecal resection.",collected_by:University of New South Wales,96.5,95.7,100,,,Good,2018-05-30T20:57:48.645Z,2018-05-30T20:57:48.645Z
2858,203.1,Campylobacter rectus strain ATCC 33238,negative,,203,Complete,ATCC 33238,,,,,,,,2020-04-23T00:00:00Z,,PRJNA284987,SAMN03737987,GCA_004803795.1,,CP012543,,"USDA, ARS, WRRC",,Sanger dideoxy sequencing; 454; Illumina;,814x,Newbler v. 2.6,1,,1,2571679,44.719734,3081,2276,Mouth,oral,,1974,USA,USA: Boston,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,This genome is part of a larger study to sequence the genomes of all validly-described taxa within the genus Campylobacter,sample_type:cell culture,97,96.5,,,,Good,2020-06-03T10:59:10.731Z,2020-06-03T10:59:10.731Z
3085,210.8698,Helicobacter pylori strain 3192,negative,,210,Complete,3192,,,,,,,,2021-11-21T00:00:00Z,,PRJNA773563,SAMN22488069,GCA_020906585.1,,CP086760,,Shanghai Jiao Tong University,,Illumina; Oxford Nanopore,604.0x,Unicycle v. v0.4.9,1,,1,1637585,38.718845,1627,1521,None,,,1/1/20,,China,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Helicobacter pylori 3192,sample_type:human,99.9,99.6,,,,Good,2021-12-24T23:35:20.610Z,2021-12-24T23:35:20.610Z
3138,213.62,Helicobacter cinaedi strain 2017D-0197,negative,,213,Complete,2017D-0197,,,,MLST.Helicobacter_cinaedi.4,,,,2020-10-26T00:00:00Z,,PRJNA239251,SAMN15354330,GCA_014931155.1,,CP063086,,Centers for Disease Control and Prevention,,PacBio,231.939x,HGAP v. 3,1,,1,2218389,38.32768,2392,2227,Blood,blood,,24-Sep-17,USA,USA: GA,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Campylobacter genome sequencing,sample_type:isolate,99.3,98,,,,Good,2021-01-01T15:36:05.912Z,2021-01-01T15:36:05.912Z
3210,263.91,Francisella tularensis strain T01,negative,,263,Complete,T01,,,,,,,,2015-10-26T00:00:00Z,,PRJNA288396,SAMN03799293,GCF_001412545.1,,CP012092,,Beijing Institute of Microbiology and Epidemiology,,Illumina,150.0x,Velvet v. 1.1,,,1,1899676,31.97,2174,1663,None,clinical,,1/1/52,China,China:Tibet,,,,,,"Human, Homo sapiens",,,tularemia,,,,,,,,,,,C,,,,,To study the origin and radiation of type B tularemia in Tibet China,collected_by:Lihua Song,99.6,97.6,100,4,,Good,2016-01-17T17:39:31.131Z,2016-01-17T17:39:31.131Z
3212,264.27,Francisella tularensis subsp. novicida strain TCH2015,negative,,264,Complete,TCH2015,,,,,,,,2018-02-12T00:00:00Z,,PRJNA378245,SAMN06481648,GCA_002952075.1,,CP021490,,BCM,,PacBio,260.51x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,2000087,32.354744,1932,1879,Lymph Node,patient believed to have been infected in Guatemala,isolated from the lymph node of a 6-year-old boy from Guatemala and isolated in Texas,15-Dec,USA,"USA: Houston, TX",,,,,env_biome:lymph node,"Human, Homo sapiens",,6 years,,,,,,,,,,,,,,,,,"TCH2015 was isolated from the lymph node of a 6-year-old boy from Guatemala and isolated in Texas. Source of infection is unknown, but may potentially have ben acquired from contaminated ocean, canal, or shower water.",,99.6,98.8,100,0.8,,Good,2018-05-26T01:56:02.854Z,2018-05-26T01:56:02.854Z
3767,287.9884,Pseudomonas aeruginosa strain GIMC5002:PAT-169,negative,,287,Complete,GIMC5002:PAT-169,,,,MLST.Pseudomonas_aeruginosa.235,genotype:ST235,,,2019-09-11T00:00:00Z,,PRJNA562821,SAMN12651335,GCA_008370085.1,,"CP043549,CP043548",,N.F.Gamaleya National Research Center for Epidemiology and Microbiology,,454; Illumina,69,CLC Genomics Workbench v. 12.0,1,1,2,6499077,65.90276,6185,6128,Urine,urina,,9-Dec,Russia,Russia: Moscow,,,,,,"Human, Homo sapiens",,,no data,,,,Resistant,Computational Prediction,,,,,,,,,,,Nosocomial Pseudomonas aeruginosa stain,collected_by:Gabrielyan N.I.,99.3,97.9,,,,Good,2019-10-02T06:41:07.056Z,2019-10-02T06:41:07.056Z
3785,292.297,Burkholderia cepacia strain 39628,negative,,292,Complete,39628,,,,,,,,2020-10-06T00:00:00Z,,PRJNA438725,SAMN08724754,GCA_014854795.1,,"CP032009,CP032011,CP032010",,"University of Nevada, Reno",,PacBio,16.04X,"SMRT v. 2.3.0, HGAP v. 3",3,,3,8403907,66.80368,8278,8437,Sputum,sputum,,8-Apr-14,Laos,Laos,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Identification of Burkholderia cepacia strains expressing a unique capsular polysaccharide antigen.,sample_type:bactera,99.4,93.9,,,,Good,2020-11-29T05:30:03.775Z,2020-11-29T05:30:03.775Z
3800,294.494,Pseudomonas fluorescens strain NCTC9428,negative,,294,Complete,NCTC9428,not available: to be reported later,,,,,NCTC:9428,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA3881054,GCA_900636825.1,,LR134318,,SC,,,,,1,,1,6033966,58.964104,5636,5345,None,not available: to be reported later,,1900/1954,United Kingdom,United Kingdom: London,,,,,,"Human, Homo sapiens",,,,,,host_health_state:not available: to be reported later,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.4,97.4,,,,Good,2019-02-01T13:48:01.728Z,2019-02-01T13:48:01.728Z
3913,303.754,Pseudomonas putida strain SWMUB4,negative,,303,Complete,SWMUB4,,,,,,,,2020-11-02T00:00:00Z,,PRJNA668445,SAMN16409504,GCA_015168335.1,,"CP063456,CP063457",,Southwest Medical University,,Oxford Nanopore,150.0x,Canu v. 1.5,1,1,2,6024098,62.51077,5627,,None,,,10/25/18,China,"China: No. 319, Zhongshan Road, Luzhou, Sichuan",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Genome sequence of Pseudomonas putida SWMUB4,sample_type:whole organism,98.7,96.8,,,,Good,2020-11-30T02:19:25.976Z,2020-11-30T02:19:25.976Z
3919,316.574,Pseudomonas stutzeri strain ZDHY95,negative,,316,Complete,ZDHY95,,,,,,,,2020-11-24T00:00:00Z,,PRJNA669156,SAMN16439930,GCA_015680045.1,,"CP063358,CP063359",,The First Affiliated Hospital of Zhengzhou University,,Oxford Nanopore; Illumina NovaSeq,200.0x,Unicycler v. v0.4.7; SPAdes v. v3.9.1,1,1,2,4588580,63.95532,4363,4261,Cerebrospinal Fluid,cerebrospinal fluid,,20-Apr-19,China,China:Henan,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Pseudomonas stutzeri with plasmid co-producing blaVIM-2 and blaCARB-4,sample_type:Cerebrospinal fluid,98.6,96,,,,Good,2021-01-01T16:58:10.235Z,2021-01-01T16:58:10.235Z
4214,446.995,Legionella pneumophila strain 80-045,negative,,446,Complete,80-045,,,,,,,,2021-08-13T00:00:00Z,,PRJDB12006,SAMD00393827,GCA_019974095.1,,AP024961,,"Department of Bacteriology I, National Institute of Infectious Diseases",,Illumina MiSeq; ONT MinION,91x,Unicycler v. 0.4.8,1,,1,3438257,38.24708,3216,2994,Lung,lung,,1980,,Japan,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Whole-genome sequencing of Legionella pneumophila strain 80-045 that caused the first case of Legionnaires' disease in Japan,,99.8,99.3,,,,Good,2021-11-30T03:52:09.963Z,2021-11-30T03:52:09.963Z
4219,450.9,Legionella longbeachae strain B41211CHC,negative,,450,Complete,B41211CHC,1,,,,,,,2020-03-19T00:00:00Z,,PRJNA577762,SAMN13042258,GCA_011465395.1,,"CP045308,CP045307",,Canterbury Health Laboratories,,Oxford Nanopore GridION; Illumina MiSeq,250.0x,Flye v. 2.4.2; Unicycler v. 0.4.7,1,1,2,4077247,37.14406,3827,3469,Sputum,Sputum sample,"derived from patients hospitalized with LD in Christchurch, New Zealand",19-Sep-09,New Zealand,New Zealand: Christchurch,,,,,,"Human, Homo sapiens",,,Pneumonia,,,,,,,,,,,,,,,,"Legionella longbeachae serogroup 1, predominantly found in soil and composted plant material, causes the majority of cases of Legionnaires’ disease (LD) in New Zealand. The goal of this study is to produce complete genome sequence of L. longbeachae serogroup 1 isolates derived from patients hospitalized with LD in Christchurch, New Zealand.",collected_by:Cantebury Health Laboratories,96.6,94.3,,,,Good,2020-03-27T23:09:55.563Z,2020-03-27T23:09:55.563Z
4222,451.12,Tatlockia micdadei strain NZ2016,negative,,451,Complete,NZ2016,,,,,,,,2017-04-11T00:00:00Z,,PRJNA380664,SAMN06645976,,,CP020615,,University of Canterbury,,PacBio RS II,225x,Canu v. 1.3,1,,1,3250164,40.51,3079,2840,None,,,2016,New Zealand,New Zealand: Waikato,,,,,env_biome:not applicable,"Human, Homo sapiens",female,55,,,,,,,,,,,,,,,,,"Legionella is a large, highly diverse genus of pathogenic bacteria that globally infect amoeba and human macrophages, where they cause a severe form of pneumonia known as Legionnaire’s disease. While Legionella pneumophila and Legionella longbeachae species are responsible for the majority of these cases, some have been attributed to the relatively unstudied Legionella micdadei. The full genomes of two clinical isolates of L. micdadei from New Zealand's north and south islands were sequenced in order to explore their pathogenicity and the genomic diversity of the Legionella genus.",,97,93.9,100,6,,Good,2017-05-28T13:12:46.832Z,2017-05-28T13:12:46.832Z
4526,470.9821,Acinetobacter baumannii strain AbCAN2,negative,,470,Complete,AbCAN2,,,,,,,,2020-01-07T00:00:00Z,,PRJNA575861,SAMN12912378,GCA_009833005.1,,CP045428,,Washington University School of Medicine,,PacBio,311.0x,HGAP v. 2016-02-25,1,,1,3809822,39.038544,3729,3559,Tailbone,Coccygeal isolate,,2015,Canada,Canada: Edmonton,,,,,,"Human, Homo sapiens",,,Infection,,,,Susceptible,Computational Prediction,,,,,,,,,,,Genome annotation of Acinetobacter baumannii pathogenic isolate,collected_by:University of Alberta Hospital,96.9,95.4,,,,Good,2020-02-01T00:28:50.782Z,2020-02-01T00:28:50.782Z
4550,480.345,Moraxella catarrhalis strain 5P47B2,negative,,480,Complete,5P47B2,,,,MLST.Moraxella_catarrhalis.544,,,,2018-12-26T00:00:00Z,,PRJNA509208,SAMN10536188,GCA_003971365.1,,CP034666,,"Institute for Genome Sciences, University of Maryland, Baltimore",,PacBio Sequel,29x,canu v. 1.4,1,,1,1933669,41.50043,1989,2002,Sputum,sputum,,7-Jan-99,USA,"USA: Buffalo, NY",,,,,,"Human, Homo sapiens",,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,,,"Moraxella catarrhalis persists in COPD with profound clinical and pathogenetic consequences. Most strains express the major surface antigen Hag/MID on acquisition and then shut off expression, suggesting that Hag/MID is critical for initial colonization and cessation of expression facilitates persistence. Genomes sequences are used to analyze changes in DNA associated with adhesin expression.","collected_by:Univerty at Buffalo, T. Murphy",99.6,99,,,,Good,2019-01-31T19:43:47.675Z,2019-01-31T19:43:47.675Z
4571,483.52,Neisseria cinerea strain FDAARGOS_871 strain Not applicable,negative,,483,Complete,Not applicable,,,,MLST.Neisseria_spp.9338,,DSM:4630,,2020-12-14T00:00:00Z,,PRJNA231221,SAMN13450401,GCA_016028715.1,,CP065726,,US Food and Drug Administration,,Pacbio; Illumina,2111x,"SMRT v. 6.0.0, HGAP v. 4",1,,1,1832901,50.902096,1929,1749,None,,,,,,,,,,,,,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:DSMZ,99.5,99.3,,,,Good,2021-01-01T19:32:35.039Z,2021-01-01T19:32:35.039Z
4627,485.9947,Neisseria gonorrhoeae strain CT213,negative,,485,Complete,CT213,,,,,,,,2021-07-28T00:00:00Z,,PRJNA607374,SAMN14131123,GCA_019380275.1,,"CP048929,CP048930,CP048931,CP048932",,"Faculty of Medicine Siriraj Hospital, Mahidol University",,Illumina NovaSeq and Oxford Nanopore,1566.400443x,Unicycler v. 0.4.4,1,3,4,2219615,52.50523,2680,2226,Urine,urethra,,1/15/10,Thailand,Thailand: Bangkok,,,,,,Homo sapiens,,15,gonorrhea,,,,,,,,,,,,,,,,To explore the genomic dynamics of co-evolution between Neisseria gonorrhoeae and Schaalia turicensis,collected_by:Natakorn Nokchan,99.3,98.6,,,,Good,2021-08-26T12:45:48.174Z,2021-08-26T12:45:48.174Z
4630,486.36,Neisseria lactamica strain Y92-1009,negative,,486,Complete,Y92-1009,,,,,,,,2017-03-07T00:00:00Z,,PRJNA331097,SAMN05437355,GCF_002022745.1,,CP019894,NZ_CP019894.1,University of Southampton,,PacBio; Illumina HiSeq,300.0x,Celera Assembler v. 2015-APR,1,,1,2146723,52.34,2412,,Respiratory,Nasopharynx,isolated during the course of a carriage study from the nasopharynx of a young child in Ireland in 1992,11-Oct,United Kingdom,United Kingdom: Sheffield,,,,,env_biome:Human Body,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"We present the high quality draft assembly of a sample of N.lactamica Y92-1009 (accession number) cell bank purified stock used to artificially induce nasopharyngeal carriage in humans. This gram negative, dipplococcoid bacterium is an organism of worldwide clinical interest due to its observed inverse carriage relationship with the meningococcus, principle agent of bacterial meningitis, in young children. The organism was originally isolated during the course of a carriage study from the nasopharynx of a young child in Ireland in 1992. This SMRT cell sequenced draft assembly consists of a single contig corrected using reads sequenced on Illumina Miseq 2000 of the same isolate.",,99.5,99.3,100,,,Good,2017-03-20T08:59:58.380Z,2017-03-20T08:59:58.380Z
4741,487.517,Neisseria meningitidis strain NMA510612,negative,,487,Complete,NMA510612,,,,,,,,2014-05-21T00:00:00Z,24812217,PRJNA239655,SAMN02709031,GCF_000626595.1,,CP007524,NZ_CP007524.1,"Institute of Pathogen Biology, CAMS",,Sanger dideoxy sequencing; 454,,Newbler v. 2.6,1,,1,2188020,51.83,2494,2461,Throat,throat swab,,30-Apr-06,China,China,,,,,,"Human, Homo sapiens",,,bacterial meningitis,,,,,,Negative,Cocci,,,,,,,,,to understand the genetic background of serogroup A neisseria meningitidis isolate,"isolate:patient;collected_by:Xu, Li",99.6,99.3,100,,,Good,2016-01-17T15:34:50.647Z,2016-01-17T15:34:50.647Z
4744,488.146,Neisseria mucosa strain FDAARGOS_758 strain Not applicable,negative,,488,Complete,Not applicable,,,,MLST.Neisseria_spp.10149,,FDA:FDAARGOS_758,,2020-06-04T00:00:00Z,,PRJNA231221,SAMN11056473,GCA_013267835.1,,CP053939,,US Food and Drug Administration,,Pacbio; Illumina,1389.17x,"SMRT v. 2.3.0, HGAP v. 3",1,,1,2224757,49.657288,2223,2044,Sputum,expectorated sputum,,,USA,USA:VA,,,,,,"Human, Homo sapiens",male,31Y,Cystic fibrosis,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","collected_by:BEI Resources, American Type and Culture Collection (ATCC)",97.7,96.5,,,,Good,2020-07-01T03:54:07.580Z,2020-07-01T03:54:07.580Z
4753,490.6,Neisseria sicca strain FDAARGOS_260,negative,,490,Complete,FDAARGOS_260,,,,,,FDA:FDAARGOS_260,,2017-03-29T00:00:00Z,,PRJNA231221,SAMN04875586,,,CP020452,,US Food and Drug Administration,,PacBio,16.04441661x,HGAP v. 3,1,,1,2783913,50.95,3074,2678,Blood,Blood,,15-Sep-14,USA,USA:DC,,,,,,"Human, Homo sapiens",male,42Y,Infection with Neisseria sicca,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:George Washington University,99.2,98.4,100,1.3,,Good,2017-05-28T05:26:23.396Z,2017-05-28T05:26:23.396Z
4758,495.31,Neisseria elongata strain M15910,negative,,495,Complete,M15910,,,,,,,,2018-08-01T00:00:00Z,,PRJNA428178,SAMN09704972,GCA_003351685.1,,CP031255,,Centers for Disease Control and Prevention,,PacBio,63.36362252x,HGAP v. 3,1,,1,2534634,53.913544,2854,,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Assemblies for pathogens that are known to cause bacterial meningitis and other closely related species,collected_by:Centers for Disease Control and Prevention,97.7,97,98,3.6,,Good,2018-09-30T04:05:46.387Z,2018-09-30T04:05:46.387Z
4763,504.11,Kingella kingae strain KWG1,negative,,504,Complete,KWG1,,,,MLST.Kingella_kingae.41,,,,2015-11-10T00:00:00Z,,PRJEB9502,SAMEA3477627,GCF_001458475.1,,LN869922,,"INSERM, IAME, UMR 1137",,,,,1,,1,2140065,46.48,2464,2251,Throat,oropharynx,isolated in continental Europe whose blaTEM-1 gene was found to be chromosomically inserted for the first time in this species,2013,France,France,,,,,,"Human, Homo sapiens",,,,,,host_health_state:arthritis,,,,,,,,,,,,,We describe the genome of the first penicillinase-producing Kingella kingae strain (KWG1) isolated in continental Europe whose blaTEM-1 gene was found to be chromosomically inserted for the first time in this species.;genome length too large,,97.9,96.8,99.2,,,Good,2016-01-30T15:09:42.543Z,2016-01-30T15:09:42.543Z
4779,518.9,Bordetella bronchiseptica strain FDAARGOS_693,negative,,518,Complete,FDAARGOS_693,,,,,,FDA:FDAARGOS_693,,2020-04-12T00:00:00Z,,PRJNA231221,SAMN11056408,GCA_012273255.1,,CP050967,,US Food and Drug Administration,,Pacbio; Illumina,493.26x,canu v. 1.4,1,,1,5094150,68.322235,4808,4719,None,clinical isolate,,,USA,USA:MN,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Mayo Clinic,98.2,97.5,,,,Good,2020-04-26T14:32:49.347Z,2020-04-26T14:32:49.347Z
4861,519.98,Bordetella parapertussis strain CIDM-BPP2,negative,,519,Complete,CIDM-BPP2,,,,MLST.Bordetella_spp.19,,,,2021-03-16T00:00:00Z,,PRJNA695314,SAMN18200433,GCA_017357185.1,,CP071602,,Centre for Infectious Diseases and Microbiology - Public Health,,Oxford Nanopore; Illumina,72x,Flye v. 2.7b; Racon v. 1.3.1; Medaka v.,1,,1,4775256,68.101814,4614,4418,Respiratory,respiratory,,1993,Australia,Australia,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Genomic evaluation of Bordetella spp. originating from Australia,collected_by:Centre for Infectious Diseases and Microbiology - Public Health,99.8,99.5,,,,Good,2021-03-28T02:05:14.917Z,2021-03-28T02:05:14.917Z
5404,520.999,Bordetella pertussis strain J185,negative,,520,Complete,J185,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,SAMN08136991,GCA_004007095.1,,CP025343,,Centers for Disease Control and Prevention,,PacBio RSII; Illumina HiSeq,344x,HGAP v. 3,1,,1,4106374,67.70654,4098,3925,Respiratory,,,2013,USA,USA: IN,,,,,,"Human, Homo sapiens",,,pertussis,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,99.5,98.5,,,,Good,2019-02-01T04:49:35.483Z,2019-02-01T04:49:35.483Z
5421,536.61,Chromobacterium violaceum strain FDAARGOS_635 strain Not applicable,negative,,536,Complete,Not applicable,,,,,,FDA:FDAARGOS_635,,2020-04-12T00:00:00Z,,PRJNA231221,SAMN11056350,GCA_012273555.1,,"CP050992,CP050991",,US Food and Drug Administration,,Pacbio; Illumina,753.81x,canu v. 1.4,1,1,2,4800763,65.04681,4615,4407,None,clinical isolate,,,USA,USA: KY,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:University of Louisville,97.3,96.6,,,,Good,2020-04-26T14:36:19.314Z,2020-04-26T14:36:19.314Z
5431,545.68,Citrobacter koseri strain FDAARGOS_530 strain Not applicable,negative,,545,Complete,Not applicable,,,,,,FDA:FDAARGOS_530,,2018-11-21T00:00:00Z,,PRJNA231221,SAMN10163225,GCA_003812405.1,,CP033780,,US Food and Drug Administration,,Pacbio; Illumina,26.80x,CA v. 8.2,1,,1,4581001,53.865215,4421,4281,Respiratory,Endotracheal aspirate,,4/1/16,,,,,,,,"Human, Homo sapiens",female,8Y,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,99.9,99.3,,,,Good,2018-11-30T03:11:59.553Z,2018-11-30T03:11:59.553Z
5476,546.94,Citrobacter freundii strain P10159,negative,,546,Complete,P10159,,biovar r,,MLST.Citrobacter_freundii.252,,,,2015-09-11T00:00:00Z,,PRJNA293024,SAMN03996567,GCA_001281005.1,,CP012554,NZ_CP012554.1,Beijing Institute of Microbiology and Epidemiology,,IonTorrent,112X,Newbler v. v2.9,1,,1,5080321,51.68,5024,4768,Urine,Patient urine,"isolated from urine sample of a patient with esophageal carcinoma in China on August, 2013",13-Aug,China,China,,,,,,"Human, Homo sapiens",,,esophageal carcinoma,,,,,,,,,,,C,,,,,"Citrobacter freundii strain P10159 was isolated from urine sample of a patient with esophageal carcinoma in China on August, 2013. Base on the 16S rRNA gene sequencing, VITEK 2 (BioM�rieux) and Bruker MALDI Biotyper analysis, the strain P10159 was was identified as Citrobacter freundii.",sample_type:cell,99.4,98.3,99.1,0.3,,Good,2016-01-17T17:06:05.190Z,2016-01-17T17:06:05.190Z
5483,548.624,Klebsiella aerogenes strain KA_P10_L5_03.19,negative,,548,Complete,KA_P10_L5_03.19,,,,,,,,2019-09-29T00:00:00Z,,PRJNA562727,SAMN12807522,GCA_008727695.1,,"CP044214,CP044215,CP044216",,Public Health England,,Oxford Nanopore MiniION; Illumina HiSeq,160.0x,miniasm v. 0.2 r168 dirty; Racon x 3 v.,1,2,3,5398116,54.651863,5397,5171,Stool,rectal swab,,19-Mar,United Kingdom,United Kingdom:London,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"This study examined the genetic environment of IMP carbapenemase genes among bacterial isolates from four London hospitals and a Welsh hospital. IMP carbapenemase genes, which hydrolyse carbapenem antibiotics, are relatively rare in the UK. However, in some hospitals they are problematic and are generally found in multiple strains and species, suggesting that they are present on mobile genetic element(s). This study examined isolates of Klebsiella pneumoniae, Klebsiella quasipneumoniae, Enterobacter cloacae complex, Klebsiella aerogenes and Citrobacter freundii in order to better understand the epidemiology of IMP positive isolates in relevant hospitals and to inform interventions to prevent further spread.",sample_type:pure culture;collected_by:London hospital,99.9,97.3,,,,Good,2019-10-27T17:10:18.163Z,2019-10-27T17:10:18.163Z
5484,549.24,Pantoea agglomerans strain FDAARGOS_160,negative,,549,Complete,FDAARGOS_160,,,,,,FDA:FDAARGOS_160,,2016-02-11T00:00:00Z,,PRJNA231221,SAMN03996307,GCF_001558735.1,"SRR2822440,SRR2822441,SRR2822442","CP014129,CP014126,CP014127,CP014128","NZ_CP014129.1,NZ_CP014126.1,NZ_CP014127.1,NZ_CP014128.1",US Food and Drug Administration,,Pacbio,24.205x,HGAP3 v. Oct 2014,1,3,4,4808813,55.06,4761,4393,Wound,Wound swab,,5/23/14,USA,USA:DC,,,,,,"Human, Homo sapiens",male,5Y,Foreign Body,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:Children's National Hospital,99.6,97.4,100,,,Good,2016-03-01T20:48:05.614Z,2016-03-01T20:48:05.614Z
5528,550.642,Enterobacter cloacae strain colR/S,negative,,550,Complete,colR/S,,,,MLST.Enterobacter_cloacae.252,,,,2016-04-15T00:00:00Z,24982068,PRJNA263343,SAMN03099688,GCA_001620245.1,,"CP010512,CP010513",,Emory University,,PacBio,50.0x,Celera Assembler v. wgs-8.1,,1,2,4852104,55.55,5001,4082,Respiratory,bronchoalveolar lavage from kidney transplant patient,,2013,USA,USA: Georgia: Atlanta,,,,,,"Human, Homo sapiens",,,kidney transplant,,,,,,,,,,,,,,,,Whole genome sequence of a nosocomial pathogen isolated from the bronchoalveolar lavage of a kidney transplant patient,collected_by:Emory University,99,94.5,99.7,7.3,,Good,2016-04-28T11:47:14.879Z,2016-04-28T11:47:14.879Z
6277,562.9316,Escherichia coli strain ZH063,negative,,562,Complete,ZH063,,,,MLST.Escherichia_coli_1.131,,,,2016-02-29T00:00:00Z,,PRJNA307507,SAMN04381853,GCF_001577325.1,,"CP014522,CP014523,CP014524","NZ_CP014522.1,NZ_CP014523.1,NZ_CP014524.1",University of Minnesota,,PacBio,100x,HGAP v. 3,1,2,3,5197049,50.73,5326,5104,None,,,2002,Canada,Canada: Winnipeg,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,Comparative sequencing of ExPEC ST131,,99.8,98,100,0.4,,Good,2016-03-18T09:16:10.778Z,2016-03-18T09:16:10.778Z
6280,564.45,Escherichia fergusonii strain ATCC 35471,negative,,564,Complete,ATCC 35471,,,,MLST.Escherichia_coli_1.4419,,ATCC: 35471,,2019-08-22T00:00:00Z,,PRJNA218110,SAMN01916802,GCA_008064895.1,,"CP042945,CP042943,CP042944",,CDC,,PacBio,123.44X,HGAP v. 3,1,2,3,4755297,49.945988,4688,,Stool,feces,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,99,97.9,,,,Good,2019-10-01T22:00:02.529Z,2019-10-01T22:00:02.529Z
6285,569.68,Hafnia alvei strain CBA7135,negative,,569,Complete,CBA7135,,,,,,,,2018-06-18T00:00:00Z,,PRJNA390219,SAMN07206916,GCA_003253795.1,,CP021971,,Korea Food Research Institute,,PacBio,135.0x,HGAP v. 3.0,1,,1,4498956,48.888386,4161,3980,Stool,adult feces,,11/17/16,South Korea,South Korea: Bundang,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,CBA7135 strain was isolated from Korean adult feces,sample_type:cell culture,98.9,97.3,99,,,Good,2018-07-16T07:56:18.291Z,2018-07-16T07:56:18.291Z
6318,571.99,Klebsiella oxytoca strain KoPF10,negative,,571,Complete,KoPF10,,,,MLST.Klebsiella_oxytoca.48,,,,2021-04-15T00:00:00Z,,PRJNA683049,SAMN18675296,GCA_017968865.1,,CP072914,,University of Texas at Dallas,,Illumina NextSeq; Oxford Nanopore MinION,323.5x,Unicycler v. 0.4.8,1,,1,5822988,55.015312,5656,5346,Urine,urine,,2018-05,USA,"USA: Dallas, Texas",,,,,,Homo sapiens,female,,Chronic Cystitis,,,host_description:Postmenopausal,,,,,,,,,,,,,"Recurrent Urinary Tract Infection (rUTI) poses a major health issue, especially among postmenopausal women. Klebsiella spp. account for ~15%-17% of rUTIs, with Klebsiella pneumoniae being the most prevalent. We report the complete genome sequences of six Klebsiella spp. isolates acquired from the urine of postmenopausal women diagnosed with rUTI.",collected_by:UT Southwestern Medical Center/ UT Dallas,99.2,97.1,,,,Good,2021-04-25T19:45:41.029Z,2021-04-25T19:45:41.029Z
6998,573.9779,Klebsiella pneumoniae strain kp757,negative,,573,Complete,kp757,,,,MLST.Klebsiella_pneumoniae.86,,,,2017-05-02T00:00:00Z,,PRJNA317547,SAMN04621179,,,CP015120,,USAMRIID,,PacBio,215,HGAP v. 2.3,1,,1,5264852,57.56,5174,5106,None,,,2015,USA,United States,,,,,,"Human, Homo sapiens",,,pneumonia,,,,,,,,,,,,,,,,Genomic investigation of drug-resistant isolates of Klebsiella pneumoniae,collected_by:USAMRIID,99.6,98.4,100,0.7,,Good,2017-05-29T10:10:56.599Z,2017-05-29T10:10:56.599Z
7023,582.609,Morganella morganii strain CTX51T,negative,,582,Complete,CTX51T,,,,,,,,2021-11-22T00:00:00Z,,PRJNA549513,SAMN19659029,GCA_020911745.1,,"CP076623,CP076624",,Fred Hutchinson Cancer Research Institute,,PacBio Sequel,110x,Microbial assembly v. 1,1,1,2,4193911,50.42744,4201,3863,Gut,adenocarcinoma in cecum,,,,,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"Complete closed genome and associated methylome efforts for bacteria grown in isolation from multiple sites across the human microbiota (oral, nasal, skin, gastrointestinal tract, reproductive tract).",sample_type:surgical resection,98,95.9,,,,Good,2021-12-24T23:46:24.910Z,2021-12-24T23:46:24.910Z
7062,584.85,Proteus mirabilis strain FDAARGOS_60,negative,,584,Complete,FDAARGOS_60,,,,,,,,2015-04-22T00:00:00Z,,PRJNA231221,SAMN02934509,GCF_000784015.1,"SRR1596450,SRR1596451,SRR1596452",JTBW01000000,,US Food and Drug Administration,,PacBio,14.22x,HGAP v. 2.0,,,1,4105509,38.91,3922,3559,Skin,Skin swab,,14-Oct-13,USA,United States,,,,,,"Human, Homo sapiens",female,16Y,Cellulitis,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:Children's National Hospital;isolate:not applicable,98.7,96.9,100,0.5,,Good,2016-01-17T15:41:01.252Z,2016-01-17T15:41:01.252Z
7067,585.52,Proteus vulgaris strain FDAARGOS_556 strain Not applicable,negative,,585,Complete,Not applicable,,,,,,FDA:FDAARGOS_556,,2018-11-21T00:00:00Z,,PRJNA231221,SAMN10163249,GCA_003812525.1,,CP033736,,US Food and Drug Administration,,Pacbio; Illumina,26.53x,Canu v. 1.4,1,,1,4158443,37.98441,3963,3812,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:University of North Carolina,99,97.8,,,,Good,2018-11-30T03:11:14.397Z,2018-11-30T03:11:14.397Z
7085,587.58,Providencia rettgeri strain FDAARGOS_330,negative,,587,Complete,FDAARGOS_330,,,,,,FDA:FDAARGOS_330,,2018-03-09T00:00:00Z,,PRJNA231221,SAMN06173343,GCA_002984195.1,,CP027418,,US Food and Drug Administration,,PacBio; Illumina,15.0368768789957x,"SMRT v. 2.3.0, HGAP v. 3.0",1,,1,4518601,40.144814,4290,4109,Urine,urine,,24-Jan-15,USA,USA:DC,,,,,,"Human, Homo sapiens",female,10Y,Urinary tract infection,,,,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,98.9,98.2,100,,,Good,2018-05-26T05:51:41.189Z,2018-05-26T05:51:41.189Z
7090,588.46,Providencia stuartii strain FDAARGOS_291,negative,,588,Complete,FDAARGOS_291,,,,,,FDA:FDAARGOS_291,,2018-03-09T00:00:00Z,,PRJNA231221,SAMN06173304,GCA_002983665.1,,CP027398,,US Food and Drug Administration,,PacBio; Illumina,15.34x,CA v. 8.2,1,,1,4394489,41.449097,4323,4014,Urine,urine,,1-Mar-14,USA,USA:DC,,,,,,"Human, Homo sapiens",male,,,,,,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:George Washington University,99.6,98.2,100,0.7,,Good,2018-05-26T05:48:15.512Z,2018-05-26T05:48:15.512Z
7100,611.359,Salmonella enterica subsp. enterica serovar Heidelberg strain CFSAN067218,negative,,611,Complete,CFSAN067218,Heidelberg,,,MLST.Salmonella_enterica.15,,,,2018-12-31T00:00:00Z,,PRJNA215355,SAMN08737531,GCA_003986635.1,,"CP028311,CP028312,CP028313",,FDA/CFSAN,,PacBio,496.0x,HGAP v. 3.0,1,2,3,4954994,52.086987,5185,5000,None,,,2011,USA,USA:PA,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Listeria monocytogenes Database: isolates from the Food and Drug Administration, Center for Food Safety and Applied Nutrition",collected_by:Dudley Lab/Penn State/PADOH,99.6,99.1,,,,Good,2019-01-31T23:18:57.274Z,2019-01-31T23:18:57.274Z
7153,615.999,Serratia marcescens strain 4928STDY7387938,negative,,615,Complete,4928STDY7387938,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,SAMEA4623347,GCA_902166755.1,,LR607375,,SC,,,,,1,,1,5046965,60.38327,4651,,Stool,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,"Human, Homo sapiens",,,,,,host_health_state:carriage,,,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,98.7,97.7,,,,Good,2019-10-03T08:02:25.337Z,2019-10-03T08:02:25.337Z
7175,621.85,Shigella boydii strain ATCC 9210,negative,,621,Complete,ATCC 9210,,,,,,ATCC:9210,,2015-06-03T00:00:00Z,,PRJNA284097,SAMN03699691,GCF_001027225.1,"SRR2029654,SRR3169819,SRR3883613",CP011511,NZ_CP011511.1,KRIBB,,PacBio,77.0x,HGAP v. SMRT Analysis v2.1,1,,1,4574246,51.19,5060,4485,Stool,Cases of diarrhea,,,,,,,,,,"Human, Homo sapiens",,,Dysentery,,,,,,,,,,,C,,,,,Comparative genomic study for different Shigella species;many frameshifted proteins,,99.6,98,100,,,Good,2016-01-17T16:07:07.051Z,2016-01-17T16:07:07.051Z
7182,622.541,Shigella dysenteriae strain HNCMB 20080,negative,,622,Complete,HNCMB 20080,,,,,,,,2020-11-13T00:00:00Z,,PRJNA662859,SAMN16094609,GCA_015475595.1,,"CP061527,CP061528,CP061529",,Justus-Liebig-University Giessen,,Illumina MiSeq; Nanopore Minion,170.0x,Unicycler v. 0.4.7,1,2,3,4405684,51.231884,5173,,None,,,1954,Hungary,Hungary,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,We present the genome sequence of a historical Shigella dysenteriae strain isolated in 1954 from a patient in Hungary,,99.5,98.5,,,,Good,2020-11-30T11:23:58.342Z,2020-11-30T11:23:58.342Z
7201,623.999,Shigella flexneri strain FDAARGOS_535 strain Not applicable,negative,,623,Complete,Not applicable,,,,,,FDA:FDAARGOS_535,,2018-12-02T00:00:00Z,,PRJNA231221,SAMN10163230,GCA_003855135.1,,"CP034060,CP034059,CP034061,CP034062,CP034063,CP034064,CP034065",,US Food and Drug Administration,,Pacbio; Illumina,15.85x,"SMRT v. 2.3.0, HGAP v. 3.0, SPAdes v.",1,6,7,4872568,50.567936,5553,4956,Stool,stool,,4/1/16,,,,,,,,"Human, Homo sapiens",male,11Y,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,99.6,97.6,,,,Good,2019-01-30T08:44:24.503Z,2019-01-30T08:44:24.503Z
7235,624.637,Shigella sonnei strain FDAARGOS_90,negative,,624,Complete,FDAARGOS_90,,,,,,FDA:FDAARGOS_90,,2016-02-11T00:00:00Z,,PRJNA231221,SAMN03996263,GCF_001558295.1,,"CP014099,CP014096,CP014097,CP014098,CP014100,CP014101","NZ_CP014099.1,NZ_CP014096.1,NZ_CP014097.1,NZ_CP014098.1,NZ_CP014100.1,NZ_CP014101.1",US Food and Drug Administration,,Pacbio,23.647x,HGAP3 v. Oct 2014,1,5,6,4988242,51,5424,5100,Stool,Stool,,9/8/13,USA,USA:DC,,,,,,"Human, Homo sapiens",female,5Y,Diarrhea,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:Children's National Hospital,99.8,97.5,100,2.1,,Good,2016-03-01T19:36:03.859Z,2016-03-01T19:36:03.859Z
7239,630.33,Yersinia enterocolitica strain ATCC 9610,negative,,630,Complete,ATCC 9610,,,,MLST.Yersinia_spp.154,,ATCC:9610,,2014-09-16T00:00:00Z,,PRJNA243535,SAMN02887290,GCF_000755055.1,"SRR2180266,SRR2180267",JPDV01000000,,Los Alamos National Laboratory,,454; Illumina,200.0x,Newbler v. 2.6; Velvet v. 1.2.08; AllPaths,,,1,4538553,47.28,4367,4084,None,,,,USA,USA: New York,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Coccobacilli,,,,,,,,,Yersinia enterocolitica ATCC 9610 Genome Assembly,biomaterial_provider:USAMRIID,100,99.6,100,0.3,,Good,2016-01-17T15:40:02.222Z,2016-01-17T15:40:02.222Z
7241,631.41,Yersinia intermedia strain FDAARGOS_729 strain Not applicable,negative,,631,Complete,Not applicable,,,,MLST.Yersinia_spp.39,,FDA:FDAARGOS_729,,2019-12-05T00:00:00Z,,PRJNA231221,SAMN11056444,GCA_009730075.1,,CP046294,,US Food and Drug Administration,,Pacbio; Illumina,688.53x,"SMRT v. 2.3.0, HGAP v. 3",1,,1,4928916,47.58316,4752,4410,None,clinical isolate,,,USA,USA:MN,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Mayo Clinic,97.1,95.7,,,,Good,2019-12-31T17:07:55.090Z,2019-12-31T17:07:55.090Z
7245,632.705,Yersinia pestis strain S19960127,negative,,632,Complete,S19960127,,,,MLST.Yersinia_spp.79,,,,2020-11-02T00:00:00Z,,PRJNA577233,SAMN13021983,GCA_015190655.1,,"CP045640,CP045636,CP045637,CP045638,CP045639",,National institute for communicable disease control and prevention,,PacBio RSII,30.0x,SOAPdenovo v. 2.3,1,4,5,4852443,47.670277,4763,4575,None,Tibetan,,8/26/96,China,China:Tibet,,,,,,"Human, Homo sapiens",,,plague,,,,,,,,,,,,,,,,genome sequence of Yersinia S19960127,collected_by:Center for Disease Control and Prevention,99.9,98.6,,,,Good,2020-11-30T02:26:38.726Z,2020-11-30T02:26:38.726Z
7253,633.88,Yersinia pseudotuberculosis strain NZYP4713,negative,,633,Complete,NZYP4713,,,,MLST.Yersinia_pseudotuberculosis.42,,,,2017-01-02T00:00:00Z,,PRJEB14046,SAMEA3988158,GCF_900092345.1,,"LT596221,LT596222","NZ_LT596221.1,NZ_LT596222.1",UNIVERSITY OF MELBOURNE,,,,,1,1,2,4794091,47.51,4514,,Stool,Faeces,,2014,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,This study performed comparative genomics a large temporal and geographically diverse collection of isolates belonging to the Y. pseudotuberculosis complex to explore the genomic epidemiology of a sustained outbreak of yersiniosis in New Zealand.,,100,99.5,100,,,Good,2017-01-18T15:50:02.526Z,2017-01-18T15:50:02.526Z
7262,644.752,Aeromonas hydrophila strain 71317,negative,,644,Complete,71317,,,,MLST.Aeromonas_spp.134,,not collected,,2021-10-10T00:00:00Z,,PRJNA759416,SAMN21168046,GCA_020405385.1,,CP084353,,Ningbo First Hospital,,Oxford Nanopore,320x,ABySS v. 2021-02-01T00:00:00,1,,1,4695915,61.693962,4279,4123,Blood,blood,,6/5/20,China,China:Ningbo,,,,,,Homo sapiens,male,73,cholecystitis,,,host_disease_outcome:recovery,,,,,,,,,,,,,Antibiotic Resistance Determinants and Virulence Factors of Aeromonas in Ningbo,collected_by:Xing-bei Weng,99.8,99.6,,,,Good,2021-12-24T08:20:46.753Z,2021-12-24T08:20:46.753Z
7280,648.77,Aeromonas caviae strain FDAARGOS_72,negative,,648,Complete,FDAARGOS_72,,,,,,,,2015-04-27T00:00:00Z,,PRJNA231221,SAMN02934523,GCF_000783775.1,"SRR1609060,SRR1609061,SRR1609062",JTBK01000000,,US Food and Drug Administration,,PacBio,21.5x,Celera Assembler v. 8.1,,,1,4517515,61.68,4540,3342,Stool,Stool,,16-Sep-13,USA,United States,,,,,,"Human, Homo sapiens",male,11M,Diarrhea,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:Children's National Hospital;isolate:not applicable,99,92.4,100,5.1,,Good,2016-01-17T15:40:56.323Z,2016-01-17T15:40:56.323Z
7291,654.657,Aeromonas veronii strain 71506,negative,,654,Complete,71506,,,,,,not collected,,2021-10-27T00:00:00Z,,PRJNA759416,SAMN21168054,GCA_020640955.1,,"CP085465,CP085466,CP085467",,Ningbo First Hospital,,Oxford Nanopore,320x,ABySS v. 2021-02-01T00:00:00,1,2,3,4692576,58.420067,4331,4122,Bile,bile,,12/24/20,China,China:Ningbo,,,,,,Homo sapiens,male,72,cholecystitis,,,host_disease_outcome:recovery,,,,,,,,,,,,,Antibiotic Resistance Determinants and Virulence Factors of Aeromonas in Ningbo,collected_by:Xing-bei Weng,99.4,98.2,,,,Good,2021-12-24T16:45:01.259Z,2021-12-24T16:45:01.259Z
7326,666.5676,Vibrio cholerae strain IDH-03329,negative,,666,Complete,IDH-03329,,,,MLST.Vibrio_cholerae.69,,,,2021-05-27T00:00:00Z,,PRJDB11362,SAMD00290839,GCA_019704235.1,,"AP024553,AP024554",,Hosei university,,MinION; Illumina MiSeq,105x,flye v. 2.8.1,2,,2,4108356,47.483227,3844,,Stool,stool from cholera patient,isolated in Kolkata were generated by using short reads obtained by illumina sequencer and long reads by nanopore sequencer,12/1/10,India,India,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Complete genomic sequences of V. cholerae O1 isolated in Kolkata were generated by using short reads obtained by illumina sequencer and long reads by nanopore sequencer.,,99.8,97.9,,,,Good,2021-08-26T18:54:58.006Z,2021-08-26T18:54:58.006Z
7331,670.961,Vibrio parahaemolyticus strain FORC_023,negative,,670,Complete,FORC_023,,,,,,,,2016-10-11T00:00:00Z,,PRJNA284329,SAMN03701448,GCF_001758605.1,SRR2032397,"CP012950,CP012951","NZ_CP012950.1,NZ_CP012951.1",Korea Research Institute of Bioscience and Biotechnology,,Illumina; PacBio,440.84x,CLCbio CLC Genomics Workbench v. 7.5.1;,2,,2,5015214,45.44,4605,4337,None,patient,,2014-10,South Korea,South Korea: Pusan,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,Mesophilic,30 C,,Facultative,Aquatic,food-borne disease,"Genome sequencing project of Vibrio parahaemolyticus FORC_023, isolated from food-borne outbreak samples in Busan, South Korea",sample_type:cell culture,99.8,99.3,99.6,,,Good,2016-11-17T03:37:04.967Z,2016-11-17T03:37:04.967Z
7339,672.851,Vibrio vulnificus strain FDAARGOS_663 strain Not applicable,negative,,672,Complete,Not applicable,,,,MLST.Vibrio_vulnificus.3,,FDA:FDAARGOS_663,,2019-09-25T00:00:00Z,,PRJNA231221,SAMN11056378,GCA_008693685.1,,"CP044068,CP044069",,US Food and Drug Administration,,Pacbio; Illumina,907.19x,canu v. 1.4,2,,2,4974815,46.715687,4712,4473,None,clinical isolate,,,USA,USA: KY,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:University of Louisville,99.6,97.5,,,,Good,2019-10-02T19:09:31.128Z,2019-10-02T19:09:31.128Z
7340,673.5,Grimontia hollisae strain ATCC 33564,positive,,673,Complete,ATCC 33564,,,,,,FDA:FDAARGOS_111,,2016-02-11T00:00:00Z,,PRJNA231221,SAMN03996327,GCF_001558255.1,"SRR2817810,SRR2817811,SRR2817812,SRR2817813","CP014056,CP014055","NZ_CP014056.1,NZ_CP014055.1",US Food and Drug Administration,,Pacbio,23.958x,HGAP3 v. Nov 2014,2,,2,3998273,49.51,3843,3511,None,,,,USA,USA:MD,,,,,,"Human, Homo sapiens",,,Vibrio infection,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:FDA CFSAN,99.9,97.8,97.3,3.7,,Good,2016-03-01T19:48:19.251Z,2016-03-01T19:48:19.251Z
7343,676.305,Vibrio fluvialis strain 19-VB00936,negative,,676,Complete,19-VB00936,,,,,,,,2021-04-26T00:00:00Z,,PRJNA722921,SAMN18795813,GCA_018140575.1,,"CP073273,CP073274",,German Federal Institute for Risk Assessment,,Illumina; Oxford Nanopore MinION,100.0x,Unicycler v. v0.4.8,2,,2,4808142,50.140594,4488,4325,Wound,foot,,2019,,Baltic Sea,,,,,,Homo sapiens,,,wound infection,,,,,,,,,,,,,,,,Vibrio fluvialis 19-VB00936 isolated from a wound infection,collected_by:Helios Hanseklinikum Stralsund,99.5,97.3,,,,Good,2021-06-02T17:41:13.303Z,2021-06-02T17:41:13.303Z
7358,686.93,Vibrio cholerae O1 biovar El Tor strain C6709,negative,,686,Complete,C6709,El Tor,,,MLST.Vibrio_cholerae.69,,,,2020-05-13T00:00:00Z,,PRJNA598947,SAMN13734988,GCA_013085105.1,,"CP047297,CP047298",,EPFL,,PacBio,343.0x,HGAP v. 3,2,,2,4090614,47.437805,3841,3666,None,,,1991,Peru,Peru,,,,,,"Human, Homo sapiens",,,cholera,,,,,,,,,,,,,,,,The goal of this study was to de novo assemble diverse pandemic V. cholerae strains and compare their closed genomes.,passage_history:provided by Reidl lab,97.6,97.1,,,,Good,2020-06-04T13:41:16.763Z,2020-06-04T13:41:16.763Z
7450,725.21,Haemophilus influenzae biotype aegyptius strain HE15/F3028,negative,,725,Complete,HE15/F3028,,,,MLST.Haemophilus_influenzae.65,,,,2019-09-19T00:00:00Z,,PRJNA563784,SAMN12687935,GCA_008586825.1,,CP043771,,Griffith University,,PacBio Sequel,245.6x,HGAP v. 4,1,,1,1984979,38.220154,2035,1941,Cerebrospinal Fluid,CSF,,1988,Brazil,Brazil: Fartura,,,,,,"Human, Homo sapiens",,,Brazilian Purpuric Fever (BPF),,,,,,,,,,,,,,,,"Closed annotated genomes of five strains of Haemophilus influenzae biogroup aegyptius, responsible for purelent conjunctivitis and Brazilian Purpuric fever",,99.1,98.4,,,,Good,2019-10-02T10:42:37.508Z,2019-10-02T10:42:37.508Z
7457,726.44,Haemophilus haemolyticus strain 2019-19,negative,,726,Complete,2019-19,,,,MLST.Haemophilus_influenzae.379,,,,2021-08-31T00:00:00Z,,PRJDB10631,SAMD00251501,GCA_019973675.1,,AP024093,,Tokyo University of Pharmacy and Life Sciences,,GridION; DNB Seq-G400,1158x,Unicycler v. 0.4.7,1,,1,1895310,38.514492,1811,1771,None,paediatric patient,isolated from a paediatric patient,2019,,not collected,,,,,,Homo sapiens,,,,,,,,,Negative,Bacilli,No,,,,,,,,Whole-genome sequence of quinolone high level resistant Haemophilus haemolyticus 2019-19 isolated from a paediatric patient.,,99.6,99.3,,,,Good,2021-12-24T00:36:58.758Z,2021-12-24T00:36:58.758Z
7528,727.972,Haemophilus influenzae strain NML-Hia-1,negative,,727,Complete,NML-Hia-1,a,,,MLST.Haemophilus_influenzae.23,,,,2016-10-31T00:00:00Z,,PRJNA328024,SAMN05714732,GCF_001856725.1,,CP017811,NZ_CP017811.1,Public Health Agency of Canada,,PacBio,436x,Celera Assembler v. APRIL-2016,1,,1,1829217,38.02,1784,1699,Blood,blood,,2011,Canada,Canada: Manitoba,,,,,,"Human, Homo sapiens",,,Invasive disease,,,,,,,,,,,,,,,,"A closed, whole genome sequence of Haemophilus influenzae serotype a",collected_by:National Microbiology Laboratory,99.6,98.7,100,0.6,,Good,2016-11-19T06:22:02.457Z,2016-11-19T06:22:02.457Z
7543,729.347,Haemophilus parainfluenzae strain NCTC10665,negative,,729,Complete,NCTC10665,not available: to be reported later,,,,,NCTC:10665,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA104062569,GCA_900638025.1,,LR134481,,SC,,,,,1,,1,2062405,39.371464,1999,1960,Mouth,saliva,,1969,,,,,,,,"Human, Homo sapiens",,,,,,host_health_state:not available: to be reported later,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.7,98.5,,,,Good,2019-02-01T14:08:12.739Z,2019-02-01T14:08:12.739Z
7570,730.57,[Haemophilus] ducreyi strain NCTC11483,negative,,730,Complete,NCTC11483,not available: to be reported later,,,,,NCTC:11483,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA4412686,GCA_900637315.1,,LR134364,,SC,,,,,1,,1,1594261,37.946987,1569,1521,None,not available: to be reported later,,1900/1982,United Kingdom,United Kingdom: Sheffield,,,,,,"Human, Homo sapiens",,,,,,host_health_state:not available: to be reported later,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.9,98.5,,,,Good,2019-02-01T13:53:55.010Z,2019-02-01T13:53:55.010Z
7583,747.973,Pasteurella multocida strain NCTC8282,negative,,747,Complete,NCTC8282,not available: to be reported later,,,,,NCTC:8282,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA104200666,GCA_900638095.1,,LR134488,,SC,,,,,1,,1,2409583,37.538486,2190,2143,Wound,Dog bite,,1900/1952,,,,,,,,"Human, Homo sapiens",,,,,,host_health_state:not available: to be reported later,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.4,99,,,,Good,2019-02-01T14:10:23.531Z,2019-02-01T14:10:23.531Z
7593,753.27,Pasteurella canis strain HL1500,negative,,753,Complete,HL1500,,,,,,,,2021-09-20T00:00:00Z,,PRJNA758715,SAMN21032959,GCA_020042685.1,,"CP083396,CP083397",,Hallym University,,Oxford Nanopore MinION; Illumina MiSeq,416.0x,Unicycler v. 0.4.8,1,1,2,2188044,36.77417,2008,1975,Pus,Pus,,2017,,South Korea,,,,,,Homo sapiens,,,Inflammation,,,,,,,,,,,,,,,,"Pasteurella canis HL1500, clinical isolate",collected_by:Kangdong Sacred Hospital,99.6,99.6,,,,Good,2021-12-24T01:34:17.528Z,2021-12-24T01:34:17.528Z
7594,754.3,Pasteurella dagmatis strain NCTC11617,negative,,754,Complete,NCTC11617,,,,,,NCTC:11617,,2017-08-15T00:00:00Z,,PRJEB6403,SAMEA4362423,GCA_900186835.1,,LT906448,,SC,,,,,1,,1,2287213,37.53,2055,2011,Respiratory,nose swab,,1900/1985,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.2,98.9,98.9,,,Good,2017-09-29T14:26:41.263Z,2017-09-29T14:26:41.263Z
7619,774.13,Bartonella bacilliformis strain KC584,negative,,774,Complete,KC584,,,,,,ATCC:35686,,2019-11-04T00:00:00Z,,PRJNA579486,SAMN13112075,GCA_009498695.1,,CP045671,,Institute for Medical Microbiology and Infection Control,,PacBio Sequel; Illumina MiSeq,500.0x,Unicycler v. v.0.4.8,1,,1,1411655,38.23052,1329,1169,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,This study aims to determine the complete genome sequence of Bartonella bacilliformis strain KC584 (ATCC® 35686™),sample_type:Microbe sample,99.8,99.4,,,,Good,2019-11-25T13:47:41.166Z,2019-11-25T13:47:41.166Z
7623,777.26,Coxiella burnetii strain 3345937,negative,,777,Complete,3345937,,,,,,,,2016-02-25T00:00:00Z,,PRJNA310186,SAMN04448129,GCF_001572765.1,,"CP014354,CP014355",,Central Veterinary Institute part of Wageningen UR,,Illumina,285.7,Spades v. 3.6.2,,1,2,2013572,42.25,2468,2110,None,,,2010,Netherlands,Netherlands,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,The aim of the sequencing project is to see the similarities in genomes of veterinary and Human strains to find the source of infection of Q-fever in the Netherlands,sample_type:cell-culture,99.6,98.7,100,,,Good,2016-03-18T07:09:30.533Z,2016-03-18T07:09:30.533Z
7643,784.27,Orientia tsutsugamushi strain Wuj/2014,negative,,784,Complete,Wuj/2014,,,,,,,,2019-09-25T00:00:00Z,,PRJNA563989,SAMN12697410,GCA_008693345.1,,CP044031,,Zhejiang Province Center for Disease Control and Prevention,,Illumina HiSeq; PacBio,411.0x,ABySS v. 2.0.2; CANU v. 1.0; GapCloser v.,1,,1,1972387,30.451174,2486,2066,None,blood from a febrile patient,,5-Jun-14,China,China:Zhejiang province,,,,,,"Human, Homo sapiens",,,Scrub typhus,,,,,,,,,,,,,,,,"Complete genome sequences of Orientia tsutsugamushi strains from Zhejiang province,China",collected_by:Qunying Lu,99.8,99.3,,,,Good,2019-10-02T18:57:16.433Z,2019-10-02T18:57:16.433Z
7691,813.94,Chlamydia trachomatis strain F-6068,negative,,813,Complete,F-6068,serovar s,,,MLST.Chlamydiales_spp.38,,,,2016-06-03T00:00:00Z,,PRJNA316787,SAMN04590091,GCF_001655575.1,SRR3318875,"CP015306,CP015307","NZ_CP015306.1,NZ_CP015307.1",University of Vienna,,Illumina,799,AMOScmp v. 3.1.0; MaSuRCA v. 2.3.0rc1;,1,1,2,1050231,41.27,971,917,None,Patient sample,,1990,Germany,Germany: Jena,,,,,,"Human, Homo sapiens",,,Chlamydial Infection,,,,,,,,,,,,,,,,"Chlamydia trachomatis, agent of ocular, urogenital and lymph system infections in humans, is highly abundant and within its serovars E, F and D are the most successful ones, causing sexually transmitted disease. Despite this, the number of public available genome sequences and in general the overall knowledge on genome level of the serovars E and F, is low. Here we re-sequenced six E and F clinical samples and one E lab strain, in order to identify the genetic variance in these serovars.","collected_by:Juergen Roedel, Eberhard Straube",99.9,99.8,100,,,Good,2016-07-05T18:27:48.066Z,2016-07-05T18:27:48.066Z
7700,817.86,Bacteroides fragilis strain S14,negative,,817,Complete,S14,,,,,,,,2016-07-08T00:00:00Z,,PRJNA290855,SAMN03921941,GCF_001682215.1,,CP012706,NZ_CP012706.1,Seqomics Ltd,,Illumina MiSeq,73.0x,CLC Genomics Workbench Tool v. 8.0.2;,1,,1,4902215,43.15,4214,3813,None,human patient,,2014,Hungary,Hungary: Szeged,,,,,,"Human, Homo sapiens",,,bacterial infection,,,,,,,,,,,C,,,,,pathogenic strain isolated from human infection site,"collected_by:Jozsef Soki, University of Szeged",99.9,99.9,100,,,Good,2016-08-26T19:18:24.328Z,2016-08-26T19:18:24.328Z
7716,818.23,Bacteroides thetaiotaomicron strain 7330,negative,,818,Complete,7330,,,,,,,,2015-10-15T00:00:00Z,26430127,PRJNA289334,SAMN03852684,GCA_001314975.1,"SRR2652131,SRR2652132,SRR2652133",CP012937,NZ_CP012937.1,Washington University in St. Louis,,Illumina MiSeq; PacBio,395X,HGAP 2.0 and Celera v. AUG-2014,1,,1,6487685,42.69,5316,5071,Stool,feces,,11-Oct-09,USA,USA:Woods Hole,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Three Bacteroides species has been mono-cultured. DNA was extracted and sequenced with Pacbio and Illumina, and assembled.",sample_type:cell culture,99.9,99.6,100,,,Good,2016-01-17T17:15:28.599Z,2016-01-17T17:15:28.599Z
7720,820.5511,Bacteroides uniformis strain JCM13288,negative,,820,Complete,JCM13288,,,,,,,,2021-06-10T00:00:00Z,33043794,PRJNA636247,SAMN15069607,GCA_018831525.1,,"CP054204,CP054199,CP054200,CP054203,CP054202,CP054201",,National Agri-Food Biotechnology Institute,,Oxford Nanopore MiniION,140.0x,canu v. 1.7,1,5,6,5329115,46.233154,5158,,Stool,feces,,1/5/19,Japan,Japan,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Whole genome sequence of Bacteroides uniformis strain JCM 13288.,sample_type:whole organism;biomaterial_provider:JCM,99.5,95.6,,,,Good,2021-06-26T05:06:01.461Z,2021-06-26T05:06:01.461Z
7725,821.4651,Phocaeicola vulgatus strain BFG-191,negative,,821,Complete,BFG-191,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,SAMN15547037,GCA_020091465.1,,"CP081912,CP081909,CP081910,CP081911",,National Institute of Allergy and Infectious Disease,,PacBio Sequel,502x,HGAP/FALCON v. v. 6.0,1,3,4,5293332,42.42683,4803,4344,Abdomen,Peritoneal Fluid,,1987,USA,USA:Bethesda,,,,,,Homo sapiens,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,100,99.7,,,,Good,2021-12-24T03:19:28.068Z,2021-12-24T03:19:28.068Z
7731,823.377,Parabacteroides distasonis strain BFG-238,negative,,823,Complete,BFG-238,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,SAMN15546933,GCA_020091445.1,,"CP081908,CP081907",,National Institute of Allergy and Infectious Disease,,PacBio Sequel,448x,HGAP/FALCON v. v. 6.0,1,1,2,5562109,45.104744,4940,4650,None,Biopsy,,1987,USA,USA:Bethesda,,,,,,Homo sapiens,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,99.3,98.2,,,,Good,2021-12-24T03:19:29.828Z,2021-12-24T03:19:29.828Z
7732,824.5,Campylobacter gracilis strain ATCC 33236,negative,,824,Complete,ATCC 33236,,,,,,ATCC:33236,,2015-08-03T00:00:00Z,,PRJNA290037,SAMN03862076,GCF_001190745.1,,CP012196,NZ_CP012196.1,"USDA, ARS, WRRC",,Sanger dideoxy sequencing; 454; Illumina,689x,Newbler v. 2.6,1,,1,2281652,46.56,2701,2103,Mouth,oral,,1977,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,First closed genome of Campylobacter gracilis,sample_type:cell culture,97.2,96.7,97.3,1.8,,Good,2016-01-17T16:42:17Z,2016-01-17T16:42:17Z
7793,837.83,Porphyromonas gingivalis strain A7436,negative,,837,Complete,A7436,,,,MLST.Porphyromonas_gingivalis.25,,,,2015-08-11T00:00:00Z,,PRJNA276132,SAMN03366764,GCF_001263815.1,,CP011995,NZ_CP011995.1,University of Florida,,454; Sanger,57.34x,Velvet v. 0.7.63; Newbler v. 2.3,1,,1,2367029,48.33,2268,2004,Mouth,subgingival plaque,,1985,USA,"USA: Atlanta, GA, CDC Anaerobic Diseases",,,,,"env_biome:Oral cavity, periodontitis patient","Human, Homo sapiens",,,Refractory periodontitis,,,,,,Negative,Bacilli,No,,Mesophilic,37,,Anaerobic,HostAssociated,Periodontitis,"This study was performed to elucidate the genetic backgrounds responsible for phenotypic differences among 4 strains of P. gingivalis, and compare them with other, currently available genomic sequences to provide a clearer understanding of virulence phenotypes of this bacterium.",,99.9,99.8,100,,,Good,2016-01-17T17:01:42.870Z,2016-01-17T17:01:42.870Z
7795,851.301,Fusobacterium nucleatum strain Fn12230,negative,,851,Complete,Fn12230,,,,,,,,2020-05-21T00:00:00Z,,PRJNA632750,SAMN14918738,GCA_013137915.1,,"CP053468,CP053470,CP053469",,Columbia University,,Illumina HiSeq; PacBio,350.0x,Uncycler v. v0.4.8-beta,1,2,3,2473944,26.962736,2454,2423,Mouth,oral,,not collected,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Genome sequencing and assembly of Fusobacterium nucleatum strain Fn12230 and identification of variation for F. nucleatum lam variant,sample_type:not collected,99,98.5,,,,Good,2020-06-05T02:51:15.524Z,2020-06-05T02:51:15.524Z
7797,856.21,Fusobacterium varium strain NCTC10560,negative,,856,Complete,NCTC10560,not available: to be reported later,,,,,NCTC:10560,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA24554668,GCA_900637705.1,,LR134390,,SC,,,,,1,,1,3302398,29.332775,3519,3398,Stool,feces,,1942,USA,USA: New York,,,,,,"Human, Homo sapiens",,,,,,host_health_state:not available: to be reported later,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.7,95,,,,Good,2019-02-01T14:01:47.123Z,2019-02-01T14:01:47.123Z
7824,860.19,Fusobacterium periodonticum strain 2_1_31,negative,,860,Complete,2_1_31,,,,,,,,2018-03-26T00:00:00Z,,PRJNA433545,SAMN08501101,GCA_003019755.1,,CP028108,,Virginia Tech,,"Illumina, MinION",70x,Unicycler v. 0.4.3,1,,1,2541084,28.127523,2507,2477,Gut,Colon,,,,,,,,,env_biome:terrestrial biome [ENVO:00000446],"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Complete Fusobacterium genomes generated by MinION and Illumina sequencing, followed by assembly with Unicycler.",,99.5,99.1,100,,,Good,2018-05-31T00:24:07.567Z,2018-05-31T00:24:07.567Z
7826,861.5,Fusobacterium ulcerans strain NCTC12112,negative,,861,Complete,NCTC12112,,,,,,NCTC:12112,,2018-06-17T00:00:00Z,,PRJEB6403,SAMEA3178012,GCA_900478315.1,,LS483487,,SC,,,,,1,,1,3539037,30.547264,3282,3233,Skin,Skin Ulcer,,1900/2003,Papua New Guinea,Papua New Guinea,,,,,,"Human, Homo sapiens",,,,,,host_health_state:Skin Ulcer,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,98.5,97,100,,,Good,2018-07-16T23:45:28.266Z,2018-07-16T23:45:28.266Z
4,1017.4,Capnocytophaga gingivalis strain H1496,negative,,1017,Complete,H1496,,,,,,,,2017-09-14T00:00:00Z,,PRJNA369395,SAMN06289147,GCA_002302415.1,,CP022386,,Centers for Disease Control and Prevention,,PacBio; Illumina MiSeq,211.3x,Canu v. 1.4,1,,1,2838633,40.09,2818,2662,Sputum,Sputum,,18-Apr-00,USA,USA: Ohio,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,select isolates within the Capnocytophaga genus were biochemically characterized and sequenced for taxonomic evaluations,sample_type:cell culture,98.8,98.5,100,,,Good,2017-09-28T23:30:54.243Z,2017-09-28T23:30:54.243Z
7,1019.5,Capnocytophaga sputigena strain NCTC11097,negative,,1019,Complete,NCTC11097,not available: to be reported later,,,,,NCTC:11097,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA104200653,GCA_900638125.1,,LR134489,,SC,,,,,1,,1,2933908,38.733868,2726,2668,Blood,Blood culture,,1974,United Kingdom,United Kingdom,,,,,,"Human, Homo sapiens",,,,,,host_health_state:disease,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99,99,,,,Good,2019-02-01T14:11:59.356Z,2019-02-01T14:11:59.356Z
175,1260.177,Finegoldia magna strain FDAARGOS_764 strain Not applicable,positive,,1260,Complete,Not applicable,,,,,,FDA:FDAARGOS_764,,2020-06-04T00:00:00Z,,PRJNA231221,SAMN11056479,GCA_013267535.1,,CP054000,,US Food and Drug Administration,,Pacbio; Illumina,1616.75x,"SMRT v. 2.3.0, HGAP v. 3",1,,1,2090058,31.992174,1987,1944,Vagina,vagina,,,USA,USA:VA,,,,,,"Human, Homo sapiens",female,,Bacterial vaginosis,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),98.9,98.5,,,,Good,2020-07-01T03:44:33.866Z,2020-07-01T03:44:33.866Z
915,1282.4634,Staphylococcus epidermidis strain NBRC 113846,positive,,1282,Complete,NBRC 113846,,,,MLST.Staphylococcus_epidermidis.2,,,,2021-09-30T00:00:00Z,,PRJNA747117,SAMN21163584,GCA_020181395.1,,"CP084008,CP084009,CP084010,CP084011",,"National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute",,Illumina MiSeq; Oxford Nanopore MinION,362.0x,Flye v. 2.8.3; Racon v. 1.4.20; Medaka v.,1,3,4,2520735,32.148994,2380,2306,Skin,human skin,,2018,,Japan,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,This work develops defined microbial mock communities to serve as control reagents for human fecal microbiota measurements by metagenome or amplicon (targeted loci) sequencing.,sample_type:pure culture,99.9,99.9,,,,Good,2021-12-24T05:23:09.519Z,2021-12-24T05:23:09.519Z
923,1283.98,Staphylococcus haemolyticus strain MSA_JNM60C2,positive,,1283,Complete,MSA_JNM60C2,,,,,genotype:ST-1,,,2021-01-19T00:00:00Z,,PRJNA669251,SAMN16871746,GCA_016695445.1,,CP065356,,National Institute of Biomedical Genomics,,Ilumina,421.0x,Bowtie v. 2,1,,1,2511057,32.812016,2471,2400,None,Preterm neonate vaginally delivered and admitted to SNCU with respiratory distress,isolated from the nares of the admitted neonates,31-Aug-18,India,"India: College of Medicine and JNM Hospital, Kalyani, West Bengal",,,,,,"Human, Homo sapiens",,8 days,Premature birth,,,,,,,,,,,,,,,,"Preterm neonates are often admitted to the SNCU after birth due to respiratory distress because of incomplete lung development. This study was undertaken to understand the nasal colonization patterns in such neonates. In this study, multidrug resistant Staphylococcus haemolyticus was found to be the major species that was isolated from the nares of the admitted neonates.",collected_by:National Institute of Biomedical genomics,99.8,98.9,,,,Good,2021-02-01T06:21:20.771Z,2021-02-01T06:21:20.771Z
929,1292.16,Staphylococcus warneri strain FDAARGOS_754 strain Not applicable,positive,,1292,Complete,Not applicable,,,,,,FDA:FDAARGOS_754,,2020-06-04T00:00:00Z,,PRJNA231221,SAMN11056469,GCA_013267715.1,,"CP054017,CP054016",,US Food and Drug Administration,,Pacbio; Illumina,1331.87x,"SMRT v. 2.3.0, HGAP v. 3",1,1,2,2460001,32.78454,2394,2324,Skin,normal skin of the right arm,,,USA,USA:VA,,,,,,"Human, Homo sapiens",male,57Y,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),98.4,98.2,,,,Good,2020-07-01T03:49:06.396Z,2020-07-01T03:49:06.396Z
946,1302.83,Streptococcus gordonii strain FDAARGOS_257,positive,,1302,Complete,FDAARGOS_257,,,,,,FDA:FDAARGOS_257,,2017-03-29T00:00:00Z,,PRJNA231221,SAMN04875583,,,CP020450,,US Food and Drug Administration,,PacBio,24.23x,CA v. 8.2,1,,1,2222466,40.42,2265,2111,Blood,Blood,,22-Aug-14,USA,USA:DC,,,,,,"Human, Homo sapiens",female,,Infection with Streptococcus gordonii,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:George Washington University,99.9,98.3,99.5,4,,Good,2017-05-28T05:04:50.054Z,2017-05-28T05:04:50.054Z
976,1307.4627,Streptococcus suis strain GX69,positive,,1307,Complete,GX69,serovar 7,,,MLST.Streptococcus_suis.373,,,,2021-10-13T00:00:00Z,,PRJNA702910,SAMN18029937,GCA_020462325.1,,CP071806,,National Institute for Communicable Disease Control and Prevention,,Illumina NovaSeq,845x,SOAPdenovo v. SOAPdenovo 2.04,1,,1,2388171,40.844143,2424,2277,None,,,2016,,China,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Streptococcus suis serotype 7 genome sequences,"sample_type:pure cultures of bacteria;collected_by:State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention",99.4,99,,,,Good,2021-12-24T11:09:47.683Z,2021-12-24T11:09:47.683Z
993,1309.331,Streptococcus mutans strain P1,positive,,1309,Complete,P1,c,,,,,,,2020-03-29T00:00:00Z,,PRJNA613248,SAMN14397573,GCA_011765545.1,,CP050273,,University of Florida,,PacBio,50x,Celera Assembler v. 8.3rc2,1,,1,2085371,36.865864,2069,1962,Mouth,root canal,,15-Mar,Brazil,Brazil,,,,,,"Human, Homo sapiens",,,endodontic infection; primary endodontic infection - Patient #1,,,,,,,,,,,,,,,,These strains were isolated from subjects with primary or secondary endodontic infections,collected_by:Augusto R. Lima,98.8,98.6,,,,Good,2020-04-12T02:25:57.923Z,2020-04-12T02:25:57.923Z
997,1310.8,Streptococcus sobrinus strain NIDR 6715-15,positive,,1310,Complete,NIDR 6715-15,,,,,,,,2018-05-30T00:00:00Z,,PRJNA471712,SAMN09232465,GCA_003176815.1,,CP029559,,University of Illinois at Urbana-Champaign,,Illumina MiSeq,300x,SPAdes v. 3.11.1,1,,1,2144746,43.66023,2154,1996,Mouth,Human dental plaque,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Streptococcus sobrinus is a Gram-positive oral pathogen. Lactic acid produced by Streptococcus sobrinus causes dental caries. The goal of this study was to assemble the first complete genomes of two strains of Streptococcus sobrinus.,sample_type:Cell culture,99.2,98.5,98.8,1.9,,Good,2018-07-15T20:33:31.508Z,2018-07-15T20:33:31.508Z
1049,1311.983,Streptococcus agalactiae strain NGBS357,positive,,1311,Complete,NGBS357,,,,MLST.Streptococcus_agalactiae.297,,,,2016-08-25T00:00:00Z,,PRJNA293858,SAMN04007152,GCF_001712835.1,,CP012503,NZ_CP012503.1,Public Health Ontario,,PacBio; Illumina,missing,,1,,1,2172875,35.6,2147,2046,None,,,2011,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,Closed whole genome sequence of mosaic NGBS375 group B Streptococcus strain,,99.9,99.8,100,,,Good,2016-09-12T00:20:10.820Z,2016-09-12T00:20:10.820Z
1172,1313.39228,Streptococcus pneumoniae strain SCAID PHRX1-2021,positive,,1313,Complete,SCAID PHRX1-2021,,,,MLST.Streptococcus_pneumoniae.377,,,,2021-09-09T00:00:00Z,,PRJNA754843,SAMN20982453,GCA_019915285.1,,CP082820,,Scientific Center for Anti-infectious Drugs (SCAID),,PacBio Sequel,386x,Canu v. 2.0,1,,1,2098200,39.720524,2188,2032,Respiratory,Swab from Pharynx,,5/18/21,Kazakhstan,Kazakhstan: Almaty,,,,,,Homo sapiens,male,69,pneumonia,,,host_disease_outcome:Recovery;host_disease_stage:Acute pneumonia,Susceptible;Resistant;Intermediate,Computational Prediction,,,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",99.5,99,,,,Good,2021-12-23T23:35:18.752Z,2021-12-23T23:35:18.752Z
1360,1314.999,Streptococcus pyogenes strain emm22.8,positive,,1314,Complete,emm22.8,,,,MLST.Streptococcus_pyogenes.360,,,,2019-05-06T00:00:00Z,,PRJNA454341,SAMN10793316,GCA_005161605.1,,CP035438,,University of Melbourne,,PacBio,80x,HGAP v. 2,1,,1,1950616,38.319946,2023,1919,Skin,skin,,,India,India,,,,,,"Human, Homo sapiens",,,Skin,,,,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,100,99.8,,,,Good,2019-07-16T00:18:07.153Z,2019-07-16T00:18:07.153Z
1369,1319.3,Streptococcus sp. 'group B' strain FDAARGOS_229,positive,,1319,Complete,FDAARGOS_229,GBS,,,MLST.Streptococcus_agalactiae.17,,FDA:FDAARGOS_229,,2017-03-29T00:00:00Z,,PRJNA231221,SAMN04875566,,,CP020432,,US Food and Drug Administration,,PacBio,17.49622562x,HGAP v. 3,1,,1,2178064,35.62,2284,2151,Cerebrospinal Fluid,CSF,,11-Jul-14,USA,USA:DC,,,,,,"Human, Homo sapiens",female,6W,Meningitis,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:Children's National Hospital,99.9,98.8,100,3,,Good,2017-05-28T05:11:32.294Z,2017-05-28T05:11:32.294Z
1374,1328.24,Streptococcus anginosus strain J4206,positive,,1328,Complete,J4206,,,,,genotype:Daptomycin resistant,,,2016-08-02T00:00:00Z,,PRJNA270893,SAMN03271571,GCA_001697145.1,,CP012719,,University of Oklahoma Health Sciences Center,,Illumina,628x,Geneious v. 6.1.8,1,,1,2001352,38.62,1953,1912,Blood,Blood,,10-Jun,USA,"USA: San Antonio, TX",,,,,,"Human, Homo sapiens",male,47,Bacteremia,,,,,,,,,,,,,,,,Genomic sequence of a daptomycin-resistant human pathogen.,collected_by:University of Texas Health Science Center at San Antonio,99.6,99.3,98.3,0.3,,Good,2016-09-11T17:36:48.869Z,2016-09-11T17:36:48.869Z
1389,1338.85,Streptococcus intermedius strain FDAARGOS_769 strain Not applicable,positive,,1338,Complete,Not applicable,,,,,,FDA:FDAARGOS_769,,2020-06-04T00:00:00Z,,PRJNA231221,SAMN11056484,GCA_013267515.1,,CP053999,,US Food and Drug Administration,,Pacbio; Illumina,2037.3x,"SMRT v. 2.3.0, HGAP v. 3",1,,1,1933377,37.717785,1978,1875,Mouth,dental plaque,,,USA,USA:VA,,,,,,"Human, Homo sapiens",female,4Y,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),98.4,98.1,,,,Good,2020-07-01T03:46:37.353Z,2020-07-01T03:46:37.353Z
1427,1349.244,Streptococcus uberis strain NCTC4674,positive,,1349,Complete,NCTC4674,not available: to be reported later,,,,,NCTC:4674,,2018-06-17T00:00:00Z,,PRJEB6403,SAMEA3956095,GCA_900475695.1,,LS483408,,SC,,,,,1,,1,2024265,36.52852,1979,1951,None,not available: to be reported later,,1900/1932,United Kingdom,United Kingdom: London,,,,,,"Human, Homo sapiens",,,,,,host_health_state:Mastitis,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.4,98.5,100,1.9,,Good,2018-07-16T22:54:38.093Z,2018-07-16T22:54:38.093Z
1615,1352.8996,Enterococcus faecium strain VRE,positive,,1352,Complete,VRE,,,,,genotype:VanA,,,2019-11-23T00:00:00Z,,PRJNA589567,SAMN13283502,GCA_009697285.1,,"CP046077,CP046079,CP046074,CP046075,CP046078,CP046076",,Public Health Agency of Canada,,Illumina; Oxford Nanopore MiniION,73.0x,SPAdes v. 1.6,1,5,6,3347130,37.67658,3434,3245,None,,,8/11/17,Canada,Canada,,,,,,"Human, Homo sapiens",,,BSI,,,,,,,,,,,,,,,,"Enterococcus faecium, ST1478",collected_by:CNISP,98,96.2,,,,Good,2019-12-31T05:32:45.798Z,2019-12-31T05:32:45.798Z
1651,1353.8,Enterococcus gallinarum strain FDAARGOS_163,positive,,1353,Complete,FDAARGOS_163,,,,,,FDA:FDAARGOS_163,,2016-02-11T00:00:00Z,,PRJNA231221,SAMN03996308,GCF_001558875.1,"SRR2822448,SRR2822449","CP014067,CP014068","NZ_CP014067.1,NZ_CP014068.1",US Food and Drug Administration,,Pacbio,25.024x,HGAP3 v. Oct 2014,1,1,2,3821349,42.32,3733,3476,Skin,Elbow swab,,5/23/14,USA,USA:DC,,,,,,"Human, Homo sapiens",male,6Y,Septic Arthritis/Cellulitis,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:Children's National Hospital,99.9,98.2,99.8,1.9,,Good,2016-03-01T20:26:00.209Z,2016-03-01T20:26:00.209Z
1654,1354.41,Enterococcus hirae strain FDAARGOS_234,positive,,1354,Complete,FDAARGOS_234,,,,,,FDA:FDAARGOS_234,,2017-08-30T00:00:00Z,,PRJNA231221,SAMN04875571,GCA_002278015.1,,CP023011,,US Food and Drug Administration,,PacBio,26.47x,CA v. 8.2,1,,1,2845444,36.99,2700,2503,Skin,Abscess,,14-Sep-14,USA,USA:DC,,,,,,"Human, Homo sapiens",male,19Y,Gluteal abscess,,,,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,98.8,97.6,100,2,,Good,2017-09-28T21:30:59.256Z,2017-09-28T21:30:59.256Z
1684,1390.556,Bacillus amyloliquefaciens strain ONU 553,positive,,1390,Complete,ONU 553,,,,,,,,2019-09-03T00:00:00Z,,PRJNA562567,SAMN12625031,GCA_008244925.1,,CP043416,,Odessa National after I.I. Mechnikov,,Illumina MiSeq,12.0x,Newbler v. 2.8,1,,1,3934563,46.688286,3953,,None,bottom sediment,isolated from Black Sea bottom sediments on depth 183 m for screening antagonistically active bacteria against oportunistic human and plant pathogens,30-Mar-11,Ukraine,Ukraine,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Strain Bacillus amyloliquefaciens ONU 553 was isolated from Black Sea bottom sediments on depth 183 m for screening antagonistically active bacteria against oportunistic human and plant pathogens.,sample_type:sediment kern,99.4,98.4,,,,Good,2019-10-02T03:20:07.759Z,2019-10-02T03:20:07.759Z
1688,1392.92,Bacillus anthracis BA1035,positive,,1392,Complete,BA1035,,,,MLST.Bacillus_cereus.3,,,,2015-02-05T00:00:00Z,-,PRJNA238135,SAMN03010427,GCA_000832725.1,"SRR2174564,SRR2174565","CP009700.1,CP009699.1,CP009698.1","NZ_CP009700.1,NZ_CP009699.1,NZ_CP009698.1",Los Alamos National Laboratory,,Illumina; 454,323x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,1,2,3,5487255,35.23,5852,5746,None,Human Clinical,,,South Africa,South Africa,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,,,,,,,,Genome sequencing of Bacillus anthracis BA1035,,100,99.3,100,,,Good,2015-03-12T13:43:22.795Z,2015-03-16T03:17:09.594Z
1694,1396.2548,Bacillus cereus strain JHU,positive,,1396,Complete,JHU,,,,,,,,2019-12-10T00:00:00Z,,PRJNA591929,SAMN13391868,GCA_009738575.1,,"CP046511,CP046512,CP046513",,Johns Hopkins University,,Oxford Nanopore; Illumina HiSeq,210.0x,Canu v. v1.8,1,2,3,6127422,34.898624,6505,5896,None,young female patient,,2019-03,USA,USA,,,,,,"Human, Homo sapiens",,,"cancer, immunosuppressed",,,,,,,,,,,,,,,,clinical isolate,collected_by:David Nauen,97.9,95,,,,Good,2019-12-31T20:22:36.050Z,2019-12-31T20:22:36.050Z
1702,1402.452,Bacillus licheniformis strain KS28,positive,,1402,Complete,KS28,,,,,,,,2020-09-21T00:00:00Z,,PRJNA558883,SAMN12501148,GCA_014672855.1,,CP043490,,Korea Centers for Disease Control & Prevention (KCDC),,IonTorrent; PacBio,181.0x,SPAdes v. 3.1,1,,1,4384483,45.813587,5556,4481,Blood,blood,,2016-06,South Korea,South Korea,,,,,,"Human, Homo sapiens",,,Absorbent pulmonary edema,,,,,,,,,,,,,,,,A clinical isolate of Bacillus licheniformis,collected_by:Gyeongsang National University,99.6,92.9,,,,Good,2020-11-28T19:25:32.089Z,2020-11-28T19:25:32.089Z
1709,1408.387,Bacillus pumilus strain UAMX,positive,,1408,Complete,UAMX,,,,,,,,2020-07-19T00:00:00Z,27018166,PRJNA645214,SAMN15498547,GCA_013423765.1,,CP058951,,Universidad Autonoma Metropolitana,,PacBio RSII,2.0x,CANU v. 1.8,1,,1,3854893,41.70772,4046,3850,Stool,feces,,1-Jan-05,Mexico,Mexico,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,The aim of this study is know role of Bacillus pumilus on gut human microbiota.Actualy Bacillus genus is not considerated that part of normal gut human microbiota. We want know influence of Bacillus over gut human microbiota.,sample_type:SINGLE STRAIN,97.1,95,,,,Good,2020-07-28T14:54:31.362Z,2020-07-28T14:54:31.362Z
1721,1423.45,Bacillus subtilis strain TLO3,positive,,1423,Complete,TLO3,,,,,,,,2017-09-12T00:00:00Z,,PRJNA401163,SAMN07598856,GCA_002290305.1,,CP023257,,Northwest University for Nationalities,,PacBio,136.0x,SOAPec v. MAY-2017,1,,1,4072939,43.61,4465,4182,Mouth,dental plaque,,4/10/17,China,China: Gansu,,,,,env_biome:Human,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Bacteriostasis of oral bacillus subtilis,,99.8,98.9,100,0.4,,Good,2017-09-28T22:02:37.864Z,2017-09-28T22:02:37.864Z
1724,1428.252,Bacillus thuringiensis 97-27,positive,,1428,Complete,97-27,,,,MLST.Bacillus_cereus.113,,,,2015-02-05T00:00:00Z,-,PRJNA238236,SAMN03223175,GCA_000833085.1,"SRR2175478,SRR2175479","CP010088.1,CP010087.1","NZ_CP010088.1,NZ_CP010087.1",Los Alamos National Laboratory,,Illumina; 454,332x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,1,1,2,5312686,35.36,5477,5327,None,,,2006,,,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,,,,,,,,Genome sequencing of Bacillus thuringiensis 97-27,,99.9,99.6,99.8,,,Good,2015-03-12T13:44:10.685Z,2015-03-16T03:17:09.594Z
1780,1491.662,Clostridium botulinum strain CDC_69094,positive,,1491,Complete,CDC_69094,,,,MLST.Clostridium_botulinum.6,,,,2016-11-16T00:00:00Z,,PRJNA301978,SAMN04262333,GCF_001879605.1,,CP013246,NZ_CP013246.1,Los Alamos National Laboratory,,Illumina; PacBio,309x; 263x,Velvet v. 1.2.08; HGAP v. 3; Phrap SPS,1,,1,4089027,28.14,3854,3711,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,C,,Anaerobic,,,Clostridium botulinum CDC_69094 annotated genome assembly,sample_type:Microbial isolate,100,99.5,100,,,Good,2017-01-16T02:35:56.957Z,2017-01-16T02:35:56.957Z
1786,1492.235,Clostridium butyricum strain CBUT,positive,,1492,Complete,CBUT,,,,,,,,2021-04-30T00:00:00Z,,PRJNA722306,SAMN18751771,GCA_018140655.1,,"CP073277,CP073278",,Pendulum Therapeutics,,PacBio Sequel; Illumina MiSeq,95x,Canu v. 2.0,1,1,2,4488390,28.778494,4047,3923,None,,,9/22/16,USA,USA,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"A growing body of evidence suggests that specific, naturally occurring gut bacteria are under-represented in the intestinal tracts of subjects with type 2 diabetes (T2D) and that their functions, like gut barrier stability and butyrate production, are important to glucose and insulin homeostasis. The objective of this study was to test the hypothesis that enteral exposure to microbes with these proposed functions can safely improve clinical measures of glycemic control and thereby play a role in the overall dietary management of diabetes.",sample_type:cell culture,97.7,95.7,,,,Good,2021-06-02T17:41:08.558Z,2021-06-02T17:41:08.558Z
1921,1496.897,Peptoclostridium difficile strain 08ACD0030,negative,,1496,Complete,Human,,,,,,,,2016-02-29T00:00:00Z,,PRJNA274772,SAMN03332454,GCF_001577795.1,SRR1793541,CP010888,NZ_CP010888.1,Canadian Science Centre for Human and Animal Health,,PacBio,51x,SMRT Analysis v. 2.3.0,1,,1,4167076,28.82,3820,3627,Stool,Stool sample (feces),,2005,Canada,Canada: Ontario,,,,,,"Human, Homo sapiens",,,"Enterocolitis, Pseudomembranous",,,,,,Positive,Bacilli,,,,,,Anaerobic,,,This isolate is involved in a study analysing North American Pulsed Field type 4 (NAP4) Clostridium difficile in Canada through genomic analysis.,collected_by:Public Health Agency of Canada,99.9,99.3,100,0.6,,Good,2016-03-18T09:28:46.069Z,2016-03-18T09:28:46.069Z
1927,1502.338,Clostridium perfringens strain CBA7123,positive,,1502,Complete,CBA7123,,,,,,,,2016-08-25T00:00:00Z,,PRJDB5093,SAMD00057672,GCA_002355795.1,,"AP017630,AP017631",,Korea Basic Science Institute,,PacBio,282.57x,PacBio SMRT Analysis v. 2.3.0,2,,2,3135010,28.52,2836,,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"The genomic data of Clostridium perfringens CBA7123 belonging to the family Clostridiaceae of the phylum Firmicutes, were obtained using the PacBio platform. The draft genome of Clostridium perfringens CBA7123 contains, 3,135,010 bp. Detailed genomic analyses and comparative studies with other bacterial genomes will give further information and insight into the metabolism of bacterial species.",,99.5,98.5,100,1.1,,Good,2017-11-23T01:46:01.251Z,2017-11-23T01:46:01.251Z
2150,1639.993,Listeria monocytogenes strain L2626,positive,,1639,Complete,L2626,1/2a,,,MLST.Listeria_monocytogenes.561,,,,2015-06-03T00:00:00Z,,PRJNA243256,SAMN02713641,GCF_001027245.1,,CP007684,NZ_CP007684.1,Cornell University,,PacBio,,HGAP and Quiver v. October 2013,1,,1,2907486,38,2874,2825,None,human host,,2011,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,Yes,,,,,,HostAssociated,Listeriosis,Listeria monocytogenes L2626 obtained from human clinical isolate,,99.9,99.5,100,,,Good,2016-01-17T16:07:07.473Z,2016-01-17T16:07:07.473Z
2157,1655.52,Actinomyces naeslundii strain ATCC 27039,negative,,1655,Complete,ATCC 27039,,,,,,ATCC 27039,,2016-10-26T00:00:00Z,,PRJDB5207,SAMD00064391,GCA_002355915.1,,AP017894,,Osaka Dental University,,PacBio RS II,200x,HGAP algorithm in the SMRT Analysis v. 2.3,1,,1,3040449,68.44,3548,3229,Wound,abdominal wound abscess,isolated from abdominal wound abscess,1969,USA,USA:Georgia,,,,,env_biome:human-associated habitat,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,No,,Mesophilic,,,Anaerobic,HostAssociated,abscess,"We present here the complete genome sequence of Actinomyces naeslundii ATCC 27039, a strain isolated from abdominal wound abscess. This strain is amenable to genetic manipulation by transformation and so provides a useful foundation for more detailed investigation of this species.",,94.9,89.4,97.3,18,High CheckM contamination score,Poor,2017-11-23T01:49:24.235Z,2017-11-23T01:49:24.235Z
2158,1659.4,Actinomyces israelii strain NCTC12972,negative,,1659,Complete,NCTC12972,not available: to be reported later,,,,,NCTC:12972,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA4364212,GCA_900637225.1,,LR134357,,SC,,,,,1,,1,2572997,64.12013,2206,2145,Brain,brain abscess,,1948,USA,United States,,,,,,"Human, Homo sapiens",,,,,,host_health_state:disease,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,97.3,96.7,,,,Good,2019-02-01T13:53:10.434Z,2019-02-01T13:53:10.434Z
2173,1689.18,Bifidobacterium dentium strain NCTC11816,positive,,1689,Complete,NCTC11816,not available: to be reported later,,,,,NCTC:11816,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA4076722,GCA_900637175.1,,LR134349,,SC,,,,,1,,1,2635828,58.538986,2240,2138,Mouth,Dental caries,,1900/1974,,,,,,,,"Human, Homo sapiens",,,,,,host_health_state:disease,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.9,99.9,,,,Good,2019-02-01T13:50:49.831Z,2019-02-01T13:50:49.831Z
2180,1717.498,Corynebacterium diphtheriae strain NCTC7838,positive,,1717,Complete,NCTC7838,not available: to be reported later,,,MLST.Corynebacterium_diphtheriae.10,,NCTC:7838,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA104318198,GCA_900638715.1,,LR134537,,SC,,,,,1,,1,2435114,53.466736,2396,2287,None,not available: to be reported later,,1900/1949,United Kingdom,United Kingdom: Newcastle,,,,,,"Human, Homo sapiens",,,,,,host_health_state:not available: to be reported later,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.9,99.3,,,,Good,2019-02-01T14:22:47.419Z,2019-02-01T14:22:47.419Z
2181,1719.86,Corynebacterium pseudotuberculosis strain 48252,positive,,1719,Complete,48252,,,,,,,,2014-07-17T00:00:00Z,25189581,PRJNA254108,SAMN02899720,GCA_000730365.1,SRR2984614,CP008922.1,NZ_CP008922.1,"Oslo University Hospital, Rikshopitalet",,PacBio,,HGAP v. v3,1,,1,2338139,52.2,2211,2227,Lung,,isolated form a patient with Corynebacterium pseudotubeculosis pneumonia,,,,,,,,,"Human, Homo sapiens",,,Corynebacterium pseudotubeculosis pneumonia,,,,,,,,,,,,,,,,The strain was isolated form a patient with Corynebacterium pseudotubeculosis pneumonia.,,98.7,97.7,100,0.3,,Good,2014-12-08T23:13:34.956Z,2015-03-16T03:17:09.594Z
2200,1747.94,Propionibacterium acnes strain KCOM 1861 (= ChDC B594),positive,,1747,Complete,KCOM 1861 (= ChDC B594),,,,MLST.Propionibacterium_acnes.79,,,,2015-09-11T00:00:00Z,,PRJNA270126,SAMN03263080,GCF_001281065.1,,CP012647,NZ_CP012647.1,Chosun University,,Illumina HiSeq,1331.0x,ALLPATHS_LG v. 47944; SSPACE v. 2.3.1;,1,,1,2522438,59.99,2450,2212,Bone,Osteomyelitis,,3/1/05,Korea,Korea: Gwangju,,,,,env_biome:Osteomyelitis,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,No,,,37C,,Anaerobic,HostAssociated,,Analyzing virulence factors of Propionibacterium acnes KCOM 1861,,99.3,98.9,100,,,Good,2016-02-29T18:07:19.632Z,2016-02-29T18:07:19.632Z
2203,1764.226,Mycobacterium avium strain CECT 7407,positive,,1764,Complete,CECT 7407,,,,,,CECT:7407,,2020-12-01T00:00:00Z,33239374,PRJNA592874,SAMN13441622,,,"JAAILH010000133,JAAILH010000123,JAAILH010000124,JAAILH010000126,JAAILH010000127,JAAILH010000129,JAAILH010000130",,Veterinary Health Surveillance Center (VISAVET),,Illumina MiSeq,220.0x,SPAdes v. 3.13.0,122,11,133,5429090,68.944,5324,5142,Respiratory,respiratory secretion,,2008,Spain,Spain,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Detection of an IS6110-like sequence in M. avium that interferes with PCR detection of MTBC species in bovine tissues using IS6110-specific Real-Time PCR,sample_type:type strain,98.8,97.4,,,,Good,2021-01-02T05:43:50.902Z,2021-01-02T05:43:50.902Z
2209,1766.51,Mycolicibacterium fortuitum strain W6,positive,,1766,Complete,W6,,,,,,,,2021-10-04T00:00:00Z,33162087,PRJNA656902,SAMN15806911,GCA_020227835.1,,CP060410,,University of Wisconsin-Madison,,Illumina MiSeq,100x,SPAdes v. 3.14.1,1,,1,6555851,66.0852,6492,6306,Sputum,sputum,,,,USA,,,,,,Homo sapiens,,,Mycobacterium avium complex disease,,,,,,,,,,,,,,,,Genotypic analysis of NTM isolates from human and milk samples in Wisconsin,collected_by:Wisconsin state lab of hygiene (WSLH),99.1,97.6,,,,Good,2021-12-24T06:00:17.210Z,2021-12-24T06:00:17.210Z
2223,1767.9,Mycobacterium intracellulare strain FLAC0181,positive,,1767,Complete,FLAC0181,,,,,,,,2017-09-05T00:00:00Z,,PRJNA315990,SAMN07528789,GCA_002285675.1,,"CP023149,CP023150",,University of Michigan Medical School,,Illumina HiSeq,150X,SPAdes v. 3.9.0,1,1,2,5638643,67.92,5426,5269,None,,,2014,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of M. abscessus complex isolates.,collected_by:Lindsay J. Caverly,99.3,98.4,100,,,Good,2017-09-28T21:52:39.352Z,2017-09-28T21:52:39.352Z
2489,1773.31,Mycobacterium tuberculosis UT205,positive,Mycobacterium tuberculosis UT205,1097669,Complete,,,,,,,,,2012-02-24T00:00:00Z,22404577,PRJNA162183,SAMEA2272432,GCA_000304555.1,,HE608151.1,,,,,,,1,,1,4418088,63.3,4212,3804,Sputum,sputum,,,Colombia,,,,,,,"Human, Homo sapiens",male,33,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,,,Tuberculosis,-,,99.6,99.3,100,,,Good,2014-12-08T22:12:21.985Z,2015-03-16T03:17:09.594Z
2637,1773.9612,Mycobacterium tuberculosis strain TBMENG-03,positive,,1773,Complete,TBMENG-03,,,,,,,,2018-07-09T00:00:00Z,,PRJNA453104,SAMN08973501,GCA_003293655.1,,CP029065,,National JALMA Institute for Leprosy and Other Mycobacterial Diseases,,Illumina NextSeq,1.0x,SPAdes v. V3.9.0,1,,1,4359659,65.55878,4396,4218,Sputum,sputum,,12-Apr-16,India,India,,,,,,"Human, Homo sapiens",male,36,Tuberculous meningitis,,,host_disease_stage:Accute,Susceptible,Computational Prediction,,,,,,,,,,,To study the genetic variations between bacilli causing Tuberculous meningitis & Pulmonary tuberculosis,collected_by:NRL-National JALMA Institute for Leprosy & Other Mycobacterial Diseases,99.8,99,98.9,2.1,,Good,2018-07-16T12:37:37.040Z,2018-07-16T12:37:37.040Z
2641,1774.88,Mycobacteroides chelonae strain MOTT36W,positive,,1774,Complete,MOTT36W,,,,,,,,2018-08-15T00:00:00Z,,PRJNA484844,SAMN09770287,GCA_003390495.1,,CP031516,,Seoul National University College of Medicine,,pacBio and illumina Hi-Seq,57.37x,HGAP v. 2.1,1,,1,5106636,64.11773,5044,,Sputum,sputum sample,,2010,South Korea,"South Korea: Asan medical center, Seoul",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Mycobacterium chelonae Genome sequencing and assembly,sample_type:cultured bacteria,99,98,100,,,Good,2018-09-30T16:40:44.807Z,2018-09-30T16:40:44.807Z
2644,1778.5,Mycobacterium gordonae strain X7091,positive,,1778,Complete,X7091,,,,,,,,2021-03-01T00:00:00Z,,PRJNA703698,SAMN18021193,GCA_017086405.1,,"CP070973,CP070974",,"Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College",,PacBio RSII,110.0x,Celera Assembler v. Dec-2020,1,1,2,7319570,66.666664,6699,,Skin,skin biopsy,,7/1/19,China,China:Jiangsu,,,,,,Homo sapiens,,,Mycobacteriaceae,,,,,,,,,,,,,,,,Description of Mycobacterium gordonae subsp. camsnse subsp. nov,"collected_by:Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College",98.9,97.1,,,,Good,2021-03-27T20:53:07.527Z,2021-03-27T20:53:07.527Z
2645,1781.9,Mycobacterium marinum strain MMA1,positive,,1781,Complete,MMA1,,,,,,,,2021-01-22T00:00:00Z,33336253,PRJNA630296,SAMN14832045,GCA_016745295.1,,CP058277,,NIH,,PacBio Sequel,260.0x,HGAP v. 6.0,1,,1,6321947,65.798386,5595,5228,Skin,elbow skin biopsy from patient with disseminated infection,,27-Apr-18,USA,USA:Maryland,,,,,,"Human, Homo sapiens",,,Disseminated Mycobacterium marinum infection,,,,,,,,,,,,,,,,Whole genome sequencing of serial M. marinum isolates from a single patient with disseminated disease,collected_by:NIAID,99.5,98.1,,,,Good,2021-02-01T07:56:05.626Z,2021-02-01T07:56:05.626Z
2646,1784.14,Mycobacterium simiae strain MO323,positive,,1784,Complete,MO323,,,,,,BEI<USA>:NR-4434,,2016-03-10T00:00:00Z,,PRJNA276839,SAMN03381263,GCF_001584765.1,,CP010996,,BEI Resources/American Type,,Illumina,98.87,CLC Genomics Workbench v. 7.0.2,,,1,5938797,66.28,5793,5056,Lung,Bronchiae,,6/14/89,USA,USA: Texas: San Antonio,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,A clinical isolate of Mycobacterium simiae obtained from a bronchial lavage,,98.5,96.7,100,4.4,,Good,2016-03-18T15:42:51.890Z,2016-03-18T15:42:51.890Z
2654,1802.8,Mycolicibacterium farcinogenes strain BKK/CU-MFGLA-001,positive,,1802,Complete,BKK/CU-MFGLA-001,,,,,,,,2021-08-24T00:00:00Z,,PRJNA749947,SAMN20463125,GCA_019739095.1,,CP080510,,Chulalongkorn University,,Oxford Nanopore MiniION,22x,Flye v. 2.8.3,1,,1,6276329,66.40089,6060,5919,Liver,liver,,2019,Thailand,Thailand: Bangkok,,,,,,Homo sapiens,,,Liver abscessus,,,,,,,,,,,,,,,,Mycobacterium app isolated from patients in Thailand,collected_by:King Chulalongkorn Memorial Hospital,99,97.2,,,,Good,2021-09-29T12:24:52.242Z,2021-09-29T12:24:52.242Z
2668,1806.25,Mycobacterium tuberculosis variant microti strain Mycobacterium microti Maus IV,positive,,1806,Complete,Mycobacterium microti Maus IV,,,,,,ATCC 35782,,2021-01-25T00:00:00Z,,PRJEB40500,SAMEA7336318,GCA_904810355.1,,LR882497,,IP,,,,,1,,1,4385022,65.61625,4260,,None,Human clinical isolate,isolated from voles in the UK in the 1930's and was kindly supplied by M. J. Colston; (2) Mycobacterium microti ATCC 35782 (also designated as TMC 1608 [M,1999,Germany,Germany,,,,,,"Human, Homo sapiens",,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,,,"We performed whole-genome sequencing of the five following Mycobacterium microti strains: (1) Mycobacterium microti OV254, which was originally isolated from voles in the UK in the 1930's and was kindly supplied by M. J. Colston; (2) Mycobacterium microti ATCC 35782 (also designated as TMC 1608 [M.P. Prague]), which was purchased from the American Type Culture Collection; (3) Mycobacterium microti 94-2272, which was isolated in 1988 from the perfusion fluid of a 41-year-old dialysis patient and was kindly provided by L. M. Parsons; (4) Mycobacterium microti Maus III (also known as strain 6740/00), which was obtained from the collection of the National Reference Center for Mycobacteria, Forschungszentrum Borstel, Germany; and (5) Mycobacterium microti Maus IV (also known as strain 1479/99), which was obtained from the collection of the National Reference Center for Mycobacteria, Forschungszentrum Borstel, Germany. On one hand, genomic DNA of M. microti strain were prepared using the SMRTbell Template library preparation kit and sequenced at the Biomics platform of the Institut Pasteur (Paris, France) using the PacBio SMRT long-read sequencing technology (Chemistry v2.1; Sequel ICS v5.0.1; SMRT Link v5.0.1). On the other hand, genomic DNA of M. microti strains were sequenced using the Illumina paired-end short-read sequencing technology. Strains OV254, ATCC 35782, 94-2272 and Maus IV were sequenced at the Wellcome Trust Sanger Institute (Hinxton, UK) using a Genome Analyzer IIx device, while strain Maus III was sequenced at the Biomics platform of the Institut Pasteur (Paris, France) using a HiSeq 2500 device. First, Raw PacBio subreads were assembled using Canu and generated supercontigs were then organized as compared to the genome of M. bovis BCG Pasteur 1173P2 using MeDuSa. Second, Illumina read pairs were trimmed using Trimmomatic. Complete read pairs were then assembled using SPAdes and providing either raw PacBio subreads or the scaffolds of PacBio supercontigs. Illumina contigs thus generated were then compared to the PacBio scaffolds using BLASTN to correct erroneous arrangements and to fill undefined gaps. Third, Illumina read pairs were mapped against the resulting assembled genome using BWA-MEM. Variants were then called using VarScan to detect and correct sequencing errors within whole-genome assemblies.",,99.3,98.6,,,,Good,2021-02-01T08:19:46.224Z,2021-02-01T08:19:46.224Z
2673,1809.3,Mycobacterium ulcerans strain JKD8049,positive,,1809,Complete,JKD8049,,,,,,,,2021-10-26T00:00:00Z,,PRJNA771185,SAMN22253492,GCA_020616615.1,,"CP085200,CP085201",,University of Melbourne,,Oxford Nanopore,240.0x,FLYE v. 2021,1,1,2,5789332,65.41058,5720,5159,Skin,,,2004,Australia,"Australia: Point Lonsdale, Victoria",,,,,,Homo sapiens,male,,Buruli ulcer,,,,,,,,,,,,,,,,Complete genome of Mycobacterium ulcerans strain JKD8049,collected_by:Victorian Infectious Diseases Reference Laboratory,99.7,98.5,,,,Good,2021-12-24T14:43:14.568Z,2021-12-24T14:43:14.568Z
2860,2047.689,Rothia dentocariosa strain FDAARGOS_752 strain Not applicable,negative,,2047,Complete,Not applicable,,,,,,FDA:FDAARGOS_752,,2020-06-04T00:00:00Z,,PRJNA231221,SAMN11056467,GCA_013267735.1,,CP054018,,US Food and Drug Administration,,Pacbio; Illumina,1267.78x,Canu v. 1.7,1,,1,2533415,53.801647,2308,2126,Sputum,expectorated sputum,,,USA,USA:VA,,,,,,"Human, Homo sapiens",male,32Y,Cystic fibrosis,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),99.1,98.7,,,,Good,2020-07-01T03:49:05.538Z,2020-07-01T03:49:05.538Z
2862,2055.18,Gordonia terrae strain JH63,positive,,2055,Complete,JH63,,,,,,,,2020-01-11T00:00:00Z,,PRJNA597702,SAMN13680426,GCA_009856645.1,,"CP047235,CP047236",,Changwon National University,,PacBio RSII,96.0x,HGAP v. 2.3,1,1,2,5338743,67.85895,4955,4684,Skin,skin,,2017-07,South Korea,South Korea: Changwon,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,cholesterol degradation,sample_type:whole organism,96.7,95.9,,,,Good,2020-02-07T13:50:54.571Z,2020-02-07T13:50:54.571Z
2891,2098.79,Mycoplasma hominis strain 8958,negative,,2098,Complete,8958,,,,,,,,2020-06-23T00:00:00Z,,PRJNA429440,SAMN15042588,GCA_013371665.1,,CP055142,,University Hospital of Dusseldorf,,Nanopore + Illumina,966x,Canu v. 1.6,1,,1,680851,26.995335,588,570,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing and comparison of multiple M. hominis isolates.,,97,96.7,,,,Good,2020-07-02T03:46:20.104Z,2020-07-02T03:46:20.104Z
3130,2104.464,Mycoplasma pneumoniae strain 10-980,negative,,2104,Complete,10-980,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,SAMN11472195,GCA_009948395.1,,CP039790,,Chungbuk National University Hospital,,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,,1,816424,40.00997,786,742,Respiratory,nasophraynx,,2010,South Korea,South Korea: Seoul,,,,,,"Human, Homo sapiens",,,Pneumonia,,,,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,99.4,99.3,,,,Good,2020-04-11T21:08:35.725Z,2020-04-11T21:08:35.725Z
3140,2130.41,Ureaplasma urealyticum strain 315,positive,,2130,Complete,315,,,,,,,,2019-07-09T00:00:00Z,,PRJNA513930,SAMN10716289,GCA_006777105.1,,CP039963,,"Sir Run Run Shaw Hospital, Zhejiang University School of Medicine",,Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.7,1,,1,853955,25.740232,679,660,Semen,male semen,,2016-06,China,China,,,,,,"Human, Homo sapiens",,,infertility,,,,,,,,,,,,,,,,A clinical Ureaplasma urealyticum isolated from infertile male,collected_by:Department of Clinical Laboratory Sir Run Run Shaw Hospital Zhejiang University School of Medicine,99.9,99.3,,,,Good,2019-09-30T16:41:20.652Z,2019-09-30T16:41:20.652Z
3221,2702.191,Gardnerella vaginalis strain FDAARGOS_568 strain Not applicable,negative,,2702,Complete,Not applicable,,,,,,FDA:FDAARGOS_568,,2018-11-21T00:00:00Z,,PRJNA231221,SAMN10163192,GCA_003812765.1,,CP033836,,US Food and Drug Administration,,Pacbio; Illumina,29.50x,Canu v. 1.2,1,,1,1716590,41.263084,1435,1415,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID,98.7,98.4,,,,Good,2018-11-30T03:08:12.896Z,2018-11-30T03:08:12.896Z
1385,13373.94,Burkholderia mallei strain FDAARGOS_590 strain Not applicable,negative,,13373,Complete,Not applicable,,,,"MLST.Burkholderia_cepacia_complex.734,MLST.Burkholderia_pseudomallei.40",genotype:UNK,FDA:FDAARGOS_590,,2018-12-14T00:00:00Z,,PRJNA231221,SAMN10228570,GCA_003933045.1,,RKJU01000000,,US Food and Drug Administration,,Pacbio; Illumina,37.30x,Canu v. 1.7,2,,2,5864677,68.48184,6265,6174,None,clinical isolate,,,China,China,,,,,,"Human, Homo sapiens",male,,Glanders-melioidosis,,,host_description:Not applicable;host_disease_outcome:fatal,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID,99.7,98,,,,Good,2019-01-31T06:15:40.498Z,2019-01-31T06:15:40.498Z
3248,28035.9,Staphylococcus lugdunensis strain FDAARGOS_143,positive,,28035,Complete,FDAARGOS_143,,,,MLST.Staphylococcus_lugdunensis.26,,FDA:FDAARGOS_143,,2016-02-11T00:00:00Z,,PRJNA231221,SAMN03996287,GCA_001558815.1,"SRR2820656,SRR2820657",CP014023,NZ_CP014023.1,US Food and Drug Administration,,Pacbio,21.54x,Celera v. 8.2,1,,1,2613826,33.95,2476,2373,Abscess,Abscess,,3/12/14,USA,USA:DC,,,,,,"Human, Homo sapiens",male,16Y,Abscess,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:Children's National Hospital,98.8,98,97.8,,,Good,2016-03-01T20:01:02.118Z,2016-03-01T20:01:02.118Z
3253,28037.232,Streptococcus mitis strain SVGS_061,positive,,28037,Complete,SVGS_061,serovar GS_061,,,,,,,2016-02-12T00:00:00Z,,PRJNA311086,SAMN04461788,GCF_001560895.1,,CP014326,NZ_CP014326.1,MD Anderson,,PacBio/Illumina,151x,HGAP/HybridSpades/Seqman NGen v.,1,,1,2167922,39.97,2007,1954,Blood,blood,,14-Dec-11,USA,"USA: Houston, Texas, MD Anderson Cancer Center",,,,,,"Human, Homo sapiens",male,25,viridans group streptococcal shock syndrome,,,host_description:Neutropenic Cancer Patient (AML);host_health_state:neutropenic,,,,,,,,C,,,,viridans group streptococcal shock syndrome,"While typically a commensal, Streptococcus mitis is frequently the cause causes invasive infections inn compromised individuals. The strain reported (SVGS_061) caused VGS shock syndrome in a neutropenic cancer patient. The investigation of this strain may aid in determining the cause of pathogeneisis of invasions caused by Streptococcus mitis.",collected_by:MD Anderson Cancer Center,99.9,99.4,100,0.3,,Good,2016-03-01T20:25:33.232Z,2016-03-01T20:25:33.232Z
3256,28080.85,Campylobacter upsaliensis strain FDAARGOS_736,negative,,28080,Complete,FDAARGOS_736,,,,,,FDA:FDAARGOS_736,,2020-08-05T00:00:00Z,,PRJNA231221,SAMN11056451,GCA_014068875.1,,"CP059682,CP059683",,US Food and Drug Administration,,Pacbio; Illumina,1908.97x,"SMRT v. 2.3.0, HGAP v. 3",1,1,2,1650243,34.83486,1716,1668,Gut,gastrointestinal tract,,,USA,USA:VA,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),99,98.7,,,,Good,2020-08-22T09:14:49.862Z,2020-08-22T09:14:49.862Z
3259,28090.112,Acinetobacter lwoffii strain FDAARGOS_557,negative,,28090,Complete,FDAARGOS_557,,,,,,FDA:FDAARGOS_557,,2020-06-17T00:00:00Z,,PRJNA231221,SAMN10163181,GCA_013349205.1,,"CP054803,CP054806,CP054805,CP054804",,US Food and Drug Administration,,Pacbio; Illumina,1326.92x,"SMRT v. 2.3.0, HGAP v. 3",1,3,4,3767090,42.87972,3814,3552,None,clinical isolate,,,USA,USA:MN,,,,,,"Human, Homo sapiens",not applicable,,,,,host_disease_outcome:Not applicable;host_health_state:Not applicable;host_description:Not applicable;host_disease_stage:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Mayo Clinic,97,95,,,,Good,2020-07-01T17:50:09.662Z,2020-07-01T17:50:09.662Z
3260,28091.9,Neisseria weaveri strain NCTC12742,negative,,28091,Complete,NCTC12742,not available: to be reported later,,,,,NCTC:12742,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA104338429,GCA_900638685.1,,LR134533,,SC,,,,,1,,1,2238481,49.0882,2295,2020,Wound,wound,,1974,Sweden,Sweden: Gothenberg,,,,,,"Human, Homo sapiens",,,,,,host_health_state:not available: to be reported later,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,97.7,97.3,,,,Good,2019-02-01T14:22:36.880Z,2019-02-01T14:22:36.880Z
3274,28116.7,Bacteroides ovatus strain ATCC 8483,negative,,28116,Complete,ATCC 8483,,,,,,ATCC:8483,,2015-10-15T00:00:00Z,26430127,PRJNA289334,SAMN03852683,GCA_001314995.1,"SRR2637631,SRR2637689,SRR2641383",CP012938,NZ_CP012938.1,Washington University in St. Louis,,PacBio; Illumina MiSeq,350X,HGAP 2.0 and Celera v. AUG-2014,1,,1,6472489,41.88,5084,4910,Stool,feces,,11-Oct-09,USA,USA:Woods Hole,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Three Bacteroides species has been mono-cultured. DNA was extracted and sequenced with Pacbio and Illumina, and assembled.",sample_type:cell culture,99.6,99.2,98.7,,,Good,2016-01-17T17:15:28.903Z,2016-01-17T17:15:28.903Z
3275,28118.6,Odoribacter splanchnicus strain NCTC10825,negative,,28118,Complete,NCTC10825,,,,,,NCTC:10825,,2017-08-15T00:00:00Z,,PRJEB6403,SAMEA44545918,GCA_900187175.1,,LT906459,,SC,,,,,1,,1,4392177,43.36,3994,3684,Abdomen,Abdominal abscess,,1968,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.8,99.6,100,0.4,,Good,2017-09-29T14:28:14.734Z,2017-09-29T14:28:14.734Z
3280,28129.6,Prevotella denticola strain F0105,negative,,28129,Complete,F0105,,,,,,,,2021-04-28T00:00:00Z,,PRJNA282954,SAMN18352179,GCA_018141825.1,,CP073339,,The Forsyth Institute,,PacBio Sequel,348x,Pacbio MA v. 9.0.0.92188,1,,1,3027740,49.960926,2856,2372,Mouth,human oral cavity,,1988-10,USA,"USA: Blacksberg, Virginia",,,634 m,,,Homo sapiens,male,14,,,,,,,,,,,,C,,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02165;collected_by:Moores, Virginia Polytechnic Institute",98.2,97.6,,,,Good,2021-06-02T17:45:06.131Z,2021-06-02T17:45:06.131Z
3292,28131.7,Prevotella intermedia strain strain 17,negative,,28131,Complete,17,,,,,,ATCC 25611,Yes,2017-01-18T00:00:00Z,,PRJNA313956,SAMN04529095,GCF_001953935.1,,"CP019302,CP019303","NZ_CP019302.1,NZ_CP019303.1",The Forsyth Institute,,PacBio,200.0x,Celera Assembler v. June 2016; HGAP v.,2,,2,2736315,43.45,2745,2385,Mouth,periodontal pocket,,1992,Japan,Japan,,,,,,"Human, Homo sapiens",,,periodontal disease,,,,,,,,,,,C,,,,,Re-sequencing of the Prevotella intermedia type strain ATCC25611 and clinical isolate Prevotella intermedia strain-17 (January 2016) using using a PacBio RS II system (Pacific Biosciences) on a single-molecule real-time (SMRT) cell using PacBio P6-C4 chemistry.,"collected_by:Fukushima, H, Moroi H, Inoue J, Onoe T, Ezaki T, Yabuuchi E, Leung KP, Walker CB, Clark WB, Sagawa H.",98.4,97.9,100,,,Good,2017-03-20T05:03:11.160Z,2017-03-20T05:03:11.160Z
3303,28132.5,Prevotella melaninogenica strain GAI 07411,negative,,28132,Complete,GAI 07411,,,,,,,,2017-09-01T00:00:00Z,,PRJDB5703,SAMD00078755,GCA_003609775.1,,"AP018049,AP018050,AP018051",,"Department of Pediatric Dentistry, Nagasaki University Graduate School of Biomedical Sciences",,PacBio RSII,246x,HGAP v. 3,2,1,3,3090326,40.773464,2520,2410,Vagina,vagina,isolated from not only periodontal pockets but also purulent infections,,Japan,Japan,,,,,,"Human, Homo sapiens",female,,,,,,,,,,,,,,,,,,"Prevotella melaninogenica is frequently isolated from not only periodontal pockets but also purulent infections. Similar to all species of the genus Prevotella, it is strictly anaerobic, gram-negative bacterium with non-spore forming coccobacilli. We used to the generation sequencing technique (PacBio RS II) to sequence the whole genome of Prevotella melaninogenica GAI 07411 isolated from the vagina. A number of potent virulence factors possessed by bacteria belonging to phylum Bacteroidetes were suggested by analyzing the genomic information. Therefore, the genomic information is indispensable to evaluate the pathogenicity and host interactions. This genomic information may provide insight into the functional activity of this strain.","biomaterial_provider:Life science Research Center, Gifu University",98.6,97.9,,,,Good,2018-11-28T19:42:18.486Z,2018-11-28T19:42:18.486Z
3305,28133.9,Prevotella nigrescens strain F0630,negative,,28133,Complete,F0630,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,SAMN18352192,GCA_018127845.1,,"CP072335,CP072336",,The Forsyth Institute,,PacBio Sequel,168x,Pacbio MA v. 9.0.0.92188,2,,2,2928207,42.697666,2814,2394,Mouth,human oral cavity,,5/7/15,USA,"USA: Cambridge, Massachusetts",,,12 m,,,Homo sapiens,male,48,,,,,,,,,,,,C,,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02185;collected_by:Pallavi Murugkar, Forsyth Institute",98,97.5,,,,Good,2021-06-02T17:19:33.397Z,2021-06-02T17:19:33.397Z
3306,28135.5,Prevotella oris strain NCTC13071,negative,,28135,Complete,NCTC13071,not available: to be reported later,,,,,NCTC:13071,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA4535752,GCA_900637655.1,,LR134384,,SC,,,,,1,,1,3168212,43.97916,2957,2703,Mouth,Gingival sulcus,,1900/1982,,,,,,,,"Human, Homo sapiens",,,,,,host_health_state:not available: to be reported later,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,98.7,97.9,,,,Good,2019-02-01T14:01:17.468Z,2019-02-01T14:01:17.468Z
3307,28137.14,Prevotella veroralis strain F0319,negative,,28137,Complete,F0319,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,SAMN18352189,GCA_018127765.1,,"CP072330,CP072331,CP072332",,The Forsyth Institute,,PacBio Sequel,377x,Pacbio MA v. 9.0.0.92188,2,1,3,2990547,41.92387,2755,2384,Mouth,human oral cavity,,1985-09,USA,"USA: Blacksberg, Virginia",,,634 m,,,Homo sapiens,male,11,,,,,,,,,,,,C,,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02188;collected_by:Moores, Virginia Polytechnic Institute",98.3,97.6,,,,Good,2021-04-26T00:37:32.049Z,2021-04-26T00:37:32.049Z
3308,28152.31,Yersinia kristensenii strain ATCC BAA-2637,negative,,28152,Complete,ATCC BAA-2637,,,,MLST.Yersinia_spp.84,,ATCC: BAA-2637,,2018-09-27T00:00:00Z,,PRJNA484516,SAMN09765716,GCA_003600645.1,,"CP032482,CP032483,CP032484",,Mayo Clinic,,Illumina MiSeq,200.0x,SPAdes v. JAN-2014,1,2,3,4448883,47.492855,4249,3996,Stool,feces,,11-Jan,USA,"USA: Rochester, MN",,,,,,"Human, Homo sapiens",,,diarrhea,,,,Susceptible;Intermediate,AMR Panel,,,,,,,,,,,Whole genome sequencing of Yersinia kristensenii EPLC-04,collected_by:Mayo Clinic,99.8,99,,,,Good,2018-11-28T18:35:59.012Z,2018-11-28T18:35:59.012Z
3314,28188.26,Capnocytophaga canimorsus strain NCTC11921,negative,,28188,Complete,NCTC11921,not available: to be reported later,,,,,NCTC:11921,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA104210801,GCA_900638435.1,,LR134513,,SC,,,,,1,,1,2528270,36.11173,2415,2220,Blood,blood,,1900/1986,,,,,,,,"Human, Homo sapiens",,,,,,host_health_state:disease,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,98.2,98,,,,Good,2019-02-01T14:17:23.662Z,2019-02-01T14:17:23.662Z
3315,28189.7,Capnocytophaga cynodegmi strain G7591,negative,,28189,Complete,G7591,,,,,,,,2017-09-14T00:00:00Z,,PRJNA369395,SAMN06754876,GCA_002302475.1,,CP022378,,Centers for Disease Control and Prevention,,PacBio; Illumina MiSeq,422.2x,Canu v. 1.4,1,,1,2640475,34.26,2396,2271,None,,,15-Jun-92,USA,USA: California,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,select isolates within the Capnocytophaga genus were biochemically characterized and sequenced for taxonomic evaluations,sample_type:cell culture,99.3,99.1,100,,,Good,2017-09-28T23:31:02.059Z,2017-09-28T23:31:02.059Z
3332,28449.59,Neisseria subflava strain M18660,negative,,28449,Complete,M18660,,,,,,,,2018-08-01T00:00:00Z,,PRJNA428178,SAMN09704641,GCA_003351665.1,,CP031251,,Centers for Disease Control and Prevention,,PacBio,107.0048358x,HGAP v. 3,1,,1,2321871,48.984116,2286,,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Assemblies for pathogens that are known to cause bacterial meningitis and other closely related species,collected_by:Centers for Disease Control and Prevention,99,97.9,100,0.7,,Good,2018-09-30T04:03:36.071Z,2018-09-30T04:03:36.071Z
3409,28450.9,Burkholderia pseudomallei strain BDP,negative,,28450,Complete,BDP,,,,MLST.Burkholderia_pseudomallei.36,,,,2014-09-18T00:00:00Z,25414490,PRJNA256982,SAMN02945025,GCA_000755765.1,,"CP009209.1,CP009210.1","NZ_CP009209.1,NZ_CP009210.1",Los Alamos National Laboratory,,Illumina; 454; PacBio,616x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,2,,2,7442161,67.891,7303,6117,Brain,brain,,1994,Australia,"Australia: Darwin, Northern Territory",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Genome sequencing of Burkholderia pseudomallei BDP,,99.2,95.6,100,0.4,,Good,2014-12-08T23:15:28.435Z,2015-03-16T03:17:09.594Z
3781,28901.9943,Salmonella enterica strain R19_2839,negative,,28901,Complete,R19.2839,Typhi,,,MLST.Salmonella_enterica.1,,,,2019-12-09T00:00:00Z,,PRJNA478278,SAMN13219579,GCA_009734305.1,,"CP046429,CP046430",,"Centers for Disease Control, Taiwan",,Illumina MiSeq; Oxford Nanopore,100.0x,unicycler v. v0.4.6,1,1,2,4896053,52.060158,5169,4698,Blood,blood,,2019,India,India:Pakistan,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"This BioProject contains the whole genome sequence data uploaded by Centers for Disease Control, Taiwan","collected_by:Centers of Disease Control, Taiwan",97.1,95.9,,,,Good,2019-12-31T18:26:41.326Z,2019-12-31T18:26:41.326Z
3787,29382.24,Staphylococcus cohnii strain FDAARGOS_334,positive,,29382,Complete,FDAARGOS_334,,,,MLST.Staphylococcus_aureus.102,,FDA:FDAARGOS_334,,2018-03-09T00:00:00Z,,PRJNA231221,SAMN06173347,GCA_002984565.1,,"CP027422,CP027420,CP027419,CP027421,CP027423,CP027424",,US Food and Drug Administration,,PacBio; Illumina,14.3396902102485x,"SMRT v. 2.3.0, HGAP v. 3.0",1,5,6,2661282,32.58839,2610,2503,Blood,peripheral blood,,22-Feb-15,USA,USA:DC,,,,,,"Human, Homo sapiens",female,10D,Contaminant,,,,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,99,98.5,98.2,1.8,,Good,2018-05-26T05:52:02.912Z,2018-05-26T05:52:02.912Z
3797,29385.324,Staphylococcus saprophyticus strain UTI-045,positive,,29385,Complete,UTI-045,,,,,,,,2020-06-18T00:00:00Z,,PRJNA636387,SAMN15089826,GCA_013358365.1,,"CP054831,CP054832,CP054833,CP054834,CP054835",,Santa Clara University,,"Illumina MiSeq, Oxford Nanopore MiniION",189.0x,Unicycler v. 0.4.8,1,4,5,2744227,33.14314,2730,2637,Urine,urine,"isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections",2019,USA,USA: California,,,,,,"Human, Homo sapiens",female,,,,,,,,,,,,,,,,,,"Several species of bacteria have been identified as major causes of urinary tract infection, but the prevalence of different bacteria can vary significantly, depending on location, timing, and demographics of the population being studied. This study is directed at identifying shared genomic and phenotypic traits in bacteria isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections.",sample_type:whole organism,98,97.2,,,,Good,2020-07-01T18:53:08.758Z,2020-07-01T18:53:08.758Z
3798,29391.22,Gemella morbillorum strain FDAARGOS_741 strain Not applicable,positive,,29391,Complete,Not applicable,,,,,,FDA:FDAARGOS_741,,2019-12-05T00:00:00Z,,PRJNA231221,SAMN11056456,GCA_009730315.1,,CP046314,,US Food and Drug Administration,,Pacbio; Illumina,1742.58x,canu v. 1.4,1,,1,1779451,30.929764,1667,1621,Sputum,expectorated sputum,,,USA,USA:VA,,,,,,"Human, Homo sapiens",male,27Y,Cystic fibrosis,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),99,99,,,,Good,2019-12-31T17:07:56.995Z,2019-12-31T17:07:56.995Z
3811,29430.79,Acinetobacter haemolyticus strain AN59,negative,,29430,Complete,AN59,,,,MLST.Acinetobacter_baumannii_2.86,,,,2020-01-16T00:00:00Z,,PRJNA311558,SAMN09927975,GCA_009892245.1,,"CP031972,CP031975,CP031974,CP031973",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",,Illumina MiSeq and PacBio RSII,296x,Unicycler v. 0.4.1,1,3,4,3694983,39.536716,3637,3467,Abdomen,Peritoneal dialysis liquid,,6-Apr-16,Mexico,Mexico: Puebla,,,,,,"Human, Homo sapiens",male,13 years,Acinetobacter infection,,,host_description:Patient was at the Emergency services,,,,,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital para el Nino Poblano,95.9,94.8,,,,Good,2020-02-01T18:10:02.800Z,2020-02-01T18:10:02.800Z
3897,29459.643,Brucella melitensis strain VB12455,negative,,29459,Complete,VB12455,,,,,,,,2019-10-13T00:00:00Z,,PRJNA575951,SAMN12917575,GCA_009017395.1,,"CP044985,CP044986",,Christian Medical College and Hospital,,Oxford Nanopore MiniION; IonTorrent,200.0x,Canu v. 1.8; Unicycler v. 0.4.7,2,,2,3311723,57.21747,3594,3301,Blood,blood,,28-Apr-19,India,India,,,,,,"Human, Homo sapiens",,,Bacterimia,,,,,,,,,,,,,,,,Brucella melitensis complete genome,collected_by:Christian Medical College and Hospital Vellore,99.9,97.5,,,,Good,2019-10-27T23:58:48.244Z,2019-10-27T23:58:48.244Z
3898,29466.62,Veillonella parvula strain NCTC11810,negative,,29466,Complete,NCTC11810,,,,,,NCTC:11810,,2017-08-15T00:00:00Z,,PRJEB6403,SAMEA4063028,GCA_900186885.1,,LT906445,,SC,,,,,1,,1,2132142,38.63,1887,1862,Gut,Intestinal tract,,1900/1981,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,100,99.9,100,,,Good,2017-09-29T14:26:44.760Z,2017-09-29T14:26:44.760Z
3899,29484.38,Yersinia frederiksenii strain FDAARGOS_417,negative,,29484,Complete,FDAARGOS_417,,,,,,FDA:FDAARGOS_417,,2017-10-18T00:00:00Z,,PRJNA231221,SAMN07312461,GCA_002591095.1,,CP023962,,US Food and Drug Administration,,PacBio; Illumina,12.18x,"SMRT v. 2.3.0, HGAP v. 3",1,,1,5000678,47.64,4781,4517,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID < MIDI < DCC < ATCC,99.6,97.9,100,0.5,,Good,2017-11-24T16:45:31.923Z,2017-11-24T16:45:31.923Z
3930,32019.101,Campylobacter fetus subsp. fetus strain CITCf02,negative,,32019,Complete,CITCf02,,,,MLST.Campylobacter_fetus.3,,,,2021-04-10T00:00:00Z,,PRJNA716563,SAMN18438775,GCA_017896405.1,,CP072665,,Munster Technological University,,Nanopore; Illumina,100.0x,SPAdes v. 3.11.1,1,,1,1766884,33.290527,1781,,Blood,blood,,2019,Ireland,Ireland,,,,,,Homo sapiens,,,endocarditis,,,,,,,,,,,,,,,,Genomic comparison of Campylobacter fetus strains isolated from a case of recurrent prosthetic valve endocarditis,collected_by:Caoimhe Lynch,99.9,99.6,,,,Good,2021-06-02T15:57:15.705Z,2021-06-02T15:57:15.705Z
3931,32021.6,Campylobacter jejuni subsp. doylei strain FDAARGOS_295,negative,,32021,Complete,FDAARGOS_295,O:17 (Penner),,ST-1845,MLST.Campylobacter_jejuni.1845,,FDA:FDAARGOS_295,,2018-03-09T00:00:00Z,,PRJNA231221,SAMN06173308,GCA_002983725.1,,CP027403,,US Food and Drug Administration,,PacBio; Illumina,25.18x,CA v. 8.2,1,,1,1845051,30.571512,2086,1914,Blood,"blood culture from a patient in Cape Town, South Africa",,1997,USA,USA:VA,,,,,,"Human, Homo sapiens",female,2Y 5M,Campylobacter infection,,,host_description:Bacteremia,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.;many frameshifted proteins","collected_by:ATCC < RE Mandrell, A Lastovica",99.5,98.8,100,2.6,,Good,2018-05-26T05:45:55.274Z,2018-05-26T05:45:55.274Z
3951,32022.895,Campylobacter jejuni subsp. jejuni strain GB19,negative,,32022,Complete,GB19,,,,MLST.Campylobacter_jejuni.61,,,,2021-03-16T00:00:00Z,,PRJNA348673,SAMN05871073,GCA_017357085.1,,"CP071592,CP071593",,"Erasmus University Medical Centre, Rotterdam, the Netherlands",,Illumina MiSeq,154.0x,Newbler v. 2.3; Geneious Reference,1,1,2,1676753,30.461727,1756,1685,Stool,feces,isolated from the feces of a patient with GBS,1998,Netherlands,Netherlands,,,,,,Homo sapiens,,,Guillain Barr� Syndrome,,,,,,,,,,,,,,,,The foodborne pathogen Campylobacter jejuni subsp. jejuni (Cjj) is a leading cause of human acute gastroenteritis and also the most important antecedent for Guillain-Barr� syndrome (GBS). We have determined the genome sequence of a Cjj strain isolated from the feces of a patient with GBS.,"collected_by:ErasmusMC, Netherlands",99.9,99.8,,,,Good,2021-03-28T02:00:02.993Z,2021-03-28T02:00:02.993Z
3953,33010.11,Propionibacterium avidum strain DPC 6544,positive,,33010,Complete,DPC 6544,,,,,,,,2016-08-26T00:00:00Z,,PRJNA339124,SAMN05579890,GCF_001714705.1,,CP016954,NZ_CP016954.1,University College Cork,,PacBio,287.8x,INVIEW DE NOVO GENOME 2.0 v. MAR-2015,1,,1,2729848,63.43,2594,2389,Stool,infant fecal swab,,2012,Ireland,Ireland,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Propionibacterium avidum DPC 6544 was sequenced after animal studies suggested probiotic potential.,sample_type:cell culture,99.4,98.2,100,0.8,,Good,2016-09-12T02:00:26.359Z,2016-09-12T02:00:26.359Z
3961,33892.42,Mycobacterium tuberculosis variant bovis BCG strain BCG_S49,positive,,33892,Complete,BCG_S49,,,,,,,,2018-10-31T00:00:00Z,,PRJNA498011,SAMN10278076,GCA_003704015.1,,CP033311,,University of Pretoria,,Illumina MiSeq,100.0x,CLC NGS Cell v. 7,1,,1,4294423,65.41946,4402,4232,Lung,superficial swab,,5-Aug-14,South Africa,South Africa,,,,,,"Human, Homo sapiens",male,8 months 1o days,Tuberculosis,,,host_description:infant,Susceptible,Computational Prediction,,,,,,,,,,,Clinical BCG isolates were sequenced and compared to reference BCG genome to identify genetic variations,collected_by:Lesedi Modipane,99.6,98.3,,,,Good,2018-11-29T08:31:32.061Z,2018-11-29T08:31:32.061Z
3964,33894.96,Mycobacterium tuberculosis variant africanum strain Various,positive,,33894,Complete,Various,,,,,,,,2021-01-25T00:00:00Z,,PRJEB42445,SAMEA104679305,GCA_905183075.1,,LR993208,,Institut Pasteur,,,,,1,,1,4374993,65.596016,4271,,None,human,,2007,France,France,,,,,,Homo sapiens,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,,,"We performed whole-genome assembly of the two following strains of the mycobacterium tuberculosis complex: (1) Mycobacterium africanum 01 (lineage L6); and (2) Mycobacterium africanum 65 (lineage L5.1). Genome sequencing was performed at the Biomics platform of the Institut Pasteur (Paris, France) using a HiSeq 2500 device. Illumina read pairs were first trimmed using Trimmomatic v0.36 (parameters: LEADING 28; TRAILING 28; SLIDINGWINDOW windowSize 5, requiredQuality 28; MINLEN 50; AVGQUAL 28). Complete read pairs were then assembled using SPAdes v3.10.1 (parameters: --careful; -k 21,33,55; --phred-offset 33). Generated contigs were finally organized as compared to the reference genome of Mycobacterium africanum GM041182 using MeDuSa v1.6 (default parameters).",,99.3,98.5,,,,Good,2021-02-27T23:31:52.306Z,2021-02-27T23:31:52.306Z
3965,33945.25,Enterococcus avium strain 352,positive,,33945,Complete,352,,,,,,,,2019-05-14T00:00:00Z,31049078,PRJNA506876,SAMN10475309,GCA_005347505.1,,"CP034169,CP034168",,shandong University,,Illumina; PacBio,210.0x,ABySS v. 2.2; CANU v. OCT-2018; blasR v.,1,1,2,4882096,38.916748,5023,4759,Bile,bile from holelithiasis patient,,2/25/18,China,China,,,,,,"Human, Homo sapiens",,,Cholelithiasis,,,,,,,,,,,,,,,,Genome Sequencing of Enterococcus avium,collected_by:Lixiang Li,97.9,93.9,,,,Good,2019-07-17T11:51:00.715Z,2019-07-17T11:51:00.715Z
3969,34062.31,Moraxella osloensis strain NP7,negative,,34062,Complete,NP7,,,,,,KCTC:52864,,2017-11-06T00:00:00Z,,PRJNA398109,SAMN07501685,,,"CP024443,CP024444,CP024445,CP024446,CP024447,CP024448,CP024449,CP024450",,Changwon National University,,PacBio,270.0x,SMRTpipe HGAP v. 3.0,1,7,8,2730583,43.05,2687,2458,Skin,skin swab,,9/22/16,South Korea,South Korea: Changwon,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Catabolism of skin microbe,sample_type:single cell,93.1,91.9,84.9,2.2,,Good,2017-11-24T17:14:17.830Z,2017-11-24T17:14:17.830Z
3971,34105.52,Streptobacillus moniliformis strain BK14232,negative,,34105,Complete,BK14232,,,,,,,,2021-07-25T00:00:00Z,,PRJNA746743,SAMN20239707,GCA_019334605.1,,CP079714,,Jena University Hospital,,Oxford Nanopore GridION,24.0x,flye v. 2.8,1,,1,1655770,26.184494,1744,1585,Joint,putrid secret,,2021-06,Germany,Germany,,,,,,Homo sapiens,,,left-sided periprosthetic infection,,,,,,,,,,,,,,,,Streptobacillus moniliformis clinical isolate,collected_by:UKJ,99.8,96.2,,,,Good,2021-08-01T21:22:13.074Z,2021-08-01T21:22:13.074Z
3983,35703.76,Citrobacter amalonaticus strain 133355-SW-C4-Cam,negative,,35703,Complete,133355-SW-C4-Cam,,,,,,,,2019-07-14T00:00:00Z,,PRJNA543044,SAMN11653541,GCA_006965505.1,,"CP041362,CP041363",,University of Bern,,Oxford Nanopore MiniION; Illumina NovaSeq,40.0x,Canu v. v1.7.1; Pilon v. v1.22,1,1,2,4804472,53.34116,4644,4495,None,,,2019-04,Switzerland,Switzerland: Bern,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of a Citrobacter amalonaticus ESBL Positive,sample_type:stools,99.2,97.9,,,,Good,2019-09-30T17:55:59.419Z,2019-09-30T17:55:59.419Z
3986,35790.36,Rickettsia japonica strain LA4/2015,negative,,35790,Complete,LA4/2015,,,,,,,,2018-09-05T00:00:00Z,,PRJNA486884,SAMN09862435,GCA_003454715.1,,CP032049,,Zhejiang Province Center for Disease Control and Prevention,,Illumina,56.2x,SOAPdenovo v. v2.04; GapCloser v.,1,,1,1283254,32.35135,1696,1516,Blood,blood,,21-Sep-15,China,China: Zhejiang Provinc,,,,,,"Human, Homo sapiens",,,Japanese spotted fever,,,,,,,,,,,,,,,,"Nine Japanese spotted fever cases in southeastern China were confirmed, and one Rickettsia japonica strain was isolated. Genome sequencing and assembly were performed.",collected_by:Qunying Lu,99.7,99.3,100,1.6,,Good,2018-10-02T08:31:25.179Z,2018-10-02T08:31:25.179Z
4042,35814.8,Bordetella holmesii strain H558,negative,,35814,Complete,H558,,,,MLST.Bordetella_spp.80,,,,2021-02-03T00:00:00Z,,PRJNA287884,SAMN12525353,GCA_016804285.1,,CP043142,,Centers for Disease Control and Prevention,,PacBio RSII; Illumina HiSeq,563x,HGAP v. 3,1,,1,3696594,62.690006,3808,3608,None,,,2010,USA,USA: IN,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to characterize genomes of Bordetella species other than B. pertussis. Members of the genus Bordetella cause respiratory and opportunistic infection in a variety of hosts. These data are being made available to facilitate comparative analyses for the study of this important group of bacterial pathogens.,,98,96.6,,,,Good,2021-02-27T17:42:13.823Z,2021-02-27T17:42:13.823Z
4081,36809.776,Mycobacteroides abscessus strain W7,positive,,36809,Complete,W7,,,,,,,,2021-10-04T00:00:00Z,33162087,PRJNA656902,SAMN15806907,GCA_020227595.1,,CP060408,,University of Wisconsin-Madison,,Illumina MiSeq,100x,SPAdes v. 3.14.1,1,,1,4802793,64.278046,4799,4698,Urine,urine,,,,USA,,,,,,Homo sapiens,,,Mycobacterium avium complex disease,,,,,,,,,,,,,,,,Genotypic analysis of NTM isolates from human and milk samples in Wisconsin,collected_by:Wisconsin state lab of hygiene (WSLH),98.6,97.8,,,,Good,2021-12-24T06:00:06.968Z,2021-12-24T06:00:06.968Z
4083,37326.9,Nocardia brasiliensis strain FDAARGOS_352,positive,,37326,Complete,FDAARGOS_352,,,,,,FDA:FDAARGOS_352,,2017-06-27T00:00:00Z,,PRJNA231221,SAMN06173365,,,CP022088,,US Food and Drug Administration,,PacBio,14.5210323611477x,"SMRT v. 2.3.0, HGAP v. 3.0",1,,1,8934655,68.24,8661,8052,Skin,"Mycetomatous lesion of the thigh, leg, and foot",,1909,Brazil,Brazil,,,,,,"Human, Homo sapiens",,,Nocardiosis (actinomycosis),,,host_description:Limited motion of the knee,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID < Inst. Pasteur,98.1,93.6,99.6,2.5,,Good,2017-07-23T02:40:32.540Z,2017-07-23T02:40:32.540Z
4086,37329.73,Nocardia farcinica strain SZ 1509,positive,,37329,Complete,SZ 1509,,,,,,,,2021-11-18T00:00:00Z,,PRJNA777769,SAMN22875803,GCA_020883195.1,,"CP086599,CP086600,CP086601,CP086602,CP086603",,"National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Contr",,PacBio,254.0x,HGAP v. 2.3,1,4,5,6613629,70.62712,6474,6192,None,,,2015-09,China,China: Shenzhen,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Whole-genome sequencing of Nocardia,sample_type:whole organism;collected_by:Yanlin Che,99.3,97.9,,,,Good,2021-12-24T23:20:08.017Z,2021-12-24T23:20:08.017Z
4095,37734.92,Enterococcus casseliflavus strain 4928STDY7387870,positive,,37734,Complete,4928STDY7387870,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,SAMEA4623294,GCA_902166785.1,,LR607377,,SC,,,,,1,,1,3744746,43.36827,3173,,Stool,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,"Human, Homo sapiens",,,,,,host_health_state:carriage,,,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,99.6,98.7,,,,Good,2019-10-03T08:01:17.046Z,2019-10-03T08:01:17.046Z
4098,38289.55,Corynebacterium jeikeium strain FDAARGOS_574 strain Not applicable,positive,,38289,Complete,Not applicable,,,,,,FDA:FDAARGOS_574,,2018-12-19T00:00:00Z,,PRJNA231221,SAMN10163223,GCA_003955985.1,,"CP033784,CP033785,CP033786",,US Food and Drug Administration,,Pacbio; Illumina,30.13x,Canu v. 1.4,1,2,3,2528170,58.812065,2247,2150,Gut,Drainage from GT site,,3/10/16,,,,,,,,"Human, Homo sapiens",female,20Y,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,97,96.4,,,,Good,2019-01-31T16:58:12.483Z,2019-01-31T16:58:12.483Z
4099,38323.36,Bartonella henselae strain Houston-I,negative,,38323,Complete,Houston-I,,,,MLST.Bartonella_henselae.1,,ATCC 49882,,2017-10-27T00:00:00Z,,PRJNA382325,SAMN06703471,GCA_002735245.1,,CP020742,,Agroscope,,PacBio,398x,HGAP v. 3,1,,1,1955425,38.27,2027,1685,None,ATCC49882,,1/13/95,Germany,Germany: Tubingen,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing of the Bartonella henselae Houston-I ATCC49882 variant-1,sample_type:culture;collected_by:Prof. Christoph Dehio;passage_history:Grown on CBA /5% Sheep blood,99.9,99.3,100,0.9,,Good,2017-11-24T17:01:03.410Z,2017-11-24T17:01:03.410Z
4100,38347.3,Leptospira interrogans serovar Hardjo-prajitno strain Hardjoprajitno,negative,,38347,Complete,Hardjoprajitno,serovar Hardjo,,,"MLST.Leptospira_spp.20,MLST.Leptospira_spp_2.6,MLST.Leptospira_spp_3.74",,,,2015-11-13T00:00:00Z,,PRJNA296687,SAMN04102139,GCA_001443305.1,SRR3647069,"CP013147,CP013148",,INDICASAT-AIP,,Illumina MiSeq,300x,"SPAdes, PAGIT package v. SEP-2015",2,,2,4692322,34.78,4663,3754,Kidney,kidney,,1970,Indonesia,Indonesia,,,,,,"Human, Homo sapiens",,,Leptospirosis,,,,,,,,,,,C,,,,,"A project to sequence the genome of Leptospira interrogans serovar Hardjo (strain Hardjoprajitno). DNA sequencing was conducted by Dr Sreekumari Rajeev from Ross University School of Veterinary Medicine (St. Kitts & Nevis). Assembly and analysis was done in collaboration with the Bioinformatics Lab of INDICASAT AIP (Panama). The strain used in this project, which belongs to the serogroup Sejroe, is a lab-adapted strain used in microscopic agglutination testing in veterinary labs in USA for the last 39-40 years.",collected_by:Unknown,99.6,99.1,100,0.7,,Good,2016-01-17T17:48:04.567Z,2016-01-17T17:48:04.567Z
4103,39777.9,Veillonella atypica strain OK5,negative,,39777,Complete,OK5,,,,,,,,2017-04-10T00:00:00Z,,PRJNA380512,SAMN06644703,,,CP020566,,University of Oklahoma HSC,,Illumina MiSeq; Illumina NextSeq,157.0x,CLC NGS Cell v. 2.3,1,,1,2071952,39.11,1857,1826,None,,,7/15/11,USA,United States,,,,,env_biome:human oral,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,to study the biology of Veillonella atypica in human oral cavity at the genetic level.,sample_type:single cell,99,99,100,,,Good,2017-05-28T10:08:49.937Z,2017-05-28T10:08:49.937Z
4104,39778.224,Veillonella dispar strain NCTC11831,negative,,39778,Complete,NCTC11831,not available: to be reported later,,,,,NCTC:11831,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA4442464,GCA_900637515.1,,LR134375,,SC,,,,,1,,1,2116915,38.867832,1948,1935,Mouth,Mouth,,1950,,,,,,,,"Human, Homo sapiens",,,,,,host_health_state:not available: to be reported later,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.6,99.5,,,,Good,2019-02-01T13:55:19.172Z,2019-02-01T13:55:19.172Z
4111,40041.89,Streptococcus equi subsp. zooepidemicus strain NCTC11854,positive,,40041,Complete,NCTC11854,,,,MLST.Streptococcus_zooepidemicus.65,,NCTC:11854,,2019-05-10T00:00:00Z,,PRJEB6403,SAMEA3307893,GCA_901472575.1,,LR590471,,SC,,,,,1,,1,2177900,41.573673,2174,1978,Blood,blood,,1914/1984,United Kingdom,United Kingdom,,,,,,"Human, Homo sapiens",,,,,,host_health_state:Septicaemia,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.9,99.7,,,,Good,2019-07-16T07:42:39.888Z,2019-07-16T07:42:39.888Z
4118,40091.23,Helcococcus kunzii strain H10,negative,,40091,Complete,H10,,,,,,,,2021-08-30T00:00:00Z,,PRJNA600407,SAMN14604363,GCA_019797965.1,,CP068729,,INSERM U1047,,Illumina HiSeq,750.0x,SPAdes v. 3.10.0,1,,1,2052171,29.617798,1871,1810,Blood,interstitial fluid [UBERON:0000913],,2013-08,France,France:Cahors,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Decrease of Staphylococcus aureus virulence by Helcococcus kunzii H13 in a Caenorhabditis elegans model,,97.3,96.7,,,,Good,2021-12-23T21:57:23.240Z,2021-12-23T21:57:23.240Z
4120,40215.125,Acinetobacter junii strain INC8271,negative,,40215,Complete,INC8271,,,,MLST.Acinetobacter_baumannii_2.635,,,,2021-05-05T00:00:00Z,,PRJNA716062,SAMN18393338,GCA_018281725.1,,CP071973,,Universidad Nacional Autonoma de Mexico,,BGISEQ,787.6x,Unicycler v. 0.4.7,1,,1,3530883,38.55752,3443,3281,Blood,Blood,"isolated from a patient with adenocarcinoma who developed polymicrobial bacteremia, with Acinetobacter, Escherichia coli and Krebsiella",4/28/18,Mexico,"Mexico: Av. San Fernando 22, Belisario Domnguez Secc 16, Mexico City",,,,,,Homo sapiens,male,61,Bacteremia,,,host_disease_outcome:Death,,,,,,,,,,,,,"Complete sequence of a strain of Acinetobacter junii isolated from a patient with adenocarcinoma who developed polymicrobial bacteremia, with Acinetobacter, Escherichia coli and Krebsiella. Acinetobacter junii was only ampicillin resistent",collected_by:INCAN,98.6,97.3,,,,Good,2021-06-02T21:37:53.483Z,2021-06-02T21:37:53.483Z
4121,40216.95,Acinetobacter radioresistens strain FDAARGOS_731,negative,,40216,Complete,FDAARGOS_731,,,,,,FDA:FDAARGOS_731,,2020-08-05T00:00:00Z,,PRJNA231221,SAMN11056446,GCA_014069095.1,,"CP059684,CP059685,CP059686,CP059688,CP059689,CP059687",,US Food and Drug Administration,,Pacbio; Illumina,1015.66x,"SMRT v. 2.3.0, HGAP v. 3",1,5,6,3377444,41.51613,3300,3146,Skin,normal skin of the right arm,,,USA,USA:VA,,,,,,"Human, Homo sapiens",male,57Y,,,,host_health_state:Not applicable;host_description:Not applicable;host_disease_stage:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),97.6,97.4,,,,Good,2020-08-22T09:21:40.239Z,2020-08-22T09:21:40.239Z
4140,40324.97,Stenotrophomonas maltophilia strain NCTC10498,negative,,40324,Complete,NCTC10498,not available: to be reported later,,,MLST.Stenotrophomonas_maltophilia.31,,NCTC:10498,,2018-06-17T00:00:00Z,,PRJEB6403,SAMEA3956094,GCA_900475685.1,,LS483406,,SC,,,,,1,,1,4661352,66.44806,4315,4184,Throat,Oropharyngeal swab,,1957,,,,,,,,"Human, Homo sapiens",,,,,,host_health_state:not available: to be reported later,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.6,99.2,99.9,,,Good,2018-07-16T22:56:47.059Z,2018-07-16T22:56:47.059Z
4158,42897.88,Shigella flexneri 2a strain 1508,negative,,42897,Complete,1508,2a,,,,,,,2018-07-17T00:00:00Z,,PRJNA379672,SAMN06617562,GCA_003324695.1,,"CP030915,CP030916,CP030917",,Hangzhou Normal University,,PacBio; Illumina HiSeq; Sanger,128.59x,HGAP v. 2.0,1,2,3,5028868,50.67749,5858,5383,None,hospitalized patients,,2015,China,China: Hangzhou,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Antimicrobial resistance study;many frameshifted proteins,sample_type:cell culture,99.7,97.9,100,0.4,,Good,2018-09-29T19:10:18.331Z,2018-09-29T19:10:18.331Z
4172,43767.6,Rhodococcus hoagii strain WY,positive,,43767,Complete,WY,,,,,,,,2019-07-21T00:00:00Z,,PRJNA554230,SAMN12259024,GCA_007197835.1,,"CP041647,CP041646",,Wenzhou Medical University,,PacBio RSII,50.0x,Canu v. v1.5,1,1,2,5213571,68.69251,5053,4790,Sputum,sputum,,4/5/14,China,China: Lishui,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"The aim of this study is to determine the complete genome sequence of Rhodococcus equi WY. Then, comparative genomics analysis will be performed to characterize the genetic diversity and genome evolution of Rhodococcus equi.",,99.8,99.1,,,,Good,2019-10-01T03:27:49.755Z,2019-10-01T03:27:49.755Z
4174,43770.575,Corynebacterium striatum strain 216,positive,,43770,Complete,216,,,,,,,,2017-12-04T00:00:00Z,,PRJNA278886,SAMN05178544,GCA_002804085.1,,CP024932,,Brigham & Women's Hospital,,PacBio,500.0x,HGAP v. v.4,1,,1,3031488,59.02,2955,2790,Respiratory,Tracheal aspirate,,2016,USA,USA:Boston,,,,,,"Human, Homo sapiens",male,62,,,,host_subject_id:CORYNE-2,,,,,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.,collected_by:Xiaomin Zhao,97.6,96.6,100,,,Good,2018-01-01T02:27:51.944Z,2018-01-01T02:27:51.944Z
4175,43771.9,Corynebacterium urealyticum strain NCTC12011,positive,,43771,Complete,NCTC12011,,,,,,NCTC:12011,,2017-08-15T00:00:00Z,,PRJEB6403,SAMEA4530651,GCA_900187235.1,,LT906481,,SC,,,,,1,,1,2377532,64.16,2040,2005,None,,,1900/1988,,,,,,,,"Human, Homo sapiens",,,,,,host_health_state:Bladder Stone,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,96.6,96.2,99.4,,,Good,2017-09-29T14:27:56.298Z,2017-09-29T14:27:56.298Z
4192,44275.5,Leptospira interrogans serovar Copenhageni strain FDAARGOS_203,negative,,44275,Complete,FDAARGOS_203,Copenhageni,,,"MLST.Leptospira_spp.17,MLST.Leptospira_spp_2.47,MLST.Leptospira_spp_3.2",,FDA:FDAARGOS_203,,2017-03-29T00:00:00Z,,PRJNA231221,SAMN04875540,,,"CP020414,CP020413",,US Food and Drug Administration,,PacBio,15.3569892514686x,HGAP v. 3,1,1,2,4630574,35.05,4780,4087,None,Human clinical sample,,1996,Brazil,Brazil,,,,,,"Human, Homo sapiens",,,Leptospirosis,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.","collected_by:ATCC < D Haake, A Ko",99.7,98.7,100,0.4,,Good,2017-05-28T04:59:27.317Z,2017-05-28T04:59:27.317Z
4194,44454.4,Mycobacterium avium subsp. avium DJO-44271,positive,,44454,Complete,DJO-44271,,,,,,,,2014-10-31T00:00:00Z,-,PRJNA263498,SAMN03103573,GCA_000770235.1,,CP009614.1,NZ_CP009614.1,BEI Resources/American Type,,Illumina,107.46,CLC Genomics Workbench v. 7.0.2,1,,1,5011264,69.1,4777,4438,None,Human fluid,,2009,USA,USA: Texas,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,,,,,,,,Whole genome sequencing of several mycobacterial species,,98.1,97.3,98.2,,,Good,2015-03-12T13:54:24.065Z,2015-03-16T03:17:09.594Z
4220,45067.5,Legionella lansingensis strain NCTC12830,negative,,45067,Complete,NCTC12830,,,,,,NCTC:12830,,2017-08-15T00:00:00Z,,PRJEB6403,SAMEA44548918,GCA_900187355.1,,LT906451,,SC,,,,,1,,1,2989256,40.7,2811,2696,Respiratory,Bronchoscopy washings,,1900/1994,,,,,,,,"Human, Homo sapiens",,,,,,host_health_state:chronic lymphocytic leukemia,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,96.7,96.4,100,0.7,,Good,2017-09-29T14:28:31.312Z,2017-09-29T14:28:31.312Z
4265,46503.2312,Parabacteroides merdae strain BFG-280,negative,,46503,Complete,BFG-280,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,SAMN15546958,GCA_020091365.1,,CP081901,,National Institute of Allergy and Infectious Disease,,PacBio Sequel,375x,HGAP/FALCON v. v. 6.0,1,,1,4559639,45.413727,4023,3621,Blood,blood,,1989,USA,USA:Bethesda,,,,,,Homo sapiens,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,99.1,98.3,,,,Good,2021-12-24T03:16:10.266Z,2021-12-24T03:16:10.266Z
4269,46506.2062,Bacteroides stercoris strain BFG-121,negative,,46506,Complete,BFG-121,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,SAMN15547175,GCA_020091485.1,,CP081913,,National Institute of Allergy and Infectious Disease,,PacBio Sequel,457x,Canu v. v. 1.6,1,,1,3883826,45.835884,3469,3142,None,,,,USA,USA:Bethesda,,,,,,Homo sapiens,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,99.6,99,,,,Good,2021-12-24T03:19:16.807Z,2021-12-24T03:19:16.807Z
4531,47678.1147,Bacteroides caccae strain BFG-100,negative,,47678,Complete,BFG-100,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,SAMN15547129,GCA_020091545.1,,CP081920,,National Institute of Allergy and Infectious Disease,,PacBio Sequel,443x,HGAP/FALCON v. v. 6.0,1,,1,5022820,42.504448,4422,4035,None,,,1985,USA,USA:Bethesda,,,,,,Homo sapiens,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,99.8,99,,,,Good,2021-12-24T03:19:37.666Z,2021-12-24T03:19:37.666Z
4535,47880.53,Pseudomonas fulva strain ZDHY414,negative,,47880,Complete,ZDHY414,,,,,,,,2020-11-24T00:00:00Z,,PRJNA678569,SAMN16807128,GCA_015679225.1,,"CP064946,CP064948,CP064947",,The First Affiliated Hospital of Zhengzhou University,,Illumina NovaSeq; Oxford Nanopore,200.0x,Unicycler v. v3.9.1,1,2,3,5757765,60.649487,5556,5268,Lung,pleural fluid in respiratory ICU,,17-May-19,China,China:Henan,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Pseudomonas fulva producing VIM-24 isolated from pleural fluid in respiratory ICU,sample_type:pleural fluid,99,97,,,,Good,2021-01-01T16:57:39.034Z,2021-01-01T16:57:39.034Z
4536,47885.35,Pseudomonas oryzihabitans strain FDAARGOS_657 strain Not applicable,negative,,47885,Complete,Not applicable,,,,,,FDA:FDAARGOS_657,,2019-09-25T00:00:00Z,,PRJNA231221,SAMN11056372,GCA_008693825.1,,"CP044074,CP044072,CP044073",,US Food and Drug Administration,,Pacbio; Illumina,874.34x,canu v. 1.4,1,2,3,5264913,65.86141,4910,4782,None,clinical isolate,,,USA,USA: KY,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:University of Louisville,98,95.5,,,,Good,2019-10-02T19:15:40.528Z,2019-10-02T19:15:40.528Z
4537,47886.9,Pseudomonas luteola strain FDAARGOS_637 strain Not applicable,negative,,47886,Complete,Not applicable,,,,,,FDA:FDAARGOS_637,,2019-09-25T00:00:00Z,,PRJNA231221,SAMN11056352,GCA_008693965.1,,"CP044086,CP044085,CP044084,CP044087,CP044088",,US Food and Drug Administration,,Pacbio; Illumina,657.89x,canu v. 1.4,2,3,5,5901383,55.42072,5925,5494,None,clinical isolate,,,USA,USA: KY,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:University of Louisville,97.3,94.1,,,,Good,2019-10-02T19:18:11.829Z,2019-10-02T19:18:11.829Z
4569,48296.84,Acinetobacter pittii strain IEC338SC,negative,,48296,Complete,IEC338SC,,,,"MLST.Acinetobacter_baumannii_1.1582,MLST.Acinetobacter_baumannii_2.1076",,,,2016-04-08T00:00:00Z,,PRJNA316135,SAMN04576523,GCF_001617545.1,,"CP015145,CP015147,CP015148,CP015146","NZ_CP015145.1,NZ_CP015147.1,NZ_CP015148.1,NZ_CP015146.1",Universidade de Sao Paulo,,Illumina MiSeq,123x,SPAdes v. 3.6.2,1,3,4,3957199,38.67,3791,3689,Respiratory,tracheal secretion,"isolated from a patient in Bel�m, Brazil, suffering from nosocomial mechanical ventilator associated pneumonia",14-Apr-14,Brazil,Brazil: Belem,,,,,,"Human, Homo sapiens",female,71,bacterial pneumonia,,,,,,,,,,,,,,,,"This Acinetobacter pittii strain presented resistance to carbapenems and was isolated from a patient in Bel�m, Brazil, suffering from nosocomial mechanical ventilator associated pneumonia.",collected_by:Fundacao Santa Casa de Misericordia do Para;passage_history:4,98.9,98.2,100,,,Good,2016-04-28T10:16:41.468Z,2016-04-28T10:16:41.468Z
5412,52773.3,Actinomyces meyeri strain W712,negative,,52773,Complete,W712,,,,,,,,2015-08-06T00:00:00Z,,PRJNA282954,SAMN03704036,GCF_001262055.1,,CP012072,NZ_CP012072.1,The Forsyth Institute,,PacBio,197x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,2049088,65.51,1797,1667,None,curette,,1984,United Kingdom,United Kingdom: London,,,,,env_biome:Human oral cavity,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,Forsyth oral bacterial genomes,,99.3,99,100,0.4,,Good,2016-01-17T17:01:19.461Z,2016-01-17T17:01:19.461Z
5415,53345.74,Enterococcus durans strain 4928STDY7387704,positive,,53345,Complete,4928STDY7387704,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,SAMEA104694341,GCA_902166615.1,,LR607372,,SC,,,,,1,,1,3195719,37.98997,3092,,Stool,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,"Human, Homo sapiens",,,,,,host_health_state:carriage,,,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,98.5,97.4,,,,Good,2019-10-03T07:51:29.977Z,2019-10-03T07:51:29.977Z
5417,53346.53,Enterococcus mundtii strain Pe103,positive,,53346,Complete,Pe103,,,,,,,,2019-05-06T00:00:00Z,,PRJNA453425,SAMN08978749,GCA_005158285.1,,"CP029066,CP029067,CP029068",,Korea Food Research Institute,,PacBio,303.0x,HGAP v. 3.0,1,2,3,3204082,38.43553,3167,3010,Stool,Korean adult feces,,2/5/18,South Korea,South Korea: Seoul,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Pe103 strain was isolated from Korean adult feces,sample_type:cell culture,99,98,,,,Good,2019-07-17T15:16:56.160Z,2019-07-17T15:16:56.160Z
5418,53436.3,Treponema pallidum subsp. endemicum strain Iraq B,negative,,53436,Complete,Iraq B,,,,,,,,2019-02-14T00:00:00Z,,PRJNA428415,SAMN08290048,GCA_004194495.1,,CP032303,,"Masaryk University, Faculty of Medicine",,Illumina MiSeq,1000.0x,IDBA_UD v. 1.1.1,1,,1,1137653,52.778217,1034,1062,Wound,lesion,,1951,Iraq,Iraq,,,,,,"Human, Homo sapiens",female,7 years,endemic syphilis,,,,,,,,,,,,,,,,"Complete genome sequencing of Treponema pallidum subsp. endemicum strain Iraq B, the causative agent of endemic syphilis.",,,,,,,Good,2019-07-13T18:28:25.126Z,2019-07-13T18:28:25.126Z
7005,57706.84,Citrobacter braakii strain FDAARGOS_638 strain Not applicable,negative,,57706,Complete,Not applicable,,,,,,FDA:FDAARGOS_638,,2020-06-03T00:00:00Z,,PRJNA231221,SAMN11056353,,,"JABRWN010000002,JABRWN010000001,JABRWN010000003",,US Food and Drug Administration,,Pacbio; Illumina,396.45x,"SMRT v. 2.3.0, HGAP v. 3",1,2,3,5441974,52.04424,5229,5007,None,clinical isolate,,,USA,USA: KY,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:University of Louisville,96.5,94.5,,,,Good,2020-07-01T03:48:45.581Z,2020-07-01T03:48:45.581Z
7009,57975.9,Burkholderia thailandensis strain 2003015869,negative,,57975,Complete,2003015869,,,,"MLST.Burkholderia_cepacia_complex.544,MLST.Burkholderia_pseudomallei.101",,,,2016-09-02T00:00:00Z,,PRJNA279182,SAMN03449126,GCF_001718295.1,SRR1956433,"CP013360,CP013361","NZ_CP013360.1,NZ_CP013361.1",Northern Arizona University,,PacBio,50x,HGAP v. 2.0,2,,2,6729001,67.68,6805,5799,None,,,2003,USA,USA: Texas,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequence analysis of diverse Burkholderia genomes,collected_by:NAU subculture,99,95.9,100,,,Good,2016-11-15T21:01:17.643Z,2016-11-15T21:01:17.643Z
7097,59201.739,Salmonella enterica subsp. enterica strain FDAARGOS_317,negative,,59201,Complete,FDAARGOS_317,Typhimurium,,,MLST.Salmonella_enterica.19,,FDA:FDAARGOS_317,,2018-03-09T00:00:00Z,,PRJNA231221,SAMN06173330,GCA_002984285.1,,"CP027410,CP027409",,US Food and Drug Administration,,PacBio; Illumina,24.4046237608933x,"SMRT v. 2.3.0, HGAP v. 3.0",1,1,2,5192855,52.16017,5524,5299,Stool,stool,,2012,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:FDA CVM < CDC,99.7,99,100,0.3,,Good,2018-05-26T05:54:34.683Z,2018-05-26T05:54:34.683Z
7099,60552.42,Burkholderia vietnamiensis strain AU1233,negative,,60552,Complete,AU1233,,,,,,,,2016-09-02T00:00:00Z,,PRJNA279182,SAMN03449402,GCF_001718775.1,SRR1956465,"CP013433,CP013434","NZ_CP013433.1,NZ_CP013434.1",Northern Arizona University,,PacBio,50x,HGAP v. 2.0,2,,2,6835067,66.86,6899,5867,Blood,CF Blood,,1999,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequence analysis of diverse Burkholderia genomes,collected_by:UMich - John Lipuma,99.6,95.7,100,,,Good,2016-11-15T21:53:15.162Z,2016-11-15T21:53:15.162Z
7162,61645.92,Enterobacter asburiae strain ENIPBJ-CG1,negative,,61645,Complete,ENIPBJ-CG1,,,,MLST.Enterobacter_cloacae.384,,,,2016-04-08T00:00:00Z,,PRJNA314550,SAMN04538166,GCA_001617645.1,,CP014993,,"Institute of Pathogen Biology,Chinese Academy Medical Sciences & Peking Union Medical College",,Sanger dideoxy sequencing; IonTorrent;,missing,Newbler v. v2.8,,,1,4648696,55.76,4794,4725,None,,,7/3/14,China,China:Beijing,,,,,env_biome:Clinical,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,It is a project about whole genome sequencing of several clinical bacterias in China;many frameshifted proteins,,99.3,92.7,99.7,10,,Good,2016-04-28T10:17:33.402Z,2016-04-28T10:17:33.402Z
7163,61648.5,Kluyvera intermedia strain CAV1151,negative,,61648,Complete,CAV1151,,,,,,,,2015-06-09T00:00:00Z,,PRJNA246471,SAMN03733692,GCF_001022135.1,SRR2965721,"CP011602,CP011600,CP011601,CP011599,CP011598","NZ_CP011602.1,NZ_CP011600.1,NZ_CP011601.1,NZ_CP011599.1,NZ_CP011598.1",University of Oxford,,PacBio,89X,HGAP3 v. 2.2.0,1,4,5,6166452,52.47,6373,5685,Stool,Perirectal,,2009-09,USA,USA:Virginia,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",collected_by:Clinical Microbiology University of Virginia Health System,99.3,96.9,99.6,1.9,,Good,2016-01-17T16:05:41.690Z,2016-01-17T16:05:41.690Z
7165,61652.8,Serratia rubidaea strain 1122,negative,,61652,Complete,1122,,,,,,,,2016-02-25T00:00:00Z,,PRJNA311262,SAMN04481172,GCF_001572725.1,,CP014474,NZ_CP014474.1,Beijing Institute of Microbiology and Epidemiology,,Illumina; IonTorrent,139,Newbler v. 2.9,1,,1,4922834,59.2,4673,4486,Sputum,sputum,isolated from a patient in China,15-May-14,China,China: Beijing,,,,,env_biome:sputum,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,"Serratia rubidaea mainly exsits in soil, water and food, and normally it’s non-pathogenic. But when patients’ immunity decreased, it can cause invasive infection, such as pulmonary infection and traumatic infection.We report here the first complete genome sequence of Serratia rubidaea, isolated from a patient in China. We hope that this sequence will help for genomic comparisons of the Serratia genus.",,99.2,97.4,99.4,0.4,,Good,2016-03-18T07:58:08.823Z,2016-03-18T07:58:08.823Z
7287,65058.66,Corynebacterium ulcerans strain 131001,positive,,65058,Complete,131001,,,,,,,,2015-09-14T00:00:00Z,,PRJNA273964,SAMN03316967,GCF_001281445.1,,CP010818,NZ_CP010818.1,Federal University of Minas Gerais,,,,,1,,1,2483321,53.31,2317,2301,None,human,isolated from human,,,,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,No,,Unknown,37,,Facultative,HostAssociated,,"Corynebacterium ulcerans is an emergent pathogen that infects a variety of wild and domesticated animals and humans. It is associated to a growing number of cases of a diphtheriae-like disease around the world. We present the complete genome sequence of C. ulcerans strain 131001, isolated from human.",,98.7,97.9,100,,,Good,2016-01-17T17:06:12.403Z,2016-01-17T17:06:12.403Z
7348,67824.43,Citrobacter farmeri strain CCRI-24236,negative,,67824,Complete,CCRI-24236,,,,,genotype:blaKPC-2,,,2021-09-01T00:00:00Z,,PRJNA744893,SAMN20153794,GCA_019803045.1,,"CP081314,CP081315,CP081316,CP081317,CP081318",,Universite Laval,,PacBio; Illumina MiSeq,100.0x,HGAP v. JUNE-2011,1,4,5,5406671,52.793724,5319,5096,Stool,anal swab,,2017,Canada,Canada: Quebec City,,,,,,Homo sapiens,male,69,pancreatitis (colonization),,,host_disease_outcome:recovered after operation,,,,,,,,,,,,,two isolates producing KPC-2 carbapenemase isolated from a single patient,collected_by:Hotel-Dieu de Quebec,99.3,97.1,,,,Good,2021-12-23T22:20:30.351Z,2021-12-23T22:20:30.351Z
7349,67826.48,Citrobacter sedlakii strain 3347089II,negative,,67826,Complete,3347089II,,,,,,,,2021-04-22T00:00:00Z,,PRJNA698767,SAMN17736025,GCA_018128425.1,,"CP071070,CP071071,CP071072",,,,Illumina NovaSeq; Oxford Nanopore MiniION,170x,Unicycler v. 0.4.8,1,2,3,4967243,54.34697,4860,4624,Skin,outer malleolus,,2020,Switzerland,Switzerland,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,99.6,98.3,,,,Good,2021-04-26T00:41:08.925Z,2021-04-26T00:41:08.925Z
7352,67827.25,Citrobacter werkmanii strain FDAARGOS_616 strain Not applicable,negative,,67827,Complete,Not applicable,,,,,,FDA:FDAARGOS_616,,2019-09-25T00:00:00Z,,PRJNA231221,SAMN11056331,GCA_008693645.1,,"CP044101,CP044100",,US Food and Drug Administration,,Pacbio; Illumina,732.05x,"SMRT v. 2.3.0, HGAP v. 3",1,1,2,5049303,52.254204,4882,4731,None,clinical isolate,,,USA,USA: MI,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:University of Michigan Health System,99.5,98.2,,,,Good,2019-10-02T19:08:26.661Z,2019-10-02T19:08:26.661Z
7369,70346.7,Acinetobacter variabilis strain RYU24,negative,,70346,Complete,RYU24,,,,,,,,2021-03-30T00:00:00Z,,PRJDB10565,SAMD00246909,GCA_018409485.1,,AP024524,,"Department of Microbiology, Juntendo University School of Medicine",,Illumina MiSeq; Oxford Nanopore MinION,160x,Unicycler v. 0.4.6,1,,1,3198423,42.381603,3103,3025,Stool,human fecal,isolated in various countries and regions worldwide,2012,Japan,"Japan:Okinawa, Naha",,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"The emergence and dissemination of drug-resistant Acinetobacter species have been recognized as a serious health concern worldwide. Drug-resistant Acinetobacter baumannii has been one of the most important nosocomial pathogens with the highest incidence rate of isolation among Acinetobacter species. The genus Acinetobacter composes 62 distinct species with validly published names and several species with effectively published names awaiting validation. Acinetobacter variabilis was originally classified as Acinetobacter DNA group 15 TU using DNA-DNA hybridization by Tjernberg and Ursing in 1989. Later, Acinetobacter DNA group 15 TU was proposed as Acinetobacter variabilis sp. nov. in 2015 by Krizova L., et al. Since NDM-1 metallo-beta-lactamase (MBL) producing Klebsiella pneumoniae and Escherichia coli was initially detected in 2008 in Sweden, NDM-type MBL producers have become endemic in the India, and these organisms were isolated in various countries and regions worldwide. Although NDM-type MBL producers seem to be not yet spreading in Japan, there is at least four reports of NDM producing clinical isolates, including an isolate of E. coli producing NDM-1 MBL obtained from a patient traveling India for business in March 2009, and two isolates of NDM-5 MBL producing E. coli and NDM-1 MBL producing K. pneumoniae obtained from two foreigners from Bangladesh and Indonesia, respectively, and an isolate of E. coli producing NDM-7 obtained from a patient with history of admission in India. In Acinetobacter species, an isolate of NDM-1 MBL producing A. baumannii was obtained from a patient in Japan. The methylation of 16S rRNA confers high resistance to all clinically important aminoglycosides in Gram-negative organism. Clinical isolates of Klebsiella pneumoniae harboring the armA, a 16S rRNA methylase, and Pseudomonas aeruginosa harboring the rmtA, another one, were identified in 2003 in France, Japan, and the other countries since 2003. To date, 10 plasmid-associated 16S rRNA methylase genes, armA, rmtA-H and npmA, have been identified in human and animal. In this study, we analysis a clinical isolate of A. variabilis producing both NDM-1 MBL and OXA-420 carbapenemases, and ArmA 16S rRNA methylase obtained from a patient in Japan.",,99,98.3,,,,Good,2021-06-03T04:04:35.110Z,2021-06-03T04:04:35.110Z
7374,71452.51,Enterococcus raffinosus strain CX012922,positive,,71452,Complete,CX012922,,,,,,,,2021-08-30T00:00:00Z,,PRJNA756165,SAMN20857173,GCA_019797905.1,,"CP081846,CP081847",,Shenzhen University,,Oxford Nanopore PromethION; Illumina,300.0x,unicycler v. v0.4.9b,1,1,2,3811651,39.574844,3800,3663,Stool,feces,,1/22/21,China,China:Guangzhou,,,,,,Homo sapiens,,,Crohn disease,,,,,,,,,,,,,,,,Complete genome of Enterococcus raffinosus,collected_by:Zhao Hailan,97.5,94.8,,,,Good,2021-12-23T21:57:44.627Z,2021-12-23T21:57:44.627Z
7380,72361.9,Bacillus vallismortis strain Bac111,positive,,72361,Complete,Bac111,,,,,,,,2018-10-21T00:00:00Z,,PRJNA412146,SAMN10146793,GCA_003667885.1,,CP033052,,King Abdullah University of Science and Technology,,PacBio,337X,Celera Assembler v. 2,1,,1,3958372,44.150295,4137,,None,Red Sea lagoons-Micorbial Mat,"isolated from the Red Sea, specifically three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS) collected from Rabigh harbor lagoon (39°0′35",2012-04,Saudi Arabia,Saudi Arabia:Rabigh harbor lagoon,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"We sequenced genomes isolated from the Red Sea, specifically three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS) collected from Rabigh harbor lagoon (39°0′35.762′′ E, 22°45′5.582′′ N) and Al-Kharrar lagoon (38°54′39.638′′ E, 22°54′50.251′′ N) in Saudi Arabia. MN mud was sampled from the coastal lagoon of the Red Sea alongside mangrove tree. MM was sampled approximately 7.5 m away from the coastal lagoon. BS refers to sediments with no contact with lagoon water at high tide.",sample_type:cell culture,99.5,98.7,,,,Good,2018-11-29T02:53:08.140Z,2018-11-29T02:53:08.140Z
7446,72407.978,Klebsiella pneumoniae subsp. pneumoniae strain BR21,negative,,72407,Complete,BR21,,,,MLST.Klebsiella_pneumoniae.437,,,,2018-02-02T00:00:00Z,,PRJNA358426,SAMN06173549,GCA_002951595.1,,"CP018885,CP018886,CP018887",,University of California,,PacBio,100.0x,PacBio v. HGAP.2,1,2,3,5708729,57.192398,5887,5951,Urine,urine,,2009,Brazil,Brazil: Rio de Janeiro,,,,,,"Human, Homo sapiens",,,urinary tract infection,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,,High-level carbapenem resistance in KPC-producing Klebsiella pneumoniae emerges from subpopulations that undergo distinct stepwise transcriptional programs from a population exposed to a lethal carbapenem dose.,collected_by:Federal University of Rio de Janeiro,99.3,97.7,99.7,0.3,,Good,2018-05-26T02:00:37.477Z,2018-05-26T02:00:37.477Z
7529,72759.16,Staphylococcus aureus subsp. anaerobius strain Zhenghai,positive,,1280,Complete,Zhenghai,Not applicable,,,MLST.Staphylococcus_aureus.5,genotype:ST5,Not applicable,,2019-11-04T00:00:00Z,,PRJNA494949,SAMN10227280,GCA_009497915.1,,CP033117,,"Ningbo Municipal Centre for Disease Control and Prevention, Ningbo, Zhejiang Province, China",,Illumina MiSeq,60.0x,SPAdes v. 3.12.0,1,,1,2744906,32.87197,2757,2773,Pus,Pus,,10/10/17,China,China: Zhejiang province,,,Not applicable,Not applicable,temperature:39 degree Celsius,"Human, Homo sapiens",,,,,,,Susceptible,Computational Prediction,,,,,,,,,,,Staphylococcal foodborne intoxication is caused by various staphylococcal enterotoxins (SEs). SED is one of such enterotoxins. This project was aimed to investigate an food poisoning outbreak caused by a SED-positive strain.,sample_type:Whole organism;biomaterial_provider:Not applicable;collected_by:Qifa Song;identified_by:Qifa song;lab_host:Not applicable;mating_type:Not applicable;passage_history:Not applicable;specimen_voucher:Not applicable,100,100,,,,Good,2019-11-25T13:27:09.994Z,2019-11-25T13:27:09.994Z
7576,74426.49,Collinsella aerofaciens strain indica,positive,,74426,Complete,indica,,,,,,,,2017-10-30T00:00:00Z,,PRJNA415274,SAMN07821249,GCA_002736145.1,,CP024160,,Translational Health Science and Technology Institute,,Illumina HiSeq; Nanpore,225.0x,SPAdes v. SEP-2017,1,,1,2306349,60.12,1981,1920,Stool,stool,,23-May-17,India,India: Faridabad,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Collinsella aerofaciens, a rod-shaped non-motile obligate anaerobe, is the mostabundant Actinobacteria in the gastrointestinal tract of healthy humans. Altered abundance of C. aerofaciens may be linked with several health disorders including irritable bowel syndrome. In the present study, we report the complete genome sequence of C. aerofaciens strain Indica.",sample_type:stool sample,97.1,96.6,100,,,Good,2017-11-26T21:32:00.024Z,2017-11-26T21:32:00.024Z
7596,76123.5,Prevotella enoeca strain F0113,negative,,76123,Complete,F0113,,,,,,,,2015-11-17T00:00:00Z,,PRJNA282954,SAMN04260158,GCA_001444445.1,,CP013195,NZ_CP013195.1,The Forsyth Institute,,PacBio,366x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,2861432,46.47,2644,2366,None,curette,,Jun-90,USA,"USA: Blacksberg, VA",,,,,env_biome:oral cavity,"Human, Homo sapiens",male,45 years,,,,,,,,,,,,C,,,,,Forsyth oral bacterial genomes,,98.7,98.4,98.7,,,Good,2016-01-17T17:48:13.621Z,2016-01-17T17:48:13.621Z
7602,76759.43,Pseudomonas monteilii strain 170918607,negative,,76759,Complete,170918607,,,,,,,,2020-03-02T00:00:00Z,,PRJNA562122,SAMN12634701,GCA_011045675.1,,CP043395,,Beijing Institute of Microbiology and Epidemiology,,PacBio RSII,100.0x,HGAP v. v3.0,1,,1,5802791,62.04866,5606,5477,None,Drainage,,2017,China,China:Jiangsu,,,,,,"Human, Homo sapiens",,,Uremia,,,,,,,,,,,,,,,,Complete sequence of chromosome of strain 170918607,,96.2,94.6,,,,Good,2020-03-27T14:39:21.256Z,2020-03-27T14:39:21.256Z
7606,76856.6,Fusobacterium nucleatum subsp. nucleatum strain 25586,negative,,76856,Complete,25586,,,,,,,,2018-03-26T00:00:00Z,,PRJNA433545,SAMN08706662,GCA_003019295.1,,CP028101,,Virginia Tech,,"Illumina, MinION",60x,Unicycler v. 0.4.3,1,,1,2180101,27.14012,2065,2025,Mouth,Oral cavity,,,,,,,,,env_biome:terrestrial biome [ENVO:00000446],"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Complete Fusobacterium genomes generated by MinION and Illumina sequencing, followed by assembly with Unicycler.",,99.9,99.7,100,,,Good,2018-05-31T00:28:53.785Z,2018-05-31T00:28:53.785Z
7612,76857.9,Fusobacterium nucleatum subsp. polymorphum strain NCTC10562,negative,,76857,Complete,NCTC10562,,,,,,,,2015-05-09T00:00:00Z,,PRJEB6403,SAMEA2479572,GCF_001457555.1,"ERR526296,ERR526297","LN831027,LN831028","NZ_LN831027.1,NZ_LN831028.1",SC,,,,,1,1,2,2455060,26.99,2351,2334,Mouth,inflamed gingiva,,1951,USA,United States,,,,,,"Human, Homo sapiens",,,,,,host_health_state:disease,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.6,99.2,100,,,Good,2016-01-30T13:20:00.089Z,2016-01-30T13:20:00.089Z
7618,76859.52,Fusobacterium nucleatum subsp. animalis strain THCT5A4,negative,,76859,Complete,THCT5A4,,,,,,,,2021-08-11T00:00:00Z,,PRJNA704481,SAMN18042963,GCA_019552125.1,,CP071099,,"Shanghai Tenth People's Hospital, Tongji University School of Medicine",,Illumina HiSeq; PacBio RSII,456x for Illumina Data and 479x for,Celera Assembler v. v8.3,1,,1,2490990,27.07,2360,2301,Gut,Gut,isolated from colorectal cancer tissues were sequenced,2018,China,China: Shanghai,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Complete genomes of Fusobacterium strains isolated from colorectal cancer tissues were sequenced. The study aimed to provide understandings of the genomic characteristics of the gut microbes that may involve in the pathogenesis of colorectal cancer.,sample_type:whole organism,99.7,99.5,,,,Good,2021-08-26T16:04:56.667Z,2021-08-26T16:04:56.667Z
7642,78331.182,Mycobacterium canettii strain Percy1105,positive,,78331,Complete,Percy1105,,,,,,,,2021-11-27T00:00:00Z,,PRJEB48348,SAMEA2149742,GCA_918429295.1,,OU917917,,Institut Pasteur,,,,,1,,1,4422085,65.583755,4267,,None,patients between 1983 and 2013 mostly,isolated from patients between 1983 and 2013 mostly in the Republic of Djibouti,,,Republic,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"We performed the whole-genome assembly of available sequencing read datasets (SRA Study ERP002514) from Mycobacterium canettii strains, which were isolated from patients between 1983 and 2013 mostly in the Republic of Djibouti. Illumina read pairs were first trimmed using Trimmomatic v0.36 (parameters: LEADING 20; TRAILING 20; SLIDINGWINDOW windowSize 5, requiredQuality 20; MINLEN 50; AVGQUAL 20). Complete read pairs were then assembled using SPAdes v3.10.1 (parameters: --careful; -k 21,33,55,77,99,127 according to read length; --phred-offset 33). Generated contigs were finally organized as compared to the closest reference genome of Mycobacterium canettii available (STB-A, STB-D or STB-L) using MeDuSa v1.6 (default parameters).",,99,98.1,,,,Good,2021-12-25T16:43:14.743Z,2021-12-25T16:43:14.743Z
7733,83262.23,Mycobacterium immunogenum strain FLAC016,positive,,83262,Complete,FLAC016,,,,,,,,2016-06-28T00:00:00Z,,PRJNA315990,SAMN05244438,GCF_001677135.1,SRR3666121,CP016189,NZ_CP016189.1,University of Michigan Medical School,,Illumina,150 X,SPAdes v. 3.5.0,1,,1,5604845,64.26,5610,5437,None,,,2013,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of M. abscessus complex isolates.,collected_by:Lindsay J. Caverly,98.4,97.3,94.7,0.1,,Good,2016-09-11T10:20:25.225Z,2016-09-11T10:20:25.225Z
7734,83331.22,Mycobacterium tuberculosis CDC1551,positive,Mycobacterium tuberculosis CDC1551,83331,Complete,CDC1551,,,,,,,,2002-09-10T00:00:00Z,12218036,PRJNA223,,GCA_000008585.1,,AE000516,NC_002755,TIGR,complete,,,,1,,1,4403837,65.6,4403,4189,None,"clothing factory worker from the Kentucky/Tennessee, USA, region","isolate from a clothing factory worker from the Kentucky/Tennessee, USA, region",,USA,"Kentucky/Tennessee, USA",,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,No,No,Mesophilic,37,,Aerobic,Host-associated,Tuberculosis,"Mycobacterium tuberculosis strain CDC1551. This strain, also nicknamed ""Oshkosh"", is a recent clinical isolate from a clothing factory worker from the Kentucky/Tennessee, USA, region. It is highly contagious, infecting approximately 80% of the patient's social contacts. However, this strain has not caused epidemics in man and is sensitive to a wide range of drugs. It is also highly virulent in a mouse lung model, producing several orders of magnitude more bacteria than the H37Rv strain when inoculated.",,99.9,99.8,100,2.1,,Good,2014-12-08T22:12:09.953Z,2015-03-16T03:17:09.594Z
7736,83332.293,Mycobacterium tuberculosis H37Rv,positive,,83332,Complete,H37Rv,,,,,,ATCC: TMC 102,,2014-09-26T00:00:00Z,,PRJNA260834,SAMN03067436,GCF_000831245.1,,CP009480,NZ_CP009480.1,BEI Resources/American Type,,Illumina,207.93,CLC Genomics Workbench v. 7.0.2,1,,1,4396119,65.61,4360,4010,Lung,Derivative of strain H37,isolated from a human lung in NY 1905,1934,USA,USA:New York,,,,,,"Human, Homo sapiens",,,Tuberculosis,,,,,,,,,,,,,,,,"Parent strain, H37, was isolated from a human lung in NY 1905. In 1934 the strain was dissociated into rough/smooth, virulent/attenuated variants. This strain corresponds to the virulent variant.",isolate:27294D-2;collected_by:W. Steenken,99.3,99.3,100,,,Good,2016-01-17T15:43:15.113Z,2016-01-17T15:43:15.113Z
7737,83333.442,Escherichia coli K-12 strain MG655,negative,,83333,Complete,MG655,,,,"MLST.Escherichia_coli_1.453,MLST.Escherichia_coli_2.86",,,,2018-04-02T00:00:00Z,,PRJNA389368,SAMN07196156,GCA_003028735.1,,CP028306,,Rehman Medical Institute,,Illumina MiSeq,30X,SPAdes v. 3.10.1,1,,1,4736591,50.777607,4665,,Urine,urine,,6-Dec-16,Pakistan,"Pakistan: Sheikh Zaid Hospital, Lahore",,,,,,"Human, Homo sapiens",,,Urinary tract infection,,,,,,,,,,,,,,,,"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","collected_by:Asma Manzoor, Nabila Ishaq",99.6,98.8,100,0.4,,Good,2018-05-30T23:17:18.045Z,2018-05-30T23:17:18.045Z
7766,83334.615,Escherichia coli O157:H7 strain 6535NalR,negative,,83334,Complete,6535NalR,O157:H7,,,MLST.Escherichia_coli_1.11,,,,2021-12-12T00:00:00Z,,PRJNA750123,SAMN20437390,GCA_021166415.1,,"CP089034,CP089035",,University of Texas at San Antonio,,"PacBio, IlluminaMiSeq",154x,HGAP v. 2.3.0,1,1,2,5737031,50.494514,6063,5644,None,laboratory mutant of 6535,,2013,USA,USA: Minnesota,,,,,,Homo sapiens,,,STEC infection,,,,,,,,,,,,,,,,Strains associated with an EHEC O157:H7 laboratory co-infection,,100,99.6,,,,Good,2021-12-25T04:45:44.508Z,2021-12-25T04:45:44.508Z
7769,83554.74,Chlamydia psittaci strain GIMC 2005:CpsCP1,negative,,83554,Complete,GIMC 2005:CpsCP1,,,,,genotype:ST24,,,2017-11-06T00:00:00Z,,PRJNA413811,SAMN07767758,GCA_002752735.1,,"CP024451,CP024452",,N.F.Gamaleya Research Center for Epidemiology and Microbiology,,Illumina,145,"CLC Genomics Workbench v. 8.5.1, 9.5.2",1,1,2,1179934,39.02,1028,1028,Joint,synovial fluid,,1971,Russia,Russia: Moscow,,,,,,"Human, Homo sapiens",,,arthritis,,,,,,,,,,,,,,,,the strain was isolated from synovial fluid of the patient with arthritis,"collected_by:Shatkin A.A., Kolkova N.I.",99.6,99.5,100,,,Good,2017-11-26T01:45:33.389Z,2017-11-26T01:45:33.389Z
7776,83558.19,Chlamydia pneumoniae strain PB2,negative,,83558,Complete,PB2,,,,,,,,2015-05-09T00:00:00Z,,PRJEB8246,SAMEA3212830,GCA_001007145.1,,LN847241,NZ_LN847241.1,University of Vienna,,,,,1,,1,1228126,40.58,1141,1131,Respiratory,PBMC,isolated from the respiratory tract and shared more than 99% sequence identity,,Germany,Germany:Luebeck,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Chlamydia pneumoniae (Cpn) are obligate intracellular bacteria that cause acute infections of the upper and lower respiratory tract and have been implicated in chronic inflammatory diseases. Although of significant clinical relevance, complete genome sequences of only four clinical Cpn strains have been obtained. All of them were isolated from the respiratory tract and shared more than 99% sequence identity. Here we investigate genetic differences on the whole-genome level that are related to Cpn tissue tropism and pathogenicity. We have sequenced the genomes of 18 clinical isolates from different anatomical sites (e.g. lung, blood, coronary arteries) of diseased patients, and one animal isolate. In total 1,363 SNP loci and 184 InDels have been identified in the genomes of all clinical Cpn isolates. These are distributed throughout the whole chlamydial genome and enriched in highly variable regions. The genomes show clear evidence of recombination in at least one potential region but no phage insertions. The tyrP gene was always encoded as single copy in all vascular isolates. Phylogenetic reconstruction revealed distinct evolutionary lineages containing primarily non-respiratory Cpn isolates. In one of these, clinical isolates from coronary arteries and blood monocytes were closely grouped together. They could be distinguished from all other isolates by characteristic nsSNPs in genes involved in RB to EB transition, inclusion membrane formation, bacterial stress response and metabolism. This study substantially expands the genomic data of Cpn and elucidates its evolutionary history. Cpn genetic differences related to tissue tropism not only indicate a specific role of the pathogen in the development of chronic disease, but also suggest the development of pathogen-oriented diagnostic strategies in the future.",isolate:PB2,99.8,99.7,100,,,Good,2016-01-17T16:02:18.021Z,2016-01-17T16:02:18.021Z
7794,84112.3,Eggerthella lenta strain C592,positive,,84112,Complete,C592,,,,,,,,2017-05-17T00:00:00Z,,PRJNA384908,SAMN06853954,,,CP021140,,University of Illinois,,Illumina HiSeq; Oxford Nanopore MinION,71.0x,"SPAdes v. 3.9,0",1,,1,3593204,64.3,3305,,None,,,3/1/16,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Eggerthella lenta C592 genome,sample_type:Cell culture,99.8,99.3,100,,,Good,2017-05-30T00:16:45.826Z,2017-05-30T00:16:45.826Z
7807,85698.5,Achromobacter xylosoxidans strain FDAARGOS_150,negative,,85698,Complete,FDAARGOS_150,,,,MLST.Achromobacter_spp.205,,FDA:FDAARGOS_150,,2016-02-11T00:00:00Z,,PRJNA231221,SAMN03996294,GCA_001559195.1,"SRR2821366,SRR2821367,SRR2821368,SRR2821369",CP014028,,US Food and Drug Administration,,Pacbio,22.682x,HGAP3 v. Nov 2014,1,,1,6263082,67.81,7353,5634,Sputum,Sputum,,4/8/14,USA,USA:DC,,,,,,"Human, Homo sapiens",female,37Y,Cystic Fibrosis,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:Children's National Hospital,97.6,81.7,96.2,21.6,High CheckM contamination score,Poor,2016-03-01T21:19:05.002Z,2016-03-01T21:19:05.002Z
7812,85962.8,Helicobacter pylori 26695,negative,Helicobacter pylori 26695,85962,Complete,26695,,,,MLST.Helicobacter_pylori.181,,,,1997-08-07T00:00:00Z,9252185,PRJNA233,,GCA_000008525.1,,AE000511,NC_000915,TIGR,complete,,,,1,,1,1667867,38.9,1674,1576,None,patient,"isolated from a patient in the United Kingdom who had gastritis before 1987, this strain has undergone repeated subculturing prior to being sequenced",,United Kingdom,United Kingdom,,,,,,"Human, Homo sapiens",,,,,,,,,-,Spiral,Yes,,Mesophilic,37,,Aerobic,Host-associated,Gastritis;Peptic ulcer disease,"Helicobacter pylori strain 26695. This strain was originally isolated from a patient in the United Kingdom who had gastritis before 1987, this strain has undergone repeated subculturing prior to being sequenced.",,99.8,99.3,100,0.9,,Good,2014-12-08T22:11:43.331Z,2015-03-16T03:17:09.594Z
7814,85963.7,Helicobacter pylori J99,negative,Helicobacter pylori J99,85963,Complete,J99,,,,MLST.Helicobacter_pylori.199,,,,1999-01-29T00:00:00Z,9923682,PRJNA234,,GCA_000008785.1,,AE001439,NC_000921,ASTRA,complete,,,,1,,1,1643831,39.2,1623,1489,Stomach,patient with duodenal ulcer,isolated in 1994 in the USA from a patient with duodenal ulcer,1994,USA,United States,,,,,,"Human, Homo sapiens",,,duodenal ulcer,,,,,,-,Spiral,Yes,,Mesophilic,37,,Aerobic,Host-associated,Gastritis;Peptic ulcer disease,Helicobacter pylori strain J99. This strain was isolated in 1994 in the USA from a patient with duodenal ulcer. It has undergone little subculturing prior to being sequenced.,,99.9,99.9,100,0.3,,Good,2014-12-08T22:11:45.029Z,2015-03-16T03:17:09.594Z
7847,87883.77,Burkholderia multivorans strain AU1185,negative,,87883,Complete,AU1185,,,,MLST.Burkholderia_cepacia_complex.18,,,,2016-09-02T00:00:00Z,,PRJNA279182,SAMN03449401,GCF_001718755.1,SRR1956464,"CP013430,CP013431,CP013432","NZ_CP013430.1,NZ_CP013431.1,NZ_CP013432.1",Northern Arizona University,,PacBio,50x,HGAP v. 2.0,3,,3,6620936,66.87,6600,5784,Skin,Thigh Biopsy,,1999,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequence analysis of diverse Burkholderia genomes,collected_by:UMich - John Lipuma,99.6,97,100,1.5,,Good,2016-11-15T22:04:43.756Z,2016-11-15T22:04:43.756Z
7854,90062.4,Leptospira interrogans serovar Icterohaemorrhagiae strain Langkawi,negative,,90062,Complete,Langkawi,Icterohaemorrhagiae,,,MLST.Leptospira_spp_3.74,,,,2020-10-07T00:00:00Z,,PRJNA564735,SAMN12721651,GCA_014858895.1,,"CP043876,CP043877,CP043878,CP043879",,Leibniz Institute DSMZ,,PacBio RSII; Illumina MiSeq,150.0x,HGAP v. 3,2,2,4,4885316,35.221817,4995,4316,None,,,2004,Netherlands,Netherlands,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Part of Leptospira interrogans comparative genomics study,"sample_type:cell culture;biomaterial_provider:Leptospirosis Reference Centre, Amsterdam",99.9,99.7,,,,Good,2020-11-29T06:18:54.249Z,2020-11-29T06:18:54.249Z
7855,90245.4,Oligella urethralis strain FDAARGOS_329,negative,,90245,Complete,FDAARGOS_329,,,,,,FDA:FDAARGOS_329,,2018-03-09T00:00:00Z,,PRJNA231221,SAMN06173342,GCA_002984485.1,,CP027417,,US Food and Drug Administration,,PacBio; Illumina,16.56x,CA v. 8.2,1,,1,2511315,46.081474,2451,2329,Ear,left ear swab,,15-Jan-15,USA,USA:DC,,,,,,"Human, Homo sapiens",male,14Y,Chronic otorrhea,,,,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,94.1,93.7,96.1,,,Good,2018-05-26T05:51:32.949Z,2018-05-26T05:51:32.949Z
7867,90370.93,Salmonella enterica subsp. enterica serovar Typhi strain B/SF/13/03/195,negative,,90370,Complete,B/SF/13/03/195,Typhi,,,,,,,2015-09-29T00:00:00Z,,PRJNA286162,SAMN03765689,GCA_001302625.1,,CP012151,,Universiti Sains Malaysia,,PacBio,184.0x,Celera Assembler v. HGAP.2,1,,1,4798993,52.03,5141,4352,None,carrier foodhandler,,13-Apr,Malaysia,Malaysia: Kelantan,,,,,,"Human, Homo sapiens",,,Typhoid fever,,,,,,,,,,,C,,,,,Genome sequencing of Salmonella enterica subsp. enterica serovar Typhi str. B/SF/13/03/195;many frameshifted proteins,collected_by:Kelantan Health Department,99.7,97.6,100,2.1,,Good,2016-01-17T17:12:24.621Z,2016-01-17T17:12:24.621Z
7931,90371.903,Salmonella enterica subsp. enterica serovar Typhimurium strain FORC_015,negative,,90371,Complete,FORC_015,Typhimurium,,,MLST.Salmonella_enterica.413,,,,2015-05-07T00:00:00Z,,PRJNA282346,SAMN03568791,GCF_000993725.1,SRR1997852,CP011365,NZ_CP011365.1,Korea Research Institute of Bioscience and Biotechnology,,PacBio RS II,161x,SMRT Analysis v. 2.3.0,1,,1,4759372,52.14,4787,4288,Blood,blood,isolated from human blood in South Korea,1-Oct-13,South Korea,South Korea,,,,,env_biome:none,"Human, Homo sapiens",,,,,,,,,,,,,Mesophilic,37 C,,Facultative,HostAssociated,pathogen infecting humans,A strain (FORC_015) of Salmonella enterica subsp. enterica serovar Typhimurium was isolated from human blood in South Korea. The complete genome sequence for this strain was obtained by PacBio RS II sequencing technology.,"sample_type:blood culture;biomaterial_provider:125 Gwak-ro, Yuseoung-gu",99.7,99,97.4,1.5,,Good,2016-01-17T15:58:23.212Z,2016-01-17T15:58:23.212Z
7942,91891.57,Legionella pneumophila subsp. pneumophila strain Albuquerque 1 (D-7474) strain Albuquerque 1 (D-7474),negative,,91891,Complete,Albuquerque 1 (D-7474,1,,,,genotype:ST1,,,2018-03-15T00:00:00Z,29427765,PRJNA376177,SAMN06928753,GCA_003004315.1,,"CP021286,CP021287",,Centers for Disease Control and Prevention,,PacBio,88.63x,HGAP v. HGAP3,1,1,2,3638556,38.282413,3486,,None,,,1977,USA,"USA: New Mexico, Albuquerque",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Comparison of genomes of Legionella pneumophila isolates from different subspecies,sample_type:human lung tissue,99.8,98.6,100,3.3,,Good,2018-05-26T06:46:39.193Z,2018-05-26T06:46:39.193Z
7948,91892.16,Legionella pneumophila subsp. fraseri strain D-4058,negative,,91892,Complete,D-4058,1,,,,genotype:ST150,,,2018-03-15T00:00:00Z,29427765,PRJNA376177,SAMN06928763,GCA_003004215.1,,"CP021277,CP021278",,Centers for Disease Control and Prevention,,PacBio,77.34x,HGAP v. HGAP3,1,1,2,3625177,38.25303,3436,,None,,,1994,USA,"USA: Connecticut, Bridgeport",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Comparison of genomes of Legionella pneumophila isolates from different subspecies,sample_type:sputum,99.9,99.6,100,,,Good,2018-05-26T06:45:55.156Z,2018-05-26T06:45:55.156Z
7949,93061.132,Staphylococcus aureus subsp. aureus NCTC 8325 strain NCTC8325,positive,,93061,Complete,NCTC8325,Serological Group A,,,MLST.Staphylococcus_aureus.8,,NCTC:8325,,2018-06-17T00:00:00Z,,PRJEB6403,SAMEA3672889,GCA_900475245.1,,LS483365,,SC,,,,,1,,1,2830002,32.880154,2677,2618,Eye,Conjunctiva,,1943,United Kingdom,United Kingdom: Oxford,,,,,,"Human, Homo sapiens",,,,,,host_health_state:Corneal Cancer,Susceptible,Computational Prediction,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,100,99.9,100,,,Good,2018-07-16T22:44:32.870Z,2018-07-16T22:44:32.870Z
7956,95485.5,Burkholderia stabilis strain ATCC BAA-67,negative,,95485,Complete,ATCC BAA-67,,,,MLST.Burkholderia_cepacia_complex.51,,ATCC:BAA-67,,2016-09-22T00:00:00Z,,PRJNA328254,SAMN05367054,GCF_001742165.1,"SRR3939695,SRR3939696","CP016442,CP016443,CP016444","NZ_CP016442.1,NZ_CP016443.1,NZ_CP016444.1",Centers for Disease Control and Prevention,,PacBio,105x,RS_HGAP_Assembly v. 3,3,,3,8527947,66.42,8522,7567,Sputum,sputum from a cystic fibrosis patient,,1993,Belgium,Belgium: Leuven,,,,,,"Human, Homo sapiens",,,Cystic fibrosis,,,,,,,,,,,,,,,,First complete genome for Burkholderia stabilis.,"collected_by:Verbiest L., Universitair Ziekenhuis Leuven",98.9,94.4,100,3.6,,Good,2016-11-16T16:15:59.061Z,2016-11-16T16:15:59.061Z
7972,95486.86,Burkholderia cenocepacia strain 895,negative,,95486,Complete,895,,,,MLST.Burkholderia_cepacia_complex.628,,,,2016-04-04T00:00:00Z,,PRJNA316047,SAMN04574071,GCF_001606135.1,,"CP015036,CP015037,CP015038","NZ_CP015036.1,NZ_CP015037.1,NZ_CP015038.1",University of Malaya,,PacBio,317.74x,HGAP v. 2,2,1,3,8731481,66.76,8681,7808,Blood,Cord blood,,17-Aug-14,Malaysia,Malaysia: Kuala Lumpur,,,,,,"Human, Homo sapiens",female,1 day old,Bacterial infection,,,,,,,,,,,,,,,,Whole genome sequencing of Burkholderia cenocepacia 895,collected_by:Cheong Yuet Meng,99.2,94.4,100,,,Good,2016-04-28T01:52:54.946Z,2016-04-28T01:52:54.946Z
8,102611.3,Helicobacter pylori J166,negative,,102611,Complete,J166,,,,MLST.Helicobacter_pylori.204,,,,2014-05-08T00:00:00Z,24924186,PRJNA245313,SAMN02736817,GCA_000685625.1,,CP007603.1,NZ_CP007603.1,Penn State University,,Sanger dideoxy sequencing; 454; Illumina,,Newbler v. May-2009,1,,1,1650561,38.9,1630,1454,Stomach,human stomach,,1995,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Human clinical H. pylori strain used for experimental infection of rhesus monkeys,,99.8,99.6,100,,,Good,2014-12-08T22:28:46.086Z,2015-03-16T03:17:09.594Z
9,102618.7,Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 strain NCTC11637,negative,,102618,Complete,NCTC11637,,,,MLST.Helicobacter_pylori.3327,,NCTC:11637,,2018-06-17T00:00:00Z,,PRJEB6403,SAMEA3178013,GCA_900478295.1,,LS483488,,SC,,,,,1,,1,1680937,38.825607,1709,1601,Stomach,Gastric Antrum,,1984,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.5,99.1,100,0.4,,Good,2018-07-16T23:42:33.236Z,2018-07-16T23:42:33.236Z
13,103855.15,Bordetella hinzii strain F582,negative,,103855,Complete,F582,,,,,,ATCC:51730,,2015-07-16T00:00:00Z,,PRJNA287884,SAMN03790813,GCF_001078275.1,,CP012076,NZ_CP012076.1,Centers for Disease Control and Prevention,,PacBio RSII; Illumina HiSeq,482x,HGAP v. 3,1,,1,4912977,67.06,4617,4559,Blood,blood,,1994,USA,USA: WA,,,,,,"Human, Homo sapiens",male,,Bacteremia,,,host_health_state:AIDS patient,,,,,,,,,,,,,This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to characterize genomes of Bordetella species other than B. pertussis. Members of the genus Bordetella cause respiratory and opportunistic infection in a variety of hosts. These data are being made available to facilitate comparative analyses for the study of this important group of bacterial pathogens.,"collected_by:B.T. Cookson, U. of Washington",97.7,96,100,,,Good,2016-01-17T16:20:51.242Z,2016-01-17T16:20:51.242Z
27,106648.24,Acinetobacter bereziniae strain XH901,negative,,106648,Complete,XH901,,,,,,,,2017-12-06T00:00:00Z,,PRJNA355181,SAMN06066181,GCA_002813045.1,,CP018259,,Zhejiang University,,Pacbio,50x,Canu v. 1.3,1,,1,4509124,38.09,4360,4170,Blood,blood,,2016,China,China: Zhejiang,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,colistin resistant Acinetobacter haemolyticus XH900,collected_by:Yunsong Yu,97.7,96.5,97.2,2.4,,Good,2018-01-01T04:10:31.331Z,2018-01-01T04:10:31.331Z
35,106654.48,Acinetobacter nosocomialis strain SSA3,negative,,106654,Complete,SSA3,,,,"MLST.Acinetobacter_baumannii_1.958,MLST.Acinetobacter_baumannii_2.433",,,,2017-04-10T00:00:00Z,,PRJNA380857,SAMN06650244,,,"CP020588,CP020587",,Yonsei University College of medicine,,PacBio,490x,HGAP v. 3,1,1,2,4142356,38.71,4034,3931,Blood,blood,,2013-09,South Korea,South Korea: Seoul,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,comparative genomics of blaOXA-23-carrying Acinetobacter strains,collected_by:KARMS,99.1,98.2,100,,,Good,2017-05-28T10:08:04.197Z,2017-05-28T10:08:04.197Z
48,110505.9,Mycobacterium heckeshornense strain JCM 15655,positive,,110505,Complete,JCM 15655,,,,,,,Yes,2020-12-25T00:00:00Z,,PRJDB10874,SAMD00265704,GCA_016592155.1,,AP024237,,"Mycobacteriology, National Institute of Infectious Diseases",,ONT MinION; Illumina Miniseq,192x,Canu v. 1.8; Shovill v. 1.0.4,1,,1,4957188,65.9294,5019,4840,None,,,1994,Germany,Germany,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,,,,,,,,"Mycobacterium (M.) heckeshornense is a slow growing, scotochromogenic, thermophilic non-tuberculous mycobacterial (NTM) species. Both biochemical and phylogenetic analyses indicated that M. heckeshornense is closely related to M. xenopi and M. botniense. We determined the complete genome sequence of M. heckeshornense type strain JCM 15655T, helping us to understand characteristics of this pathogen.",,98.7,97.3,,,,Good,2021-02-01T05:23:40.151Z,2021-02-01T05:23:40.151Z
79,115711.1,Chlamydophila pneumoniae AR39,negative,Chlamydophila pneumoniae AR39,115711,Complete,AR39,,,,,,,,2000-02-24T00:00:00Z,10684935,PRJNA247,SAMN02641564,GCA_000091085.1,,"AE002163,AE002161",NC_002180,TIGR,complete,,,,1,,1,1229853,40.6,1168,1112,Respiratory,University of Washington student with acute respiratory (=AR) tract infection,"Isolated from a University of Washington student with acute respiratory (=AR) tract infection in 1983, and epidemiologically distinct from Chlamydophila pneumoniae strain CWL029",1983,USA,USA: Wyoming,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,Mesophilic,37,,,Host-associated,Pharyngitis,"Chlamydophila pneumoniae strain AR39. Isolated from a University of Washington student with acute respiratory (=AR) tract infection in 1983, and epidemiologically distinct from Chlamydophila pneumoniae strain CWL029.",,99.7,99.7,100,,,Good,2014-12-08T22:10:54.551Z,2015-03-16T03:17:09.594Z
91,119602.564,Streptococcus dysgalactiae subsp. equisimilis strain 89,positive,,119602,Complete,89,,,,MLST.Streptococcus_dysgalactiae_equisimilis.29,,,,2020-08-08T00:00:00Z,,PRJDB10330,SAMD00238723,GCA_014192695.1,,AP023393,,"Department of Microbiology, Graduate School of Medicine, Kyoto University",,Illumina MiSeq; Oxford Nanopore,362x,Unicycler v. 0.4.8,1,,1,2158609,39.4316,2147,2075,None,,,1998,,,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Cocci,,,,,,,,,"We determined complete genome sequence of three Streptococcus species, S. pyogenes, S. suis, and S. dysgalactiae. Among these three species, S. pyogenes and S. dysagalactiae have recognized as causative agents occasionally causing sever disease (ex. toxic shock syndrome) to human. On the other hand, S. suis is one of the major zoonotic agent and cause a variety of infections in individuals working in close contact with swine or pork products. In this study, we focus on the gene sets or genomic regions contributing to their pathogenicity, based on the complete genome sequence of three Streptococcus species.",,98.2,97.6,,,,Good,2020-08-22T13:48:18.088Z,2020-08-22T13:48:18.088Z
113,119856.8,Francisella tularensis subsp. tularensis WY96,negative,,119856,Complete,WY96,,,,,,,,2015-02-09T00:00:00Z,-,PRJNA240119,SAMN02769653,GCA_000834965.1,"SRR1284499,SRR1284500,SRR1284501","CP010103.1,CP010104.1","NZ_CP010103.1,NZ_CP010104.1",Los Alamos National Laboratory,,Illumina (short insert); Illumina (long,304x; 50x; 132x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,1,1,2,2047033,32.27,1977,1947,Wound,Wound,,2008,USA,USA: Wyoming,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,,,,,,,,,,Genome sequencing of Francisella tularensis tularensis WY96,,99.6,98.9,99.2,0.8,,Good,2015-03-12T13:40:17.630Z,2015-03-16T03:17:09.594Z
116,119857.297,Francisella tularensis subsp. holarctica strain 2015321842,negative,,119857,Complete,2015321842,,,,,,,,2021-07-06T00:00:00Z,,PRJNA721727,SAMN18737166,GCA_019134795.1,,CP073125,,USAMRIID,,PacBio,200x,HGAP v. 4,1,,1,1890509,32.175358,2173,1849,Lung,pleural,,2015,USA,USA: KY,,,,,,Homo sapiens,,,Tularemia,,,,,,,,,,,,,,,,Complete sequencing and characterization of 10 Francisella tularensis strains to be used for vaccine and treatment testing,collected_by:Minnesota Public Health,99.9,98.5,,,,Good,2021-08-01T16:45:31.447Z,2021-08-01T16:45:31.447Z
130,120959.23,Mycobacterium kubicae strain NJH_MKUB2,positive,,120959,Complete,NJH_MKUB2,,,,,,,,2020-08-21T00:00:00Z,,PRJNA575747,SAMN12910286,GCA_014263335.1,,"CP045075,CP045076,CP045077,CP045078,CP045079,CP045080",,National Jewish Health,,Oxford Nanopore MiniION; Illumina HiSeq,425x,Unicycler v. 0.4.4,1,5,6,6272472,65.98746,6215,5921,Lung,Bronchial Alveolar lavage,,2017,USA,USA,,,,,,"Human, Homo sapiens",male,,,,,,,,,,,,,,,,,,We provide the complete genome assemblies of Nontuberculous Mycobacteria (NTM) isolates sequenced at National Jewish Health. The genomes were sequenced and resolved using hybrid assembly of Illumina HiSeq and ONT MinION sequencing reads.,collected_by:National Jewish Health,97.6,95.5,,,,Good,2020-09-06T00:03:01.388Z,2020-09-06T00:03:01.388Z
142,123899.23,Bordetella trematum strain F581,negative,,123899,Complete,F581,,,,,,ATCC:700309,,2019-01-03T00:00:00Z,,PRJNA287884,SAMN05333717,GCA_003991115.1,,CP016340,,Centers for Disease Control and Prevention,,PacBio RSII; Illumina MiSeq,185x,HGAP v. 3,1,,1,4476250,65.546295,4190,4047,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to characterize genomes of Bordetella species other than B. pertussis. Members of the genus Bordetella cause respiratory and opportunistic infection in a variety of hosts. These data are being made available to facilitate comparative analyses for the study of this important group of bacterial pathogens.,,98.3,96.5,,,,Good,2019-02-01T00:13:41.826Z,2019-02-01T00:13:41.826Z
193,126385.6,Providencia alcalifaciens strain FDAARGOS_408,negative,,126385,Complete,FDAARGOS_408,,,,,,FDA:FDAARGOS_408,,2017-09-28T00:00:00Z,,PRJNA231221,SAMN07312452,GCA_002393505.1,,CP023536,,US Food and Drug Administration,,PacBio; Illumina,16.55x,"SMRT v. 2.3.0, HGAP v. 3",1,,1,3990106,41.99,3777,3644,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID,98.9,98.2,100,,,Good,2017-11-25T03:22:27.432Z,2017-11-25T03:22:27.432Z
1050,131111.13,Schaalia turicensis strain CT001,negative,,131111,Complete,CT001,,,,,,,,2021-07-28T00:00:00Z,,PRJNA607374,SAMN14131124,GCA_019380255.1,,CP048928,,"Faculty of Medicine Siriraj Hospital, Mahidol University",,Illumina NovaSeq and Oxford Nanopore,1443.414545x,Unicycler v. 0.4.4,1,,1,1912310,57.120342,1727,1630,Urine,urethra,,1/15/10,Thailand,Thailand: Bangkok,,,,,,Homo sapiens,,15,gonorrhea,,,,,,,,,,,,,,,,To explore the genomic dynamics of co-evolution between Neisseria gonorrhoeae and Schaalia turicensis,collected_by:Natakorn Nokchan,97.3,97.1,,,,Good,2021-08-26T12:45:47.705Z,2021-08-26T12:45:47.705Z
1655,135487.8,Nocardia cyriacigeorgica strain MDA3349 strain MDA3349 ancestor,positive,,135487,Complete,MDA3349 ancestor,,,,,,,,2018-02-22T00:00:00Z,,PRJNA432572,SAMN08458266,GCA_002949635.1,,"CP026746,CP026745",,Rice University,,PacBio; Illumina HiSeq,43.0x,Canu v. 1.4,1,1,2,6462637,68.284355,6114,5803,None,laboratory,,2016,USA,USA: Texas,,,,,,"Human, Homo sapiens",,,nocardiosis,,,,,,,,,,,,,,,,Multiple pathogenic isolates of Nocardia nova and Nocardia cyriageorgica were adapted to trimethoprim-sulfamethoxazole using experimental evolution. Whole genome sequencing was used to identify mutations conferring resistance.,collected_by:Heer Mehta,98.9,97.9,100,,,Good,2018-05-26T01:46:11.032Z,2018-05-26T01:46:11.032Z
1678,138677.3,Chlamydophila pneumoniae J138,negative,Chlamydophila pneumoniae J138,138677,Complete,J138,,,,,,,,2000-06-28T00:00:00Z,"1,083,975,310,871,360",PRJNA257,,GCA_000011165.1,,BA000008,NC_002491,"Yamaguchi Univ., Japan",complete,,,,1,,1,1226565,40.6,1177,1069,Respiratory,the pharyngeal mucosa of a 5 year old male patient with acute bronchitis,Isolated in Japan in 1994 from the pharyngeal mucosa of a 5 year old male patient with acute bronchitis,1994,Japan,Japan,,,,,,"Human, Homo sapiens",male,5,acute bronchitis,,,,,,-,Rod,,,Mesophilic,37,,,Host-associated,Pharyngitis;Bronchitis;Pneumonitis,Chlamydophila pneumoniae strain J138. Isolated in Japan in 1994 from the pharyngeal mucosa of a 5 year old male patient with acute bronchitis.,,99.7,99.7,100,1.7,,Good,2014-12-08T22:10:54.586Z,2015-03-16T03:17:09.594Z
1728,143387.63,Fusobacterium necrophorum subsp. funduliforme strain F1260,negative,,143387,Complete,F1260,,,,,,,,2018-11-15T00:00:00Z,,PRJNA354964,SAMN06234847,GCA_003732525.1,,CP019306,,Aarhus University,,PacBio,300.0x,HGAP v. 3,1,,1,2288480,35.214333,2336,2219,Blood,Blood,,2000,Denmark,Denmark,,,,,,"Human, Homo sapiens",,,Lemierre's syndrome,,,,,,,,,,,,,,,,Closed genome of a human strain of Fusobacterium necrophorum subsp. funduliforme,collected_by:Lena Hagelskjaer,96.8,96.2,,,,Good,2018-11-29T11:03:39.990Z,2018-11-29T11:03:39.990Z
1774,148942.549,Streptococcus equi subsp. equi strain NCTC12091,positive,,148942,Complete,NCTC12091,not available: to be reported later,,,MLST.Streptococcus_zooepidemicus.212,,NCTC:12091,,2018-12-19T00:00:00Z,,PRJEB6403,SAMEA3572409,GCA_900636415.1,,LR134273,,SC,,,,,1,,1,2081938,41.578663,2077,1881,Blood,Blood culture,,1987,United Kingdom,United Kingdom: Northallerton,,,,,,"Human, Homo sapiens",,,,,,host_health_state:disease,,,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,99.9,99.9,,,,Good,2019-02-01T13:29:25.407Z,2019-02-01T13:29:25.407Z
1866,149539.896,Salmonella enterica subsp. enterica serovar Enteritidis strain 81-1705,negative,,149539,Complete,81-1705,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,SAMN06050734,GCA_002763415.1,,"CP018651,CP018652,CP018653,CP018654",,FDA,,PacBio,missing,HGAP v. 3.0,1,3,4,4991608,52.03,5273,5022,None,Human,,1981,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,Resistant,AMR Panel,,,,,,,,,,,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,99.6,99,100,1.8,,Good,2017-11-24T17:24:24.538Z,2017-11-24T17:24:24.538Z
1923,150053.3,Yersinia enterocolitica subsp. palearctica strain Y1,negative,,150053,Complete,Y1,O:3,,,MLST.Yersinia_spp.18,,,,2019-03-25T00:00:00Z,,PRJNA480560,SAMN09641678,GCA_004368055.1,,"CP030980,CP030981",,Helmholtz Centre for Infection Research,,PacBio; Illumina MiSeq,159x,HGAP SMRTPortal v. 2.3.0,1,1,2,4594706,46.95382,4575,4258,None,,,2007,Germany,Germany,,,,,,"Human, Homo sapiens",,,Yersiniosis,,,,,,,,,,,,,,,,"The aim of the study was to sequence and annotate the genome of the clinical isolate of Y. enterocolitica Y1 (O:3/4). Additionally, the transcriptome of this isolate was compared to the transcriptome of Y. enterocolitica 8081v (O:8/1B).","collected_by:E. Strauch, BfR",99.4,97.8,,,,Good,2019-07-15T18:12:36.489Z,2019-07-15T18:12:36.489Z
1929,152500.5,Burkholderia dolosa strain FDAARGOS_562 strain Not applicable,negative,,152500,Complete,Not applicable,,,,MLST.Burkholderia_cepacia_complex.472,,FDA:FDAARGOS_562,,2018-11-21T00:00:00Z,,PRJNA231221,SAMN10163186,GCA_003813045.1,,"CP033838,CP033839,CP033840",,US Food and Drug Administration,,Pacbio; Illumina,14.64x,"SMRT v. 2.3.0, HGAP v. 3.0",3,,3,6409101,67.00798,6569,5875,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID < Northern Arizona University < Michigan State University (USA),99.4,95.9,,,,Good,2018-11-30T03:25:26.817Z,2018-11-30T03:25:26.817Z
1942,155322.253,Bacillus toyonensis strain BV-17,positive,,155322,Complete,BV-17,,,,MLST.Bacillus_cereus.72,,,,2019-12-25T00:00:00Z,,PRJNA594461,SAMN13518956,GCA_009799785.1,,CP047044,,Peking University Cancer Hospital & Institute,,Illumina,0.9888x,ABySS v. MAY-2019,1,,1,5351266,35.392185,5531,5266,None,,,2019-04,China,China,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,a new Bacillus cereus genome,,97.9,97,,,,Good,2020-02-07T13:50:54.571Z,2020-02-07T13:50:54.571Z
1944,155615.5,Fusobacterium nucleatum subsp. vincentii strain KCOM 2931,negative,,155615,Complete,KCOM 2931,,,,,,,,2017-11-13T00:00:00Z,,PRJNA415900,SAMN07837329,GCA_002764055.1,,CP024749,,Korean Collection for Oral Microbiology,,PacBio,467.0x,RS HGAP v. 3.0,1,,1,2087706,27.21,1985,1962,Mouth,Subgingival dental plaque,,4/24/15,Korea,Korea: Gwangju,,,,,,"Human, Homo sapiens",,,periodontitis,,,,,,,,,,,,,,,,Genome sequencing of Fusobacterium nucleatum subsp. vincentii KCOM 2931,collected_by:Korean Collection for Oral Microbiology,99.9,99.7,100,,,Good,2017-11-24T17:23:37Z,2017-11-24T17:23:37Z
1945,155864.21,Escherichia coli O157:H7 str. EDL933,negative,,155864,Complete,EDL933,,,,"MLST.Escherichia_coli_1.453,MLST.Escherichia_coli_2.86",,,,2018-04-02T00:00:00Z,,PRJNA389368,SAMN07196157,GCA_003028715.1,,CP028305,,Rehman Medical Institute,,Illumina MiSeq,30X,SPAdes v. 3.10.1,1,,1,4709911,50.763325,4635,,Urine,urine,,6-Dec-16,Pakistan,"Pakistan: Sheikh Zaid Hospital, Lahore",,,,,,"Human, Homo sapiens",,,Urinary tract infection,,,,,,,,,,,,,,,,"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","collected_by:Asma Manzoor, Nabila Ishaq",99.6,98.7,96.8,1.5,,Good,2018-05-30T23:17:23.107Z,2018-05-30T23:17:23.107Z
2016,158836.977,Enterobacter hormaechei strain MSB1_8J,negative,,158836,Complete,MSB1_8J,,,,MLST.Enterobacter_cloacae.114,,,,2020-12-20T00:00:00Z,,PRJNA646837,SAMN17054651,GCA_016126855.1,,"CP065939,CP065940,CP065941,CP065942",,Monash University,,Oxford Nanopore MinION; Illumina HiSeq,38.0x,Unicycler v. 0.4,1,3,4,5201113,54.731747,5154,4937,Stool,rectal swab,,2014,Australia,Australia: Melbourne,,,,,,"Human, Homo sapiens",,,carriage,,,,,,,,,,,,,,,,Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU,"collected_by:Microbiology Unit & Department of Infectious Diseases, Alfred Hospital",99.6,98.2,,,,Good,2021-01-01T20:41:41.861Z,2021-01-01T20:41:41.861Z
2017,158879.11,Staphylococcus aureus subsp. aureus N315,positive,Staphylococcus aureus subsp. aureus N315,158879,Complete,N315,,,,MLST.Staphylococcus_aureus.5,,,,2001-06-22T00:00:00Z,11418146,PRJNA264,,GCA_000009645.1,,"BA000018,AP003139","NC_002745,NC_003140",Juntendo Univ.|NITE,complete,,,,1,1,2,2839469,32.8,2734,2619,Respiratory,pharyngeal smear of a Japanese patient,isolated in 1982 from a pharyngeal smear of a Japanese patient,1982,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,30-37,,Facultative,Host-associated,Toxic shock syndrome;Scarlet fever,Staphylococcus aureus subsp. aureus strain N315. This strain is a methicillin-resistant (MRSA) strain isolated in 1982 from a pharyngeal smear of a Japanese patient.,,100,99.9,100,,,Good,2014-12-08T22:13:24.904Z,2015-03-16T03:17:09.594Z
2020,160490.1,Streptococcus pyogenes M1 GAS,positive,Streptococcus pyogenes M1 GAS,160490,Complete,M1 GAS,,,,MLST.Streptococcus_pyogenes.28,,,,2001-04-11T00:00:00Z,11296296,PRJNA269,SAMN02604089,GCA_000006785.2,,AE004092,NC_002737,University of Oklahoma,complete,,,,1,,1,1852441,38.5,1919,1697,Wound,patient with a wound infection,isolated from a patient with a wound infection,,,,,,,,,"Human, Homo sapiens",,,wound infection,,,,,,+,Coccus,No,No,Mesophilic,30-35,Non-halophilic,Facultative,Host-associated,,Streptococcus pyogenes strain M1 GAS. This strain is also known as group A streptococci (GAS). This organism is a strict human pathogen that was isolated from a patient with a wound infection.,,99.9,99.9,100,0.9,,Good,2014-12-08T22:13:35.807Z,2015-03-16T03:17:09.594Z
2021,160491.19,Streptococcus pyogenes str. Manfredo,positive,Streptococcus pyogenes str. Manfredo,160491,Complete,Manfredo,serovar M5,,,MLST.Streptococcus_pyogenes.99,,,,2007-03-29T00:00:00Z,17012393,PRJNA270,SAMEA1705956,GCA_000009385.1,,AM295007,NC_009332,Wellcome Trust Sanger Institute,complete,,,,1,,1,1841271,38.6,1935,1745,None,patient,isolated from a patient in the 1950's in Chicago,1950's,USA,USA: Chicago,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,30-35,Non-halophilic,Facultative,Host-associated,,Streptococcus pyogenes strain Manfredo. This strain is a serotype M5 strain associated with acute rheumatic fever isolated from a patient in the 1950's in Chicago.,,99.9,99.6,100,,,Good,2014-12-08T22:13:36.002Z,2015-03-16T03:17:09.594Z
2172,168807.7,Escherichia coli O127:H6 strain EPEC E2348/69 variety 2,negative,,168807,Complete,EPEC E2348/69 variety 2,,,,"MLST.Escherichia_coli_1.15,MLST.Escherichia_coli_2.491",,,,2017-10-28T00:00:00Z,,PRJEB18716,SAMEA35192668,GCA_900149915.1,,LT827011,,CNB/CSIC,,,,,1,,1,4848621,50.567574,4906,4436,None,Sanger Centre via Imperial College,,2012,United Kingdom,United Kingdom,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,The strain EPEC E2348/69 variety 2 was obtained from the Sanger Centre via the Imperial College. The sequence was obtained using NGS and the reads were assembled using NC_011601.1 as reference.,,99.9,98.8,99.6,,,Good,2018-07-16T16:44:24.512Z,2018-07-16T16:44:24.512Z
2175,170187.11,Streptococcus pneumoniae TIGR4,positive,Streptococcus pneumoniae TIGR4,170187,Complete,TIGR4,serovar 4,,,,,,,2001-07-21T00:00:00Z,11463916,PRJNA277,,GCA_000006885.1,,AE005672,NC_003028,TIGR,complete,,,,1,,1,2160842,39.7,2328,2105,Blood,the blood of a 30 year old male patient,"isolate from the blood of a 30 year old male patient in Kongsvinger, Norway",,Norway,"Kongsvinger, Norway",,,,,,"Human, Homo sapiens",male,30,,,,,,,+,Coccus,No,No,Mesophilic,30-35,,Facultative,Multiple,Pneumonia;Meningitis;Bacteremia;Sinusitis;Otitis media;Conjunctivitis,"Streptococcus pneumoniae strain TIGR4. This strain is a highly virulent capsular serotype 4 clinical isolate from the blood of a 30 year old male patient in Kongsvinger, Norway.",,99.6,99,100,0.3,,Good,2014-12-08T22:13:35.364Z,2015-03-16T03:17:09.594Z
2202,176279.9,Staphylococcus epidermidis RP62A,positive,Staphylococcus epidermidis RP62A,176279,Complete,RP62A,,,,MLST.Staphylococcus_epidermidis.10,,,,2005-01-18T00:00:00Z,15774886,PRJNA64,SAMN02603975,GCA_000011925.1,,"CP000029,CP000028","NC_002976,NC_006663",TIGR,complete,,,,1,1,2,2643840,32.1,2503,2526,Urine,patient with intravascular catheter-associated sepsis,isolated from a patient with intravascular catheter-associated sepsis,,,,,,,,,"Human, Homo sapiens",,,intravascular catheter-associated sepsis,,,,,,+,Coccus,No,No,Mesophilic,30-37,,Facultative,Host-associated,Toxic shock syndrome;Scarlet fever,"Staphylococcus epidermidis strain RP62A. This strain is a strongly adherent, slime-producing, pathogenic strain isolated from a patient with intravascular catheter-associated sepsis.",,100,100,100,,,Good,2014-12-08T22:13:26Z,2015-03-16T03:17:09.594Z
2642,177416.18,Francisella tularensis subsp. tularensis SCHU S4,negative,Francisella tularensis subsp. tularensis SCHU S4,177416,Complete,Schu S4,,,,,,,,2004-12-17T00:00:00Z,15640799,PRJNA9,,GCA_000008985.1,,AJ749949,NC_006570,"Swedish Defence Research Agency|Defence Science and Technology Laboratory, UK|Uppsala Univ.",complete,,,,1,,1,1892819,32.3,2097,1603,None,human case of tularemia,isolated from a human case of tularemia in 1951,1951,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,No,,,-,,Aerobic,Aquatic,Tularemia,"Francisella tularensis subsp. tularensis strain Schu S4. This subspecies is virulent in humans, and the strain is a clinical isolate that is also virulent in an animal model. Originally isolated from a human case of tularemia in 1951. Genome analysis indicates the presence of a large number of pseudogenes, many that disrupt important metabolic pathways, which is the reason for the exacting nutritional requirements of this organism. There is a duplicated pathogenicity island that has also been detected in strain LVS and mutations in the iglA, iglC, or pdpD genes affect the ability of the pathogen to survive in macrophages. The genome also contains genes for type IV pili production and capsular polysaccharide genes similar to those of Bacillus anthracis as well as numerous ABC transporters. There are a large number of insertion sequences including a mariner element, which is a transposon typically found in eukaryotes and is the first instance of this element to be found in a microbe, which may have acquired it during transit through one of the insect vectors.",,100,99.8,100,,,Good,2014-12-08T22:11:39.248Z,2015-03-16T03:17:09.594Z
2665,180434.86,Morganella morganii subsp. morganii strain 12304,negative,,180434,Complete,12304,,,,,,,,2021-06-09T00:00:00Z,,PRJNA673775,SAMN16623060,GCA_018802585.1,,CP064832,,Beijing Institute of Microbiology and Epidemiology,,PacBio RSII,100x,HGAP v. v3.0,1,,1,3950614,51.154808,3995,3689,None,,,2013,China,China:Wenzhou,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,The chromosome sequences of Morganella morganii,sample_type:cell culture,98,97,,,,Good,2021-06-26T03:33:17.323Z,2021-06-26T03:33:17.323Z
2683,182082.4,Chlamydophila pneumoniae TW-183,negative,Chlamydophila pneumoniae TW-183,182082,Complete,TW-183,,,,,,,Yes,2003-07-25T00:00:00Z,,PRJNA420,SAMN02602979,GCA_000007205.1,,AE009440,NC_005043,ALTANA Pharma,complete,,,,1,,1,1225935,40.6,1148,1113,Eye,child's conjunctiva (the membranes lining the eyelid) during a trachoma vaccine trial,isolated in 1965 from a child's conjunctiva (the membranes lining the eyelid) during a trachoma vaccine trial in Taiwan,1965,Taiwan,Taiwan,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,Mesophilic,37,,,Host-associated,Pharyngitis;Bronchitis;Pneumonitis,"Chlamydophila pneumoniae strain TW-183. This is the type strain for Chlamydophila pneumoniae. An ocular isolate first isolated in 1965 from a child's conjunctiva (the membranes lining the eyelid) during a trachoma vaccine trial in Taiwan. However, it naturally causes respiratory rather than ocular infections.",,99.9,99.9,100,,,Good,2014-12-08T22:10:54.633Z,2015-03-16T03:17:09.594Z
2684,183192.3,Escherichia coli O157:H- strain 3072/96,negative,,183192,Complete,3072/96,O157:H-,,,"MLST.Escherichia_coli_2.523,MLST.Escherichia_coli_1.11",,,,2021-02-11T00:00:00Z,,PRJNA415351,SAMN07821902,GCA_016864435.1,,"CP028590,CP028591",,University of Hohenheim,,PacBio,200.0x,HGAP3 algorithm v. 2.3,1,1,2,5684545,50.480663,6153,5949,None,patient suffering from HUS,isolated in Germany 1999 from a stool sample of a patient suffering from HUS (Schmidt et al,1996/1997,Germany,Germany,,,,,,Homo sapiens,,,HUS (Schmidt et al,,,,,,,,,,,,,,,,"The goal of this project is the complete sequencing (genome and possible plasmids) of a single sorbitol-fermenting enterohemorrhagic Escherichia coli (EHEC) O157:H- strain 3072/96 isolated in Germany 1999 from a stool sample of a patient suffering from HUS (Schmidt et al., 1999).","collected_by:Institute for Hygiene and Microbiology, University of Wuerzburg, Germany",99.9,99.5,,,,Good,2021-02-28T01:54:23.928Z,2021-02-28T01:54:23.928Z
2686,185332.6,Vibrio cholerae O37 strain ATCC 25872,negative,,185332,Complete,ATCC 25872,O37,,,MLST.Vibrio_cholerae.68,,ATCC:25872,,2021-05-11T00:00:00Z,,PRJNA599000,SAMN13736322,GCA_018336415.1,,"CP047305,CP047306",,EPFL,,PacBio Sequel,1796.0x,HGAP v. 4,2,,2,4018449,47.5633,3720,3576,Gut,,,1965,Czechoslovakia,Czechoslovakia,,,,,,Homo sapiens,,,gastroenteritis/cholera,,,,,,,,,,,,,,,,The goal of this study was understand the regulatory circuit of the type VI secretion system (T6SS) in non-pandemic but toxigenic V. cholerae.,passage_history:E. Aldova->O. Felsenfeld->ATTC->M. Blokesch,99.9,99.6,,,,Good,2021-06-02T22:48:20.176Z,2021-06-02T22:48:20.176Z
2687,189518.3,Leptospira interrogans serovar Lai str. 56601,negative,Leptospira interrogans serovar Lai str. 56601,189518,Complete,56601,serovar Lai,,,"MLST.Leptospira_spp.1,MLST.Leptospira_spp_2.7,MLST.Leptospira_spp_3.47",,,,2003-04-25T00:00:00Z,12712204,PRJNA293,SAMN02603127,GCA_000092565.1,,"AE010300,AE010301","NC_004342,NC_004343","Chinese National HGC, Shanghai",complete,,,,2,,2,4691184,35,4665,4724,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,Spiral,Yes,No,Mesophilic,28-30,,Aerobic,Host-associated,Leptospirosis,"Leptospira interrogans serovar Lai str. 56601. This strain has been maintained by the National Institute for Communicable Disease Control and Prevention, at the Chinese Center for Disease Control and Prevention in Beijing, China, and is a pathogenic strain.",,99.8,99.6,100,,,Good,2014-12-08T22:11:57.844Z,2015-03-16T03:17:09.594Z
2689,192222.6,Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819,negative,Campylobacter jejuni subsp. jejuni NCTC 11168,192222,Complete,NCTC 11168,,,,MLST.Campylobacter_jejuni.43,,NCTC 11168,,2000-02-25T00:00:00Z,"1,068,820,417,565,660",PRJNA8,SAMEA1705929,GCA_000009085.1,,AL111168,NC_002163,Wellcome Trust Sanger Institute,complete,,,,1,,1,1641481,30.5,1702,1623,Stool,diarrheic patient,isolated from a diarrheic patient in 1977 and minimally passaged,1977,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Spiral,Yes,No,Mesophilic,-,,Microaerophilic,Multiple,Food poisoning,"Campylobacter jejuni strain NCTC11168. This strain (originally 5636/77) was isolated from a diarrheic patient in 1977 and minimally passaged. This strain displays aberrant virulence phenotypes in animal models and tissue culture. Contains many homopolymeric tracts in the genome which result in hypervariable sequences in many genes having to do with cell surface structures. These sequences result in hypervarible antigenic diversity and immune evasion. Overall, the genome contains very few repetitive DNA sequences and very few coding regions arranged in operons. Pathogenicity factors include cytolethal-distending toxin, hemolysin-like toxins, and a type II secretion system.",,100,99.9,100,,,Good,2014-12-08T22:10:47.711Z,2015-03-16T03:17:09.594Z
2691,193567.3,Streptococcus pyogenes SSI-1,positive,Streptococcus pyogenes SSI-1,193567,Complete,SSI-1,serovar M3,,,MLST.Streptococcus_pyogenes.15,,,,2003-06-12T00:00:00Z,12799345,PRJNA301,,GCA_000011285.1,,BA000034,NC_004606,Osaka Univ.,complete,,,,1,,1,1894275,38.6,2009,1861,Blood,toxic-shock patient,"isolated from a toxic-shock patient in Japan and often associated with severe invasive infections, necrotizing fasciitis, and death",,Japan,Japan,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,30-35,Non-halophilic,Facultative,Host-associated,,"Streptococcus pyogenes strain SSI-1. This strain is a serotype M3 strain that was isolated from a toxic-shock patient in Japan and often associated with severe invasive infections, necrotizing fasciitis, and death.",,99.9,99.7,100,,,Good,2014-12-08T22:13:35.973Z,2015-03-16T03:17:09.594Z
2701,196620.5,Staphylococcus aureus subsp. aureus MW2,positive,Staphylococcus aureus subsp. aureus MW2,196620,Complete,MW2,,,,MLST.Staphylococcus_aureus.1,,,,2002-06-05T00:00:00Z,12044378,PRJNA306,,GCA_000011265.1,,BA000033,NC_003923,NITE,complete,,,,1,,1,2820462,32.8,2712,2632,None,community acquired,This strain is a community-acquired methicillin-resistant (MSRA) strain,1998,USA,USA: North Dakota,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,30-37,,Facultative,Host-associated,Toxic shock syndrome;Scarlet fever,Staphylococcus aureus subsp. aureus strain MW2. This strain is a community-acquired methicillin-resistant (MSRA) strain and is one of the major pathogens causing community-acquired infections in the Midwestern USA. Several fatal infections were attributed to this strain in the late 1990's.,,100,100,100,,,Good,2014-12-08T22:13:24.860Z,2015-03-16T03:17:09.594Z
2832,198214.7,Shigella flexneri 2a str. 301,negative,Shigella flexneri 2a str. 301,198214,Complete,301,,,,,,,,2002-10-18T00:00:00Z,12384590,PRJNA310,SAMN02603599,GCA_000006925.2,,"AE005674,AF386526","NC_004337,NC_004851",Microbial Genome Center of ChMPH,complete,,,,1,1,2,4828821,50.7,5527,4440,None,patient,"isolated in 1984 from a patient in Beijing, China",1984,China,China: Beijing,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,Mesophilic,37,,Facultative,Host-associated,Dysentery,"Shigella flexneri 2a str. 301. This strain was isolated in 1984 from a patient in Beijing, China. It is similar to pathogenic Escherichia coli except for the more numerous insertion sequences and contains a virulence plasmid (pCP301).",,99.6,97.5,100,,,Good,2014-12-08T22:12:54.946Z,2015-03-16T03:17:09.594Z
2840,199310.4,Escherichia coli CFT073,negative,Escherichia coli CFT073,199310,Complete,CFT073,,,UPEC,"MLST.Escherichia_coli_1.73,MLST.Escherichia_coli_2.4",,,,2002-12-10T00:00:00Z,"124,711,572,182,540",PRJNA313,SAMN02604094,GCA_000007445.1,,AE014075,NC_004431,"University of Wisconsin-Madison, USA",complete,,,,1,,1,5231428,50.5,5142,5339,None,,isolated at the University of Maryland Hospital,,USA,USA: Maryland,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,37,,Facultative,Host-associated,Urinary tract infection,"Escherichia coli strain CFT073. This strain (CFT073; O6:K2:H1) is uropathogenic E. coli (UPEC) one of the most common causes of non-hospital-acquired urinary tract infections. There are numerous important differences between EHEC and UPEC, namely the loss of specific virulence factors such as the type III secretion system and plasmid- and phage-associated PAIs. UPEC has gained fimbrial operons, including genes for production of Pap pili, as well as other virulence factors that allow it to colonize the urinary tract.",,99.9,97.9,100,1.1,,Good,2014-12-08T22:11:23.529Z,2015-03-16T03:17:09.594Z
2859,203275.8,Tannerella forsythia ATCC 43037,negative,Tannerella forsythia ATCC 43037,203275,Complete,ATCC 43037,,,,,,ATCC 43037,Yes,2011-12-15T00:00:00Z,,PRJNA319,,GCA_000238215.1,,CP003191,NC_016610,TIGR,unfinished,,,,1,,1,3405521,46.98,2908,3001,Abdomen,human periodontal pocket,isolated from a human periodontal pocket in Massachusetts and is the type strain for this organism,,USA,Massachusetts,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,No,,Mesophilic,37,,Anaerobic,Host-associated,Periodontitis,Tannerella forsythensis strain ATCC 43037. Tannerella forsythensis strain ATCC 43037 was isolated from a human periodontal pocket in Massachusetts and is the type strain for this organism.,,100,99.9,100,,,Good,2014-12-08T22:13:40.370Z,2015-03-16T03:17:09.594Z
2864,205920.11,Ehrlichia chaffeensis str. Arkansas,negative,Ehrlichia chaffeensis str. Arkansas,205920,Complete,Arkansas,,,,,,,,2006-02-21T00:00:00Z,16482227,PRJNA325,SAMN02604010,GCA_000013145.1,,CP000236,NC_007799,TIGR,complete,,,,1,,1,1176248,30.1,992,1105,None,patient,obtained from a patient on an army base in Arkansas in 1990,1990,USA,USA: Arkansas,,,,,,"Human, Homo sapiens",,,,,,,,,,Rod,,,,-,,,Host-associated,Human monocytic ehrlichiosis,"Ehrlichia chaffeensis strain Arkansas. This strain is the first isolate of Ehrlichia chaffeensis, which was obtained from a patient on an army base in Arkansas in 1990.",,99.4,98.7,100,,,Good,2014-12-08T22:11:10.023Z,2015-03-16T03:17:09.594Z
2876,208224.79,Enterobacter kobei strain C16,negative,,208224,Complete,C16,,,,MLST.Enterobacter_cloacae.191,,,,2019-10-09T00:00:00Z,,PRJNA550014,SAMN12289356,GCA_008931545.1,,"CP042578,CP042579,CP042580,CP042581",,University of Oxford,,Oxford Nanopore MiniION,1557x,Unicycler v. SEP-2017,1,3,4,5366747,54.398296,5423,5232,None,clinical sample,,12-Mar-09,Australia,Australia: Sydney,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,99,97.6,,,,Good,2019-10-27T21:58:29.744Z,2019-10-27T21:58:29.744Z
2877,208962.68,Escherichia albertii strain 1551-2,negative,,208962,Complete,1551-2,,,,MLST.Escherichia_coli_1.984,,,,2018-01-22T00:00:00Z,,PRJNA421872,SAMN08159313,GCA_002895205.1,,CP025317,,Federal University of Sao Paulo,,PacBio,139.18x,SMRT Link v. v4.0.0,1,,1,4730877,49.864326,4878,4695,None,,,1989,Brazil,Brazil: Sao Paulo state,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"The sequenced escherichia albertii strain was previously classified as atypical enteropathogenic Escherichia coli. Because of its invasive ability and potential intracellular persistence in vitro, knowledge about its genome could help identify potential effectors or pathogenic islands that could be involved in the pathogenicity of this strain",sample_type:Single cell,99.4,97.6,97.8,0.4,,Good,2018-05-25T19:34:31.654Z,2018-05-25T19:34:31.654Z
2878,208963.12,Pseudomonas aeruginosa UCBPP-PA14,negative,Pseudomonas aeruginosa UCBPP-PA14,208963,Complete,UCBPP-PA14,,,,MLST.Pseudomonas_aeruginosa.253,,,,2006-10-06T00:00:00Z,17038190,PRJNA386,SAMN02603591,GCA_000014625.1,,CP000438,NC_008463,Massachusetts General Hospital|Harvard Medical School Partners Healthcare Center for Genetics and Genomics,complete,,,,1,,1,6537648,66.3,6022,5892,Burn,human burn patient,isolate from a human burn patient,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,25-30,,Aerobic,Multiple,,"Pseudomonas aeruginosa strain UCBPP-PA14. This strain is a human clinical isolate from a human burn patient. It is infectious in mice, Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana. It is an excellent model for the study of pathogenesis and biofilm formation.",,99.8,99.3,99.7,,,Good,2014-12-08T22:12:37.968Z,2015-03-16T03:17:09.594Z
3086,210007.7,Streptococcus mutans UA159,positive,Streptococcus mutans UA159,210007,Complete,UA159,serovar c,,,,,,,2002-10-25T00:00:00Z,12397186,PRJNA333,SAMN02604090,GCA_000007465.2,,AE014133,NC_004350,University of Oklahoma,complete,,,,1,,1,2030921,36.8,1926,1960,Mouth,child with active dental caries,isolated from a child with active dental caries in 1982,1982,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,37,,Facultative,Host-associated,Dental caries,Streptococcus mutans strain UA159. This strain is a serotype c strain isolated from a child with active dental caries in 1982.,,100,99.9,100,,,Good,2014-12-08T22:13:32.351Z,2015-03-16T03:17:09.594Z
3131,211110.3,Streptococcus agalactiae NEM316,positive,Streptococcus agalactiae NEM316,211110,Complete,NEM316,serovar III,,,MLST.Streptococcus_agalactiae.23,,,,2002-10-02T00:00:00Z,12354221,PRJNA334,SAMEA3138330,GCA_000196055.1,,AL732656,NC_004368,Institut Pasteur,complete,,,,1,,1,2211485,35.6,2186,2094,Blood,case of fatal septicemia,isolated from a case of fatal septicemia,,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,37,,Facultative,Host-associated,Meningitis,Streptococcus agalactiae strain NEM316. This strain is a serotype III strain isolated from a case of fatal septicemia. Type III is responsible for 80% of neonatal GBS (group B streptococcal) meningitis.,,99.9,99.9,100,,,Good,2014-12-08T22:13:29.373Z,2015-03-16T03:17:09.594Z
3133,211880.31,Leptospira interrogans serovar Canicola strain 782,negative,,211880,Complete,782,Canicola,,,,,,,2020-10-07T00:00:00Z,,PRJNA564737,SAMN12721654,GCA_014858915.1,,"CP043884,CP043885,CP043886,CP043887,CP043890,CP043888,CP043889",,Leibniz Institute DSMZ,,PacBio RSII; Illumina MiSeq,359.0x,HGAP v. 3,2,5,7,5308174,35.20124,5551,4791,None,,,2014,Malaysia,Malaysia:Klang,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Part of Leptospira interrogans comparative genomics study,sample_type:cell culture,99.9,99.5,,,,Good,2020-11-29T06:19:07.830Z,2020-11-29T06:19:07.830Z
3134,212042.8,Anaplasma phagocytophilum HZ,negative,Anaplasma phagocytophilum HZ,212042,Complete,HZ,,,,MLST.Anaplasma_phagocytophilum.161,,,,2006-02-21T00:00:00Z,16482227,PRJNA336,,GCA_000013125.1,,CP000235,NC_007797,TIGR,complete,,,,1,,1,1471282,41.6,1506,1264,None,patient,"Isolated from a patient in New York, USA, in 1995",1995,USA,New York USA,,,,,,"Human, Homo sapiens",,,,,,,,,-,,,,Mesophilic,37,,Aerobic,Host-associated,Human granulocytic anaplasmosis,"Anaplasma phagocytophilum strain HZ. Isolated from a patient in New York, USA, in 1995.",,99.8,98.4,100,,,Good,2014-12-08T22:10:05.086Z,2015-03-16T03:17:09.594Z
3142,214092.21,Yersinia pestis CO92,negative,Yersinia pestis CO92,214092,Complete,CO92,,,,MLST.Yersinia_spp.79,,,,2001-10-05T00:00:00Z,"115,863,601,283,453,000,000,000",PRJNA34,SAMEA1705942,GCA_000009065.1,,"AL590842,AL117189,AL109969,AL117211","NC_003143,NC_003131,NC_003132,NC_003134",Wellcome Trust Sanger Institute,complete,,,,1,3,4,4829855,47.6,4666,4066,Lung,patient who died of pneumonic plague after acquiring the disease from an infected cat,isolated in the USA from a patient who died of pneumonic plague after acquiring the disease from an infected cat,,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,Mesophilic,28-30,,Facultative,Multiple,Bubonic plague,Yersinia pestis strain CO92. This strain is a recent Orientalis subtype isolated in the USA from a patient who died of pneumonic plague after acquiring the disease from an infected cat. This strain is 50 Kbp larger than the Yersinia pestis KIM10+ genome due to numerous insertions.,,99.6,98.5,100,,,Good,2014-12-08T22:13:51.215Z,2015-03-16T03:17:09.594Z
3143,216592.36,Escherichia coli 042,negative,,216592,Complete,42,,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.471",,,,2019-09-18T00:00:00Z,,PRJNA560158,SAMN12569951,GCA_008042015.2,,"CP042934,CP042935,CP042936",,University of Bern,,Illumina NovaSeq and Oxford Nanopore,50.0x,CANU v. 1.7,1,2,3,4789860,50.55037,4850,4586,Stool,stool,,2-Aug-19,Switzerland,Switzerland,,,,,,"Human, Homo sapiens",,,colonization,,,,,,,,,,,,,,,,Shedding of OXA-181-carbapenemase-producing Escherichia coli from companion animals after hospitalization and humans in Switzerland.,collected_by:Odette J. Bernasconi,99.3,98.4,,,,Good,2019-10-01T21:43:09.539Z,2019-10-01T21:43:09.539Z
3144,216594.6,Mycobacterium marinum M,positive,Mycobacterium marinum M,216594,Complete,M,,,,,,,,2008-04-15T00:00:00Z,18403782,PRJNA16725,SAMN02604327,GCA_000018345.1,,"CP000854,CP000895","NC_010612,NC_010604",Wellcome Trust Sanger Institute,complete,,,,1,1,2,6660144,65.7,5880,5452,None,human,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,No,No,Mesophilic,32,,Aerobic,Multiple,Tuberculosis;Dermatitis;Arthritis,Mycobacterium marinum strain M. This strain is a well-studied human isolate that is susceptible to a relatively wider range of antibiotics than other M. marinum isolates and thus has a potential to be easier to use in genetic and molecular biological studies.,,99.6,98.2,100,5.7,,Good,2014-12-08T22:12:07.612Z,2015-03-16T03:17:09.594Z
3145,218496.4,Tropheryma whipplei TW08/27,positive,Tropheryma whipplei TW08/27,218496,Complete,TW08/27,,,,,,,,2003-02-28T00:00:00Z,12606174,PRJNA354,SAMEA1705925,GCA_000196075.1,,BX072543,NC_004551,Wellcome Trust Sanger Institute,complete,,,,1,,1,925938,46.3,982,783,Cerebrospinal Fluid,the cerebrospinal fluid a woman who had suffered severe weight loss,isolated from the cerebrospinal fluid a woman who had suffered severe weight loss in Germany,,Germany,Germany,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,No,No,Mesophilic,37,,Aerobic,Host-associated,Whipple's disease,Tropheryma whipplei strain TW08/27. This strain was isolated from the cerebrospinal fluid a woman who had suffered severe weight loss in Germany. The patient had been treated with antibiotics followed by a year of no treatment prior to the sample being taken.,,97,96.8,92.4,,,Good,2014-12-08T22:13:43.172Z,2015-03-16T03:17:09.594Z
3146,220341.7,Salmonella enterica subsp. enterica serovar Typhi str. CT18,negative,Salmonella enterica subsp. enterica serovar Typhi str. CT18,220341,Complete,CT18,serovar Typhi,,,MLST.Salmonella_enterica.2,,,,2001-10-26T00:00:00Z,11677608,PRJNA236,SAMEA1705914,GCA_000195995.1,,"AL513382,AL513383,AL513384","NC_003198,NC_003384,NC_003385",Wellcome Trust Sanger Institute,complete,,,,1,1,3,5133713,51.9,5297,4758,Blood,isolated from blood,isolated from blood,1993,Viet Nam,Vietnam: Mekong Delta region,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,37,,Facultative,Host-associated,Typhoid fever,"Salmonella enterica subsp. enterica serovar Typhi. This serovar is a human-specific organism that causes the life-threatening illness Typhoid fever which is acquired by coming into contact with contaminated food or water. Annually, 17 million people are infected, with 600,000 fatalities, mostly in developing countries. It contains multiple fimbrial operons that may be used to create extracellular appendages for attachment and entry into host intestinal epithelial cells.  Salmonella enterica subsp. enterica serovar Typhi strain CT18. This strain is a multidrug resistant strain of Salmonella typhi. It contains a large number of pseudogenes as compared to related organisms. CT18 also has two plasmids, pHCM1 and pHCM2, which mediate drug resistance and may also encode virulence functions.",,99.6,98.1,100,0.3,,Good,2014-12-08T22:12:52.348Z,2015-03-16T03:17:09.594Z
3151,222805.8,Mycobacterium chimaera strain AUSMDU00007395,positive,,222805,Complete,AUSMDU00007395,,,,,,,,2019-11-17T00:00:00Z,,PRJNA556438,SAMN13191638,GCA_009664715.1,,"CP045963,CP045964,CP045965,CP045966,CP045967,CP045968",,Microbiological Diagnostic Unit,,"PacBio RSII, Illumina NextSeq",154x,Unicycler v. 0.4.6,1,5,6,6384143,67.500854,6243,5915,None,,,2016,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,98,96.2,,,,Good,2019-12-30T20:34:30.675Z,2019-12-30T20:34:30.675Z
3152,224914.11,Brucella melitensis bv. 1 str. 16M,negative,Brucella melitensis bv. 1 str. 16M,224914,Complete,16M,,biovar 1,,MLST.Brucella_spp.7,,,,2002-01-05T00:00:00Z,"1,175,668,812,271,120",PRJNA180,,GCA_000007125.1,,"AE008917,AE008918","NC_003317,NC_003318",Integrated Genomics,complete,,,,2,,2,3294931,57.2,3499,3198,None,infected goat,isolated from an infected goat and is pathogenic in humans,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Coccobacillus,,,Mesophilic,37,,Aerobic,Host-associated,Brucellosis,Brucella melitensisstrain 16M. This strain was isolated from an infected goat and is pathogenic in humans.,,99.9,99.6,100,,,Good,2014-12-08T22:10:39.527Z,2015-03-16T03:17:09.594Z
3154,226185.9,Enterococcus faecalis V583,positive,Enterococcus faecalis V583,226185,Complete,V583,,,,MLST.Enterococcus_faecalis.6,,,,2003-03-29T00:00:00Z,12663927,PRJNA70,,GCA_000007785.1,,"AE016830,AE016833,AE016831,AE016832","NC_004668,NC_004669,NC_004671,NC_004670",TIGR,complete,,,,1,3,4,3359974,37.4,3243,3265,Blood,blood culture derived from a chronically-infected patient,came from a blood culture derived from a chronically-infected patient in 1987 from Barnes Hospital in St,1987,USA,"St. Louis, Missouri",,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,,,Mesophilic,37,,Facultative,Multiple,Bacteremia;Endocarditis;Urinary tract infection,"Enterococcus faecalis strain V583. This strain is one of the first vancomycin-resistant strains isolated. This isolate came from a blood culture derived from a chronically-infected patient in 1987 from Barnes Hospital in St. Louis, Missouri. This strain was found to lack the cytolysin gene and a surface adhesin, Esp, that contributes to urinary tract infections. Mobile genetic elements make up one quarter of the genome.",,100,99.9,100,0.7,,Good,2014-12-08T22:11:15.346Z,2015-03-16T03:17:09.594Z
3159,242231.1,Neisseria gonorrhoeae FA 1090,negative,Neisseria gonorrhoeae FA 1090,242231,Complete,FA 1090,,,,,,,,2005-02-14T00:00:00Z,,PRJNA23,SAMN02604088,GCA_000006845.1,,AE004969,NC_002946,University of Oklahoma,complete,,,,1,,1,2153922,52.7,2628,2002,Skin,patient with disseminated gonococcal infections,isolated from a patient with disseminated gonococcal infections,,,,,,,,,"Human, Homo sapiens",,,disseminated gonococcal infections,,,,,,-,Coccus,,,Mesophilic,35-37,,Aerobic,Host-associated,Gonorrhea,Neisseria gonorrhoeae strain FA 1090. A serum-resistant streptomycin-resistant proline-requiring strain isolated from a patient with disseminated gonococcal infections.,,99.6,98.7,99.4,1.2,,Good,2014-12-08T22:12:24.876Z,2015-03-16T03:17:09.594Z
3160,242619.8,Porphyromonas gingivalis W83,negative,Porphyromonas gingivalis W83,242619,Complete,W83,,,,MLST.Porphyromonas_gingivalis.24,,,,2003-09-02T00:00:00Z,,PRJNA48,SAMN02603720,GCA_000007585.1,,AE015924,NC_002950,Porphyromonas gingivalis Genome Project|TIGR|The Forsyth Institute,complete,,,,1,,1,2343476,48.3,2078,1909,None,unknown human infection,"isolated by H. Werner in the 1950s in Bonn, Germany, from an unknown human infection",1950,Germany,Germany: Bonn,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,No,No,Mesophilic,37,Non-halophilic,Anaerobic,Host-associated,Periodontitis,"Porphyromonas gingivalis strain W83. This strain (also known as HG66) is virulent in a mouse model and has been extensively studied. It was originally isolated by H. Werner in the 1950s in Bonn, Germany, from an unknown human infection.",,100,99.7,100,,,Good,2014-12-08T22:12:33.101Z,2015-03-16T03:17:09.594Z
3161,243160.12,Burkholderia mallei ATCC 23344,negative,Burkholderia mallei ATCC 23344,243160,Complete,ATCC 23344,,,,"MLST.Burkholderia_cepacia_complex.734,MLST.Burkholderia_pseudomallei.40",,ATCC 23344,Yes,2004-09-21T00:00:00Z,,PRJNA171,SAMN02603987,GCA_000011705.1,,"CP000010,CP000011","NC_006348,NC_006349",TIGR,complete,,,,2,,2,5835527,68.5,5724,5024,None,Chinese patient,came from a Chinese patient in Burma who had glanders in 1944,1944,Burma,Burma,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,No,,Mesophilic,-,,,Host-associated,Glanders;Pneumonia,"Burkholderia mallei strain ATCC 23344. This type strain (ATCC 23344; NBL 7; China 7; 3873; EY 2233; RH627) came from a Chinese patient in Burma who had glanders in 1944. The genome of this organism carries a large number of insertion sequences as compared to the related Bukholderia pseudomallei, and a large number of simple sequence repeats that may function in antigenic variation of cell surface proteins.",,99.8,99,99.7,,,Good,2014-12-08T22:10:42.036Z,2015-03-16T03:17:09.594Z
3162,243243.7,Mycobacterium avium 104,positive,Mycobacterium avium 104,243243,Complete,104,,,,,,,,2006-11-20T00:00:00Z,,PRJNA88,SAMN02603981,GCA_000014985.1,,CP000479,NC_008595,TIGR,complete,,,,1,,1,5475491,69,5214,5120,None,AIDS patient and has been characterized for virulence,"derived from an AIDS patient and has been characterized for virulence in the murine model of low-dose aerosol infection in that it could colonize the lung, proliferate within the tissue and disseminate to other organs",,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,No,No,Mesophilic,37,,Aerobic,Host-associated,Pulmonary tuberculosis,"Mycobacterium avium strain 104. This strain is a common representative of the species complex. It was derived from an AIDS patient and has been characterized for virulence in the murine model of low-dose aerosol infection in that it could colonize the lung, proliferate within the tissue and disseminate to other organs. This strain will be used for comparative analysis with other Mycobacterium species.",,98.6,97.6,99.1,0.9,,Good,2014-12-08T22:12:05.899Z,2015-03-16T03:17:09.594Z
3163,243273.25,Mycoplasma genitalium G37,negative,Mycoplasma genitalium G37,243273,Complete,G37,,,,,,,Yes,1995-10-20T00:00:00Z,"75,699,938,253,680,800,000,000,000,000",PRJNA97,,GCA_000027325.1,,L43967,NC_000908,TIGR,complete,,,,1,,1,580076,31.7,542,475,Urine,male patient with nongonococcal urethritis,isolated as a urethral specimen from a male patient with nongonococcal urethritis,,,,,,,,,"Human, Homo sapiens",male,,nongonococcal urethritis,,,,,,-,Sphere,Yes,No,Mesophilic,37,Non-halophilic,Facultative,Host-associated,Urinary tract infection;respritory tract infection,Mycoplasma genitalium strain G-37. This strain was isolated as a urethral specimen from a male patient with nongonococcal urethritis. This is the type strain for the species and is used for comparative genomics.,,99.8,99.6,100,,,Good,2014-12-08T22:12:24.039Z,2015-03-16T03:17:09.594Z
3165,243276.9,Treponema pallidum subsp. pallidum str. Nichols,negative,,243276,Complete,Nichols,,,,,,,,2014-01-30T00:00:00Z,24058545,PRJNA30655,SAMN02603005,GCF_000410535.2,,CP004010,,Baylor College of Medicine,,454 GS20; Illumina GA,44X; 55X,CLC Bio Workbench,1,,1,1139633,52.79,1029,978,Brain,neurosyphilitic patient,isolated in 1912 from a neurosyphilitic patient and is virulent,1912,,,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Spirilla,No,,Mesophilic,,,Anaerobic,HostAssociated,Syphilis,"Treponema pallidum subsp. pallidum  This organism is the causative agent of endemic and venereal syphilis. This sexual transmitted disease was first discovered in Europe at the end of the fifteenth century, however, the causative agent was not identified until 1905. At one time syphilis was the third most commonly reported communicable disease in the USA. Syphilis is characterized by multiple clinical stages and long periods of latent, asymptomatic infection. Although effective therapies have been available since the introduction of penicillin, syphilis remains a global health problem Treponema pallidum subsp. pallidum strain Nichols. This strain was originally isolated in 1912 from a neurosyphilitic patient and is virulent.",,99.9,99.7,37.6,,Low CheckM completeness score,Poor,2016-01-17T15:30:52.911Z,2016-01-17T15:30:52.911Z
3166,244319.35,Escherichia coli O26:H11 strain FWSEC0001,negative,,244319,Complete,FWSEC0001,O26:H11,,,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2019-05-03T00:00:00Z,,PRJNA287560,SAMN08768102,GCA_005037725.2,,NELP01000000,,National Microbiology Laboratory,,Illumina MiSeq;Oxford Nanopore MinION,66.48x;325.05x,Unicycler;Canu v. 0.4.4.0;1.7,1,3,4,5803315,50.620842,6391,6195,None,Clinical: Human (Homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2002,Canada,"Canada:British Columbia,Vancouver",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,Mesophilic,37 C,,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,99.6,98.6,,,,Good,2019-07-14T19:19:01.916Z,2019-07-14T19:19:01.916Z
3180,244366.656,Klebsiella variicola strain JNQH579,negative,,244366,Complete,JNQH579,,,,MLST.Klebsiella_pneumoniae.2013,,,,2021-07-15T00:00:00Z,,PRJNA702614,SAMN20064304,GCA_019222805.1,,"CP078146,CP078147,CP078148",,The First Affiliated Hospital of Shandong First Medical University,,IonTorrent,129.0x,Flye v. 2.8.3,1,2,3,6149961,56.655514,6215,5865,Sputum,sputum,isolated from China,3/21/21,China,China: Shandong,,,,,,Homo sapiens,,,pneumoniae,,,,,,,,,,,,,,,,"The studies are aimed at determining the characteristics of epidemiology, antimicrobial resistance and pathogenicity for carbapenem resistant enterobacteriaceae, especially for strains isolated from China.",collected_by:Mingju Hao,99.8,97.1,,,,Good,2021-08-01T17:54:31.113Z,2021-08-01T17:54:31.113Z
3181,247156.8,Nocardia farcinica IFM 10152,positive,Nocardia farcinica IFM 10152,247156,Complete,IFM 10152,,,,,,,Yes,2004-10-07T00:00:00Z,15466710,PRJNA13117,,GCA_000009805.1,,"AP006618,AP006619,AP006620","NC_006361,NC_006362,NC_006363","Department of Bioactive Molecules, National Institute of Infectious Diseases|Department of Molecular Function, Research Center for Pathogenic Fungi and Micobial Toxicosis|Laboratory of Genomic Information, Kitasato Institute for Life Sciences|School of Science, Kitasato University",complete,,,,1,2,3,6292344,70.7,5935,5936,Lung,the bronchus of a male Japanese patient,isolated from the bronchus of a male Japanese patient,,,,,,,,,"Human, Homo sapiens",male,,,,,,,,+,Rod,No,Yes,Mesophilic,37,Non-halophilic,Aerobic,Multiple,Nocardiosis,Nocardia farcinica strain IFM 10152. This type strain was isolated from the bronchus of a male Japanese patient.,,99.3,98.9,99.6,,,Good,2014-12-08T22:12:27.625Z,2015-03-16T03:17:09.594Z
3189,257309.4,Corynebacterium diphtheriae NCTC 13129,positive,Corynebacterium diphtheriae NCTC 13129,257309,Complete,NCTC 13129,,biovar gravis,,MLST.Corynebacterium_diphtheriae.8,,NCTC 13129,,2003-11-07T00:00:00Z,14602910,PRJNA87,SAMEA1705951,GCA_000195815.1,,BX248353,NC_002935,Wellcome Trust Sanger Institute,complete,,,,1,,1,2488635,53.5,2390,2272,Respiratory,the pharyngeal membrane of a 72-year-old unimmunized UK female with clinical diphtheria acquired during a short Baltic cruise,isolated in 1997 from the pharyngeal membrane of a 72-year-old unimmunized UK female with clinical diphtheria acquired during a short Baltic cruise,1997,United Kingdom,United Kingdom,,,,,,"Human, Homo sapiens",female,72,,,,,,,+,Rod,No,No,Mesophilic,37,,Aerobic,Multiple,Diphtheria,Corynebacterium diphtheriae biotype gravis strain NCTC13129. This strain was isolated in 1997 from the pharyngeal membrane of a 72-year-old unimmunized UK female with clinical diphtheria acquired during a short Baltic cruise. Knowing the genetic sequence of this modern strain is important for understanding how to successfully treat the disease that has recently started breaking out in the Eastern Europe.,,99.9,99.9,100,,,Good,2014-12-08T22:11:03.418Z,2015-03-16T03:17:09.594Z
3190,257311.4,Bordetella parapertussis 12822,negative,Bordetella parapertussis 12822,257311,Complete,12822,,,,MLST.Bordetella_spp.19,,,,2003-08-12T00:00:00Z,12910271,PRJNA25,SAMEA1705915,GCA_000195695.1,,BX470249,NC_002928,Wellcome Trust Sanger Institute,complete,,,,1,,1,4773551,68.1,4639,4185,None,infected infant,isolated from an infected infant in Germany in 1993,1993,Germany,Germany,,,,,,"Human, Homo sapiens",,infant,,,,,,,-,Rod,,,Mesophilic,35-37,,Aerobic,Host-associated,Respiratory tract infections,Bordetella parapertussis strain 12822 . This strain was isolated from an infected infant in Germany in 1993. The genome contains the gene for pertussis toxin but does not express it.,,99.6,99.1,100,,,Good,2014-12-08T22:10:30.454Z,2015-03-16T03:17:09.594Z
3191,257313.5,Bordetella pertussis Tohama I,negative,Bordetella pertussis Tohama I,257313,Complete,Tohama I,,,,MLST.Bordetella_spp.1,,,,2003-08-12T00:00:00Z,,PRJNA26,SAMEA1705933,GCA_000195715.1,,BX470248,NC_002929,Wellcome Trust Sanger Institute,complete,,,,1,,1,4086189,67.7,4170,3436,Respiratory,patient with whooping cough and has been studied extensively for over 40 years,isolated from a patient with whooping cough and has been studied extensively for over 40 years,,,,,,,,,"Human, Homo sapiens",,,whooping cough,,,,,,-,Rod,,,Mesophilic,35-37,,Aerobic,Host-associated,Respiratory tract infections,"Bordetella pertussis Tohama I. This strain was originally isolated from a patient with whooping cough and has been studied extensively for over 40 years. The chromosome contains a type IV secretion system for export of the pertussis toxin, a typical AB type toxin. The B subunits are involved in attachment to host cells, and the A subunit, the ADP-ribosylating factor, interferes with cell signalling pathways by increasing intracellular cAMP concentrations. The result is an inability of phagocytes to kill foreign invaders such as the bacterium.",,99.6,98.3,100,,,Good,2014-12-08T22:10:31.038Z,2015-03-16T03:17:09.594Z
3197,262727.7,Haemophilus influenzae R2846,negative,Haemophilus influenzae R2846,262727,Complete,R2846,,,,MLST.Haemophilus_influenzae.1622,,,,2004-02-12T00:00:00Z,,PRJNA9620,SAMN02604260,GCA_000165575.1,,CP002276,NC_017452.1,"University of Washington; Seattle Biomedical Research Institute|University of Oklahoma Health Sciences Center, Pediatrics, USA, Oklahoma City|University of Washington, Genome Center, USA, Seattle",complete,,,,1,,1,1819370,38,1775,1636,Ear,middle ear fluid of a child with acute otitis media,isolated from middle ear fluid of a child with acute otitis media,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,Mesophilic,35-37,,Facultative,Host-associated,Meningitis;Septicemia;Otitis media;Sinusitis;Bronchitis,"Haemophilus influenzae R2846. Strain R2846 (also known as Strain 12), was isolated from middle ear fluid of a child with acute otitis media. This strain is part of a complete genomic sequencing, annotation and comparison of two isolates of Haemophilus influenzae.",,99.6,99,100,1.3,,Good,2014-12-08T22:11:42.268Z,2015-03-16T03:17:09.594Z
3198,262728.6,Haemophilus influenzae R2866,negative,Haemophilus influenzae R2866,262728,Complete,R2866,,,,MLST.Haemophilus_influenzae.99,,,,2004-02-12T00:00:00Z,,PRJNA9621,SAMN02604259,GCA_000165525.1,,CP002277,NC_017451.1,"University of Washington Genome Center; Seattle Biomedical Research Institute|University of Oklahoma Health Sciences Center, Pediatrics, USA, Oklahoma City|University of Washington, Genome Center, USA, Seattle",complete,,,,1,,1,1932306,38.1,1907,1795,Blood,the blood of a child with meningitis,isolated from the blood of a child with meningitis,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,Mesophilic,35-37,,Facultative,Host-associated,Meningitis;Septicemia;Otitis media;Sinusitis;Bronchitis,"Haemophilus influenzae R2866 (Int1). Strain R2866 (also known as Int1), was isolated from the blood of a child with meningitis. This strain is unusual in that although it has no polysaccharide capsule, it caused serious, invasive disease in a child with no immunologic deficit or other predisposing medical problems.",,99.4,99.3,100,0.6,,Good,2014-12-08T22:11:42.276Z,2015-03-16T03:17:09.594Z
3213,265669.9,Listeria monocytogenes serotype 4b str. F2365,positive,Listeria monocytogenes serotype 4b str. F2365,265669,Complete,4b F2365,serovar 4b,,,MLST.Listeria_monocytogenes.1,,,,2004-04-30T00:00:00Z,15115801,PRJNA85,SAMN02603980,GCA_000008285.1,,AE017262,NC_002973,TIGR,complete,,,,1,,1,2905187,38,2867,2821,None,,"isolated in 1985 in California, USA, during an outbreak of listeriosis among patients with AIDS",1985,USA,California USA,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,Yes,,Mesophilic,30-37,,Facultative,Multiple,Listeriosis,"Listeria monocytogenes strain 4b F2365. This strain was isolated in 1985 in California, USA, during an outbreak of listeriosis among patients with AIDS. The strain is of serotype 4b and was isolated from a cheese product that caused the outbreak.",,99.9,99.4,100,,,Good,2014-12-08T22:12:00.657Z,2015-03-16T03:17:09.594Z
3215,267671.5,Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130,negative,Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130,267671,Complete,Fiocruz L1-130,serovar Copenhageni,,,"MLST.Leptospira_spp.17,MLST.Leptospira_spp_2.47,MLST.Leptospira_spp_3.2",,,,2004-03-19T00:00:00Z,15028702,PRJNA10687,SAMN02603847,GCA_000007685.1,,"AE016823,AE016824","NC_005823,NC_005824",Sao Paulo state (Brazil) Consortium,complete,,,,2,,2,4627366,35,4550,3658,None,patient with severe leptospirosis during an epidemic,isolated from a patient with severe leptospirosis during an epidemic in 1996,1996,,,,,,,,"Human, Homo sapiens",,,severe leptospirosis during an epidemic,,,,,,,Spiral,Yes,No,Mesophilic,28-30,,Aerobic,Host-associated,Leptospirosis,Leptospira interrogans serovar copenhageni strain Fiocruz L1-130. This strain was isolated from a patient with severe leptospirosis during an epidemic in 1996.,,99.8,99.7,100,,,Good,2014-12-08T22:11:56.736Z,2015-03-16T03:17:09.594Z
3216,267747.3,Propionibacterium acnes KPA171202,positive,Propionibacterium acnes KPA171202,267747,Complete,Propionibacterium acnes KPA171202,,,,MLST.Propionibacterium_acnes.5,,,,2004-08-03T00:00:00Z,15286373,PRJNA12460,SAMN02603281,GCA_000008345.1,,AE017283,NC_006085,University of Goettingen,complete,,,,1,,1,2560265,60,2422,2297,Skin,human skin,"Isolated from human skin, this strain is used for comparative genomics",,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,No,No,Mesophilic,37,Non-halophilic,Anaerobic,Host-associated,Acne,"Propionibacterium acnes strain KPA171202 . Isolated from human skin, this strain is used for comparative genomics.",,99.4,98.9,100,,,Good,2014-12-08T22:12:34.959Z,2015-03-16T03:17:09.594Z
3218,269801.1,Bacillus cereus G9241,positive,,269801,Complete,G9241,,,,MLST.Bacillus_cereus.78,,,,2015-05-28T00:00:00Z,25931591,PRJNA235894,SAMN03085864,GCF_000832805.1,"SRR2164311,SRR2164312,SRR2164313","CP009590,CP009591,CP009592,CP009589","NZ_CP009590.1,NZ_CP009591.1,NZ_CP009592.1,NZ_CP009589.1",Los Alamos National Laboratory,,Illumina; PacBio,498x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,1,3,4,5720073,35.18,5967,5683,None,Human clinical sample,,2004,USA,USA: Louisiana,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,,,,,,,,Genome sequencing of Bacillus cereus G9241,,99.9,98.8,100,0.7,,Good,2016-01-17T15:43:21.071Z,2016-01-17T15:43:21.071Z
3223,272560.6,Burkholderia pseudomallei K96243,negative,Burkholderia pseudomallei K96243,272560,Complete,K96243,,,,MLST.Burkholderia_pseudomallei.10,,,,2004-09-21T00:00:00Z,15377794,PRJNA178,,GCA_000011545.1,,"BX571965,BX571966","NC_006350,NC_006351",Wellcome Trust Sanger Institute,complete,,,,2,,2,7247547,68.1,6808,5728,None,Thailand,isolate from Thailand,,Thailand,Thailand,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,-,,Aerobic,Terrestrial,Melioidosis,"Burkholderia pseudomallei strain K96243. This strain was a clinical isolate from Thailand. The genome of this organism carries many genomic islands as compared to the related organism B. mallei, suggesting extensive horizontal transfer. Three different type III secretion systems (TTSS) are encoded on the chromosomes of this organism, two of which are similar to plant pathogenic TTSSs, while the third is similar to the Salmonella pathogenicity island, all of which may contribute to pathogenicity. Other virulence determinants include multidrug efflux pumps, secreted toxins and proteases, and various adhesins. Capsular polysaccharide may protect the organism from host defense mechanisms. This organism also carries a number of small sequence repeats which may promoter antigenic variation, similar to what was found with the B. mallei genome.",,99.3,96.4,100,,,Good,2014-12-08T22:10:42.968Z,2015-03-16T03:17:09.594Z
3224,272563.12,Peptoclostridium difficile 630,negative,,272563,Complete,630,,,,,,DSM:27543,,2015-04-15T00:00:00Z,25858846,PRJNA275406,SAMN03344097,GCF_000932055.1,,CP010905,,Leibniz Institute DSMZ,,PacBio; Illumina GAIIx,101x,HGAP SMRTPortal v. 2.3.0,1,,1,4274806,29.04,3894,3778,None,human,,1982,Switzerland,Switzerland,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Genome sequencing of the virulent and multidrug resistant Clostridium difficile 630,sample_type:cell culture,100,99.5,100,0.6,,Good,2016-01-17T15:44:43.992Z,2016-01-17T15:44:43.992Z
3225,272620.9,Klebsiella pneumoniae subsp. pneumoniae MGH 78578,negative,Klebsiella pneumoniae subsp. pneumoniae MGH 78578,272620,Complete,MGH 78578,,,,MLST.Klebsiella_pneumoniae.38,,,,2007-07-05T00:00:00Z,,PRJNA31,SAMN02603941,GCA_000016305.1,,"CP000647,CP000649,CP000650,CP000651,CP000652,CP000648","NC_009648,NC_009650,NC_009651,NC_009652,NC_009653,NC_009649",Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine,complete,,,,1,5,6,5694894,57.1,5269,5185,None,patient,isolated from a patient in 1994,1994,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,37,,Facultative,Multiple,Pneumonia;Urinary tract infection,Klebsiella pneumoniae  subsp. pneumoniae strain MGH 78578. This strain was isolated from a patient in 1994.,,99.8,99.3,100,,,Good,2014-12-08T22:11:51.136Z,2015-03-16T03:17:09.594Z
3226,272634.6,Mycoplasma pneumoniae M129,negative,Mycoplasma pneumoniae M129,272634,Complete,M129,,,,MLST.Mycoplasma_pneumoniae.1,,ATCC 29342,,1996-11-15T00:00:00Z,"894,863,310,954,595",PRJNA99,SAMN02603304,GCA_000027345.1,,U00089,NC_000912,"Heidelberg Univ., Germany",complete,,,,1,,1,816394,40,755,689,Lung,patient with atypical pneumonia,clinical isolate from a patient with atypical pneumonia,,,,,,,,,"Human, Homo sapiens",,,atypical pneumonia,,,,,,-,Sphere,Yes,No,Mesophilic,37,Non-halophilic,Facultative,Host-associated,Atypical pneumonia,Mycoplasma pneumoniae strain M129 ATCC29342. This strain is a clinical isolate from a patient with atypical pneumonia.,,99.9,99.9,100,,,Good,2014-12-08T22:12:24.433Z,2015-03-16T03:17:09.594Z
3227,272831.7,Neisseria meningitidis FAM18,negative,Neisseria meningitidis FAM18,272831,Complete,FAM18,,,,MLST.Neisseria_spp.11,,,,2007-01-04T00:00:00Z,17305430,PRJNA255,SAMEA1705939,GCA_000009465.1,,AM421808,NC_008767,Sanger Institute|NCBI,complete,,,,1,,1,2194961,51.6,2662,1917,Blood,patient with meningococcal septicemia,isolated from a patient with meningococcal septicemia,,,,,,,,,"Human, Homo sapiens",,,meningococcal septicemia,,,,,,-,Coccus,,,Mesophilic,35-37,,Aerobic,Host-associated,Meningitis;Septicemia,Neisseria meningitidis FAM18. Strain FAM18 is a member of the serogroup C ET-37 complex and was isolated from a patient with meningococcal septicemia.,,99.9,99.8,100,,,Good,2014-12-08T22:12:25.812Z,2015-03-16T03:17:09.594Z
3228,272944.4,Rickettsia conorii str. Malish 7,negative,Rickettsia conorii str. Malish 7,272944,Complete,Malish 7,,,,,,,,2000-10-13T00:00:00Z,"1,103,065,511,557,890",PRJNA42,SAMN02603141,GCA_000007025.1,,AE006914,NC_003103,CNRS,complete,,,,1,,1,1268755,32.4,1578,1374,None,human,isolated from a human in South Africa,,South Africa,South Africa,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,Mesophilic,-,,Aerobic,Host-associated,Rocky mountain spotted fever,Rickettsia conorii strain Malish 7. This strain was isolated from a human in South Africa.,,99.9,99.6,100,,,Good,2014-12-08T22:12:44.102Z,2015-03-16T03:17:09.594Z
3229,272947.5,Rickettsia prowazekii str. Madrid E,negative,Rickettsia prowazekii str. Madrid E,272947,Complete,Madrid E,,,,,,,,1998-11-21T00:00:00Z,9823893,PRJNA43,SAMEA3138318,GCA_000195735.1,,AJ235269,NC_000963,Uppsala Univ.,complete,,,,1,,1,1111523,29,924,835,None,typhus patient,isolated from a typhus patient in Madrid,,Spain,Madrid,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,Mesophilic,-,,Aerobic,Host-associated,Epidemic typhus;Mediterranean spotted fever, Rickettsia prowazekii strain Madrid E. This strain is an egg-passaged attentuated avirulent strain that has been used as a live vaccine and was originally isolated from a typhus patient in Madrid.,,99.9,99.5,100,1.6,,Good,2014-12-08T22:12:44.333Z,2015-03-16T03:17:09.594Z
3230,273121.8,Wolinella succinogenes DSM 1740,negative,Wolinella succinogenes DSM 1740,273121,Complete,DSM 1740,,,pathovar ir,,,DSM 1740,,2003-09-23T00:00:00Z,14500908,PRJNA445,SAMEA3138333,GCA_000196135.1,,BX571656,NC_005090,Max Planck Institute,complete,,,,1,,1,2110355,48.5,2098,2042,None,the rumen of a cow,isolated from the rumen of a cow and is considered nonpathogenic in both its host and in humans,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,"Spiral, Curved",Yes,,Mesophilic,-,,Microaerophilic,Host-associated,,"Wolinella succinogenes strain DSM 1740. This organism was first isolated from the rumen of a cow and is considered nonpathogenic in both its host and in humans. However, this organism contains a number of virulence genes, including some found within genomic islands, which resemble genes from Campylobacter jejuni. These include a chromosomal type IV secretion system that resembles that found on the Campylobacter jejuni virulence plasmid pVir, and the Campylobacter jejuni secreted invasion antigen B (ciaB). The chromosome also contains nitrogen-fixation genes that may have been horizontally-transferred from bacteria within the Rhizobiaciae group.",,99.7,99.6,99.2,1.2,,Good,2014-12-08T22:13:49.348Z,2015-03-16T03:17:09.594Z
3231,273123.1,Yersinia pseudotuberculosis IP 32953,negative,Yersinia pseudotuberculosis IP 32953,273123,Complete,IP 32953,serovar I,,,MLST.Yersinia_pseudotuberculosis.42,,,,2004-09-11T00:00:00Z,15358858,PRJNA12950,,GCA_000047365.1,,"BX936398,BX936400,BX936399","NC_006155,NC_006154,NC_006153",Lawrence Livermore National Laboratory|Institut Pasteur,complete,,,,1,2,3,4840898,47.6,4745,4038,None,human patient,isolated from a human patient,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,28-30,,Facultative,Multiple,Gastroenteritis,Yersinia pseudotuberculosis strain IP 32953. This strain is a fully virulent serotype I strain isolated from a human patient.,,100,99.7,100,,,Good,2014-12-08T22:13:52.208Z,2015-03-16T03:17:09.594Z
3232,279808.8,Staphylococcus haemolyticus JCSC1435,positive,Staphylococcus haemolyticus JCSC1435,279808,Complete,,,,,MLST.Staphylococcus_haemolyticus.2,,,,2005-06-30T00:00:00Z,16237012,PRJNA12508,,GCA_000009865.1,,"AP006716,AP006718,AP006719,AP006717","NC_007168,NC_007170,NC_007171,NC_007169",NITE,complete,,,,1,3,4,2697861,32.8,2638,2692,None,"Japanese inpatient at Juntendo Hospital, Tokyo,","isolated from a Japanese inpatient at Juntendo Hospital, Tokyo, in 2000",2000,Japan,Juntendo Hospital Tokyo,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,30-37,,Facultative,Host-associated,,"Staphylococcus haemolyticus JCSC1435. Staphylococcus haemolyticus JCSC1435 was isolated from a Japanese inpatient at Juntendo Hospital, Tokyo, in 2000. This strain is a highly resistant strain which has been shown to generate spontaneous antibiotic sensitive mutants. The genome sequence will provide information on the proteins involved in antibiotic resistance and in the production of antibiotic sensitive variants.",,99.9,99.9,100,,,Good,2014-12-08T22:13:26.328Z,2015-03-16T03:17:09.594Z
3293,281310.6,Haemophilus influenzae 86-028NP,negative,Haemophilus influenzae 86-028NP,281310,Complete,86-028NP,,,,MLST.Haemophilus_influenzae.33,,,,2004-04-23T00:00:00Z,"1,510,281,315,968,070",PRJNA11752,SAMN02603157,GCA_000012185.1,,CP000057,NC_007146,"Columbus Children's Research Institute and The Ohio State University, Pediatrics, USA",complete,,,,1,,1,1914490,38.2,1894,1792,None,pediatric patient with otitis media from Columbus Children's Hospital,isolate from a pediatric patient with otitis media from Columbus Children's Hospital,,USA,Columbus Children's Hospital,,,,,,"Human, Homo sapiens",,,otitis media,,,,,,-,Rod,,,Mesophilic,35-37,,Facultative,Host-associated,Meningitis;Septicemia;Otitis media;Sinusitis;Bronchitis,Haemophilus influenzae strain 86-028NP. This nontypeable strain is a clinical isolate from a pediatric patient with otitis media from Columbus Children's Hospital. It has been extensively characterized in chinchilla models of otitis media.,,99.6,99.3,100,,,Good,2014-12-08T22:11:42.174Z,2015-03-16T03:17:09.594Z
3318,283165.4,Bartonella quintana str. Toulouse,negative,Bartonella quintana str. Toulouse,283165,Complete,Toulose,,,,,,,,2004-06-24T00:00:00Z,15210978,PRJNA44,SAMEA3138248,GCA_000046685.1,,BX897700,NC_005955,Uppsala Univ.,complete,,,,1,,1,1581384,38.8,1491,1142,Blood,human blood,"isolated from human blood in Toulouse, France in 1993",1993,France,Toulouse France,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,No,Mesophilic,37,,Aerobic,Host-associated,Bacillary angiomatosis;Trench fever,"Bartonella quintana str. Toulouse. Bartonella quintana str. Toulouse was isolated from human blood in Toulouse, France in 1993. There is evidence of extensive genome reduction in comparison to other Bartonella species which may be associated with the limited host range of Bartonella quintana.",,99.7,99,100,,,Good,2014-12-08T22:10:25.990Z,2015-03-16T03:17:09.594Z
3319,283166.5,Bartonella henselae str. Houston-1,negative,Bartonella henselae str. Houston-1,283166,Complete,Houston-1,,,,MLST.Bartonella_henselae.1,,ATCC 49882,,2004-06-24T00:00:00Z,15210978,PRJNA196,SAMEA3138249,GCA_000046705.1,,BX897699,NC_005956,Uppsala Univ.,complete,,,,1,,1,1931047,38.2,1941,1488,Blood,human blood,isolated from human blood in Houston Texas,,USA,Houston Texas,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,No,Mesophilic,37,,Aerobic,Host-associated,Bacillary angiomatosis;Cat scratch fever,Bartonella henselae str. Houston-1. Bartonella henselae str. Houston-1 (ATCC 49882) was isolated from human blood in Houston Texas.,,99.9,99.3,100,,,Good,2014-12-08T22:10:25.868Z,2015-03-16T03:17:09.594Z
3325,283734.2283,Staphylococcus pseudintermedius strain AP20,positive,,283734,Complete,AP20,,,,MLST.Staphylococcus_pseudintermedius.181,,,,2019-08-05T00:00:00Z,,PRJNA475016,SAMN09378520,GCA_007833755.1,,CP031561,,"Veterinary Science, Chulalongkorn University",,Oxford Nanopore Technologies,40.0x,Canu v. 1.3,1,,1,2734754,37.498325,2699,2547,None,,,1/30/09,Thailand,Thailand:Bangkok,,,,,temperature:20,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,whole genome of MRSP isolates from dogs and humans belonging to the same ST were compared to investigate the difference of their genome component that may associated with human adaptation.,sample_type:mixed culture,99,98.6,,,,Good,2020-11-26T15:02:51.620Z,2020-11-26T15:02:51.620Z
3411,286636.3,Streptococcus pyogenes MGAS10394,positive,Streptococcus pyogenes MGAS10394,286636,Complete,MGAS10394,serovar M6,,,MLST.Streptococcus_pyogenes.382,,,,2004-07-24T00:00:00Z,15272401,PRJNA12469,SAMN02603497,GCA_000011665.1,,CP000003,NC_006086,Lab of Human Bacterial Pathogenesis,complete,,,,1,,1,1899877,38.7,1960,1886,Throat,child with pharyngitis,This strain is a serotype M6 isolate cultured from a child with pharyngitis in private elementary school in Pennsilvania.,,USA,Pennsilvania,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,35,Non-halophilic,Facultative,Host-associated,,"Streptococcus pyogenes strain MGAS10394. This strain is a serotype M6 isolate cultured from a child with pharyngitis in private elementary school in Pennsilvania. The strain contains the mefA gene encoding macrolide resistance and shown to be resistant to erythromycin, and has a chromosomal field-inversion gel-electrophoresis pattern characteristic of the serotype M6 clone causing disease on the territory of USA. It has been deposited at the American Type Culture Collection (accession no. BAA-946).",,99.8,99.7,100,,,Good,2014-12-08T22:13:35.840Z,2015-03-16T03:17:09.594Z
3417,286783.345,Salmonella enterica subsp. enterica serovar Indiana strain SI108,negative,,286783,Complete,SI108,Indiana,,,MLST.Salmonella_enterica.17,,,,2020-04-06T00:00:00Z,,PRJNA615288,SAMN14450155,GCA_012053325.1,,"CP050769,CP050770",,University of Maryland,,Illumina MiSeq; Oxford Nanopore MiniION,103x,Unicycler v. 0.4.8,1,1,2,5071476,52.011604,5216,4836,Stool,Diarrheal patient,,9/22/13,China,China:Shanghai,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,97.1,96.2,,,,Good,2020-06-03T11:17:07.429Z,2020-06-03T11:17:07.429Z
3782,290338.8,Citrobacter koseri ATCC BAA-895,negative,Citrobacter koseri ATCC BAA-895,290338,Complete,ATCC BAA-895,,,,,,ATCC BAA-895,,2007-09-11T00:00:00Z,,PRJNA12716,SAMN02603912,GCA_000018045.1,,"CP000822,CP000824,CP000823","NC_009792,NC_009794,NC_009793",Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine,complete,,,,1,2,3,4735357,53.8,4311,5008,None,human infant,isolate from a human infant,,,,,,,,,"Human, Homo sapiens",,infant,,,,,,,-,,,,Mesophilic,-,,,Multiple,Bacteremia;Meningoencephalitis;Cerebral abscesses,Citrobacter koseri ATCC BAA-895. Citrobacter koseri ATCC BAA-895 is a clinical isolate from a human infant and will be used for comparative analysis with other Citrobacter species.,,99.9,99.9,100,0.3,,Good,2014-12-08T22:10:55.751Z,2015-03-16T03:17:09.594Z
3783,290847.5,Helicobacter pylori 51,negative,Helicobacter pylori 51,290847,Complete,51,,,,MLST.Helicobacter_pylori.3033,,,,2009-10-21T00:00:00Z,,PRJNA9627,SAMN02603300,GCA_000011725.1,,CP000012,NC_017382.1,"Gyeongsang National University College of Medicine and 21c Frontier Human Functional Genome Research Project|Gyeongsang National University|KRIBB, Korea, Daejeon",complete,,,,1,,1,1589954,38.8,1600,1415,Stomach,duodenal ulcer patient who had undergone a gastrointestinal examination,isolated from a duodenal ulcer patient who had undergone a gastrointestinal examination in a hospital in South Korea,,South Korea,South Korea,,,,,,"Human, Homo sapiens",,,,,,,,,-,Spiral,Yes,,Mesophilic,37,,Aerobic,Host-associated,Gastritis;Peptic ulcer disease,Helicobacter pylori strain 51. This strain was isolated from a duodenal ulcer patient who had undergone a gastrointestinal examination in a hospital in South Korea.,,100,99.7,100,,,Good,2014-12-08T22:11:43.349Z,2015-03-16T03:17:09.594Z
3900,295405.11,Bacteroides fragilis YCH46,negative,Bacteroides fragilis YCH46,295405,Complete,YCH46,,,,,,,,2004-10-15T00:00:00Z,15466707,PRJNA13067,,GCA_000009925.1,,"AP006841,AP006842","NC_006347,NC_006297",Kitasato Univ.,complete,,,,1,1,2,5310990,43.2,4412,4625,Blood,patient with septicemia,isolated from a patient with septicemia in Japan,,Japan,Japan,,,,,,"Human, Homo sapiens",,,septicemia,,,,,,-,Rod,,,Mesophilic,37,,Anaerobic,,Diarrhea;Abscesses,"Bacteroides fragilis strain YCH46. This organism can become an opportunistic pathogen, infecting anywhere in the body and causing abcess formation. Enterotoxigenic Bacterioides fragilis (ETBF) is associated with diarrheal diseases. This strain was isolated from a patient with septicemia in Japan. Virulence functions include numerous capsular polysaccharide biosynthesis systems that are controlled by invertible promoters that are recombined by a site-specific recombinase, Mpi, that works at a set of inverted repeats found within the chromosome. This system allows a vast repertoire of variable antigens to be expressed, thereby aiding evasion of the immune system. This organism also carries a potentially conjugative plasmid, as well as a number of conjugative and mobilizable transposons.",,99.8,99.6,99.7,,,Good,2014-12-08T22:10:22.528Z,2015-03-16T03:17:09.594Z
3904,299766.91,Enterobacter hormaechei subsp. steigerwaltii strain C309,negative,,299766,Complete,C309,,,,MLST.Enterobacter_cloacae.110,,,,2018-03-22T00:00:00Z,,PRJEB25613,SAMEA104700146,GCA_900322715.1,,"LT991954,LT991955,LT991956",,CHU Clermont-ferrand,,,,,1,2,3,5200769,54.956104,5002,,None,hospital,isolated over a one-year period and originating from hospital environment,2015,France,France,,,,,,"Human, Homo sapiens",,,,,,host_health_state:diseased,,,,,,,,,,,,,"We investigated nosocomial infections involving unusual carbapenemase-producing Enterobacter cloacae complex (ECC) strains isolated over a one-year period and originating from hospital environment. Whole-genome sequence typing revealed the predominance of epidemic isolates belonging to the novel sequence type ST873 , which produced the carbapenemase VIM-4. The mechanism underlying the one-year outbreak involved the emergence of a new phylogenetic lineage within the ECC, which should be closely monitored in the context of nosocomial infections",,99.5,97.9,100,0.4,,Good,2018-05-29T17:32:31.940Z,2018-05-29T17:32:31.940Z
3908,299767.237,Enterobacter ludwigii strain 994590,negative,,299767,Complete,994590,,,,,,,,2021-11-07T00:00:00Z,,PRJNA774541,SAMN22567593,GCA_020783215.1,,CP086101,,JMI Laboratories,,Illumina MiSeq; Oxford Nanopore MinION,29.01x,Unicycler v. v0.4.9b,1,,1,4763253,54.66002,4553,4439,None,,,2017,USA,USA: California,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"We submitted 5 E. cloacae isolates to 10-day serial passage in broth microdilution with cefepime, meropenem, or ceftazidime-avibactam to evaluate MIC increases and resistance mechanisms after exposure. Post-exposure isolates displaying >2-fold changes from the parent isolate and the parent isolate were analyzed. MIC changes increased 4- to 64-fold (median: 32-fold) after cefepime, 16- to 64-fold (16-fold) after meropenem and 2- to 32-fold (8-fold) after ceftazidime-avibactam exposure. Post-exposure isolates had diverse mechanisms identified using a combination of short- and long-read whole genome sequencing",sample_type:whole genome,99.4,98.8,,,,Good,2021-12-24T20:21:43.309Z,2021-12-24T20:21:43.309Z
3909,301102.37,Enterobacter hormaechei subsp. oharae strain DSM 16687,negative,,301102,Complete,DSM 16687,,,,,,DSM:16687,,2016-09-16T00:00:00Z,,PRJNA259658,SAMN05581749,GCF_001729705.1,SRR4045260,CP017180,NZ_CP017180.1,JCVI,,PacBio,15.49x,HGAP v. 3.0.0,1,,1,4724316,55.58,4571,4427,None,,,,Germany,Germany,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Carbapenem resistance in Enterobacteriacae is increasingly due to the presence of the KPC beta-lactamase, which can be transferred on several different plasmids. The project is designed to better understand the spread of the blaKPC gene and the genetic backgrounds in which it is carried.",,99.6,98.8,100,,,Good,2016-11-16T11:19:51.328Z,2016-11-16T11:19:51.328Z
3914,306537.1,Corynebacterium jeikeium K411,positive,Corynebacterium jeikeium K411,306537,Complete,K411,,,,,,,,2005-06-27T00:00:00Z,15968079,PRJNA13967,SAMEA3283089,GCA_000006605.1,,"CR931997,AF401314","NC_007164,NC_003080",Bielefeld Univ,complete,,,,1,1,2,2476822,61.4,2127,2120,Axillia,the axilla of a bone marrow transplant patient,isolated from the axilla of a bone marrow transplant patient,,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,No,No,Mesophilic,-,Non-halophilic,Facultative,Multiple,Nosocomial infections,Corynebacterium jeikeium K411.This strain was isolated from the axilla of a bone marrow transplant patient.,,97.3,96.8,100,0.8,,Good,2014-12-08T22:11:03.768Z,2015-03-16T03:17:09.594Z
3916,312175.13,Leptospira interrogans serovar Bataviae strain 1548,negative,,312175,Complete,1548,Bataviae,,,MLST.Leptospira_spp.50,,,,2020-10-07T00:00:00Z,,PRJNA564736,SAMN12721655,GCA_014858935.1,,"CP043880,CP043881,CP043882,CP043883",,Leibniz Institute DSMZ,,PacBio RSII; Illumina MiSeq,183.0x,HGAP v. 3,1,3,4,4880112,35.157143,4959,4290,None,,,2015,Malaysia,Malaysia:Klang,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Part of Leptospira interrogans comparative genomics study,sample_type:cell culture,99.8,99.4,,,,Good,2020-11-29T06:18:51.304Z,2020-11-29T06:18:51.304Z
3917,314723.4,Borrelia hermsii DAH,negative,Borrelia hermsii DAH,314723,Complete,DAH,,,,,,,,2006-12-22T00:00:00Z,"16,796,672,223,540,300,000,000",PRJNA29637,,GCA_000012065.2,,"CP000281,CP000048,CP000280,CP000279,CP000278,CP000277,CP000276,CP000275,CP000274,CP000273",NC_010673,"Rocky Mountain Laboratories, NIAID, NIH",complete,,,,1,,1,922307,29.8,856,819,Blood,Blood,isolated from a case of relapsing fever in western Washington,,USA,"Washington, USA",,,,,,"Human, Homo sapiens",,,,,,,,,,Spiral,Yes,No,Mesophilic,-,,Aerobic,Host-associated,Tick-borne relapsing fever,Borrelia hermsii strain DAH. This strain was isolated from a case of relapsing fever in western Washington. This organism will be used for comparative genomics.,,99.9,99.9,25.5,0.1,Low CheckM completeness score,Poor,2014-12-08T22:10:32.741Z,2015-03-16T03:17:09.594Z
3925,316435.63,Escherichia coli Nissle 1917,negative,,316435,Complete,Nissle 1917,,,,"MLST.Escherichia_coli_2.4,MLST.Escherichia_coli_1.73",,,,2021-09-14T00:00:00Z,,PRJNA722272,SAMN18749717,GCA_019967895.1,,"CP082949,CP082950,CP082951",,Skolkovo Institute of Science and Technology,,Illumina NextSeq,217.0x,SPAdes v. v3.13.1,1,2,3,5064230,50.573406,5001,4717,Stool,stool,,2020,Germany,Germany:Herdecke,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Genome sequencing of a probiotic Escherichia coli strain Nissle 1917.,sample_type:cell culture,99.9,99,,,,Good,2021-12-24T00:20:28.901Z,2021-12-24T00:20:28.901Z
3928,319705.15,Mycobacterium abscessus subsp. bolletii MC1518,positive,,319705,Complete,MC1518,,,,MLST.Mycobacterium_abscessus.5,,,,2014-10-31T00:00:00Z,-,PRJNA263497,SAMN03102996,GCA_000770125.1,,CP009613.1,NZ_CP009613.1,BEI Resources/American Type,,Illumina,,CLC Genomics Workbench v. 7.0.2,1,,1,5049258,64.14,5023,4866,Sputum,sputum,,,USA,USA: Texas,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,,,,,,,,Whole genome sequencing of several mycobacterial species,,98.2,97,100,,,Good,2015-03-12T13:53:30.812Z,2015-03-16T03:17:09.594Z
3952,321314.9,Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67,negative,Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67,321314,Complete,SC-B67,serovar Choleraesuis,,,MLST.Salmonella_enterica.66,,,,2005-04-01T00:00:00Z,"1,578,149,516,257,050",PRJNA9618,SAMN02603109,GCA_000008105.1,,"AY509003,AE017220,AY509004","NC_006855,NC_006905,NC_006856",Chang Gung Memorial Hospital,complete,,,,1,2,3,4944000,52.1,5089,4634,Blood,58-year old man with sepsis and has been shown to be resistant to ciprofloxacin and ceftriaxone,isolated from a 58-year old man with sepsis and has been shown to be resistant to ciprofloxacin and ceftriaxone,,,,,,,,,"Human, Homo sapiens",,58,,,,,,,-,Rod,Yes,,Mesophilic,37,,Facultative,Host-associated,Salmonellosis;Swine paratyphoid,"Salmonella enterica subsp. enterica serovar Choleraesuis strain SC-B67. This organism is an extremely invasive serovar that is increasingly becoming resistant to multiple antibiotics such as fluoroquinolones, which severly inhibits the treatment of systemic infections caused by this organism. This strain was isolated from a 58-year old man with sepsis and has been shown to be resistant to ciprofloxacin and ceftriaxone. Mutations in the gyrase and topoisomerase genes appear to be the cause of the ciprofloxacin resistance while the presence of an ampC gene on a transmissable plasmid was responsible for ceftriaxone resistance. This organism also causes severe disease (swine paratyphoid) in pigs.",,99.6,97.3,98.9,1.6,,Good,2014-12-08T22:12:48.619Z,2015-03-16T03:17:09.594Z
3954,331112.6,Escherichia coli HS,negative,Escherichia coli HS,331112,Complete,HS,serovar O9,,Nonpathogenic,"MLST.Escherichia_coli_1.46,MLST.Escherichia_coli_2.667",,,,2007-09-10T00:00:00Z,18676672,PRJNA13959,SAMN02604037,GCA_000017765.1,,CP000802,NC_009800,TIGR,complete,,,,1,,1,4643538,50.8,4520,4378,None,laboratory scientist at Walter Reed Army Institute of Research,"isolated from a laboratory scientist at Walter Reed Army Institute of Research in 1978 (Levine, 1978)",1978,USA,Walter Reed Army Institute,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,37,,Facultative,Host-associated,,"Escherichia coli strain HS. This strain (HS; serotype O9) is a human commensal that was originally isolated from a laboratory scientist at Walter Reed Army Institute of Research in 1978 (Levine, 1978). It was obtained from Drs. Kaper and Nataro at the School of Medicine at the University of Maryland. Strain HS colonizes the human gastrointestinal tract in challenge experiments, but no overt signs of disease occur. Thus, this strain represents a genomic baseline for human gastrointestinal tract colonization. It is competent and amenable to genetic manipulation.",,99.9,99.2,99.3,,,Good,2014-12-08T22:11:25.512Z,2015-03-16T03:17:09.594Z
3955,331271.8,Burkholderia cenocepacia AU 1054,negative,Burkholderia cenocepacia AU 1054,331271,Complete,AU 1054,,,,MLST.Burkholderia_cepacia_complex.122,,,,2006-06-01T00:00:00Z,,PRJNA13919,SAMN02598326,GCA_000014085.1,,"CP000378,CP000379,CP000380","NC_008060,NC_008061,NC_008062",DOE Joint Genome Institute,complete,,,,3,,3,7279116,66.9,6759,6477,Blood,the blood of a patient with CF,isolated from the blood of a patient with CF,,,,,,,,,"Human, Homo sapiens",,,CF,,,,,,,,,,Mesophilic,-,,,,Necrotizing pneumonia,Burkholderia cenocepacia strain AU 1054. This organism (AU 1054) was isolated from the blood of a patient with CF. This microbe has three chromosomes.,,99.2,95.6,100,,,Good,2014-12-08T22:10:41.504Z,2015-03-16T03:17:09.594Z
3956,333849.47,Enterococcus faecium DO,positive,,333849,Complete,DO,,,,MLST.Enterococcus_faecium.18,,,,2015-06-08T00:00:00Z,22769602,PRJNA30627,SAMN00002237,GCA_000174395.2,,ACIY01000000,,Baylor College of Medicine,,Sanger; 454 GS20; 454 FLX,,Newbler assembler v2.3 10192009,1,3,4,3052572,37.869804,3173,3114,None,,,,USA,USA: University of Texas Medical School,,,,,env_biome:terrestrial biome [ENVO:00000446],"Human, Homo sapiens",,,,,,,,,Positive,Cocci,,,Mesophilic,,,Facultative,Multiple,"Urinary tract infection, bacteremia, endocarditis",Enterococcus faecium DO. Enterococcus faecium DO is an opportunistic pathogen that transfers vancomycin resistance to other bacteria.,,99,96.7,100,0.9,,Good,2018-09-12T12:23:42.915Z,2018-09-12T12:23:42.915Z
3957,334413.6,Finegoldia magna ATCC 29328,positive,Finegoldia magna ATCC 29328,334413,Complete,ATCC 29328,,,,,,ATCC 29328,,2008-02-14T00:00:00Z,,PRJNA18981,,GCA_000010185.1,,"AP008971,AP008972","NC_010376,NC_010371",Kitasato Univ.,complete,Sanger,10x,Phred/Phrap/Consed,1,1,2,1986740,32.1,1850,1813,Gut,,,,,,,,,,,"Human, Homo sapiens",,,,Gastrointestinal tract,,,,,+,Coccus,,,Mesophilic,-,Non-halophilic,Anaerobic,Multiple,,Finegoldia magna ATCC 29328.This strain is being sequenced for comparative genome analysis.,,99.9,99.9,100,,,Good,2014-12-08T22:11:37.761Z,2015-03-16T03:17:09.594Z
3958,336982.7,Mycobacterium tuberculosis F11,positive,Mycobacterium tuberculosis F11,336982,Complete,F11,,,,,,,,2007-06-07T00:00:00Z,,PRJNA15642,,GCA_000016925.1,,CP000717,NC_009565,Broad Institute,complete,,,,1,,1,4424435,65.6,4394,3941,Lung,tuberculosis patients during a TB epidemic,recovered from tuberculosis patients during a TB epidemic in the Western Cape of South Africa,,South Africa,Western Cape of South Africa,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,No,No,Mesophilic,37,,Aerobic,Host-associated,Tuberculosis,Mycobacterium tuberculosis strain F11. This strain (genotype F11) represents the largest portion of isolates recovered from tuberculosis patients during a TB epidemic in the Western Cape of South Africa. It is also found in other parts of the world.,,99.9,99.8,100,,,Good,2014-12-08T22:12:10.026Z,2015-03-16T03:17:09.594Z
3972,342451.11,Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305,positive,Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305,342451,Complete,ATCC 15305,,,,,,ATCC 15305,Yes,2005-08-12T00:00:00Z,16135568,PRJNA15596,,GCA_000010125.1,,"AP008934,AP008936,AP008935","NC_007350,NC_007352,NC_007351",Kitasato Univ.,complete,,,,1,2,3,2577899,33.2,2498,2514,Urine,human urine specimen,was from a human urine specimen,,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,-,,Aerobic,Host-associated,Urinary tract infection,"Staphylococcus saprophyticus  subsp. saprophyticus ATCC 15305. This strain (GTC 265; ATCC 15305) is the type strain for the species and the sequenced strain was obtained from the Japanese Society for Bacteriology (Tokyo). The original ATCC isolate was from a human urine specimen. It will be used for comparative genomics with other Staphylococcal genomes. Genomic analysis revealed that this organism does not encode many of the virulence factors found in S. aureus. It does contain a capsular polysaccharide biosynthetic locus and a genomic island encoding antibiotic resistance determinants. Virulence factors include adhesins that mediate adherence to urinary tract epithelial cells, a number of paralogous transport system, and a putative iron-uptake system as well as the aforementioned antiobiotic and polysaccharide loci.",,99.3,98.9,98.9,2.1,,Good,2014-12-08T22:13:26.535Z,2015-03-16T03:17:09.594Z
3973,342617.7,Streptococcus agalactiae CJB111,positive,,342617,Complete,CJB111,,,,MLST.Streptococcus_agalactiae.1,,,,2020-11-03T00:00:00Z,,PRJNA663970,SAMN16191206,GCA_015221735.1,,CP063198,,University of Colorado-Anschutz Medical Campus,,Illumina NextSeq; Oxford Nanopore; Sanger,472x; 310x,Unicycler v. JULY-2020,1,,1,2093987,35.52104,2078,2009,Blood,blood,isolated from a neonate with bacteremia in 1990,18-Jul-90,USA,USA,,,,,,"Human, Homo sapiens",female,55 days,bacteremia without focus,,,,,,,,,,,,,,,,CJB111 is a Group B streptococcal strain isolated from a neonate with bacteremia in 1990.,collected_by:Carol J Baker,99.8,99.8,,,,Good,2020-11-30T03:12:41.095Z,2020-11-30T03:12:41.095Z
3974,344609.11,Shigella boydii CDC 3083-94,negative,Shigella boydii CDC 3083-94,344609,Complete,BS512,serovar 18,,,,,,,2008-05-05T00:00:00Z,,PRJNA15637,SAMN02604039,GCA_000020185.1,,"CP001063,CP001059,CP001060,CP001062,CP001061,CP001058","NC_010658,NC_010657,NC_010659,NC_010660,NC_010672,NC_010656",TIGR,complete,,,,1,5,6,4874659,51,5696,4557,None,12-year-old boy,isolated from a 12-year-old boy in Arizona by Dr Nancy Stockbine,,USA,USA: Arizona,,,,,,"Human, Homo sapiens",,12,,,,,,,-,Rod,Yes,No,Mesophilic,37,Non-halophilic,Facultative,Host-associated,Dysentery,"Shigella boydii4 strain BS512. This strain (strain BS512; serotype 18) was originally isolated from a 12-year-old boy in Arizona by Dr Nancy Stockbine. It is a member of Group 1 as determined by limited sequence analysis and can invade HeLa cells. Pathogenicity and virulence have been verified during in vitro experimentation, and multiple plasmids are present in this strain.gDNA for sequencing was isolated from a stock culture provided by Dr Anthony Maurelli from Uniformed Services University of Health Sciences. Two libraries were constructed - a small insert library (4-5 kb) and a large insert library (10-12 kb) from which 20,656 and 47,348 reads were sequenced, respectively.",,98.8,96.5,100,,,Good,2014-12-08T22:12:54.508Z,2015-03-16T03:17:09.594Z
3976,345072.25,Vibrio cholerae MO10,negative,,345072,Complete,MO10,,,,MLST.Vibrio_cholerae.69,,,,2021-04-14T00:00:00Z,,PRJNA720118,SAMN18642716,,,"CP072849,CP072850",,Universite de Montreal,,PacBio Sequel,385.0x,Flye v. 2.8.1,2,,2,4072012,47.52287,3769,3608,None,,,1/1/93,India,India,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Identify accumulated mutations in V. cholerae MD lab strains.,sample_type:whole organism;lab_host:Marylise Duperthuy UdeM,99.8,99.5,,,,Good,2021-04-25T19:10:54.056Z,2021-04-25T19:10:54.056Z
3977,349747.9,Yersinia pseudotuberculosis IP 31758,negative,Yersinia pseudotuberculosis IP 31758,349747,Complete,IP31758,serovar 1b,,,MLST.Yersinia_pseudotuberculosis.2,,,,2007-07-23T00:00:00Z,17784789,PRJNA16070,SAMN02604043,GCA_000016945.1,,"CP000720,CP000719,CP000718","NC_009708,NC_009705,NC_009704",TIGR,complete,,,,1,2,3,4935125,47.2,4749,4324,Stool,the stools of a patient presenting with scarlet-like fever,isolated in 1966 from the stools of a patient presenting with scarlet-like fever in the Primorski region of the former USSR,1966,Russia,Primorski region of the former USSR,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,-,,Facultative,Multiple,Gastroenteritis,"Yersinia pseudotuberculosis strain IP 31758. This strain is serotype 1b and was isolated in 1966 from the stools of a patient presenting with scarlet-like fever in the Primorski region of the former USSR. The strain was sent to the Institut Pasteur by Dr Timofeeva (Antiplague Institute, Irkoutsk).Two libraries were constructed: a small insert library (4-5 kb) and a large insert library (10-12 kb) from which 11,818 and 49,665 reads were sequenced respectively.",,99.9,98.9,100,,,Good,2014-12-08T22:13:52.198Z,2015-03-16T03:17:09.594Z
3978,355276.3,Leptospira borgpetersenii serovar Hardjo-bovis str. L550,negative,Leptospira borgpetersenii serovar Hardjo-bovis L550,355276,Complete,L550,serovar Hardjo-bovis,,,"MLST.Leptospira_spp_2.175,MLST.Leptospira_spp_3.128",,,,2006-10-13T00:00:00Z,16973745,PRJNA16146,SAMN02603615,GCA_000013945.1,,"CP000348,CP000349","NC_008508,NC_008509",Monash University|Australian Genome Research Facility Ltd.|National Animal Disease Center|Victorian Bioinformatics Consortium,complete,,,,2,,2,3931782,40.2,4262,2945,None,human clinical sample,isolated from a human clinical sample and will be used for comparative genomics with other Leptospira species,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Spiral,Yes,No,Mesophilic,-,Non-halophilic,Aerobic,Host-associated,Leptospirosis,Leptospira borgpetersenii sv Hardjo-bovis strain L550. This strain was isolated from a human clinical sample and will be used for comparative genomics with other Leptospira species.,,99.6,97,100,1,,Good,2014-12-08T22:11:56.215Z,2015-03-16T03:17:09.594Z
3984,357244.4,Orientia tsutsugamushi str. Boryong,negative,Orientia tsutsugamushi str. Boryong,357244,Complete,Boryong,,,,MLST.Orientia_tsutsugamushi.48,,,,2007-05-15T00:00:00Z,17483455,PRJNA16180,SAMEA3138266,GCA_000063545.1,,AM494475,NC_009488,Seoul National University College of Medicine|GenoTech Genome Research Center,complete,,,,1,,1,2127051,30.5,2364,1182,None,human,"isolated from a human in 1995 in Boryong, Korea",1995,South Korea,South Korea: Boryong,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,,-,,,Host-associated,Scrub typhus,"Orientia tsutsugamushi strain Boryong. This strain was isolated from a human in 1995 in Boryong, Korea.",,99.6,99.5,100,,,Good,2014-12-08T22:12:29.034Z,2015-03-16T03:17:09.594Z
3985,357544.13,Helicobacter pylori HPAG1,negative,Helicobacter pylori HPAG1,357544,Complete,HPAG1,,,,MLST.Helicobacter_pylori.848,,,Yes,2006-06-06T00:00:00Z,16788065,PRJNA16183,SAMN02604311,GCA_000013245.1,,"CP000241,CP000242","NC_008086,NC_008087",Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine,complete,,,,1,1,2,1605736,39.1,1596,1544,Stomach,"Swedish patient with chronic atrophic gastritis, the precursor to gastric adenocarcinoma","isolated from a Swedish patient with chronic atrophic gastritis, the precursor to gastric adenocarcinoma",,,,,,,,,"Human, Homo sapiens",,,"chronic atrophic gastritis, the precursor to gastric adenocarcinoma",,,,,,-,Spiral,Yes,,Mesophilic,37,Non-halophilic,Aerobic,Host-associated,Gastric ulcer,"Helicobacter pylori HPAG1.This strain was isolated from a Swedish patient with chronic atrophic gastritis, the precursor to gastric adenocarcinoma. Since Helicobacter pylori is associated with gastric cancer, sequencing the genome of this clinical isolate, and comparing it to the two other sequenced type strains (J99 and 26695, both recovered from patients with acid peptic disease) should provide new insights about microbial factors that may contribute to tumorigenesis.",,99.8,99.6,100,0.3,,Good,2014-12-08T22:11:44.304Z,2015-03-16T03:17:09.594Z
4043,359786.13,Staphylococcus aureus subsp. aureus JH9,positive,Staphylococcus aureus subsp. aureus JH9,359786,Complete,JH9,,,,MLST.Staphylococcus_aureus.105,,,,2007-05-18T00:00:00Z,,PRJNA15757,SAMN02598343,GCA_000016805.1,,"CP000703,CP000704","NC_009487,NC_009477",DOE Joint Genome Institute,complete,,,,1,1,2,2937129,32.9,2879,2726,None,patient undergoing vancomycin treatment,isolated from a patient undergoing vancomycin treatment,,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,30-37,,Facultative,Host-associated,Toxic shock syndrome;Scarlet fever,"Staphylococcus aureus subsp. aureus strain JH9. A series of isogenic methicillin-resistant (MRSA) strains were isolated from a patient undergoing vancomycin treatment. The chronologically earliest strain (JH1) was vancomycin sensitive, while the latest strain (JH9) exhibited increased vancomycin resistance (VISA-type vancomycin resistance). Comparison of these two strains will enable understanding of the evolutionary events that occur under the selective pressure of the presence of antibiotics as well as help explain the genetic basis for vancomycin resistance.",,100,99.7,100,1.2,,Good,2014-12-08T22:13:24.693Z,2015-03-16T03:17:09.594Z
4044,359787.11,Staphylococcus aureus subsp. aureus JH1,positive,Staphylococcus aureus subsp. aureus JH1,359787,Complete,JH1,,,,MLST.Staphylococcus_aureus.105,,,,2007-06-28T00:00:00Z,,PRJNA15758,SAMN02598344,GCA_000017125.1,,"CP000736,CP000737","NC_009632,NC_009619",DOE Joint Genome Institute,complete,,,,1,1,2,2936936,32.9,2839,2780,None,patient undergoing vancomycin treatment,isolated from a patient undergoing vancomycin treatment,,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,30-37,,Facultative,Host-associated,Toxic shock syndrome;Scarlet fever,"Staphylococcus aureus subsp. aureus strain JH1. A series of isogenic methicillin-resistant (MRSA) strains were isolated from a patient undergoing vancomycin treatment. The chronologically earliest strain (JH1) was vancomycin sensitive, while the latest strain (JH9) exhibited increased vancomycin resistance (VISA-type vancomycin resistance). Comparison of these two strains will enable understanding of the evolutionary events that occur under the selective pressure of the presence of antibiotics as well as help explain the genetic basis for vancomycin resistance.",,100,99.8,100,1.2,,Good,2014-12-08T22:13:24.683Z,2015-03-16T03:17:09.594Z
4045,360102.15,Yersinia pestis Antiqua,negative,,360102,Complete,Antiqua,,,,MLST.Yersinia_spp.79,,,,2015-05-28T00:00:00Z,25931590,PRJNA240103,SAMN03174669,GCF_000834825.1,"SRR2176134,SRR2176135","CP009906,CP009905,CP009904,CP009903","NZ_CP009906.1,NZ_CP009905.1,NZ_CP009904.1,NZ_CP009903.1",Los Alamos National Laboratory,,Illumina; PacBio; 454,477x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,1,3,4,4884396,47.71,4780,4367,None,Human clinical sample,,1965,Congo,Republic of the Congo,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,Genome sequencing of Yersinia pestis Antiqua,sample_type:Microbial isolate culture,99.9,98.3,100,1,,Good,2016-01-17T15:43:27.271Z,2016-01-17T15:43:27.271Z
4046,360106.6,Campylobacter fetus subsp. fetus 82-40,negative,Campylobacter fetus subsp. fetus 82-40,360106,Complete,82-40,,,,MLST.Campylobacter_fetus.6,,,,2006-11-27T00:00:00Z,,PRJNA16293,SAMN02604050,GCA_000015085.1,,CP000487,NC_008599,TIGR,complete,,,,1,,1,1773615,33.3,1768,1719,Blood,the blood of a human patient who was having a renal transplant,isolated from the blood of a human patient who was having a renal transplant and is the best characterized isolate of this species,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Spiral,Yes,,,-,,Microaerophilic,Host-associated,Infertility;Spontaneous abortions;Septicemia;Meningitis,"Campylobacter fetus subsp. fetus 82-40. This strain (82-40) was isolated from the blood of a human patient who was having a renal transplant and is the best characterized isolate of this species.. The ratio of bloodstream infection to diarrheal illnesses for C. fetus is nearly 400-fold higher than for C. jejuni, indicating its marked propensity for invasive disease compared to C. jejuni.",,99.8,99.8,100,,,Good,2014-12-08T22:10:46.364Z,2015-03-16T03:17:09.594Z
4047,360115.5,Coxiella burnetii RSA 331,negative,Coxiella burnetii RSA 331,360115,Complete,RSA 331,,,,,,,,2007-12-05T00:00:00Z,,PRJNA16791,SAMN02604053,GCA_000018745.1,,"CP000890,CP000889","NC_010117,NC_010115",TIGR,complete,,,,1,1,2,2053744,42.7,2194,1975,Blood,the blood of an infected patient,isolated from the blood of an infected patient in northern Italy in 1945,1945,Italy,northern Italy,,,,,,"Human, Homo sapiens",,,,,,,,,-,Coccobacillus,,,Mesophilic,-,,Facultative,Multiple,Q fever,Coxiella burnetii  strain RSA 331. This strain (RSA 331; Hentzerling) is associated with acute Q fever and was isolated from the blood of an infected patient in northern Italy in 1945.,,99.9,99.3,100,,,Good,2014-12-08T22:11:04.674Z,2015-03-16T03:17:09.594Z
4048,360118.8,Burkholderia pseudomallei 406e,negative,,360118,Complete,406E,,,,MLST.Burkholderia_pseudomallei.211,,,,2015-06-02T00:00:00Z,25931592,PRJNA238550,SAMN03010441,GCF_000959145.1,"SRR1614095,SRR1614096,SRR1614097","CP009298,CP009297","NZ_CP009298.1,NZ_CP009297.1",Los Alamos National Laboratory,,Illumina; 454; PacBio,337x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,2,,2,7271506,68.09,7281,5902,None,Human,,1988,Thailand,Thailand,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,,,,,,,,Genome sequencing of Burkholderia pseudomallei 406E,,99.1,95.6,100,,,Good,2016-01-17T15:50:14.445Z,2016-01-17T15:50:14.445Z
4049,362663.9,Escherichia coli 536,negative,Escherichia coli 536,362663,Complete,536,,,UPEC,"MLST.Escherichia_coli_1.127,MLST.Escherichia_coli_2.261",,,,2006-07-13T00:00:00Z,16879640,PRJNA16235,SAMN02604181,GCA_000013305.1,,CP000247,NC_008253,University of Goettingen,complete,,,,1,,1,4938920,50.5,4773,4620,None,patient with acute pyelonephritis (inflammation of the kidney and pelvis),isolated from a patient with acute pyelonephritis (inflammation of the kidney and pelvis),,,,,,,,,"Human, Homo sapiens",,,acute pyelonephritis (inflammation of the kidney and pelvis),,,,,,-,Rod,Yes,,Mesophilic,-,,Facultative,Host-associated,Urinary tract infection,"Escherichia coli strain 536. This strain (536; O6:K15:H31) is a uropathogenic Escherichia coli (UPEC) that was isolated from a patient with acute pyelonephritis (inflammation of the kidney and pelvis). It is a model organism of extraintestinal E. coli, which are among the most common causes of non-hospital-acquired urinary tract infections (UTIs) and UPEC strains are responsible for 40% of nosocomial UTIs. Comparative genomics with other E. coli, especially UPEC strains such as CFT073 will reveal important pathogenicity traits. Studies on strain 536 have revealed at least 5 pathogenicity islands. The project is a collaboration with the group of Prof. Hacker, Institute for Molecular Infection Biology, University of Wurzburg.",,99.8,97.9,99.6,1.1,,Good,2014-12-08T22:11:20.299Z,2015-03-16T03:17:09.594Z
4052,364106.8,Escherichia coli UTI89,negative,Escherichia coli UTI89,364106,Complete,UTI89,,,UPEC,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,,,2006-04-05T00:00:00Z,16585510,PRJNA16259,SAMN00000110,GCA_000013265.1,,"CP000243,CP000244","NC_007946,NC_007941",Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine,complete,,,,1,1,2,5179971,50.6,5040,5166,Urine,woman with uncomplicated cystitis (bladder inflammation) that has been demonstrated to cause cystitis,isolated from a woman with uncomplicated cystitis (bladder inflammation) that has been demonstrated to cause cystitis in a murine urinary tract infection model,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,-,,Facultative,Host-associated,Urinary tract infection,"Escherichia coli strain UTI89. This strain (UTI89) is a uropathogenic strain isolated from a woman with uncomplicated cystitis (bladder inflammation) that has been demonstrated to cause cystitis in a murine urinary tract infection model.The genome of UTI89 showed 4 pathogenicity islands. A plasmid was found that was similar to the F plasmid but which also contained virulence genes. Comparison of a set of orthologs from this organism with other E. coli strains showed positive selection on some genes, including those for iron acquisition. Comparison with additional sequences (found in Accession Numbers DQ389000:DQ389068 and DQ440980:DQ441250) of a subset of genes from a number of isolates from patients with UTI infections and isolates from healthy individuals showed positive selection of fepE and amiA genes and some weakly positive selection for ompC.",,99.8,99.1,100,,,Good,2014-12-08T22:11:36.454Z,2015-03-16T03:17:09.594Z
4053,367737.6,Arcobacter butzleri RM4018,negative,Arcobacter butzleri RM4018,367737,Complete,RM4018,,,,MLST.Arcobacter_spp.1,,,,2007-09-27T00:00:00Z,"1,758,812,818,159,240",PRJNA16319,SAMN02604276,GCA_000014025.1,,CP000361,NC_009850,"USDA - Agricultural Research Service, USA|Agencourt Bioscience",complete,,,,1,,1,2341251,27,2275,2259,Stomach,human patient with gastroenteritis,isolated from a human patient with gastroenteritis,,,,,,,,,"Human, Homo sapiens",,,gastroenteritis,,,,,,-,Spiral,Yes,No,Mesophilic,-,,Aerobic,Multiple,Gastroenteritis;Bacteremia,Arcobacter butzleri RM4018. Arcobacter butzleri RM4018 was isolated from a human patient with gastroenteritis.,,99.9,99.8,100,4.4,,Good,2014-12-08T22:10:06.677Z,2015-03-16T03:17:09.594Z
4082,373045.6,Escherichia coli O111:NM strain FWSEC0005,negative,,373045,Complete,FWSEC0005,O111:NM,,,"MLST.Escherichia_coli_1.16,MLST.Escherichia_coli_2.480",,,,2019-05-03T00:00:00Z,,PRJNA287560,SAMN08768106,GCA_005037805.2,,NJGR01000000,,National Microbiology Laboratory,,Illumina MiSeq;Oxford Nanopore MinION,108.41x;252.38x,Unicycler;Canu v. 0.4.4.0;1.7,1,,1,5132754,50.64242,5466,5279,None,Clinical: Human (Homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2000,Canada,Canada:Saskatchewan,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,Mesophilic,37 C,,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,99.9,98.4,,,,Good,2019-07-14T19:19:29.494Z,2019-07-14T19:19:29.494Z
4089,374923.7,Shigella flexneri 1a,negative,,374923,Complete,670,1a,,,,,,,2017-08-02T00:00:00Z,,PRJNA377966,SAMN06478366,GCA_002240135.1,,"CP020086,CP020087,CP020088",,Hangzhou Normal University,,PacBio,237.11,HGAP v. 2.0,1,2,3,4899768,50.61,5645,5283,None,hospitalized patients,,2006,China,China: Hangzhou,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Antibiotic resistance study,sample_type:cell culture,99.1,97.3,100,,,Good,2017-09-28T19:43:11.753Z,2017-09-28T19:43:11.753Z
4090,374930.9,Haemophilus influenzae PittEE,negative,Haemophilus influenzae PittEE,374930,Complete,PittEE,,,,MLST.Haemophilus_influenzae.107,,,,2007-06-07T00:00:00Z,17550610,PRJNA16400,SAMN02603084,GCA_000016465.1,,CP000671,NC_009566,Allegheny-Singer Research Institute (ASRI),complete,,,,1,,1,1813033,38,1851,1619,Ear,middle-ear effusion,isolate recovered by Dr Robert Wadowsky from the middle-ear effusion of a child in Pittsburgh who was undergoing tympanostomy and ventilation tube placement for the treatment of chronic otitis media with effusion (COME).,,USA,Pittsburgh,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,Mesophilic,-,Non-halophilic,Facultative,Host-associated,Meningitis;Septicemia;Otitis media;Sinusitis;Bronchitis,"Haemophilus influenzae PittEE.Strain PittEE is a non-typeable Haemophilus influenzae (NTHi) isolate recovered by Dr Robert Wadowsky from the middle-ear effusion of a child in Pittsburgh who was undergoing tympanostomy and ventilation tube placement for the treatment of chronic otitis media with effusion (COME).  In the chinchilla model, PittEE infection induces COME but does not cause systemic disease.Sequenced and assembled using technology developed by 454 Life Sciences, Inc. (www.454.com), supplemented with double-barreled Sanger dideoxy sequencing read data from traditional clone libraries. The genome sequence is currently comprised of 6 contigs, and has been sequenced to a depth of 35X.;many frameshifted proteins",,99.6,96.8,100,4.3,,Good,2014-12-08T22:11:42.232Z,2015-03-16T03:17:09.594Z
4091,374931.1,Haemophilus influenzae PittGG,negative,Haemophilus influenzae PittGG,374931,Complete,PittGG,,,,,,,,2007-06-07T00:00:00Z,17550610,PRJNA16401,SAMN02603085,GCA_000016485.1,,CP000672,NC_009567,Allegheny-Singer Research Institute (ASRI),complete,,,,1,,1,1887192,38,2063,1667,Ear,external ear discharge,isolate recovered by Dr Robert Wadowsky from the external ear discharge of a spontaneously perforated tympanic membrane of a child in Pittsburgh  who had been diagnosed with otorrhea.,,USA,Pittsburgh,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,Mesophilic,-,Mesophilic,Facultative,Host-associated,Meningitis,"Haemophilus influenzae PittGG.Strain PittGG is a non-typeable Haemophilus influenzae (NTHi) isolate recovered by Dr Robert Wadowsky from the external ear discharge of a spontaneously perforated tympanic membrane of a child in Pittsburgh  who had been diagnosed with otorrhea.  In the chinchilla model, PittGG infection induces acute otitis media (AOM) and causes virulent, uniformly fatal, systemic disease.Sequenced and assembled using technology developed by 454 Life Sciences, Inc. (www.454.com), supplemented with double-barreled Sanger dideoxy sequencing read data from traditional clone libraries. The genome sequence is currently comprised of 60 contigs, and has been sequenced to a depth of 35X. ;many frameshifted proteins",,99.6,94.3,100,8.8,,Good,2014-12-08T22:11:42.241Z,2015-03-16T03:17:09.594Z
4092,376725.3,Escherichia coli O103:H2 strain FWSEC0007,negative,,376725,Complete,FWSEC0007,O103:H2,,,MLST.Escherichia_coli_1.17,,,,2019-05-03T00:00:00Z,,PRJNA287560,SAMN08768108,GCA_005037795.2,,NJGQ01000000,,National Microbiology Laboratory,,Illumina MiSeq;Oxford Nanopore MinION,103.12x;58.53x,Unicycler;Canu v. 0.4.4.0;1.7,1,1,2,5470829,50.687874,5856,5741,None,Clinical: Human (Homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2004,Canada,"Canada:Manitoba,Winnipeg",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,Mesophilic,37 C,,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,100,99.2,,,,Good,2019-07-14T19:22:01.208Z,2019-07-14T19:22:01.208Z
4096,381754.6,Pseudomonas aeruginosa PA7,negative,Pseudomonas aeruginosa PA7,381754,Complete,PA7,,,,MLST.Pseudomonas_aeruginosa.1195,,,,2007-07-05T00:00:00Z,20107499,PRJNA16720,SAMN02603435,GCA_000017205.1,,CP000744,NC_009656,J. Craig Venter Institute,complete,,,,1,,1,6588339,66.4,6064,6286,None,clinical isolate,This strain is a clinical isolate,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,25-30,,Aerobic,Multiple,,Pseudomonas aeruginosa PA7. This strain is a clinical isolate and will be used for comparative genomics.,,99.7,98.5,98.6,1.5,,Good,2014-12-08T22:12:37.731Z,2015-03-16T03:17:09.594Z
4101,392021.5,Rickettsia rickettsii str. 'Sheila Smith',negative,Rickettsia rickettsii str. 'Sheila Smith',392021,Complete,'Sheila Smith',,,,,,,,2007-10-02T00:00:00Z,,PRJNA9636,SAMN02603386,GCA_000018225.1,,CP000848,NC_009882,Institute for Systems Biology|University of Iowa,complete,,,,1,,1,1257710,32.5,1577,1345,None,from a patient with Rocky Mountain spotted fever,isolated from from a patient with Rocky Mountain spotted fever and will be used for comparative analysis,,,,,,,,,"Human, Homo sapiens",,,Rocky Mountain spotted fever,,,,,,-,Rod,,,Mesophilic,37,,Aerobic,Host-associated,Rocky mountain spotted fever,Rickettsia rickettsii str. 'Sheila Smith'. This strain was isolated from from a patient with Rocky Mountain spotted fever and will be used for comparative analysis.,,99.9,99.9,100,,,Good,2014-12-08T22:12:44.385Z,2015-03-16T03:17:09.594Z
4105,398577.6,Burkholderia ambifaria MC40-6,negative,Burkholderia ambifaria MC40-6,398577,Complete,MC40-6,,,,MLST.Burkholderia_cepacia_complex.136,,,,2008-04-03T00:00:00Z,,PRJNA17411,SAMN02598385,GCA_000019925.1,,"CP001025,CP001026,CP001027,CP001028","NC_010551,NC_010552,NC_010557,NC_010553",US DOE Joint Genome Institute|DOE Joint Genome Institute|JGI-PGF,complete,,,,3,1,4,7642536,66.4,6983,6697,Lung,cystic fibrosis patient,isolated from a cystic fibrosis patient,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,,,Mesophilic,-,Non-halophilic,,Multiple,Cepacia syndrome,Burkholderia ambifaria MC40-6. This strain was isolated from a cystic fibrosis patient.,,99.1,95.3,100,0.7,,Good,2014-12-08T22:10:41.334Z,2015-03-16T03:17:09.594Z
4112,400667.121,Acinetobacter baumannii ATCC 17978,negative,,400667,Complete,ATCC 17978,,,,"MLST.Acinetobacter_baumannii_1.112,MLST.Acinetobacter_baumannii_2.437",,ATCC:17978,,2020-06-24T00:00:00Z,,PRJNA629538,SAMN14779651,GCA_013372085.1,,"CP053098,CP053099,CP053100",,UC San Diego,,Illumina HiSeq; Oxford Nanopore MiniION,80.0x,Unicycler v. 0.4.2,1,2,3,4030054,38.936424,3842,3764,None,,,2017-08,USA,USA: San Diego,,,,,,"Human, Homo sapiens",,,,,,,Susceptible,Computational Prediction,,,,,,,,,,,A. baumannii ATCC 17978 hybrid assembly,sample_type:cell culture,97,96.5,,,,Good,2020-07-02T04:10:20.618Z,2020-07-02T04:10:20.618Z
4113,400673.7,Legionella pneumophila str. Corby,negative,Legionella pneumophila str. Corby,400673,Complete,Corby,,,,,,,,2007-05-24T00:00:00Z,17888731,PRJNA17491,SAMN02603241,GCA_000092545.1,,CP000675,NC_009494,"Fritz Lipmann Institute (former Institute of Molecular Biotechnology, IMB)",complete,,,,1,,1,3576470,38.5,3438,3206,None,human isolate,human isolate,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,-,,Aerobic,Host-associated,Legionellosis,Legionella pneumophila str. Corby. Legionella pneumophila str. Corby is a human isolate and will be used for comparative genomics.,,99.9,99.7,100,0.6,,Good,2014-12-08T22:11:55.697Z,2015-03-16T03:17:09.594Z
4142,405416.6,Acinetobacter baumannii ACICU,negative,Acinetobacter baumannii ACICU,405416,Complete,ACICU,,,,MLST.Acinetobacter_baumannii_2.2,,,,2008-04-15T00:00:00Z,27458211,PRJNA17827,SAMN02603140,GCA_000018445.1,,"CP000863,CP000865,CP000864","NC_010611,NC_010606,NC_010605","CNR - National Research Council|Istituto Superiore di Sanita|National Research Council, Istitute for Biomedical Technologies, Italy, Segrate",complete,,,,1,2,3,3996761,38.9,3690,3759,Cerebrospinal Fluid,CSF,isolated from an outbreak in an intensive care unit in Rome,2005,Italy,Rome,,,,,,"Human, Homo sapiens",,,,,,,Resistant,AMR Panel,-,Pleomorphic rod,,,Mesophilic,37,Non-halophilic,Aerobic,Aquatic,Nosocomial infections,Acinetobacter baumannii strain ACICU. Acinetobacter baumannii strain ACICU (also called H34)was isolated from an outbreak in an intensive care unit in Rome. This strain will be used for comparative analysis with other Acinetobacter baumannii strains.;A novel method of consensus panchromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii,,99.4,98.3,100,1,,Good,2014-12-08T22:09:34.589Z,2015-03-16T03:17:09.594Z
4143,405532.5,Bacillus cereus B4264,positive,Bacillus cereus B4264,405532,Complete,B4264,,,,MLST.Bacillus_cereus.89,,,,2008-12-17T00:00:00Z,,PRJNA17731,SAMN02604059,GCA_000021205.1,,CP001176,NC_011725,"J. Craig Venter Institute, USA, Rockville|TIGR",complete,,,,1,,1,5419036,35.3,5431,5408,Lung,case of fatal pneumonia,isolated in 1969 from a case of fatal pneumonia in a male patient,1969,,,,,,,,"Human, Homo sapiens",male,,,,,,,,+,Rod,Yes,Yes,Mesophilic,37,Non-halophilic,Aerobic,Multiple,Pneumonia,"Bacillus cereus B4264.This strain was isolated in 1969 from a case of fatal pneumonia in a male patient. B. cereus B4264 was cultured from the blood and the pleural fluid. This isolate was negative for all Laboratory Response Network (LRN) PCR assays that target pXO1 and pXO2. The isolate belongs to MLST type 89 using the MLSTDB scheme. Interestingly, this sequence type appears to be unrelated to B. anthracis. The clinical presentation resembles that of B. cereus G9241 and B. cereus 03BB102, and access to the draft genome of this isolate will allow for the comparison of strains that causes similar disease but have different genetic backgrounds and potential virulence genes.Sequence was obtained from three libraries - a fosmid library (33-39 kb; 50,162 reads), a medium insert library (10-12 kb; 11,376 reads), and a small insert library (3-5 kb; 12,413 reads).",,99.9,99,100,,,Good,2014-12-08T22:10:13.568Z,2015-03-16T03:17:09.594Z
4144,405535.8,Bacillus cereus AH820,positive,Bacillus cereus AH820,405535,Complete,AH820,,,,MLST.Bacillus_cereus.460,,,,2008-12-19T00:00:00Z,,PRJNA17711,SAMN02604057,GCA_000021785.1,,"CP001283,CP001285,CP001286,CP001284","NC_011773,NC_011777,NC_011771,NC_011776",TIGR,complete,,,,1,3,4,5588834,35.3,5873,5810,Abdomen,the periodontal pocket of a 76 year old female patient with marginal periodontitis and was further analyzed,"isolated in October 1995 in Akershus, Norway, from the periodontal pocket of a 76 year old female patient with marginal periodontitis and was further analyzed by Helgason et al",1995,Norway,Norway: Akershus,,,,,,"Human, Homo sapiens",female,76,marginal periodontitis,,,,,,+,Rod,Yes,Yes,Mesophilic,-,Non-halophilic,Aerobic,Multiple,Periodontitis,"Bacillus cereus AH820.This strain was isolated in October 1995 in Akershus, Norway, from the periodontal pocket of a 76 year old female patient with marginal periodontitis and was further analyzed by Helgason et al. (2000 J Clin Microbiol. 38, 1615-1622). B. cereus AH820 resides very close to the B. anthracis cluster using MLST analyses, and is 100% identical in all 7 loci to 3 other periodontal B. cereus isolates, suggesting that these human pathogens form a distinct clade within the group.Sequence was obtained from three libraries - a fosmid library (33-39 kb; 48,035 reads), a medium insert library (10-12 kb; 11,689 reads), and a small insert library (3-5 kb; 12;650 reads).",,99.8,98.4,99.3,0.7,,Good,2014-12-08T22:10:13.482Z,2015-03-16T03:17:09.594Z
4145,407148.6,Campylobacter jejuni subsp. jejuni 81116,negative,Campylobacter jejuni subsp. jejuni 81116,407148,Complete,81116,,,,MLST.Campylobacter_jejuni.267,,,,2007-09-20T00:00:00Z,17873037,PRJNA17953,SAMN02603008,GCA_000017905.1,,CP000814,NC_009839,BBSRC Institute of Food Research,complete,,,,1,,1,1628115,30.5,1636,1626,None,waterborne outbreak,isolated from a waterborne outbreak in 1982 and now routinely used as a laboratory strain,1982,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Spiral,Yes,No,Mesophilic,-,,Microaerophilic,Multiple,Food poisoning,Campylobacter jejuni subsp. jejuni 81116. Campylobacter jejuni subsp. jejuni 81116 is a human strain isolated from a waterborne outbreak in 1982 and now routinely used as a laboratory strain. This strain will be used for comparative analysis.,,100,99.9,100,,,Good,2014-12-08T22:10:47.263Z,2015-03-16T03:17:09.594Z
4146,409438.11,Escherichia coli SE11,negative,Escherichia coli SE11,409438,Complete,SE11,,,,"MLST.Escherichia_coli_1.156,MLST.Escherichia_coli_2.19",,,,2008-10-22T00:00:00Z,18931093,PRJNA18057,,GCA_000010385.1,,"AP009240,AP009245,AP009246,AP009242,AP009243,AP009241,AP009244","NC_011415,NC_011408,NC_011411,NC_011413,NC_011416,NC_011419,NC_011407",Kitasato Univ.,complete,Sanger,8x,Phred/Phrap/Consed,1,6,7,5155626,50.7,5048,5002,Gut,,,,,,,,,,,"Human, Homo sapiens",,,,Gastrointestinal tract,,,,,-,Rod,,,Mesophilic,37,Non-halophilic,Facultative,Host-associated,,Escherichia coli SE11.This strain is being sequenced for comparative genome analysis.,,99.9,99.5,100,,,Good,2014-12-08T22:11:34.523Z,2015-03-16T03:17:09.594Z
4147,412418.11,Borrelia recurrentis A1,negative,Borrelia recurrentis A1,412418,Complete,A1,,,,,,,,2008-09-15T00:00:00Z,,PRJNA18233,SAMN02603586,GCA_000019705.1,,"CP000993,CP000995,CP000996,CP000997,CP000998,CP000999,CP001000,CP000994","NC_011244,NC_011252,NC_011253,NC_011255,NC_011258,NC_011260,NC_011263,NC_011246",Unite des Rickettsies - Marseille|Marseille-Nice Genopole,complete,,,,1,5,8,1242163,27.5,1133,990,None,adult patient with louse-borne relapsing fever,isolated from adult patient with louse-borne relapsing fever in Ethiopia,,Ethiopia,Ethiopia,,,,,,"Human, Homo sapiens",,,louse-borne relapsing fever,,,,,,-,Spiral,Yes,No,Mesophilic,-,,Aerobic,Host-associated,Relapsing fever,Borrelia recurrentis A1. Borrelia recurrentis isolated from adult patient with louse-borne relapsing fever in Ethiopia. This organism will be used for comparative analysis with other Borrelia species.,,99.7,99.2,30.3,13.7,High CheckM contamination score;Low CheckM completeness score,Poor,2014-12-08T22:10:32.911Z,2015-03-16T03:17:09.594Z
4148,412419.2,Borrelia duttonii Ly,negative,Borrelia duttonii Ly,412419,Complete,Ly,,,,,,,,2008-09-15T00:00:00Z,18787695,PRJNA18231,SAMN02603585,GCA_000019685.1,,"CP000976,CP000978,CP000979,CP000980,CP000981,CP000982,CP000983,CP000984,CP000985,CP000986,CP000987,CP000988,CP000989,CP000990,CP000991,CP000992,CP000977","NC_011229,NC_011226,NC_011247,NC_011257,NC_011259,NC_011261,NC_011265,NC_011245,NC_011248,NC_011249,NC_011250,NC_011251,NC_011254,NC_011256,NC_011262,NC_011264,NC_011224",Unite des Rickettsies - Marseille|Marseille-Nice Genopole,complete,,,,1,15,17,1574881,28,1546,1305,None,2-year-old girl with tick-borne relapsing fever,isolated from a 2-year-old girl with tick-borne relapsing fever in Tanzania,,Tanzania,Tanzania,,,,,,"Human, Homo sapiens",,2,,,,,,,,Spiral,Yes,No,Psychrophilic,-,,Aerobic,Host-associated,Tick-borne relapsing fever,Borrelia duttonii Ly. Borrelia duttonii Ly was isolated from a 2-year-old girl with tick-borne relapsing fever in Tanzania. This organism will be used for comparative analysis with other Borrelia species.,,99.6,99.3,30.3,7.4,Low CheckM completeness score,Poor,2014-12-08T22:10:32.283Z,2015-03-16T03:17:09.594Z
4149,418136.12,Francisella tularensis subsp. tularensis WY96-3418,negative,Francisella tularensis subsp. tularensis WY96-3418,418136,Complete,WY96-3418,,,,,,,,2007-03-24T00:00:00Z,17895988,PRJNA18459,SAMN02603036,GCA_000016105.1,,CP000608,NC_009257,"BioHealthBase|Joint Genome Institute, Production Genomics Facility, Walnut Creek CA and Los Alamos National Laboratory, Los Alamos NM.|UT Southwestern Medical Center, Department of Pathology, USA, Dallas",complete,,,,1,,1,1898476,32.3,2082,1634,Wound,human finger wound,isolated from a human finger wound and is being sequenced for comparative genome analysis,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,No,,Mesophilic,-,Non-halophilic,Aerobic,Host-associated,Tularemia,Francisella tularensis subsp. tularensis WY96-3418.This strain was isolated from a human finger wound and is being sequenced for comparative genome analysis.,,100,99.4,100,0.8,,Good,2014-12-08T22:11:39.288Z,2015-03-16T03:17:09.594Z
4151,419947.8,Mycobacterium tuberculosis H37Ra,positive,Mycobacterium tuberculosis H37Ra,419947,Complete,ATCC25177,,,,,,ATCC 25177,Yes,2007-05-31T00:00:00Z,18584054,PRJNA18883,,GCA_000016145.1,,CP000611,NC_009525,"Chinese National Human Genome Center at Shanghai|Fudan University, P.R. China, Shanghai|Johns Hopkins University, Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, USA, Baltimore",complete,,,,1,,1,4419977,65.6,4412,4034,Lung,avirulent strain derived from its virulentparent strain H37,derived from its virulentparent strain H37 (isolated from a 19 year-old male patient with chronic pulmonary tuberculosis by Edward R. Baldwin in 1905) through a process of aging and dissociation from in vitro culture in 1935,,,,,,,,,"Human, Homo sapiens",male,19,chronic pulmonary tuberculosis,,,,,,+,Rod,No,No,,37,Non-halophilic,Aerobic,Host-associated,Tuberculosis,"Mycobacterium tuberculosis H37Ra. This strain (H37Ra; ATCC 25177) is an avirulent strain derived from its virulentparent strain H37 (isolated from a 19 year-old male patient with chronic pulmonary tuberculosis by Edward R. Baldwin in 1905) through a process of aging and dissociation from in vitro culture in 1935. H37Ra has several different characteristics compared with its virulent sister strain H37Rv, including a rough, raised colony morphology, loss of cord formation, loss of neutral red dye binding,decreased ability to survive under anaerobic conditions, reduced ability to survive inside macrophages, and loss of virulence in guinea pigs, mice and rabbits. Despite numerous studies in the past 70 years, the molecular basis for the loss of virulencein H37Ra has remained obscure. In this project, we determined the whole genome sequence for the H37Ra strain from ATCC (ATCC 25177). The choice of the ATCC type strain of H37Ra is important as repeated in vitro culture is known to create changes in the genome. Determination of the genome sequence of H37Ra and comparative genome analysis of H37Ra with the recently sequenced virulent sister strain H37Rv is of critical importance not only for elucidating the mechanism of attenuation of virulence in H37Ra but also for understanding the virulence and pathogenesis of M. tuberculosis.",,99.9,99.9,100,,,Good,2014-12-08T22:12:10.267Z,2015-03-16T03:17:09.594Z
4152,423212.4,Legionella pneumophila 2300/99 Alcoy,negative,Legionella pneumophila 2300/99 Alcoy,423212,Complete,2300/99 Alcoy,,,,,,,,2010-05-03T00:00:00Z,20236513,PRJNA18743,SAMN02604292,GCA_000092625.1,,CP001828,NC_014125,"Valencia University and Public Health Research Superior Center (CSISP) of Valencia's Goverment, Spain|Cavanilles Institute on Biodiversity and Evolutionary Biology|Public Health Research Center (CSISP) of Valencia s Government, Spain",complete,,,,1,,1,3516334,38.38,3346,3190,None,patient affected,isolated from a patient affected by legionellosis in Alcoy (Spain),,Spain,Spain:Alcoy,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,,Mesophilic,-,,Aerobic,Host-associated,Legionellosis,"Legionella pneumophila strain 2300/99 Alcoy. This strain (2300/99 Alcoy) belongs to serogroup 1 and is considered endemic in Spanish areas. It was isolated from a patient affected by legionellosis in Alcoy (Spain). One of the most important outbreaks was registered in Murcia (Spain) in 2001, when more than 751 cases of suspected Legionellosis were registered.",,99.9,99.6,100,1.1,,Good,2014-12-08T22:11:55.656Z,2015-03-16T03:17:09.594Z
4153,424717.5,Shigella flexneri 3a strain 888048,negative,,424717,Complete,888048,,,,,,,,2021-01-10T00:00:00Z,,PRJNA687663,SAMN17152196,GCA_016598675.1,,CP066809,,University of Bath,,Oxford Nanopore MinION; Illumina HiSeq,28.0x,Flye v. 2.7.1,1,,1,4519004,50.90664,5146,4401,Stool,stool,,20-Jan,United Kingdom,United Kingdom: London,,,,,,"Human, Homo sapiens",male,,shigellosis,,,,,,,,,,,,,,,,Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK. This study aimed to look at the location of AMR determinants in CTX-M-27-positive Shigella isolates spread through MSM in England and their relation to known plasmids in Shigella,collected_by:Public Health England,,,,,,Good,2021-02-01T05:25:34.311Z,2021-02-01T05:25:34.311Z
4154,424720.8,Shigella flexneri Y strain PE577,negative,,424720,Complete,PE577,Y,,,,,,,2019-09-12T00:00:00Z,,PRJNA533747,SAMN12588114,GCA_008370775.1,,"CP042980,CP042979,CP042978",,Michigan State University,,Illumina HiSeq,30.0x,A5 pipeline v. v. 20160825,1,2,3,4598750,50.962784,5076,4559,None,,"isolated in Adelaide, Australia and has been the laboratory host of numerous phages, including SfI, SfII, SfV, Sf6, etc",1990,Australia,Australia: Adelaide,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Shigella flexneri serotype Y is a common host to many bacteriophages. Strain PE577 was initially isolated in Adelaide, Australia and has been the laboratory host of numerous phages, including SfI, SfII, SfV, Sf6, etc. This strain has also been used to isolate many Shigella phages from the environment. The goal of this study was to sequence the entire genome of this strain for general characterization and future genetic inquiries.",sample_type:monoisolate;biomaterial_provider:C. Murray -> R. Morona -> K. Parent,99.8,97.9,,,,Good,2019-10-02T06:52:19.387Z,2019-10-02T06:52:19.387Z
4155,426430.24,Staphylococcus aureus subsp. aureus str. Newman,positive,,426430,Complete,NYU,,,,MLST.Staphylococcus_aureus.254,mlst:8,,,2017-09-18T00:00:00Z,29487865,PRJNA406184,SAMN07629846,GCA_002310435.1,,CP023390,,NYU Langone Health,,Illumina Miseq,200.0x,R studio v. 1.0.136,1,,1,2878897,32.89,2940,2964,None,Genomic DNA,,"July,2007",Japan,Tokyo,,,,,,"Human, Homo sapiens",,,invasive_infection,,,,Resistant,AMR Panel,,,,,,,,,,,A single nucleotide polymorphism in the Staphylococcus aureus virulence regulator SaeR abolishes pathogenesis,collected_by:Victor J. Torres,100,100,100,,,Good,2017-09-29T00:30:58.425Z,2017-09-29T00:30:58.425Z
4159,431946.3,Escherichia coli SE15,negative,Escherichia coli SE15,431946,Complete,SE15,,,,MLST.Escherichia_coli_1.131,,,,2009-12-14T00:00:00Z,20008064,PRJNA19053,,GCA_000010485.1,,"AP009378,AP009379","NC_013654.1,NC_013655.1",Kitasato Univ.,complete,"454, Sanger",,Phred/Phrap/Consed,1,1,2,4839683,50.7,4664,4488,Gut,,,,,,,,,,,"Human, Homo sapiens",,,,Gastrointestinal tract,,,,,-,Rod,Yes,,Mesophilic,-,Non-halophilic,Facultative,Host-associated,,Escherichia coli SE15.This strain is being sequenced for comparative genome analysis.,,99.9,99.1,100,,,Good,2014-12-08T22:11:34.531Z,2015-03-16T03:17:09.594Z
4161,431947.7,Porphyromonas gingivalis ATCC 33277,negative,Porphyromonas gingivalis ATCC 33277,431947,Complete,ATCC 33277,,,,MLST.Porphyromonas_gingivalis.96,,ATCC 33277,,2008-05-20T00:00:00Z,,PRJNA19051,,GCA_000010505.1,,AP009380,NC_010729,Kitasato Univ.,complete,Sanger,9.5x,Phred/Phrap,1,,1,2354886,48.4,2056,2090,Mouth,human gingiva is being sequenced for comparative genome analysis,isolated from human gingiva is being sequenced for comparative genome analysis,,,,,,,,,"Human, Homo sapiens",,,,Oral; Gingival crevices,,,,,-,Rod,No,No,Mesophilic,37,,Anaerobic,Host-associated,Periodontitis,Porphyromonas gingivalis ATCC 33277.This strain was isolated from human gingiva is being sequenced for comparative genome analysis.,,100,100,100,0.7,,Good,2014-12-08T22:12:32.996Z,2015-03-16T03:17:09.594Z
4162,434924.5,Coxiella burnetii CbuK_Q154,negative,Coxiella burnetii CbuK_Q154,434924,Complete,CbuK_Q154,,,,,,,,2008-11-06T00:00:00Z,19047403,PRJNA19139,,GCA_000019885.1,,"CP001020,CP001021","NC_011528,NC_011526","Rocky Mountain Laboratories|Integrated Genomics, Inc.",complete,,,,1,1,2,2102380,42.6,2147,1947,None,patient with endocarditis and contains the plasmid QpRS,isolated from a patient with endocarditis and contains the plasmid QpRS,,,,,,,,,"Human, Homo sapiens",,,endocarditis,,,,,,-,Coccobacillus,,,Mesophilic,-,,Facultative,Multiple,Q fever,Coxiella burnetii K Q154. Coxiella burnetii K Q154 was isolated from a patient with endocarditis and contains the plasmid QpRS. This strain is being sequenced for comparative genome analysis.,,99.9,99.1,100,,,Good,2014-12-08T22:11:04.643Z,2015-03-16T03:17:09.594Z
4189,439334.628,Mycobacterium avium subsp. hominissuis strain w14,positive,,439334,Complete,w14,,,,,,,,2021-10-04T00:00:00Z,33162087,PRJNA656902,SAMN15806906,GCA_020227575.1,,CP060407,,University of Wisconsin-Madison,,Illumina MiSeq,100x,SPAdes v. 3.14.1,1,,1,5098287,69.22348,4918,4755,Sputum,sputum,,,,USA,,,,,,Homo sapiens,,,Mycobacterium avium complex disease,,,,,,,,,,,,,,,,Genotypic analysis of NTM isolates from human and milk samples in Wisconsin,collected_by:Wisconsin state lab of hygiene (WSLH),98.8,97.5,,,,Good,2021-12-24T06:03:36.296Z,2021-12-24T06:03:36.296Z
4190,440524.124,"Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain L-3835",negative,,440524,Complete,L-3835,"4,[5],12:i:-",,,MLST.Salmonella_enterica.34,,,,2021-05-26T00:00:00Z,,PRJDB6430,SAMD00097512,GCA_019670145.1,,AP023288,,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",,Sequel; NextSeq500,123x,Canu v. 1.4; minimap v. 0.2-r124; racon v.,1,,1,4995025,52.146965,5035,4698,None,Homo sapiens,,2007,Japan,Japan,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) and the monophasic variant (Salmonella 4,[5],12:i:-) are the major cause of gastroenteritis for both humans and animals. Pulsed-field gel electrophoresis and multilocus variable-number tandem-repeat analysis have been used widely as subtyping methods of this pathogens in the molecular epidemiological analyses, however the results do not reflect the phylogenetic information precisely. In this study, we performed phylogenetic analysis of these serovars using whole-genome sequencing data and identified nine clades to be discriminated each other as genotypes.",,99.8,99.3,,,,Good,2021-08-26T17:53:33.377Z,2021-08-26T17:53:33.377Z
4191,441162.11,Burkholderia oklahomensis C6786,negative,,441162,Complete,C6786,,,,"MLST.Burkholderia_cepacia_complex.549,MLST.Burkholderia_pseudomallei.81",,,,2015-06-02T00:00:00Z,25931592,PRJNA238548,SAMN03075637,GCF_000959365.1,"SRR1614074,SRR1614082,SRR1614083","CP009555,CP009556","NZ_CP009555.1,NZ_CP009556.1",Los Alamos National Laboratory,,Illumina; PacBio; 454,687x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,2,,2,7135022,67.07,7365,6071,Wound,Pelvic Wound,,1973,USA,USA: Oklahoma,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,,,,,,,,Genome sequencing of Burkholderia oklahomensis C6786,,98.6,94.5,99.5,1.8,,Good,2016-01-17T15:50:18.449Z,2016-01-17T15:50:18.449Z
4193,443150.4,Mycobacterium tuberculosis CCDC5180,positive,Mycobacterium tuberculosis CCDC5180,443150,Complete,CCDC5180,,,,,,,,2011-07-05T00:00:00Z,21914894,PRJNA19583,,GCA_000270365.1,,CP001642,NC_017522.1,Beijing Genomics Institute,complete,,,,1,,1,4405981,65.59,4358,3591,Lung,patient with secondary pulmonary tuberculosis,isolated in 2004 from a patient with secondary pulmonary tuberculosis,2004,,,,,,,,"Human, Homo sapiens",,,secondary pulmonary tuberculosis,,,,,,+,Rod,No,No,Mesophilic,37,,Aerobic,Host-associated,Tuberculosis,"Mycobacterium tuberculosis CCDC 5180. This strain was isolated in 2004 from a patient with secondary pulmonary tuberculosis. Strain CCDC5180 is resistant to isoniazid, rifampicin, streptomycin and ethambutol. This strain is sequenced for comparative genomic studies.",,99.5,98.7,100,,,Good,2014-12-08T22:12:09.950Z,2015-03-16T03:17:09.594Z
4224,455434.6,Treponema pallidum subsp. pallidum SS14,negative,,455434,Complete,SS14,,,,MLST.Treponema_pallidum.19,,,,2013-12-11T00:00:00Z,24058545,PRJNA20067,SAMN00000318,GCF_000410555.1,"SRR000351,SRR029225",CP004011,,Baylor College of Medicine,,454 GS20; Illumina GA,37X; 68X,CLC Bio Workbench v.,1,,1,1139569,52.77,1032,975,None,patient with secondary syphilis,isolated in 1977 from a patient with secondary syphilis,1977,,,,,,,,"Human, Homo sapiens",,,secondary syphilis,,,,,,,Spirilla,No,,Mesophilic,,,Anaerobic,HostAssociated,Syphilis,"Treponema pallidum subsp. pallidum. This organism is the causative agent of endemic and venereal syphilis. This sexual transmitted disease was first discovered in Europe at the end of the fifteenth century, however, the causative agent was not identified until 1905. At one time syphilis was the third most commonly reported communicable disease in the USA. Syphilis is characterized by multiple clinical stages and long periods of latent, asymptomatic infection. Although effective therapies have been available since the introduction of penicillin, syphilis remains a global health problem. Treponema pallidum subsp. pallidum SS14. Treponema pallidum subsp. pallidum SS14 was isolated in 1977 from a patient with secondary syphilis. This strain is less susceptible than the Nichols strain for a number of antibiotics and will be used for comparative analysis.",,99.9,99.7,37.6,,Low CheckM completeness score,Poor,2016-01-17T15:30:53.224Z,2016-01-17T15:30:53.224Z
4270,469616.3,Fusobacterium mortiferum ATCC 9817,negative,,469616,Complete,ATCC 9817,,,,,,ATCC:9817,,2018-03-26T00:00:00Z,,PRJNA433545,SAMN08501148,GCA_003019315.1,,CP028102,,Virginia Tech,,"Illumina, MinION",43x,Unicycler v. 0.4.3,1,,1,2716766,29.288721,2664,2585,Stool,Peri-renal abscess,,,,,,,,,env_biome:terrestrial biome [ENVO:00000446],"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Complete Fusobacterium genomes generated by MinION and Illumina sequencing, followed by assembly with Unicycler.",,98.7,98.1,100,0.5,,Good,2018-07-15T14:46:24.852Z,2018-07-15T14:46:24.852Z
4271,469618.1,Fusobacterium varium ATCC 27725,negative,,469618,Complete,ATCC 27725,,,,,,ATCC:27725,,2018-03-26T00:00:00Z,,PRJNA433545,SAMN08501142,GCA_003019655.1,,"CP028103,CP028104",,Virginia Tech,,"Illumina, MinION",27x,Unicycler v. 0.4.3,1,1,2,3346458,29.345894,3144,3025,Stool,feces,,,,,,,,,env_biome:terrestrial biome [ENVO:00000446],"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Complete Fusobacterium genomes generated by MinION and Illumina sequencing, followed by assembly with Unicycler.",,99.8,99,100,,,Good,2018-05-31T00:25:40.615Z,2018-05-31T00:25:40.615Z
4527,471876.6,Streptococcus pyogenes NZ131,positive,Streptococcus pyogenes NZ131,471876,Complete,NZ131,serovar M49,,,,,,,2008-10-16T00:00:00Z,18820018,PRJNA20707,SAMN02604236,GCA_000018125.1,,CP000829,NC_011375,University of Oklahoma Health Sciences Center|University of Oklahoma's Advanced Center for Genome Technology,complete,,,,1,,1,1815785,38.6,1876,1700,None,patient with acute glomerulonephritis,isolated from a patient with acute glomerulonephritis,,,,,,,,,"Human, Homo sapiens",,,acute glomerulonephritis,,,,,,+,Coccus,No,No,Mesophilic,-,,Facultative,Host-associated,,Streptococcus pyogenes NZ131. This strain is a serotype M49 strain isolated from a patient with acute glomerulonephritis. This strain will be used for comparative analysis.,,99.9,99.7,100,1.7,,Good,2014-12-08T22:13:35.946Z,2015-03-16T03:17:09.594Z
4532,478434.4,Mycobacterium tuberculosis KZN 1435,positive,Mycobacterium tuberculosis KZN 1435,478434,Complete,KZN 1435,,,,,,,,2007-10-30T00:00:00Z,,PRJNA21055,,GCA_000023625.1,,CP001658,NC_012943,Broad Institute,complete,,,,1,,1,4398250,65.6,4388,4059,None,patient,"isolated from a patient in KwaZulu-Natal, South Africa",,South Africa,KwaZulu Natal South Africa,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,Yes,No,Mesophilic,37,,Aerobic,Host-associated,Tuberculosis,"Mycobacterium tuberculosis strain KZN 1435. M. tuberculosis strain KZN 1435 was isolated from a patient in KwaZulu-Natal, South Africa. This strain is multidrug-resistant (resistant to isoniazid and rifampin).",,99.9,99.4,100,2.1,,Good,2014-12-08T22:12:11.097Z,2015-03-16T03:17:09.594Z
4538,479437.5,Eggerthella lenta DSM 2243,positive,Eggerthella lenta DSM 2243,479437,Complete,DSM 2243,,,,,,DSM 2243,Yes,2009-04-21T00:00:00Z,21304654,PRJNA21093,SAMN00002594,GCA_000024265.1,"SRR017650,SRR017651,SRR017652",CP001726,NC_013204,US DOE Joint Genome Institute (JGI-PGF)|DOE Joint Genome Institute|JGI-PGF,complete,,,,1,,1,3632260,64.2,3212,3070,None,cases of bacteremia,isolated from cases of bacteremia,,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,No,No,Mesophilic,-,,Anaerobic,Host-associated,Bacteremia,"Eggerthella lenta DSM 2243. Eggerthella lenta DSM 2243, formerly Eubacterium lentum, is a normal member of human gastrointestinal flora. This organism has been isolated from cases of bacteremia. Eggerthella lenta DSM 2243 is the type strain and will be used for comparative analysis.",,99.8,99.8,100,,,Good,2014-12-08T22:11:09.961Z,2015-03-16T03:17:09.594Z
4551,480119.5,Acinetobacter baumannii AB0057,negative,Acinetobacter baumannii AB0057,480119,Complete,AB0057,,,,"MLST.Acinetobacter_baumannii_1.207,MLST.Acinetobacter_baumannii_2.1",oc locus:OCL3,,,2008-11-17T00:00:00Z,27458211,PRJNA21111,SAMN02603051,GCA_000021245.1,SRR1997868,"CP001182,CP001183","NC_011586,NC_011585","Case Western Reserve University|Case Western Reserve University, Department of Genetics, School of Medicine, USA, Cleveland",complete,,,,1,1,2,4059242,39.2,3770,3801,Blood,Blood,isolate from a bloodstream infection of a patient at Walter Reed Army Medical Center,2004,USA,Walter Reed Army Medical Center,,,,,,"Human, Homo sapiens",,,,,,,Resistant,AMR Panel,-,Pleomorphic rod,No,No,Mesophilic,-,,Aerobic,Multiple,Nosocomial infections,"Acinetobacter baumannii AB0057. Acinetobacter baumannii AB0057 is a multidrug-resistant isolate from a bloodstream infection of a patient at Walter Reed Army Medical Center.;A novel method of consensus panchromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii;Holt et al., Microbial Genomics, 2016.",,99.3,98.2,100,1,,Good,2014-12-08T22:09:31.953Z,2015-03-16T03:17:09.594Z
4552,482957.39,Burkholderia lata strain A05,negative,,482957,Complete,A05,,,,MLST.Burkholderia_cepacia_complex.103,,,,2018-11-05T00:00:00Z,,PRJNA419071,SAMN08042342,GCA_003711145.1,,"CP024943,CP024944,CP024945",,SAHMRI,,PacBio,1.0x,HGAP v. 3,3,,3,8787009,66.185,8913,8272,Blood,blood,,7-May-16,Australia,Australia: Adelaide,,,,,,"Human, Homo sapiens",,,cepacia syndrome,,,,,,,,,,,,,,,,Burkholderia lata strain A05 from Australasian sublineage,collected_by:SA Pathology,99,94.2,,,,Good,2018-11-29T08:55:52.518Z,2018-11-29T08:55:52.518Z
4631,486698.6,Mycobacterium riyadhense strain NTM,positive,,486698,Complete,NTM,,,,,,,,2021-02-11T00:00:00Z,,PRJNA558523,SAMN12495011,GCA_016864455.1,,CP045092,,King Faisal Specialist Hospital and Research Centre,,IonTorrent,64.0x,SPAdes v. 3.13.0,1,,1,6772223,65.10811,6779,,Lung,Lungs,,2018-10,Saudi Arabia,Saudi Arabia,,,,,,Homo sapiens,,,Tuberculosis,,,,,,,,,,,,,,,,NTM,collected_by:KFSHRC,98.5,94.3,,,,Good,2021-02-27T19:29:05.026Z,2021-02-27T19:29:05.026Z
4742,487215.4,Streptococcus pyogenes Alab49,positive,Streptococcus pyogenes Alab49,487215,Complete,Alab49,,,,MLST.Streptococcus_pyogenes.11,,,,2011-10-07T00:00:00Z,21949075,PRJNA162171,SAMN02603353,GCA_000230295.1,,CP003068.1,NC_017596.1,Institute for Genome Sciences,assembly,ABI 3730xl,,Celera Assembler,1,,1,1827308,38.58,1809,1773,None,impetigo lesion,,1986,USA,USA: Alabama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,Impetigo,Genome sequencing of a skin specialist strain of Streptococcus pyogenes.,,99.7,99.3,100,0.9,,Good,2014-12-08T22:13:35.569Z,2015-03-16T03:17:09.594Z
4743,487521.1,Mycobacterium intracellulare ATCC 13950,positive,,487521,Complete,ATCC 13950,,,,,,ATCC:13950,,2014-01-30T00:00:00Z,22535933,PRJNA82157,SAMN02603186,GCF_000277125.1,,CP003322,NC_016946.1,"Department of Microbiology and Immunology, Seoul National University",,,,,1,,1,5402402,68.1,5153,5144,None,"clinical isolates from a Korean pulmonary patient, male, 64 age, Asan medical center",,,South Korea,South Korea: Seoul,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,No,,,,,,,,"Whole genome sequence of Mycobacterium intracellulare Int-2 type, ATCC 13950.",,99.2,98.4,100,,,Good,2016-01-17T15:29:02.906Z,2016-01-17T15:29:02.906Z
4746,488446.5,Burkholderia latens strain AU17928,negative,,488446,Complete,AU17928,,,,MLST.Burkholderia_cepacia_complex.811,,,,2016-09-02T00:00:00Z,,PRJNA279182,SAMN03449404,GCF_001718795.1,SRR1956466,"CP013435,CP013438,CP013437,CP013436","NZ_CP013435.1,NZ_CP013438.1,NZ_CP013437.1,NZ_CP013436.1",Northern Arizona University,,PacBio,50x,HGAP v. 2.0,3,1,4,6614478,66.37,6541,5817,Respiratory,CF Maxillary Sinus,,2009,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequence analysis of diverse Burkholderia genomes,collected_by:UMich - John Lipuma,99.4,96.4,100,,,Good,2016-11-15T22:28:13.233Z,2016-11-15T22:28:13.233Z
4751,488447.265,Burkholderia contaminans strain SCAID TST1-2021 (11/270) strain SCAID TST1-2021 (11/270) strain SCAID TST1-2021 (11/270),negative,,488447,Complete,SCAID TST1-2021 (11/270),,,,MLST.Burkholderia_cepacia_complex.102,,,,2021-09-15T00:00:00Z,,PRJNA754843,SAMN20982457,GCA_019915365.1,,"CP082807,CP082808,CP082809,CP082810,CP082811,CP082812",,Scientific Center for Anti-infectious Drugs (SCAID),,PacBio Sequel,91x,Canu v. 2.0,3,3,6,8363142,66.25037,8297,7480,Respiratory,Swab from tracheostomic tube,,3/12/21,Kazakhstan,Kazakhstan: Almaty,,,,,,Homo sapiens,,,"Surgical Procedures, Operative",,,,Resistant;Susceptible,AMR Panel,,,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",98.4,92.3,,,,Good,2021-12-23T23:46:59.695Z,2021-12-23T23:46:59.695Z
4756,492670.328,Bacillus velezensis strain Bac57,positive,,492670,Complete,Bac57,,,,,,,,2018-10-21T00:00:00Z,,PRJNA412146,SAMN10146799,GCA_003667745.1,,"CP033054,CP033053",,King Abdullah University of Science and Technology,,PacBio,344X,Celera Assembler v. 2,1,1,2,4234898,45.866653,4379,,None,Red Sea lagoons-Mangrove Mud,"isolated from the Red Sea, specifically three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS) collected from Rabigh harbor lagoon (39°0′35",2012-04,Saudi Arabia,Saudi Arabia:Rabigh harbor lagoon,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"We sequenced genomes isolated from the Red Sea, specifically three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS) collected from Rabigh harbor lagoon (39°0′35.762′′ E, 22°45′5.582′′ N) and Al-Kharrar lagoon (38°54′39.638′′ E, 22°54′50.251′′ N) in Saudi Arabia. MN mud was sampled from the coastal lagoon of the Red Sea alongside mangrove tree. MM was sampled approximately 7.5 m away from the coastal lagoon. BS refers to sediments with no contact with lagoon water at high tide.",sample_type:cell culture,99.3,98.2,,,,Good,2018-11-29T02:50:53.130Z,2018-11-29T02:50:53.130Z
4759,498388.3,Escherichia coli C strain C,negative,,498388,Complete,C,,,,"MLST.Escherichia_coli_1.1721,MLST.Escherichia_coli_2.687",,,,2017-04-05T00:00:00Z,,PRJNA380607,SAMN06645125,,,CP020543,,Drexel University College of Medicine,,PacBio,184.0x,HGAP Assembly v. 2,1,,1,4617024,50.96,4665,4581,None,,,4/1/16,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,The last laboratory strain of E. coli to be sequnced. E. coli C is a long time laboratory strain used for phage studies. Recent data shows that it forms much better biofilm than other strains and can be used as a model organism in bacterial biofilm studies.,sample_type:bacterial culture,99.9,99.3,100,0.4,,Good,2017-05-28T07:37:09.600Z,2017-05-28T07:37:09.600Z
4765,511145.616,Escherichia coli str. K-12 substr. MG1655,negative,,511145,Complete,K-12,,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.262",,,,2017-12-17T00:00:00Z,,PRJNA421841,SAMN08158212,GCA_002843685.1,,CP025268,,Harvard Medical School,,Illumina HiSeq,69.0x,Velvet v. 2017-06-01,1,,1,4643559,50.76,4790,4687,None,,"derived strains, including the mutation to rph which causes pyrimidine starvation in minimal media, were corrected or compensated for",1/15/17,USA,USA: Boston,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"C321.deltaA was adapted over ~1,100 generations to fast growth in M9 minimal media supplemented with 1% glucose. In so doing, many off-target mutations leftover from the original recoding efforts were corrected as either direct reversions, or more often compensatory adaptive mutations. Additionally, mutations known to be endemic to all MG1655-derived strains, including the mutation to rph which causes pyrimidine starvation in minimal media, were corrected or compensated for. We present here the genome of a recoded C321 strain with no TAG codons adapted for fast growth in M9 and other defined media.",sample_type:cell culture,99.8,99.3,99.8,,,Good,2018-01-01T06:16:22.817Z,2018-01-01T06:16:22.817Z
4767,515619.6,Eubacterium rectale ATCC 33656,positive,Eubacterium rectale ATCC 33656,515619,Complete,ATCC 33656,,,,,,ATCC 33656,Yes,2009-06-04T00:00:00Z,19321416,PRJNA29071,SAMN02603082,GCA_000020605.1,,CP001107,NC_012781,"Center for Genome Sciences, Washington University School of Medicine|Laboratory of Jeffrey I. Gordon|Washington University Genome Sequencing Center",complete,,,,1,,1,3449685,41.5,3194,3621,Stool,human feces,isolated from human feces,,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,,No,,-,,Anaerobic,,,Eubacterium rectale ATCC 33656. Eubacterium rectale ATCC 33656 was isolated from human feces. This is the type strain and will be used for comparative analysis with other human gut bacteria.,,99.9,99.9,100,3.2,,Good,2014-12-08T22:11:37.208Z,2015-03-16T03:17:09.594Z
4768,515621.3,Clostridium botulinum Ba4 str. 657,positive,Clostridium botulinum Ba4 str. 657,515621,Complete,str. 657,,,,MLST.Clostridium_botulinum.7,,,,2009-05-01T00:00:00Z,18060065,PRJNA29077,SAMN02603539,GCA_000020345.1,,"CP001083,CP001082,CP001081","NC_012658,NC_012657,NC_012654",Los Alamos National Laboratory|DOE Joint Genome Institute|The J. Craig Venter Institute,complete,,,,1,2,3,4257769,28,4106,4097,None,infant botulism case,isolated from an infant botulism case in 1976,1976,,,,,,,,"Human, Homo sapiens",,infant,,,,,,,_,Rod,Yes,Yes,Mesophilic,37,,Anaerobic,Multiple,,"Clostridium botulinum Ba4 str. 657. Clostridium botulinum Ba4 str. 657 was isolated from an infant botulism case in 1976. The strain is a bivalent Ba strain, that simultaneously produces two different toxin types and will be used for comparative analysis with other Clostridium botulinum strains.",,99.5,98.8,100,,,Good,2014-12-08T22:10:56.919Z,2015-03-16T03:17:09.594Z
4862,519441.6,Streptobacillus moniliformis DSM 12112,negative,Streptobacillus moniliformis DSM 12112,519441,Complete,DSM 12112,,,,,,DSM 12112,,2009-05-08T00:00:00Z,21304670,PRJNA29309,SAMN00002603,GCA_000024565.1,"SRR017785,SRR017786,SRR017787,SRR017788","CP001779,CP001780","NC_013515,NC_013516",US DOE Joint Genome Institute (JGI-PGF)|DOE Joint Genome Institute|JGI-PGF,complete,,,,1,1,2,1673280,26.3,1509,1442,Wound,case of rat bite fever,isolated from a case of rat bite fever and will provide information on the pathogenicity and virulence mechanisms of this organism,,,,,,,,,"Human, Homo sapiens",,,rat bite fever,,,,,,-,Pleomorphic rod,No,No,Mesophilic,-,,Microaerophilic,Host-associated,Rat bite fever,Streptobacillus moniliformis DSM 12112. Streptobacillus moniliformis DSM 12112 was isolated from a case of rat bite fever and will provide information on the pathogenicity and virulence mechanisms of this organism.,,99.9,99.9,100,2.5,,Good,2014-12-08T22:13:26.999Z,2015-03-16T03:17:09.594Z
5405,521006.8,Neisseria gonorrhoeae NCCP11945,negative,Neisseria gonorrhoeae NCCP11945,521006,Complete,NCCP11945,,,,,,,,2008-07-09T00:00:00Z,18586945,PRJNA29335,SAMN02603475,GCA_000020105.1,,"CP001050,CP001051","NC_011035,NC_011034",Korea Centers for Disease Control and Prevention|Genotech corp.,complete,,,,1,1,2,2236178,52.4,2871,2674,Vagina,vaginal smear of a Korean patient,isolated in 2002 from a vaginal smear of a Korean patient,2002,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Coccus,,,Mesophilic,35-37,,Aerobic,Host-associated,Gonorrhea,"Neisseria gonorrhoeae NCCP11945. Neisseria gonorrhoeae NCCP11945 was isolated in 2002 from a vaginal smear of a Korean patient. This is a multidrug-resistant strain and will be used to understand the prevalence, antibiotic resistance, and importance of horizontal gene transfer within this important, naturally competent organism.",,97.1,96.2,89.8,1.3,,Good,2014-12-08T22:12:24.910Z,2015-03-16T03:17:09.594Z
5406,521097.5,Capnocytophaga ochracea DSM 7271,negative,Capnocytophaga ochracea DSM 7271,521097,Complete,DSM 7271,,,,,,DSM 7271,Yes,2009-04-30T00:00:00Z,21304645,PRJNA29403,SAMN00001911,GCA_000023285.1,"SRR013476,SRR013477",CP001632,NC_013162,US DOE Joint Genome Institute (JGI-PGF)|DOE Joint Genome Institute|JGI-PGF,complete,,,,1,,1,2612925,39.6,2172,2171,Mouth,the human oral cavity,isolated from the human oral cavity,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,No,Mesophilic,35-37,,Facultative,Host-associated,,"Capnocytophaga ochracea DSM 7271.  Capnocytophaga ochracea DSM 7271 was isolated from the human oral cavity. This organism causes periodontal disease and can also be an opportunistic pathogens, causing septicemia, peritonitis, endocarditis and conjunctivitis in susceptible patients. Capnocytophaga ochracea DSM 7271 is the type strain and will be sequenced for comparative analysis.",,99.9,99.9,100,,,Good,2014-12-08T22:10:51.207Z,2015-03-16T03:17:09.594Z
5408,523796.83,Staphylococcus aureus subsp. aureus ST398 strain 2012-3,positive,,523796,Complete,2012-3,,,,MLST.Staphylococcus_aureus.398,,,,2021-11-16T00:00:00Z,,PRJNA385005,SAMN06856373,GCA_020881895.1,,CP021178,,Renji Hospital,,Illumina,357.8,HGAP v. 3.0,1,,1,2715600,32.95684,2682,2689,None,,,2012-03,China,China: Shanghai,,,,,,Homo sapiens,,,fatal sepsis,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,,The first CA-MRSA ST398 genome isolated from human without livestock contact and harboring prophage 3,collected_by:Min Li,100,99.9,,,,Good,2021-12-24T23:08:58.472Z,2021-12-24T23:08:58.472Z
5409,525283.9,Fusobacterium nucleatum subsp. nucleatum ATCC 23726,negative,,525283,Complete,ATCC 23726,,,,,,ATCC:23726,,2018-03-26T00:00:00Z,,PRJNA433545,SAMN08501025,GCA_003019785.1,,CP028109,,Virginia Tech,,"Illumina, MinION",35x,Unicycler v. 0.4.3,1,,1,2299539,27.180925,2175,2112,Vagina,Urogentical Tract,,,,,,,,,env_biome:terrestrial biome [ENVO:00000446],"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Complete Fusobacterium genomes generated by MinION and Illumina sequencing, followed by assembly with Unicycler.",,99.8,99.5,100,,,Good,2018-05-31T00:23:51.777Z,2018-05-31T00:23:51.777Z
5410,525284.18,Gardnerella vaginalis ATCC 14019,negative,Gardnerella vaginalis ATCC 14019,525284,Complete,ATCC 14019,,,,,,ATCC 14019,,2009-02-12T00:00:00Z,20865041,PRJNA31473,SAMN00001462,GCA_000159155.2,"SRR010961,SRR010962,SRR088870",CP002104,NC_014644,"Baylor College of Medicine|Baylor College of Medicine, Human Genome Sequencing Center, USA, Houston",complete,"454-GS-FLX, 454-Paired-end",88.88x,Newbler/1.1.03.24,1,,1,1667350,41.5,1345,1365,None,,,,,,,,,,,"Human, Homo sapiens",,,,Urogenital tract; Vaginal,,,,,+,Rod,,,Mesophilic,-,,Anaerobic,Host-associated,Bacterial vaginosis,Gardnerella vaginalis ATCC 14019.A reference genome for the Human Microbiome Project.,,99,98.4,100,1.8,,Good,2014-12-08T22:11:40.301Z,2015-03-16T03:17:09.594Z
5411,525381.4,Streptococcus pneumoniae TCH8431/19A,positive,Streptococcus pneumoniae TCH8431/19A,525381,Complete,TCH8431/19A,,,,,,BEI HM-145,,2009-03-18T00:00:00Z,,PRJNA34659,SAMN00002223,GCA_000196595.1,"SRR014817,SRR014818",CP001993,NC_014251,Baylor College of Medicine,complete,"454-GS-FLX, Sanger",89.09x,Newbler v. 1.1.03.24,1,,1,2088772,40.2,2255,2275,Lung,,Lung,,,,,,,,,"Human, Homo sapiens",,,,Airways; Respiratory tract,,,,,+,Coccus,No,No,Mesophilic,-,,Facultative,,,Streptococcus pneumoniae TCH8431/19A.This strain will be sequenced for comparative genome analysis.,,99.6,99.1,100,0.5,,Good,2014-12-08T22:13:35.361Z,2015-03-16T03:17:09.594Z
5413,529507.6,Proteus mirabilis HI4320,negative,Proteus mirabilis HI4320,529507,Complete,HI4320,,,,,,,,2008-04-03T00:00:00Z,18375554,PRJNA12624,SAMEA1705945,GCA_000069965.1,,"AM942759,AM942760","NC_010554,NC_010555",Wellcome Trust Sanger Institute,complete,,,,1,1,2,4099895,38.9,3685,3662,Urine,human urinary tract,Proteus mirabilis is a tetracycline resistant human urinary tract isolate.,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,No,Mesophilic,37,Non-halophilic,Aerobic,Host-associated,Encephalitis;Urinary tract infection;Pyelonephritis;Pneumonia;Septicemia,Proteus mirabilis HI4320. Proteus mirabilis is a tetracycline resistant human urinary tract isolate.,,98.7,97.9,100,,,Good,2014-12-08T22:12:35.516Z,2015-03-16T03:17:09.594Z
5422,536232.3,Clostridium botulinum A2 str. Kyoto,positive,Clostridium botulinum A2 str. Kyoto,536232,Complete,Kyoto,,,,MLST.Clostridium_botulinum.2,,,,2009-04-15T00:00:00Z,,PRJNA29859,SAMN02603540,GCA_000022765.1,,CP001581,NC_012563,Los Alamos National Laboratory|DOE Joint Genome Institute|The J. Craig Venter Institute,complete,,,,1,,1,4155278,28.2,3903,3878,None,case of infant botulism,"isolated from a case of infant botulism in Kyoto, Japan in 1978 and will be use for comparative analysis with other C. botulinum strains",1978,Japan,Kyoto Japan,,,,,,"Human, Homo sapiens",,infant,,,,,,,+,Rod,Yes,Yes,Mesophilic,37,,Anaerobic,Multiple,Botulism,"Clostridium botulinum A2 Kyoto. This strain was isolated from a case of infant botulism in Kyoto, Japan in 1978 and will be use for comparative analysis with other C. botulinum strains.",,100,99.5,100,,,Good,2014-12-08T22:10:56.836Z,2015-03-16T03:17:09.594Z
5477,546272.3,Brucella melitensis ATCC 23457,negative,Brucella melitensis ATCC 23457,546272,Complete,ATCC 23457,,,,,,ATCC 23457,,2009-03-25T00:00:00Z,,PRJNA30561,SAMN02604296,GCA_000022625.1,,"CP001488,CP001489","NC_012441,NC_012442",Virginia Bioinformatics Institute|Los Alomos National Labs/Joint Genome Institute,complete,,,,2,,2,3311219,57.2,3486,3136,Blood,human blood and bone marrow samples,obtained from human blood and bone marrow samples,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Coccobacillus,,,Mesophilic,-,,Facultative,Host-associated,Brucellosis,Brucella melitensis ATCC 23457.Brucella melitensis ATCC 23457 (isolate 84) was obtained from human blood and bone marrow samples and will be used for comparative analysis.,,99.9,99.3,100,,,Good,2014-12-08T22:10:39.051Z,2015-03-16T03:17:09.594Z
5478,547048.4,Yersinia pestis biovar Medievalis str. Harbin 35,negative,Yersinia pestis biovar Medievalis str. Harbin 35,547048,Complete,Harbin 35,Medievalis,,,MLST.Yersinia_spp.79,,,,2011-01-25T00:00:00Z,,PRJNA30505,SAMN02603222,GCA_000186725.1,,"CP001608.1,CP001611.1,CP001609.1,CP001610.1","NC_017265.1,NC_017263.1,NC_017266.1,NC_017264.1",Los Alamos National Lab,complete,Sanger,,,1,3,4,4709501,48,4996,,None,human isolate from China,,,China,China,,,,,,"Human, Homo sapiens",,,,,,,,,,Rod-shaped,Motile,Nonsporulating,Mesophile,,,Facultative,Host,Bubonic plague;Pneumonic plague,"Animal Pathogen, Human Pathogen, Medical, Biothreat",,99.9,97.9,100,0.3,,Good,2014-12-08T22:13:51.962Z,2015-03-16T03:17:09.594Z
5529,553174.6,Prevotella melaninogenica ATCC 25845,negative,Prevotella melaninogenica ATCC 25845,553174,Complete,ATCC 25845,,,,,,ATCC 25845,,2009-07-08T00:00:00Z,,PRJNA31383,SAMN00001916,GCA_000144405.1,SRR013508,"CP002122,CP002123","NC_014370,NC_014371",J. Craig Venter Institute,complete,454,136x,,2,,2,3168282,41,2385,2296,Mouth,,,,,,,,,,,"Human, Homo sapiens",,,,Oral,,,,,,,,,,-,,,,,Prevotella melaninogenica ATCC 25845.A reference genome for the Human Microbiome Project.,,98.4,98.1,98.7,,,Good,2014-12-08T22:12:33.450Z,2015-03-16T03:17:09.594Z
5530,553190.4,Gardnerella vaginalis 409-05,negative,Gardnerella vaginalis 409-05,553190,Complete,409-05,,,,,,BEI HM-295,,2010-01-07T00:00:00Z,,PRJNA31001,SAMN02299422,GCA_000025205.1,,CP001849,NC_013721,J. Craig Venter Institute,complete,454,34x,CA 5.1,1,,1,1617545,42,1190,1258,Vagina,,,,,,,,,,,"Human, Homo sapiens",,,,Urogenital tract; Vaginal,,,,,,,,,,-,,Anaerobic,,,Gardnerella vaginalis  409-05.This strain is being sequenced as a reference for the Human Microbiome project (HMP).,,99.8,99.8,100,,,Good,2014-12-08T22:11:40.212Z,2015-03-16T03:17:09.594Z
5531,553199.9,Propionibacterium acnes SK137,positive,Propionibacterium acnes SK137,553199,Complete,SK137,,,,MLST.Propionibacterium_acnes.18,,BEI HM-122,,2008-11-21T00:00:00Z,,PRJNA31005,SAMN00000718,GCA_000025765.1,SRR005146,CP001977,NC_014039,J. Craig Venter Institute,complete,454-GS-FLX,22.4x,Newbler 1.1.03.24-64-7,1,,1,2495334,60.1,2383,2352,Skin,,"Acne vulgaris, folliculitis, sarcoidosis, system infection and endocarditis, postoperative infections",,,,,,,,,"Human, Homo sapiens",,,,Skin,,,,,+,Rod,No,No,Mesophilic,-,,Anaerobic,,,Propionibacterium acnes  SK137.  This strain is being sequenced as a reference for the Human Microbiome Project (HMP).,,99.5,98.6,100,,,Good,2014-12-08T22:12:34.999Z,2015-03-16T03:17:09.594Z
5532,557600.4,Acinetobacter baumannii AB307-0294,negative,Acinetobacter baumannii AB307-0294,557600,Complete,AB307-0294,,,,MLST.Acinetobacter_baumannii_2.1,,,,2008-11-24T00:00:00Z,18931120,PRJNA30993,SAMN02603889,GCA_000021145.1,,CP001172,NC_011595,"SUNY-Buffalo-CoE|Infectious Disease and Genomics, Center of  Excellence (CoE) in Bioinformatics and Life Sciences",complete,,,,1,,1,3760981,39,3409,3451,Blood,Blood,"isolated from the blood of a hospitalized patient in Buffalo, NY",1994,USA,USA: Buffalo NY,,,,,,"Human, Homo sapiens",,,,,,,,,-,Pleomorphic rod,,,Mesophilic,-,,Aerobic,Multiple,Nosocomial infections,"Acinetobacter baumannii AB307-0294. Acinetobacter baumannii AB307-0294 was isolated from the blood of a hospitalized patient in Buffalo, NY. This is a multi-drug resistant strain and will be used for comparative analysis.",,99.3,98.5,100,1.5,,Good,2014-12-08T22:09:32.203Z,2015-03-16T03:17:09.594Z
5533,561275.19,Mycobacterium bovis BCG str. Tokyo 172,positive,,561275,Complete,Tokyo 172,,,,,,,,2016-03-07T00:00:00Z,,PRJNA313242,SAMN04517448,GCF_001580385.1,,CP014566,NZ_CP014566.1,Thai Red Cross Society,,Illumina,766x,Illumina Reads v. Hiseq,1,,1,4371707,65.65,4291,4025,Lung,subculture of Mycobacterium bovis BCG str. Tokyo 172,,1988,Thailand,Thailand,,,,,,"Human, Homo sapiens",,,Tuberculosis,,,,,,,,,,,C,,,,,Mycobacterium bovis BCG,collected_by:Queen Saovabha Memorial Institute,99.8,99,100,,,Good,2016-03-18T11:15:55.054Z,2016-03-18T11:15:55.054Z
6278,562971.11,Achromobacter xylosoxidans C54,negative,,562971,Complete,C54,,,,MLST.Achromobacter_spp.7,,BEI<USA>:HM-235D,,2014-09-26T00:00:00Z,,PRJNA260837,SAMN03067439,GCF_000758265.1,,CP009448,NZ_CP009448.1,BEI Resources/American Type,,Illumina,51.1,CLC Genomics Workbench v. 7.0.2,1,,1,6131060,67.99,5668,5281,Sputum,non-cystic fibrosis bronchiectasis sputum,,6-Feb,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Phylogenetic analysis of bacterial species using whole genome sequences,,98,95,100,,,Good,2016-01-17T15:40:16.972Z,2016-01-17T15:40:16.972Z
6281,568813.3,Streptococcus suis SC84,positive,Streptococcus suis SC84,568813,Complete,SC84,,,,MLST.Streptococcus_suis.7,,,,2009-07-07T00:00:00Z,,PRJNA32239,SAMEA2272312,GCA_000026725.1,,FM252031,NC_012924,Sanger Institute|The Wellcome Trust Sanger Institute,complete,,,,1,,1,2095898,41.1,1987,1898,None,clinical isolate,Streptococcus suis SC84 is a human clinical isolate,,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,-,,Facultative,Multiple,Meningitis;Arthritis;Pneumonia,Streptococcus suis SC84. Streptococcus suis SC84 is a human clinical isolate and will be used for comparative analysis with other S. suis strains.,,99.6,99.6,100,,,Good,2014-12-08T22:13:37.617Z,2015-03-16T03:17:09.594Z
6282,568814.3,Streptococcus suis BM407,positive,Streptococcus suis BM407,568814,Complete,BM407,,,,MLST.Streptococcus_suis.1,,,,2009-07-07T00:00:00Z,19603075,PRJNA32237,SAMEA2272697,GCA_000026745.1,,"FM252032,FM252033","NC_012926,NC_012923",The Wellcome Trust Sanger Institute,complete,,,,1,1,2,2170808,41,2064,1947,None,clinical isolate,Streptococcus suis BM407 is a human clinical isolate,,,,,,,,,"Human, Homo sapiens",,,,,,,,,+,Coccus,No,No,Mesophilic,-,,Facultative,Multiple,Meningitis;Arthritis;Pneumonia,Streptococcus suis BM407. Streptococcus suis BM407 is a human clinical isolate and will be used for comparative analysis with other S. suis strains.,,99.6,99.5,100,,,Good,2014-12-08T22:13:37.441Z,2015-03-16T03:17:09.594Z
6286,569579.3,Escherichia coli NU14 strain NU14,negative,,569579,Complete,NU14,,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,,,2017-03-10T00:00:00Z,,PRJNA373796,SAMN06314223,GCF_002024865.1,,CP019777,NZ_CP019777.1,National University of Singapore and Genome Institute of Singapore,,PacBio,300.0x,HGAP3 v. 3,1,,1,5076615,50.59,5206,5102,Urine,Urine,,1986,USA,United States,,,,,,"Human, Homo sapiens",female,,Urinary tract infection,,,,,,,,,,,,,,,,Sequencing of uropathogenic E. coli strain NU14,"collected_by:Scott J. Hultgren, William R. Schwan, Anthony J. Schaeffer, James L. Duncan",99.9,99.3,100,,,Good,2017-03-20T09:03:42.395Z,2017-03-20T09:03:42.395Z
6287,570508.6,Helicobacter pylori P12,negative,Helicobacter pylori P12,570508,Complete,P12,,,,MLST.Helicobacter_pylori.3024,,,,2008-10-30T00:00:00Z,20478826,PRJNA32291,SAMN02603595,GCA_000021465.1,,"CP001217,CP001218","NC_011498,NC_011499","Max von Pettenkofer-Institut f????r Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universit????t M????nchen|Institut f????r Informatik, LFE Bioinformatik, Ludwig-Maximilians-Universit????t M????nchen",complete,,,,1,1,2,1684038,38.8,1685,1579,Stomach,patient with duodenal ulcer,isolate obtained from a patient with duodenal ulcer,,,,,,,,,"Human, Homo sapiens",,,duodenal ulcer,,,,,,-,Spiral,Yes,No,Mesophilic,-,,Microaerophilic,Host-associated,Gastritis;Peptic ulcer disease,Helicobacter pylori P12. Helicobacter pylori P12 is a clinical isolate obtained from a patient with duodenal ulcer. This organism will be used for comparative analysis.,,99.8,99.6,99.1,0.6,,Good,2014-12-08T22:11:45.260Z,2015-03-16T03:17:09.594Z
6319,572264.18,Bacillus cereus 03BB102,positive,,572264,Complete,03BB102,,,,MLST.Bacillus_cereus.11,,,,2015-05-28T00:00:00Z,25931591,PRJNA236041,SAMN03010434,GCF_000832405.1,"SRR2171418,SRR2171420","CP009318,CP009317","NZ_CP009318.1,NZ_CP009317.1",Los Alamos National Laboratory,,Illumina; 454,332x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,1,1,2,5448107,35.33,5690,5495,Blood,Human blood,,2003,USA,USA: Texas: San Antonio,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,,,,,,,,Genome sequencing of Bacillus cereus 03BB102,,99.6,98.4,100,0.7,,Good,2016-01-17T15:43:20.362Z,2016-01-17T15:43:20.362Z
6999,574093.3,Streptococcus pneumoniae AP200,positive,Streptococcus pneumoniae AP200,574093,Complete,AP200,,,,MLST.Streptococcus_pneumoniae.62,,,,2010-09-07T00:00:00Z,18070957,PRJNA32641,SAMN02603428,GCA_000146975.1,,CP002121,NC_014494,"Istituto di Teconologie Biomediche, Consiglio Nazionale delle Ricerche|Istituto Superiore di Sanit????|Istituto di Teconologie Biomediche, Consiglio Nazionale delle Ricerche, Italia|Universit???? di Siena",complete,,,,1,,1,2130580,39.51,2366,2216,Cerebrospinal Fluid,the cerebrospinal fluid of a patient with meningitis,isolate from the cerebrospinal fluid of a patient with meningitis in Italy in 2003,2003,Italy,Italy,,,,,,"Human, Homo sapiens",,,meningitis,,,,,,+,Coccus,No,No,Mesophilic,-,,Facultative,Host-associated,Pneumonia,Streptococcus pneumoniae AP200 . This strain is a clinical isolate from the cerebrospinal fluid of a patient with meningitis in Italy in 2003.,,99.6,99,100,1,,Good,2014-12-08T22:13:33.190Z,2015-03-16T03:17:09.594Z
7000,574521.7,Escherichia coli O127:H6 str. E2348/69,negative,Escherichia coli O127:H6 str. E2348/69,574521,Complete,E2348/69,,,EHEC,"MLST.Escherichia_coli_1.15,MLST.Escherichia_coli_2.491",,,,2008-11-26T00:00:00Z,,PRJNA32571,SAMEA1705959,GCA_000026545.1,,"FM180568,FM180569,FM180570","NC_011601,NC_011603,NC_011602",Wellcome Trust Sanger Institute,complete,,,,1,2,3,5069678,50.5,4903,4653,None,outbreak,"isolated in Taunton, United Kingdom, in 1969 during an outbreak of infantile diarrhea",1969,United Kingdom,United Kingdom: Taunton,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,No,Mesophilic,37,,Facultative,Host-associated,,"Escherichia coli O127:H6 E2348/69. Enteropathogenic Escherichia coli (EPEC) is an important cause of fatal infant diarrhea. EPEC induces diarrhea by attaching and effacing to host cells in the small intestine, inducing cytoskeletal rearrangements that result in pedastel formation, and then by introducing toxins into the host cell. Important virulence functions such as the type III secretion system are encoded by the locus of enterocyte effacement. Escherichia coli 0127:H6 E2348/69 is an enteropathogenic E. coli strain to be used for comparative studies with related Escherichia and Shigella species.",,99.6,98.4,99.6,,,Good,2014-12-08T22:11:32.187Z,2015-03-16T03:17:09.594Z
7001,575584.58,Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841,negative,,575584,Complete,ATCC 19606,,,,MLST.Acinetobacter_baumannii_2.52,,ATCC:19606,,2021-07-23T00:00:00Z,,PRJNA637288,SAMN15099408,GCA_019331655.1,,"CP058289,CP058290,CP058291",,Roma Tre University,,Illumina MiSeq and MinION,426x,SPAdes v. 3.13,1,2,3,3944918,39.162514,3723,3642,Urine,Urine,,10/2/14,Italy,Italy,,,,,,Homo sapiens,,,,,,,Susceptible,Computational Prediction,,,,,,,,,,,Diversity among Acinetobacter baumannii ATCC 19606T laboratory strains inferred from whole genome sequences,,99.5,99,,,,Good,2021-08-01T21:22:12.017Z,2021-08-01T21:22:12.017Z
7006,577675.3,Escherichia coli O91:H21 strain FWSEC0008,negative,,577675,Complete,FWSEC0008,O91:H21,,,MLST.Escherichia_coli_1.442,,,,2019-05-03T00:00:00Z,,PRJNA287560,SAMN08768109,GCA_005037775.2,,NFGY01000000,,National Microbiology Laboratory,,Illumina MiSeq;Oxford Nanopore MinION,98.41x;82.67x,Unicycler;Canu v. 0.4.4.0;1.7,1,1,2,5093580,50.856236,5289,5198,None,Clinical: Human (Homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",1989,Germany,Germany,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,Mesophilic,37 C,,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:Laboratory for Foodborne Zoonoses: Public Health Agency of Canada,100,99.3,,,,Good,2019-07-14T19:18:53.882Z,2019-07-14T19:18:53.882Z
7068,585054.5,Escherichia fergusonii ATCC 35469,negative,Escherichia fergusonii ATCC 35469,585054,Complete,ATCC 35469,,,,MLST.Escherichia_coli_1.5298,,ATCC 35469,,2008-12-18T00:00:00Z,19165319,PRJNA33369,SAMEA3138228,GCA_000026225.1,,"CU928158,CU928144","NC_011740,NC_011743",Genoscope,complete,,,,1,1,2,4643861,49.9,4373,4321,Stool,human feces,isolated from human feces and will be used for comparative analysis with other Escherichia species,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,No,Mesophilic,-,,Facultative,Multiple,Urinary tract infection (UTI);Bacteremia,Escherichia fergusonii ATCC 35469. Escherichia fergusonii ATCC 35469 was isolated from human feces and will be used for comparative analysis with other Escherichia species.,,99.1,98,95.9,1.5,,Good,2014-12-08T22:11:36.843Z,2015-03-16T03:17:09.594Z
7069,585055.56,Escherichia coli 55989,negative,,585055,Complete,55989,,,,MLST.Escherichia_coli_1.131,,,,2018-04-02T00:00:00Z,,PRJNA389368,SAMN07196158,GCA_003028695.1,,CP028304,,Rehman Medical Institute,,Illumina MiSeq,30X,SPAdes v. 3.10.1,1,,1,4989876,50.786613,4966,,Urine,urine,,6-Dec-16,Pakistan,"Pakistan: Sheikh Zaid Hospital, Lahore",,,,,,"Human, Homo sapiens",,,Urinary tract infection,,,,,,,,,,,,,,,,"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","collected_by:Asma Manzoor, Nabila Ishaq",99.9,98.3,100,,,Good,2018-05-30T23:17:51.825Z,2018-05-30T23:17:51.825Z
7070,585538.3,Helicobacter pylori 83,negative,Helicobacter pylori 83,585538,Complete,83,,,,MLST.Helicobacter_pylori.3034,,BEI HM-273,,2011-05-11T00:00:00Z,,PRJNA34609,SAMN00189522,GCA_000213135.1,"SRR090119,SRR090120",CP002605,NC_017375.1,Baylor College of Medicine,complete,454,38.3x,Newbler v. 2.0.0-Eclipse,1,,1,1617426,38.72,1644,1609,Stomach,,,,,,,,,,,"Human, Homo sapiens",,,,Gastrointestinal tract; Stomach,,,,,-,Spiral,Yes,No,Mesophilic,37,,Aerobic,,Gastritis;Peptic ulcer disease,Helicobacter pylori 83.Reference genome for the Human Microbiome Project,,99.5,99.1,100,0.9,,Good,2014-12-08T22:11:43.368Z,2015-03-16T03:17:09.594Z
7091,591946.4,Escherichia coli LF82,negative,Escherichia coli LF82,591946,Complete,LF82,,,AIEC,"MLST.Escherichia_coli_1.135,MLST.Escherichia_coli_2.64",,,,2009-01-27T00:00:00Z,,PRJNA33825,SAMEA3138414,GCA_000284495.1,,CU651637,NC_011993.1,Genoscope,complete,,,,1,,1,4773108,50.7,4555,4376,Stool,patient with Crohn's disease,isolated from a patient with Crohn's disease,,,,,,,,,"Human, Homo sapiens",,,Crohn's disease,,,,,,-,Rod,Yes,No,Mesophilic,-,,Facultative,Multiple,Enterocolitis,Escherichia coli LF82. Escherichia coli LF82 is an adherent-invasive E. coli (AIEC) strain isolated from a patient with Crohn's disease. AIEC strains adhere and colonize the intestinal mucosa and are able to invade and replicate in intestinal epithelial cells. This strain will be used for comparative analysis with other E. coli strains.,,99.9,99.1,100,,,Good,2014-12-08T22:11:30.332Z,2015-03-16T03:17:09.594Z
7098,592021.13,Bacillus anthracis str. A0248,positive,Bacillus anthracis str. A0248,592021,Complete,,,,,MLST.Bacillus_cereus.1,,,,2009-05-01T00:00:00Z,,PRJNA33543,SAMN02603932,GCA_000022865.1,,"CP001598,CP001599,CP001597","NC_012659,NC_012656,NC_012655",The J. Craig Venter Institute,complete,,,,1,2,3,5503926,35.2,6007,5291,None,,"isolated from USAMRIID, Ohio",,USA,Ohio,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,Yes,Yes,Mesophilic,-,,Facultative,Multiple,Anthrax,"Bacillus anthracis strain A0248. This strain (96-10355; K1256) is a human isolated from USAMRIID, Ohio.",,100,99.4,100,,,Good,2014-12-08T22:10:11.925Z,2015-03-16T03:17:09.594Z
7263,645462.3,Clostridium difficile CD196,positive,Clostridium difficile CD196,645462,Complete,CD196,,,,MLST.Clostridium_difficile.1,,,,2009-10-01T00:00:00Z,19781061,PRJNA38037,,GCA_000085225.1,,FN538970,NC_013315,Wellcome Trust Sanger Institute,complete,,,,1,,1,4110554,28.56,3669,3454,Stool,single patient with a C. difficile infection; Toxigenic,isolated from a single patient with a C. difficile infection in a hospital in Paris in 1985,1985,France,"Michigan, USA",,,,,,"Human, Homo sapiens",,,C. difficile infection,,,,,,+,Rod,Yes,Yes,Mesophilic,-,,Anaerobic,Multiple,Diarrhea;pseudomembraneous colitis,Comparative phylogenomics of Clostridium difficile; Ribotype 12,,100,100,100,,,Good,2014-12-08T22:10:58.219Z,2015-03-16T03:17:09.594Z
7265,645463.57,Clostridioides difficile R20291,positive,,645463,Complete,R20291,,,,,,,,2020-12-03T00:00:00Z,,PRJNA471285,SAMN09205946,GCA_015732555.1,,CP029423,,Leibniz Institute DSMZ,,PacBio; Illumina GAIIx,93x,HGAP SMRTPortal v. 2.3.0,1,,1,4204902,28.871326,3797,3676,None,,,2006,United Kingdom,United Kingdom,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Population Genomics of Clostridium difficile,sample_type:cell culture,100,100,,,,Good,2021-01-01T18:00:16.516Z,2021-01-01T18:00:16.516Z
7266,645464.3,Campylobacter jejuni subsp. jejuni M1,negative,Campylobacter jejuni subsp. jejuni M1,645464,Complete,M1,,,,MLST.Campylobacter_jejuni.137,,,,2010-09-28T00:00:00Z,20865039,PRJNA38041,SAMN02603174,GCA_000148705.1,,CP001900,NC_017280.1,Danish Technical University,complete,,,,1,,1,1616648,30.6,1658,1622,None,"both the patient and from the poultry flock sampled at the abattoir, thus providing a clear-cut case of the direct transmission of disease from poultry to human","isolated the M1 strain (laboratory designation 99/308) from both the patient and from the poultry flock sampled at the abattoir, thus providing a clear-cut case of the direct transmission of disease from poultry to human",,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Rod,Yes,No,Mesophilic,-,,Microaerophilic,Multiple,Gastroenteritis,"Campylobacter jejuni subsp. jejuni M1.Following a research visit to a poultry abattoir, one surveillance team member developed campylobacteriosis. We isolated the M1 strain (laboratory designation 99/308) from both the patient and from the poultry flock sampled at the abattoir, thus providing a clear-cut case of the direct transmission of disease from poultry to human. We have determined the genome sequence of the M1 strain and compared it to other previously published Campylobacter genomes. We found the M1 genome to contain many genes related to chicken colonization which are not ubiquitous in the published genomes. The M1 genome represents a confirmed pathogen and chicken colonizer useful for further comparative studies.",,99.9,99.3,100,0.6,,Good,2014-12-08T22:10:47.682Z,2015-03-16T03:17:09.594Z
7292,657310.3,Enterococcus sp. 7L76,positive,Enterococcus sp. 7L76,1351,Complete,7L76,,,,"MLST.Enterococcus_faecalis.72,MLST.Enterococcus_faecium.357",,,,2010-04-23T00:00:00Z,,PRJNA39181,SAMEA3138365,GCA_000210115.1,,FP929058,-,Wellcome Trust Sanger Institute,complete,454,16x,,1,,1,3096657,35.39,2863,2295,Gut,human intestine,cellulolytic bacterium from the human intestine,,,,,,,,,"Human, Homo sapiens",,,,Gastrointestinal tract,,,,,+,Coccus,,,,-,,,,,Enterococcus sp. 7L76. Enterococcus sp. 7L76 is a cellulolytic bacterium from the human intestine.;missing tRNA genes,,99.3,97,98.2,1.6,,Good,2014-12-08T22:11:18.132Z,2015-03-16T03:17:09.594Z
7293,657316.3,Megamonas hypermegale ART12/1,negative,Megamonas hypermegale,657316,Complete,ART12/1,,,,,,,,2010-03-25T00:00:00Z,,PRJNA39163,SAMEA3138358,GCA_000209975.1,,FP929048,-,Wellcome Trust Sanger Institute,complete,454-GS-FLX-Titanium,27x,,1,,1,2209938,30.51,2774,2118,Gut,,,,,,,,,,,"Human, Homo sapiens",,,,Gastrointestinal tract,,,,,,,,,Mesophilic,-,,Anaerobic,Host-associated,,Megamonas hypermegale ART12/1.This strain will be used for comparative genome analysis.;many frameshifted proteins;missing rRNA genes,,95.9,87.4,100,19.4,High CheckM contamination score,Poor,2014-12-08T22:12:02.044Z,2015-03-16T03:17:09.594Z
7294,657317.3,Eubacterium rectale M104/1,positive,Eubacterium rectale,657317,Complete,M104/1,,,,,,,,2010-03-25T00:00:00Z,,PRJNA39161,SAMEA3138357,GCA_000209955.1,,FP929043,-,Wellcome Trust Sanger Institute,complete,454,21x,,1,,1,3698419,39.1,3426,3212,Gut,,,,,,,,,,,"Human, Homo sapiens",,,,Gastrointestinal tract,,,,,+,Rod,,,Mesophilic,-,,Anaerobic,,,Eubacterium rectale M104/1.This strain will be used for comparative genome analysis.,,99.3,98.4,100,4.4,,Good,2014-12-08T22:11:37.228Z,2015-03-16T03:17:09.594Z
7295,657318.4,Eubacterium rectale DSM 17629,positive,Eubacterium rectale,657318,Complete,DSM 17629,,,,,,"DSM 17629, NCIMB 14373",,2010-03-25T00:00:00Z,,PRJNA39159,SAMEA3138356,GCA_000209935.1,,FP929042,-,Wellcome Trust Sanger Institute,complete,454,25x,,1,,1,3344951,40.35,3105,2898,Gut,,,,,,,,,,,"Human, Homo sapiens",,,,Gastrointestinal tract,,,,,+,Rod,,,Mesophilic,-,,Anaerobic,,,Eubacterium rectale DSM 17629.This strain will be used for comparative genome analysis.,,99.8,99.6,100,3.2,,Good,2014-12-08T22:11:37.218Z,2015-03-16T03:17:09.594Z
7296,664662.5,Borreliella bavariensis strain A104S,negative,,664662,Complete,A104S,,,,,,,,2021-06-10T00:00:00Z,33032522,PRJNA327303,SAMN05328446,GCA_018831565.1,,"CP058812,CP058813,CP058825,CP058822,CP058823,CP058817,CP058824,CP058816,CP058818,CP058819,CP058820,CP058821",,Bavarian Health and Food Safety Authority,,Illumina MiSeq; PacBio,22.0x,SPAdes v. 3.10.1; HGAP v. 3,1,13,14,1315446,27.7505,1468,,None,,,1996,Netherlands,Netherlands,,,,,,Homo sapiens,,,Lyme disease,,,,,,,,,,,,,,,,"To understand the evolutionary history of the Borrelia burgdorferi sensu lato species complex, we used NGS sequencing to obtain a strongly supported phylogeny of many genospecies belonging to this bacterial species complex. We associated host and vector associations to this phylogeny which provides an understanding of their impact on diversification of the bacteria.",collected_by:German National Reference Centre for Borrelia,96.3,95.2,,,,Good,2021-06-26T05:02:20.090Z,2021-06-26T05:02:20.090Z
7359,698737.3,Staphylococcus lugdunensis HKU09-01,positive,Staphylococcus lugdunensis HKU09-01,698737,Complete,HKU09-01,,,,MLST.Staphylococcus_lugdunensis.1,,,,2010-02-19T00:00:00Z,20047907,PRJNA42395,SAMN02603957,GCA_000025085.1,,CP001837,NC_013893,The University of Hong Kong,complete,,,,1,,1,2658366,33.9,2493,2490,Skin,patient suffering from skin and soft tissue infection,isolated from a patient suffering from skin and soft tissue infection,,,,,,,,,"Human, Homo sapiens",,,skin and soft tissue infection,,,,,,+,Cocci,No,No,Mesophilic,-,,Aerobic,Host-associated,,Staphylococcus lugdunensis HKU09-01. Complete genome sequencing of Staphylococcus lugdunensis strain HKU09-01 isolated from a patient suffering from skin and soft tissue infection.,,98.8,98.5,97.8,,,Good,2014-12-08T22:13:26.427Z,2015-03-16T03:17:09.594Z
7360,699034.5,Clostridium difficile BI1,positive,Clostridium difficile BI1,699034,Complete,BI1,,,,MLST.Clostridium_difficile.1,,,,2010-03-24T00:00:00Z,20368420,PRJNA42469,,GCA_000211235.1,,"FN668942,FN668943,FN668941",-,Wellcome Trust Sanger Institute,complete,,,,1,2,3,4464700,28.36,4101,,None,human,human strain isolated in the United States in 1988,1988,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,Yes,Yes,Mesophilic,-,,Anaerobic,Host-associated,Antibiotic-associated Diarrhea;Pseudomembraneous colitis,Clostridium difficile BI1. Clostridium difficile BI1 is a human strain isolated in the United States in 1988. This strain will be used for comparative analysis.,,99.9,99.6,100,0.6,,Good,2014-12-08T22:10:57.928Z,2015-03-16T03:17:09.594Z
7361,699035.5,Clostridium difficile M120,positive,Clostridium difficile M120,699035,Complete,M120,,,,MLST.Clostridium_difficile.11,,,,2010-03-24T00:00:00Z,20368420,PRJNA42467,,GCA_000210435.1,,FN665653,NC_017174.1,Wellcome Trust Sanger Institute,complete,,,,1,,1,4047729,28.67,3694,,None,human,human strain isolated in the United Kingdom in 2007,2007,United Kingdom,United Kingdom,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,Yes,Yes,Mesophilic,-,,Anaerobic,Multiple,Antibiotic-associated Diarrhea;Pseudomembraneous colitis,Clostridium difficile M120. Clostridium difficile M120 is a human strain isolated in the United Kingdom in 2007. This strain will be used for comparative analysis.,,99.2,98.4,100,0.6,,Good,2014-12-08T22:10:59.413Z,2015-03-16T03:17:09.594Z
7362,699036.5,Clostridium difficile CF5,positive,Clostridium difficile CF5,699036,Complete,CF5,,,,MLST.Clostridium_difficile.86,,,,2010-03-24T00:00:00Z,20368420,PRJNA42465,,GCA_000210415.1,,FN665652,-,Wellcome Trust Sanger Institute,complete,,,,1,,1,4159517,28.54,3797,,None,human,human strain isolated in the Belgium in 1995,1995,Belgium,Belgium,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,Yes,Yes,Mesophilic,-,,Anaerobic,Multiple,Antibiotic-associated Diarrhea;Pseudomembraneous colitis,Clostridium difficile CF5. Clostridium difficile CF5 is a human strain isolated in the Belgium in 1995. This strain will be used for comparative analysis.;missing tRNA genes,,100,99.5,100,1.3,,Good,2014-12-08T22:10:58.643Z,2015-03-16T03:17:09.594Z
7363,699037.5,Clostridium difficile M68,positive,Clostridium difficile M68,699037,Complete,M68,,,,MLST.Clostridium_difficile.37,,,,2010-03-24T00:00:00Z,20368420,PRJNA42463,,GCA_000210395.1,,FN668375,-,Wellcome Trust Sanger Institute,complete,,,,1,,1,4308325,28.88,3919,,None,human,human strain isolated in Ireland in 2006,2006,Ireland,Ireland,,,,,,"Human, Homo sapiens",,,,,,,,,+,Rod,Yes,Yes,Mesophilic,-,,Anaerobic,Multiple,Antibiotic-associated Diarrhea;Pseudomembraneous colitis,Clostridium difficile M68. Clostridium difficile M68is a human strain isolated in Ireland in 2006. This strain will be used for comparative analysis.,,100,99.7,100,,,Good,2014-12-08T22:10:59.422Z,2015-03-16T03:17:09.594Z
7364,699186.6,Enterococcus faecalis R712,positive,,699186,Complete,R712,,,,MLST.Enterococcus_faecalis.103,,,,2019-11-14T00:00:00Z,,PRJNA523028,SAMN10962800,GCA_009662495.1,,"CP036249,CP036247,CP036248",,Universidad El Bosque,,PacBio,114.0x,HGAP v. 2,1,2,3,3117418,37.37144,3180,3133,Blood,blood,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Enterococcus faecalis R712 Genome sequencing,collected_by:Cesar A. Arias,99.7,98.6,,,,Good,2019-11-25T21:35:47.078Z,2019-11-25T21:35:47.078Z
7365,699240.12,Clostridiales genomosp. BVAB1 strain UAB071,positive,,699240,Complete,UAB071,,biovar AB1,,,,,,2020-03-09T00:00:00Z,,PRJNA562728,SAMN12648934,GCA_011082265.1,,CP049781,,University of Maryland Baltimore,,PacBio Sequel II,2247.0x,Canu v. 1.7,1,,1,1649642,31.830544,1525,,Vagina,vagina,derived from cervicovaginal samples of seven separate women,Sep-2009/Jul-2010,USA,"USA: Birmingham, Alabama",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Bacterial Vaginosis Associated Bacteria 1 (BVAB1) is an as-yet uncultured bacterial species found in the human vagina that belongs to the family Lachnospiraceae within the order Clostridiales, and as its name suggests, is often associated with bacterial vaginosis (BV). In reproductive health, BV is of concern due to its associated risk for HIV, Chlamydia trachomatis, and Neisseria gonorrhoeae acquisition as well as preterm birth. BVAB1 has been shown to be associated with BV persistence after metronidazole treatment and increased vaginal inflammation, as well as conferring a higher risk of puerperal infections. To date, no complete genome of BVAB1 is available, which has made it difficult to understand its disease-associated features. We present here a comparative analysis including a complete genome and six metagenome-assembled genomes (MAGs) of BVAB1 derived from cervicovaginal samples of seven separate women. The complete genome was obtained from a metagenome sequenced with long-read technology on a PacBio Sequel II instrument while the others were derived from metagenomes sequenced on the Illumina HiSeq platform. The complete genome is 1.649 Mb long and encodes 1,578 genes. We propose to rename BVAB1 to “Candidatus Lachnocurva vaginae” based on phylogenetic analysis, and provide genomic evidence that this candidate species may metabolize D-lactate, produce trimethylamine (the chemical responsible for BV-associated odor), and be motile. The complete genome and assembled MAGs will be valuable resources contributing to our understanding of the heterogenous etiology of bacterial vaginosis.",sample_type:metagenomic assembly,95.9,95.5,,,,Good,2020-04-11T23:48:43.381Z,2020-04-11T23:48:43.381Z
7366,701042.4,Mycobacterium marseillense strain FLAC0026,positive,,701042,Complete,FLAC0026,,,,,,,,2017-09-05T00:00:00Z,,PRJNA315990,SAMN07528776,GCA_002285715.1,,"CP023147,CP023148",,University of Michigan Medical School,,Illumina HiSeq,150X,SPAdes v. 3.9.0,1,1,2,5285642,67.84,5032,4905,None,,,2013,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of M. abscessus complex isolates.,collected_by:Lindsay J. Caverly,99.1,98.4,100,,,Good,2017-09-28T21:52:29.496Z,2017-09-28T21:52:29.496Z
7367,701177.3,Escherichia coli O55:H7 str. CB9615,negative,Escherichia coli O55:H7 str. CB9615,701177,Complete,CB9615,,,EHEC,"MLST.Escherichia_coli_1.335,MLST.Escherichia_coli_2.553",,,,2010-03-08T00:00:00Z,20090843,PRJNA42729,SAMN02603636,GCA_000025165.1,,"CP001846,CP001847","NC_013941,NC_013942",Nankai University|Tianjin Biochip,complete,,,,1,1,2,5452353,50.5,5362,5121,Stool,infant with diarrhea,isolated from an infant with diarrhea in Germany in 2003 and confirmed to belong to the same multilocus sequence type (ST11) as the O157:H7 clone,2003,Germany,Germany,,,,,,"Human, Homo sapiens",,infant,,,,,,,-,Rod,Yes,No,Mesophilic,-,,Facultative,Multiple,Gastroenteritis,Escherichia coli O55:H7 str. CB9615. Escherichia coli O55:H7 str. CB9615 was isolated from an infant with diarrhea in Germany in 2003 and confirmed to belong to the same multilocus sequence type (ST11) as the O157:H7 clone. The O55:H7 and O157:H7 E. coli clones have been shown to be closely related and will be useful for the analysis of recombination events and mutational events.,,99.8,99.1,100,,,Good,2014-12-08T22:11:32.950Z,2015-03-16T03:17:09.594Z
7368,702439.159,Prevotella nigrescens F0103,negative,,702439,Complete,F0103,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,SAMN18352178,GCA_018127865.1,,"CP072341,CP072342,CP072340",,The Forsyth Institute,,PacBio Sequel,561x,Pacbio MA v. 9.0.0.92188,2,1,3,3069220,42.74757,3033,2575,Mouth,human oral cavity,,1988-10,USA,"USA: Blacksberg, Virginia",,,634 m,,,Homo sapiens,male,14,,,,,,,,,,,,C,,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02183;collected_by:Moores, Virginia Polytechnic Institute",98.2,97.5,,,,Good,2021-04-26T00:37:25.581Z,2021-04-26T00:37:25.581Z
7370,710686.3,Mycobacterium smegmatis JS623,positive,Mycobacterium smegmatis JS623,212767,Complete,JS623,,,,,, ,,2012-12-27T00:00:00Z,14532060,PRJNA60055,SAMN02261384,GCA_000328565.1,SRR3927264,"CP003078.1,CP003081.1,CP003080.1,CP003079.1","NC_019966.1,NC_019959.1,NC_019958.1,NC_019957.1",JGI,complete,454/Illumina,30x,1,1,2,3,7057652,65.08,7191,6753,None,Soil; human smegma,"derived from sandy garden soil (Panama City, Fla.)",,USA,"USA: Panama City, Florida",,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Rod-shaped,No,No,,37C,,Aerobe,,Cellulitis,Mycobacterium smegmatis JS623.This strain will be used for comparative genome analysis.,,96.6,94.4,98.4,8.5,,Good,2014-12-08T22:12:07.875Z,2015-03-16T03:17:09.594Z
7375,717960.3,"""[Eubacterium] cylindroides T2-87""",negative,Eubacterium cylindroides T2-87,717960,Complete,T2-87,,,,,,,,2010-04-23T00:00:00Z,,PRJNA45917,,GCA_000210615.1,,FP929041,-,metaHIT|The Wellcome Trust Sanger Institute,complete,454,19x,,1,,1,1966750,31.43,1873,1442,Gut,,,,,,,,,,,"Human, Homo sapiens",,,,Gastrointestinal tract; Gut,,,,,+,Rod,,,Mesophilic,-,,Anaerobic,,,"Eubacterium cylindroides T2-87.Gut Health Programme, Rowett Institute of Nutrition and Health, University of Aberdeen. http://www.rowett.ac.uk/divisions/ghp/",,92.3,90.1,70.6,11.8,High CheckM contamination score;Low CheckM completeness score,Poor,2014-12-08T22:13:52.494Z,2015-03-16T03:17:09.594Z
7376,718254.4,Enterobacter cloacae subsp. cloacae NCTC 9394,negative,Enterobacter cloacae subsp. cloacae NCTC 9394,718254,Complete,NCTC 9394,,,,MLST.Enterobacter_cloacae.4,,NCTC 9394,,2010-04-23T00:00:00Z,,PRJNA45967,SAMEA3138380,GCA_000210775.1,,FP929040,-,metaHIT|The Wellcome Trust Sanger Institute,complete,454,15x,,1,,1,4908759,52.69,4542,3725,Gut,,,,,,,,,,,"Human, Homo sapiens",,,,Gastrointestinal tract,,,,,-,Rod,Yes,No,Mesophilic,-,,Facultative,Multiple,,Enterobacter cloacae subsp. cloacae NCTC 9394. Project description not provided.;missing tRNA genes,,98.7,94.8,98,2.8,,Good,2014-12-08T22:11:10.871Z,2015-03-16T03:17:09.594Z
7377,722438.5,Mycoplasma pneumoniae FH,negative,,722438,Complete,FH,,,,MLST.Mycoplasma_pneumoniae.2,,ATCC:15531,,2015-08-21T00:00:00Z,26275904,PRJNA182276,SAMN03284384,GCF_001272835.1,,CP010546,NZ_CP010546.1,University of Alabama at Birmingham,,Illumina MiSeq,at least 300x,ABySS v. 1.3.7,1,,1,817207,39.98,792,706,Sputum,Sputum,,1954,USA,USA:MA,,,,,,"Human, Homo sapiens",,,pneumonia,,,,,,,,,,,,,,,Mycoplasma pneumonia,WGS of Mycoplasma pneumoniae strain FH.,collected_by:Unknown,99.9,99.9,100,,,Good,2016-01-17T17:04:00.901Z,2016-01-17T17:04:00.901Z
7379,722731.5,Mycobacterium shigaense strain SCY,positive,,722731,Complete,SCY,,,,,,,,2018-09-10T00:00:00Z,,PRJNA398420,SAMN07510626,GCA_003515645.1,,CP022927,,"Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College",,PacBio; Illumina HiSeq,100.0x,Celera Assembler v. 1.2; SOAP GapCloser,1,,1,5207883,67.232445,5029,,Skin,skin biopsy from woman,,1-Jan-13,China,China,,,,,,"Human, Homo sapiens",,,Mycobacterial disease of the skin,,,,,,,,,,,,,,,,Mycobacterium shigaense (SCY),collected_by:Hongsheng Wang,98.9,97.6,100,8.9,,Good,2018-10-03T01:26:11.221Z,2018-10-03T01:26:11.221Z
7571,741093.3,Escherichia coli Xuzhou21,negative,Escherichia coli Xuzhou21,741093,Complete,Xuzhou21,,,,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.822",,,,2011-04-08T00:00:00Z,22558360,PRJNA45823,SAMN02603645,GCA_000262125.1,,"CP001925.1,CP001927.1,CP001926.1","NC_017906.1,NC_017903.1,NC_017907.1","National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention",complete,,,,1,2,3,5516736,50.3828,5540,5183,None,,,1999,China,China,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,No,,Mesophilic,,,Facultative,Multiple,Hemolytic uremic syndrome (HUS),-,,99.9,99.6,100,0.4,,Good,2014-12-08T22:11:36.565Z,2015-03-16T03:17:09.594Z
7584,748672.3,Yersinia pseudotuberculosis str. PA3606 Pa3606,negative,,748672,Complete,Pa3606,,,,MLST.Yersinia_pseudotuberculosis.2,,,,2015-02-09T00:00:00Z,-,PRJNA239349,SAMN03223176,GCA_000834945.1,"SRR3214359,SRR3214361","CP010067.1,CP010068.1,CP010069.1","NZ_CP010067.1,NZ_CP010068.1,NZ_CP010069.1",Los Alamos National Laboratory,,Illumina; PacBio; 454,471x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,1,2,3,4830299,47.51,4462,4111,None,,,2009,Japan,Japan: Fukushima,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,No,,,,,,,Genome sequencing of Yersinia pseudotuberculosis Pa3606,,99.6,98.5,100,,,Good,2015-03-12T14:02:15.604Z,2015-03-16T03:17:09.594Z
7585,749219.3,Moraxella catarrhalis RH4,negative,Moraxella catarrhalis RH4,749219,Complete,RH4,,,,MLST.Moraxella_catarrhalis.128,,,,2010-05-11T00:00:00Z,20453089,PRJNA46869,SAMN02470825,GCA_000302495.1,,CP002005,NC_014147,Radboud University Nijmegen Medical Centre,complete,,,,1,,1,1863286,41.67,1885,1886,Blood,human blood,isolated from human blood and will be used for comparative analysis,,,,,,,,,"Human, Homo sapiens",,,,,,,,,-,Diplococcus,No,No,Mesophilic,-,,Aerobic,Host-associated,,Moraxella catarrhalis RH4. Moraxella catarrhalis RH4 was originally isolated from human blood and will be used for comparative analysis.,,99.7,99.7,100,,,Good,2014-12-08T22:12:04.863Z,2015-03-16T03:17:09.594Z
7595,754093.4,Shigella dysenteriae 1617,negative,,754093,Complete,1617,,,,,,,,2015-03-09T00:00:00Z,25743074,PRJNA218020,,GCF_000497505.1,,"CP006736,CP006737",,Igenbio Inc,,"454 GS FLX, Illumina paired end",20x,"Newbler v 2.3, CLC package workbench",1,1,2,4480198,50.98,6316,6409,None,,,,Guatemala,Guatemala,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Comparative genomics of Sd1617 to representative strains in evaluating its pathogenesis.,,99.1,95.7,99.6,2.4,,Good,2016-01-17T15:33:51.604Z,2016-01-17T15:33:51.604Z
7597,762948.4,Rothia dentocariosa ATCC 17931,negative,Rothia dentocariosa ATCC 17931,762948,Complete,ATCC 17931,,,,,,"ATCC 17931, CDC X599",,2010-05-21T00:00:00Z,,PRJNA48447,SAMN00120582,GCA_000164695.2,"SRR089543,SRR089544",CP002280,NC_014643,Baylor College of Medicine,complete,454,34.7x,Newbler v. 2.0-01162009,1,,1,2506025,53.69,2168,2217,Mouth,,,,,,,,,,,"Human, Homo sapiens",,,,Oral; Teeth,,,,,+,Coccus,,,Mesophilic,-,,Aerobic,Host-associated,,Rothia dentocariosa ATCC 17931.A reference genome for the Human Microbiome Project.,,100,99.9,100,,,Good,2014-12-08T22:12:44.911Z,2015-03-16T03:17:09.594Z
7598,765963.4,Helicobacter pylori PeCan4,negative,Helicobacter pylori PeCan4,765963,Complete,PeCan4,,,,MLST.Helicobacter_pylori.3041,,,,2010-10-01T00:00:00Z,,PRJNA49027,SAMN02603203,GCA_000148875.1,,"CP002074,CP002075","NC_014555,NC_014556",Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine,complete,,,,1,1,2,1638269,38.91,1648,1563,Stomach,Peruvian gastric cancer patient,isolated from a Peruvian gastric cancer patient,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,-,,,,,Helicobacter pylori PeCan4.This strain was isolated from a Peruvian gastric cancer patient.,,100,99.7,100,,,Good,2014-12-08T22:11:45.336Z,2015-03-16T03:17:09.594Z
7599,767031.3,Prevotella denticola F0289,negative,Prevotella denticola F0289,767031,Complete,F0289,,,,,,BEI HM-208,,2011-03-28T00:00:00Z,,PRJNA49293,SAMN00031760,GCA_000193395.1,SRR063731,CP002589,NC_015311,J. Craig Venter Institute,complete,"454, Illumina",43x,Celera Assembler v. 6.1,1,,1,2937589,50.36,2529,2386,Mouth,,Dewhirst Lab,,,,,,,,,"Human, Homo sapiens",,,,Oral,,,,,-,Rod,No,No,Mesophilic,-,,Anaerobic,Host-associated,,Prevotella denticola F0289.A reference genome for the Human Microbiome Project.,,98.2,97.8,100,1.3,,Good,2014-12-08T22:12:33.360Z,2015-03-16T03:17:09.594Z
7603,768494.3,Bacillus anthracis str. H9401,positive,Bacillus anthracis str. H9401,768494,Complete,H9401,,,,MLST.Bacillus_cereus.1,,,,2012-04-17T00:00:00Z,,PRJNA49361,SAMN02603474,GCA_000258885.1,,"CP002091.1,CP002092.1,CP002093.1","NC_017729.1,NC_017726.1,NC_017727.1",Korea Center for Disease Control & Prevention,complete,,,,1,2,3,5495471,35.2644,5853,5791,None,Korean cutaneous anthrax patient,isolate from a Korean cutaneous anthrax patient,,Korea,Korea,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,Yes,,Mesophilic,,,Facultative,Multiple,Anthrax,Bacillus anthracis str. H9401.Bacillus anthracis str. H9401 is a clinical isolate from a Korean cutaneous anthrax patient.,,100,99.3,100,0.1,,Good,2014-12-08T22:10:12.238Z,2015-03-16T03:17:09.594Z
7644,794851.3,Helicobacter pylori Sat464,negative,Helicobacter pylori Sat464,794851,Complete,Sat464,,,,MLST.Helicobacter_pylori.3043,,,,2010-10-01T00:00:00Z,,PRJNA49453,SAMN02603200,GCA_000148915.1,,"CP002071,CP002072","NC_017359.1,NC_017356.1","Dept. Molec. Microbiology, Washintgton University Medical School in Saint Louis",complete,,,,1,1,2,1567570,39.09,1566,1508,None,"Amerindian resident from Satipo region, Peru","Pure culture of strain from Amerindian resident from Satipo region, Peru",,Peru,"Satipo region, Peru",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,-,,,,,"Pure culture of strain from Amerindian resident from Satipo region, Peru.  Helicobacter pylori is a genetically diverse gastric pathogen, important in peptic ulcer desease and gastric cancer. Different genotypes predominate in different human populations",,99.9,99.7,100,,,Good,2014-12-08T22:11:46.260Z,2015-03-16T03:17:09.594Z
7811,857099.9,Streptococcus mutans OMZ175,positive,,857099,Complete,OMZ175,,,,,,,,2021-09-02T00:00:00Z,,PRJNA752369,SAMN20593762,GCA_019856215.1,,CP082153,,University of Florida,,PacBio; Sequel 2,0.98x,Flye v. 2.8,1,,1,2060302,37.06947,2042,1947,Mouth,Dental plaque,,Not applicable,,Not applicable,,,,,,Homo sapiens,,,Not applicable,,,,,,,,,,,,,,,,Whole genome sequence of strain OMZ175 of Streptococcus mutans,collected_by:Not applicable,99.9,99.4,,,,Good,2021-12-23T23:01:53.966Z,2021-12-23T23:01:53.966Z
7827,867914.5,Staphylococcus aureus LAC,positive,,867914,Complete,LAC,,,,MLST.Staphylococcus_aureus.8,,,,2020-11-13T00:00:00Z,,PRJNA639565,SAMN15239172,GCA_015475575.1,,"CP055225,CP055226",,University of Arkansas for Medical Sciences,,Illumina; Oxford Nanopore MiniION,1129.0x,Unicycler v. v0.4.4,1,1,2,2877525,32.7798,2837,2803,None,not applicable,,,,,,,,,,"Human, Homo sapiens",,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,,"The genome sequence presented here was generated using the USA300 LAC strain used by Dr Anthony R. Richardson at the University of Pittsburgh to generate a TnSeq library (Grosser et al., PLOS Pathogens, 2018). This library, and the parent strain, were obtained by the laboratory of Dr Mark S. Smeltzer at the University of Arkansas for Medical Sciences (UAMS). The genome of the parent strain was subsequently sequenced, assembled and polished at UAMS by Dr Piroon Jenjaroenpun and Ms. Duah Alkam.",sample_type:isolate,100,99.7,,,,Good,2020-11-30T11:20:51.540Z,2020-11-30T11:20:51.540Z
7848,881260.9,Enterobacter bugandensis strain EB-247,negative,,881260,Complete,EB-247,,,,MLST.Enterobacter_cloacae.495,,DSM 29888T,,2018-03-31T00:00:00Z,,PRJEB11452,SAMEA104711314,GCA_900324475.1,,LT992502,,JUSTUS LIEBIG UNIVERSITY,,,,,1,,1,4717613,55.99728,4435,,Blood,blood,"isolated from an outbreak in a neonatal unit, Tanzania, could not be assigned to any known species and was further investigated",1/5/10,Tanzania,Tanzania,,,,,,"Human, Homo sapiens",,,,,,host_health_state:diseased,,,,,,,,,,,,,"An ‘Enterobacter-like’ bacterium (EB-247T) isolated from an outbreak in a neonatal unit, Tanzania, could not be assigned to any known species and was further investigated. We used fermentation characteristics, biochemical assays and fatty acid profiles for taxonomic analysis of EB-247T, and supplemented this with information derived from sub-genome- and genome- based analysis. Phenotypic and morphological tests revealed that the isolate is a Gram-negative, rod-shaped, highly motile and facultatively anaerobic. Whole cell analysis showed that most of the fatty acids, with the exception of C17:0 Cyclo and C16:1ω6c/C16:1ω7c that were present in altered ratios, were typical for the Enterobacter species. We performed whole genome sequencing of EB-247T to perform subgenome-based phylogenetic analysis i.e. 16S rRNA, multi-locus sequence analysis (MLSA) and whole-genome-based taxonomic analysis. The draft genome of EB-247T was approximately 4.9 Mb in size with a G+C content of 56.0%. The 16S rDNA sequence of EB-247T showed > 97% similarity to all the Enterobacter species, while MLSA clustered EB-247T within Enterobacter but classified it as a separate species. Analysis using in silico DNA-DNA hybridization showed it had less than 70% sequence similarity with other Enterobacter species. The average nucleotide identity of EB-247T exhibited less than 95% sequence similarity to all the compared Enterobacter species supporting it’s a new species. From these results, we conclude that EB-247T possesses sufficient characteristics that are different from known Enterobacter species, and should be considered to be a novel species. The name Enterobacter bugandensis sp. nov. is proposed for isolate EB-247T (=DSM 29888T=NCCB 100573T).",,99.5,98.4,100,0.6,,Good,2018-05-29T17:31:13.315Z,2018-05-29T17:31:13.315Z
7850,884204.6,Burkholderia pseudomallei 1026b,negative,,884204,Complete,1026b,,,,MLST.Burkholderia_pseudomallei.102,,,,2015-06-02T00:00:00Z,25931592,PRJNA178698,SAMN03097397,GCF_000959125.1,"SRR1609221,SRR1609224,SRR1609225,SRR1609226","CP004379,CP004380","NZ_CP004379.1,NZ_CP004380.1",Los Alamos National Laboratory,,454PE; Illumina; PacBio,29x; 297x; 48x,Newbler v. 2.6; Velvet v. 1.1.05; Allpaths,2,,2,7237672,68.13,7301,5937,Blood,Septicemic melioidosis patient blood sample,,1993,Thailand,Thailand,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,,,,,,,,"Whole genome sequence of Burkholderia pseudomallei 1026b, funded by US Department of Homeland Security (DHS).",,99.2,96.2,100,,,Good,2016-01-17T15:50:14.132Z,2016-01-17T15:50:14.132Z
7851,887712.6,Chlamydia trachomatis L2c,negative,Chlamydia trachomatis L2c,887712,Complete,L2c,,,,MLST.Chlamydiales_spp.44,,,,2011-07-06T00:00:00Z,21540364,PRJNA47581,SAMN00011086,GCA_000220105.1,"SRR039361,SRR039362,SRR039363,SRR039364",CP002024,NC_015744,Emory University,complete,,,,1,,1,1038313,41.33,960,954,Stool,man with severe proctitis,isolated from a man with severe proctitis,,,,,,,,,"Human, Homo sapiens",,,severe proctitis,,,,,,,,,,,-,,,,,Chlamydia trachomatis L2c.This strain was isolated from a man with severe proctitis.,,99.8,99.7,100,,,Good,2014-12-08T22:10:54.276Z,2015-03-16T03:17:09.594Z
7852,888727.21,Eubacterium sulci ATCC 35585,positive,,888727,Complete,ATCC 35585,,,,,,ATCC:35585,,2015-08-07T00:00:00Z,,PRJNA282954,SAMN03704030,GCA_001189495.1,,CP012068,,The Forsyth Institute,,PacBio,382x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,1739380,39.920433,1619,1475,Mouth,"Subgingival plaque, gingival sulcus",,,USA,"USA: Blacksberg, VA",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,95.3,94.6,,,,Good,2019-07-17T20:11:10.258Z,2019-07-17T20:11:10.258Z
7932,908937.9,Prevotella dentalis DSM 3688,negative,,908937,Complete,DSM 3688,,,,,,DSM:3688,,2015-01-16T00:00:00Z,,PRJNA56077,SAMN02232045,GCF_000242335.1,SRR3926781,AGRS01000000,,DOE Joint Genome Institute,,454/Illumina,30x,Newbler v. 2.3,2,2,4,3350206,55.85,2893,2544,Mouth,dental root canal,,,,,,,,,env_biome:not provided; submitted under MIGS 2.1,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,This strain is part of the GEBA (A Genomic Encyclopedia of Bacteria and Archaea) project.,,98.6,98.1,100,1.3,,Good,2016-01-17T15:28:44.302Z,2016-01-17T15:28:44.302Z
7933,909952.3,Propionibacterium acnes 266,positive,Propionibacterium acnes 266,909952,Complete,266,,,,MLST.Propionibacterium_acnes.20,,,,2011-05-11T00:00:00Z,21738717,PRJNA56091,SAMN02603263,GCA_000213155.1,,CP002409,NC_017534.1,Georg-August-University Goettingen|Goettingen Genomics Laboratory,complete,,,,1,,1,2494578,60.03,2433,2348,Lung,pleuropulmonary infection,isolate from a pleuropulmonary infection,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,-,,,,,"Propionibacterium acnes 266.This strain, a human isolate from a pleuropulmonary infection, represents a member of the sequence type 18 (ST18) within the phylogenetic cluster I-1a. ST18 strains are frequently associated with disease, in particular severe acne.",,99.5,98.6,100,0.7,,Good,2014-12-08T22:12:34.213Z,2015-03-16T03:17:09.594Z
7934,910265.3,Pseudomonas aeruginosa C-NN2 strain early isolate NN2 (clone C),negative,,910265,Complete,early isolate NN2 (clone C),,,,MLST.Pseudomonas_aeruginosa.17,,,,2017-06-09T00:00:00Z,,PRJEB5222,SAMEA104083446,,,LT883143,,MHH,,,,,1,,1,6902967,66.12,6586,6601,Lung,Cystic fibrosis lung,,12/5/85,,,,,,,,Homo sapiens sapiens,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,,,In this study we closed the contig of the most common Pseudomonas aerugiosa clone C followed by an annotation step. In addition RNA-seq was performed to identify transcriptional start sites (TSS) und small RNA.,,99.9,99.2,100,0.6,,Good,2017-07-28T00:03:46.296Z,2017-07-28T00:03:46.296Z
7950,930944.6,Yersinia enterocolitica subsp. palearctica Y11,negative,Yersinia enterocolitica subsp. palearctica Y11,930944,Complete,Y11,,,,,,,,2011-01-14T00:00:00Z,21296963,PRJNA60483,SAMEA2271938,GCA_000253175.1,,"FR729477,FR745874","NC_017564.1,NC_017565.1",Max von Pettenkofer-Institute,complete,,,,1,1,2,4625880,46.97,4424,4459,None,humans and asymptomatic slaughter pigs,"isolated from humans and asymptomatic slaughter pigs in Europe, Northern Asia and Australia",,Germany,Europe Northern Asia,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,-,,,,,"Yersiniosis is the third most common bacterial enteric disease in Europe and Yersinia enterocolitica subsp. palearctica O:3/4 is the most common bioserotype isolated from humans and asymptomatic slaughter pigs in Europe, Northern Asia and Australia. Thus, deciphering of Yersinia enterocolitica subsp. palearctica O:3/4 genome will help to uncover the mechanisms behind is host adaptation strategy and successful worldwide dissemination.",,99.3,96.7,100,,,Good,2014-12-08T22:13:51.032Z,2015-03-16T03:17:09.594Z
7951,935296.3,Enterobacter aerogenes EA1509E,negative,Enterobacter aerogenes EA1509E,935296,Complete,EA1509E,,,,MLST.Enterobacter_cloacae.248,, ,,2013-01-25T00:00:00Z,23071100,PRJNA61107,SAMEA3138432,GCA_000334515.1,,"FO203353.1,FO203354.1,FO203355.1","NC_020182.1,NC_020180.1,NC_020181.1",Unit¿¿¿¿¿ de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE),complete,,,,3,,3,5591105,54.9278,5298,5499,Blood,blood culture,isolate from blood culture,,France,France:Marseille,,,,,,"Human, Homo sapiens",,,dead,,,,,,,,,,,,,,,,First genome sequence of a Multi-drug Resistant Isolate of Enterobacter aerogenes species. Clinical isolate from blood culture.,,99.3,96.7,100,1.5,,Good,2014-12-08T22:11:10.403Z,2015-03-16T03:17:09.594Z
7952,936153.3,Enterococcus faecalis 62,positive,Enterococcus faecalis 62,936153,Complete,62,,,,MLST.Enterococcus_faecalis.66,,,,2011-02-16T00:00:00Z,"1,939,307,821,398,540",PRJNA61185,SAMN02603509,GCA_000211255.1,,"CP002491,CP002492,CP002495,CP002493,CP002494",-,"Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences",complete,,,,1,3,4,3100313,37.39,3041,3027,None,healthy Norwegian baby,isolate from a healthy Norwegian baby in 2006,2006,Norway,Norway,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,-,,,,,Enterococcus faecalis EF62.Enterococcus faecalis EF62 is a commensal isolate from a healthy Norwegian baby in 2006. EF62 is a ST66 strain and is not part of any clonal complex associated with nosocomial infections. This strain will be used for comparative analysis.,,99.9,99,100,1.5,,Good,2014-12-08T22:11:11.975Z,2015-03-16T03:17:09.594Z
7953,940296.3,Neisseria gonorrhoeae TCDC-NG08107,negative,Neisseria gonorrhoeae TCDC-NG08107,940296,Complete,TCDC-NG08107,,,,,,,,2011-01-07T00:00:00Z,21257765,PRJNA61377,,,,"CP002440,CP002441",-,"Centers for Disease Control, Taiwan",complete,,,,1,,1,2154835,52.56,2694,2151,None,male patient,isolated from a male patient in May 2008,2008,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,-,,,,,Neisseria gonorrhoeaeTCDC-NG08107. Neisseria gonorrhoeaeTCDC-NG08107 was isolated from a male patient in May 2008,,98,97.4,100,,,Good,2014-12-08T22:12:24.971Z,2015-03-16T03:17:09.594Z
7954,941323.4,Escherichia coli VR50,negative,,941323,Complete,VR50,OR:K1:H-,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",,,,2015-04-02T00:00:00Z,25667270,PRJEA61445,SAMN03371467,GCF_000968515.1,,"CP011134,CP011135,CP011136,CP011137,CP011138,CP011139,CP011140,CP011141,CP011142,CP011143","NZ_CP011134.1,NZ_CP011135.1,NZ_CP011136.1,NZ_CP011137.1,NZ_CP011138.1,NZ_CP011139.1,NZ_CP011140.1,NZ_CP011141.1,NZ_CP011142.1,NZ_CP011143.1",The University of Queensland,,Pacific Biosciences SMRT sequencing,65x,SMRTanalysis v. 2.0.0,1,9,10,5196066,50.8,5282,4788,Urine,urine,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Escherichia coli VR50 is an asymptomatic bacteruria isolate.,sample_type:Bacterial culture,99.9,98.8,100,,,Good,2016-01-17T15:52:45.340Z,2016-01-17T15:52:45.340Z
7955,948564.7,Vibrio cholerae C6706,negative,,948564,Complete,C6706,El Tor,,,MLST.Vibrio_cholerae.69,,,,2020-05-13T00:00:00Z,,PRJNA598947,SAMN13734987,GCA_013085075.1,,"CP047295,CP047296",,EPFL,,PacBio,329.0x,HGAP v. 3,2,,2,4085431,47.460316,3856,3661,None,,,1991,Peru,Peru,,,,,,"Human, Homo sapiens",,,cholera,,,,,,,,,,,,,,,,The goal of this study was to de novo assemble diverse pandemic V. cholerae strains and compare their closed genomes.,passage_history:provided by Mekalanos lab,97.6,96.7,,,,Good,2020-06-04T13:44:58.124Z,2020-06-04T13:44:58.124Z
7973,985079.5,Burkholderia multivorans ATCC BAA-247,negative,,985079,Complete,BAA-247,,,,MLST.Burkholderia_cepacia_complex.650,,,,2015-06-02T00:00:00Z,25931592,PRJNA264318,SAMN03140189,GCF_000959525.1,"SRR2146909,SRR2146910,SRR2846722,SRR2846723","CP009832,CP009831,CP009830","NZ_CP009832.1,NZ_CP009831.1,NZ_CP009830.1",Los Alamos National Laboratory,,Illumina; PacBio,656x,Velvet v. 1.2.08; Phrap v. SPS - 4.24;,3,,3,6322746,67.24,6216,5589,Lung,Human Clinical Sample (Cystis Fibrosis Patient),,1992,Belgium,Belgium: Brussela,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Genome sequencing of Burkholderia multivorans BAA-247,,99.7,97.8,100,,,Good,2016-01-17T15:50:21.039Z,2016-01-17T15:50:21.039Z
7975,991915.7,Escherichia coli O121:H19 strain FWSEC0006,negative,,991915,Complete,FWSEC0006,O121:H19,,,MLST.Escherichia_coli_1.655,,,,2019-05-03T00:00:00Z,,PRJNA287560,SAMN08768107,GCA_005037715.2,,NETR01000000,,National Microbiology Laboratory,,Illumina MiSeq;Oxford Nanopore MinION,103.62x;127.66x,Unicycler;Canu v. 0.4.4.0;1.7,1,1,2,5479551,50.62349,5904,5698,None,Clinical: Human (Homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2003,Canada,Canada:Alberta,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,Mesophilic,37 C,,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,100,99.3,,,,Good,2019-07-14T19:18:45.576Z,2019-07-14T19:18:45.576Z
7976,991919.15,Escherichia coli O145:NM strain FWSEC0002,negative,,991919,Complete,FWSEC0002,O145:NM,,,"MLST.Escherichia_coli_1.32,MLST.Escherichia_coli_2.436",,,,2019-05-03T00:00:00Z,,PRJNA287560,SAMN08768103,GCA_005037815.2,,NJGT01000000,,National Microbiology Laboratory,,Illumina MiSeq;Oxford Nanopore MinION,78.00x;124.40x,Unicycler;Canu v. 0.4.4.0;1.7,1,2,3,5790057,50.641365,6315,6056,None,Clinical: Human (Homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2003,Canada,Canada:Alberta,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,Mesophilic,37 C,,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,99.6,98.8,,,,Good,2019-07-14T19:20:06.432Z,2019-07-14T19:20:06.432Z
7977,997873.77,Bacteroides caccae CL03T12C61,negative,,997873,Complete,CL03T12C61,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,SAMN16451178,GCA_018292205.1,,"CP072258,CP072259,CP072260,CP072261",,Brigham & Women's Hospital,,PacBio Sequel,164x,FALCON-Unzip v. 1.2.0,1,3,4,5499725,42.83378,4904,4473,Stool,feces,,2009-05,USA,USA: Boston,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or ""sweep"" through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.","sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",99.8,99.3,,,,Good,2021-06-02T21:45:43.857Z,2021-06-02T21:45:43.857Z
7978,997879.7,Bacteroides fragilis CL03T12C07,negative,,997879,Complete,CL03T12C07,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,SAMN16451179,GCA_018292185.1,,CP072257,,Brigham & Women's Hospital,,PacBio Sequel,380x,FALCON-Unzip v. 1.2.0,1,,1,5224217,43.464294,4613,4258,Stool,feces,,2009-05,USA,USA: Boston,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or ""sweep"" through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.","sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",100,99.8,,,,Good,2021-06-02T21:45:18.261Z,2021-06-02T21:45:18.261Z
7979,997890.6,Bacteroides uniformis CL03T12C37,negative,,997890,Complete,CL03T12C37,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,SAMN16451181,GCA_018292165.1,,"CP072255,CP072256",,Brigham & Women's Hospital,,PacBio Sequel,334x,FALCON-Unzip v. 1.2.0,1,1,2,4920161,46.203995,4345,4031,Stool,feces,,2009-05,USA,USA: Boston,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or ""sweep"" through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.","sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",99.3,98.7,,,,Good,2021-06-02T21:42:00.207Z,2021-06-02T21:42:00.207Z
7980,999416.5,Parabacteroides distasonis CL03T12C09,negative,,999416,Complete,CL03T12C09,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,SAMN16451183,GCA_018292145.1,,CP072254,,Brigham & Women's Hospital,,PacBio Sequel,321x,FALCON-Unzip v. 1.2.0,1,,1,5062790,45.130787,4358,4132,Stool,feces,,2009-05,USA,USA: Boston,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or ""sweep"" through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.","sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",99,98.1,,,,Good,2021-06-02T21:42:01.447Z,2021-06-02T21:42:01.447Z
0,1003201.3,Rickettsia typhi str. TH1527,negative,Rickettsia typhi str. TH1527,1003201,Complete,TH1527,,,,,, ,,2012-03-21T00:00:00Z,,PRJNA65219,SAMN02603529,GCA_000277285.1,,CP003397.1,NC_017066.1,Los Alamos National Lab,complete,,,,1,,1,1112372,28.9,875,838,Blood,blood of a human with murine typhus,"isolated in April 1965 Thailand from blood of a human with murine typhus in the District Hospital in Chiang Rai Province, Thailand;  This as the first case of murine typhus reported in Thailand",1965,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Rickettsia typhi strain TH1527 was isolated in April 1965 Thailand from blood of a human with murine typhus in the District Hospital in Chiang Rai Province, Thailand;  This as the first case of murine typhus reported in Thailand.  Patient diagnosed with bronchitis, fever of unknown origin, and no rash.  Isolate passaged 9 times in embyonated chicken eggs, 6 Vero E6 tissue culture passages, and pooled from 1-3 passages in mouse L929 cells.  Organism was purified from host cells by differential centrifugation and banding In Renografin density gradients and WNA was purified with Qiagen spin columns.Rickettsia. This genus, like other Rickettsial organisms such as Neorickettsia and Anaplasma, is composed of obligate intracellular bacteria. There are two groups, the spotted fever group, and the typhus group. The latter is composed of two organisms, Rickettsia prowazekii and Rickettsia typhi. The bacteria can be transmitted via an arthropod (tick, fleas, mites, and/or lice) to a host organism or maintained transstadially and transovarially in the arthropod.  When pathogenic in humans,  they target endothelial cells and sometimes macrophages. They attach via an adhesin, rickettsial outer membrane proteins A and/or B, and are internalized where they persist as cytoplasmically free organisms. Rickettsia typhi. This organism causes murine (endemic) typhus and is an obligate intracellular pathogen that infects both the flea vector and hosts such as humans, commonly  rats, and some other mammals. It is in the typhus group along with R. prowazekii, and genomic comparisons demonstrate colinearity and similarity to the genome of that organism except for two independent inversions near the origin and terminus. In the flea vector, the bacterium penetrates the gut epithelial barrier and is found in the feces which become infective. Rickettsia typhi strain TH1527. This is the first strain isolated in Thailand from a human case of murine typhus.",,99.9,99.8,100,,,Good,2014-12-08T22:12:44.531Z,2015-03-16T03:17:09.594Z
1,1006543.3,Staphylococcus aureus subsp. aureus T0131,positive,Staphylococcus aureus subsp. aureus T0131,1006543,Complete,T0131,,,,MLST.Staphylococcus_aureus.239,,,,2011-04-19T00:00:00Z,21551295,PRJNA65323,SAMN02603905,GCA_000204665.1,,CP002643,NC_017347.1,"TEDA School of Biological Sciences and Biotechnology, Nankai University|Tianjin Biochip Corporation",complete,,,,1,,1,2913900,32.8,2741,2711,None,87-year-old patient,"isolated in 2006, was recovered from an 87-year-old patient in No",2006,China,"No.3 Central Hospital in Tianjin, China",,,,,,"Human, Homo sapiens",,87,,,,,,,,,,,,-,,,,,"S. aureus strain T0131, isolated in 2006, was recovered from an 87-year-old patient in No.3 Central Hospital in Tianjin, China.",,100,99.9,100,,,Good,2014-12-08T22:13:25.097Z,2015-03-16T03:17:09.594Z
2,1009464.3,Gardnerella vaginalis HMP9231,negative,Gardnerella vaginalis HMP9231,1009464,Complete,HMP9231,,,,,,CCUG 59494,,2011-05-18T00:00:00Z,,PRJNA51067,SAMN00100736,GCA_000213955.1,SRR063794,CP002725,NC_017456.1,J. Craig Venter Institute,complete,454-GS-FLX-Titanium,39x,CA v6.1,1,,1,1726519,41.23,1376,1317,Vagina,,,,,,,,,,,"Human, Homo sapiens",,,,Urogenital tract; Endometrium,,,,,,,,,,-,,,,,A reference genome for the Human Microbiome Project. ,,98.6,98.3,99.7,0.3,,Good,2014-12-08T22:11:40.310Z,2015-03-16T03:17:09.594Z
3,1010840.4,Streptococcus pyogenes MGAS1882,positive,Streptococcus pyogenes MGAS1882,1010840,Complete,MGAS1882,,,,MLST.Streptococcus_pyogenes.172,,NR-33708,,2012-03-01T00:00:00Z,,PRJNA66081,SAMN02603945,GCA_000250925.1,,CP003121.1,NC_017053.1,The Methodist Hospital Research Institute,complete,454; Illumina,,,1,,1,1781029,38,1727,,None,,,early 1960,USA,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,Host,,-,,99.7,99.5,100,,,Good,2014-12-08T22:13:35.868Z,2015-03-16T03:17:09.594Z
10,1031746.3,Campylobacter hyointestinalis subsp. hyointestinalis LMG 9260,negative,,1031746,Complete,LMG 9260,,,,MLST.Campylobacter_hyointestinalis.5,,LMG:9260,,2016-05-16T00:00:00Z,,PRJNA66795,SAMN03737973,GCF_001643955.1,,CP015575,NZ_CP015575.1,"USDA, ARS, WRRC",,454; Illumina,1165x,Newbler v. 2.6,1,,1,1753385,33.96,1830,1678,Stool,feces,,1986,Belgium,Belgium: Brussels,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,LMG culture collection,sample_type:cell culture,98.7,98.2,100,,,Good,2016-07-05T00:18:45.867Z,2016-07-05T00:18:45.867Z
11,1032071.3,Arcobacter cryaerophilus D2610,negative,,1032071,Complete,D2610,,,,MLST.Arcobacter_spp.210,,,,2018-10-16T00:00:00Z,,PRJNA66819,SAMN03737949,GCA_003660085.1,,CP032825,,"USDA, ARS, WRRC",,Illumina HiSeq; 454,964x,Newbler v. 2.6,1,,1,2055914,27.506939,2028,1994,Blood,blood,,,USA,USA,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"USDA, ARS, WRRC",sample_type:cell culture,98.7,98.2,,,,Good,2019-07-17T02:17:27.434Z,2019-07-17T02:17:27.434Z
17,1038927.45,Escherichia coli O104:H4 strain FWSEC0009,negative,,1038927,Complete,FWSEC0009,O104:H4,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",,,,2019-05-01T00:00:00Z,,PRJNA287560,SAMN08768110,GCA_005014075.1,,"CP031902,CP031903,CP031904,CP031905",,National Microbiology Laboratory,,Illumina MiSeq;Oxford Nanopore MinION,65.55x;110.27x,Unicycler;Canu v. 0.4.4.0;1.7,1,3,4,5442997,50.65053,5768,5654,None,Clinical: Human (Homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2011,Germany,Germany,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,Mesophilic,37 C,,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:Laboratory for Foodborne Zoonoses: Public Health Agency of Canada,99.9,98.9,,,,Good,2019-07-14T19:20:31.213Z,2019-07-14T19:20:31.213Z
18,1041522.28,Mycobacterium colombiense CECT 3035 strain CECT 3035,positive,,1041522,Complete,CECT 3035,,,,,,,,2017-04-24T00:00:00Z,27818776,PRJNA383253,SAMN06760893,,,CP020821,,National University of Colombia,,PacBio,340.0x,HGAP v. Oct 2014,1,,1,5581643,68.09,5451,,Blood,blood,"isolated in other scenarios such as lymphadenopathy, subcutaneous infections and disseminated disease in HIV-negative patients in countries like Spain, France, China, Canada and Russia",2006,Colombia,Colombia,,,,,,"Human, Homo sapiens",,,HIV,,,,,,,,,,,,,,,,"M. colombiense infections were initially described in HIV patients in Bogot�, Colombia. In this initial study, M. colombiense was confirmed to be the causative agent of pulmonary disease and bacteraemia in this group of people who died of HIV/M. colombiense coinfection. After this study, M. colombiense has been isolated in other scenarios such as lymphadenopathy, subcutaneous infections and disseminated disease in HIV-negative patients in countries like Spain, France, China, Canada and Russia.",collected_by:Martha I Murcia,99,97.3,100,1.7,,Good,2017-05-29T02:38:50.921Z,2017-05-29T02:38:50.921Z
21,1045010.21,Escherichia coli O157 strain FDAARGOS_293,negative,,1045010,Complete,FDAARGOS_293,,,,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,FDA:FDAARGOS_293,,2017-06-27T00:00:00Z,,PRJNA231221,SAMN06173306,,,"CP022050,CP022051,CP022052",,US Food and Drug Administration,,PacBio,17.6648961609863x,"SMRT v. 2.3.0, HGAP v. 3.0",1,2,3,5686502,50.48,6234,5979,None,,,26-Feb-14,USA,USA:DC,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:George Washington University,99.8,98.9,100,0.7,,Good,2017-07-23T01:14:06.936Z,2017-07-23T01:14:06.936Z
22,1048254.4,Escherichia coli O104:H4 str. C227-11,negative,,1048254,Complete,C227-11,,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",,DSM -3043,,2015-07-13T00:00:00Z,,PRJNA281410,SAMN03856947,GCF_000986765.1,,"CP011331,CP011332,CP011333,CP011334,CP011335,CP011336,CP011337,CP011338","NZ_CP011331.1,NZ_CP011336.1,NZ_CP011337.1,NZ_CP011335.1,NZ_CP011338.1,NZ_CP011334.1,NZ_CP011332.1,NZ_CP011333.1",Icahn School of Medicine at Mount Sinai,,PacBio,100.0x,HGAP v. 2.0,1,7,8,5446006,50.63,5664,5275,Stool,stool sample from a 64-year-old woman from Hamburg who presented with bloody diarrhea and did not develop hemolytic uremic syndrome (HUS),,18-May-11,Denmark,Denmark,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"To obtain high quality reference assemblies of multiple bacterial genomes and conduct genome-wide analysis of DNA methylation, we sequenced three cultured isolates using a Pacific Biosciences RSII instrument. These long read sequenced isolates include Escherichia coli O104:H4 str. C227-11, Helicobacter pylori J99, and Chromohalobacter salexigens DSM-3043.""",isolate:368 shch,100,99,100,,,Good,2016-01-17T15:56:39.571Z,2016-01-17T15:56:39.571Z
23,1048264.3,Streptococcus pyogenes HKU QMH11M0907901,positive,,1048264,Complete,HKU QMH11M0907901,,,,MLST.Streptococcus_pyogenes.36,,,,2012-05-18T00:00:00Z,,PRJNA68183,SAMN02471172,GCF_000275625.1,,AFRY01000000,,"Department of Microbiology, The University of Hong Kong",,454 GS FLX titanium,48x,Newbler v. 2.5.3,1,,1,1908100,38.45,1909,1865,Blood,blood from scarlet fever outbreak,,2011,China,China: Hong Kong,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Clinical use of next generation sequencing for rapid identification of useful genomic signatures in the complete genome of an epidemic strain of emm12 Streptococcus pyogenes causing scarlet fever and bacteremia in Hong Kong. Bacteremic strain from a patient with scarlet fever in Hong Kong. Gram positive cocci in chains, beta-hemolytic on horse blood agar, bacitracin susceptible, Lancefield Group A antigen positive. The Vitek ID bionumber profile was 51043230001 which had a confidence level of 99% in its identification as Streptococcus pyogenes. Resistant to erythromycin, clindamycin and tetracycline but susceptible to penicillin G, ciprofloxacin, levofloxacin, rifampicin and vancomycin. Emm typing: emm12. MLST: ST36.",,99.9,99.9,100,0.9,,Good,2016-01-17T15:29:01.552Z,2016-01-17T15:29:01.552Z
24,1055527.3,Helicobacter pylori ELS37,negative,Helicobacter pylori ELS37,1055527,Complete,ELS37,,,,MLST.Helicobacter_pylori.3048,, ,,2012-03-23T00:00:00Z,,PRJNA69915,SAMN02604318,GCA_000255955.1,,"CP002953.1,CP002954.1","NC_017063.1,NC_017064.1",Washington University Med. School,complete,,,,1,1,2,1669876,38.8905,1663,1576,Stomach,gastric cancer patient from El Salvador rural area,isolate from gastric cancer patient from El Salvador rural area,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Clinical Helicobacter pylori isolate from gastric cancer patient from El Salvador rural area.,,100,99.3,100,,,Good,2014-12-08T22:11:43.598Z,2015-03-16T03:17:09.594Z
25,1055531.3,Helicobacter pylori Aklavik117,negative,Helicobacter pylori Aklavik117,1055531,Complete,Aklavik117,,,,MLST.Helicobacter_pylori.2935,, ,,2012-11-26T00:00:00Z,,PRJNA69923,SAMN02604323,GCA_000315955.1,,"CP003483.1,CP003485.1,CP003484.1","NC_019560.1,NC_019562.1,NC_019561.1",Washington University Medical School,complete,,,1,1,2,3,1636125,38.73,1617,1538,None,Amerindian; Clinical isolate,"Clinical isolate from Amerindian resident in Aklavik, Canada",,Canada,"Canada: Aklavik village, Northwest Territories",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Clinical isolate from Amerindian resident in Aklavik, Canada",,99.6,99.3,99.7,,,Good,2014-12-08T22:11:43.415Z,2015-03-16T03:17:09.594Z
26,1055532.3,Helicobacter pylori Aklavik86,negative,Helicobacter pylori Aklavik86,1055532,Complete,Aklavik86,,,,MLST.Helicobacter_pylori.2945,, ,,2012-11-26T00:00:00Z,,PRJNA69925,SAMN02604324,GCA_000317875.1,,"CP003476.1,CP003477.1,CP003478.1","NC_019563.1,NC_019564.1,NC_019565.1",Washington University Medical School,complete,,,1,1,2,3,1507930,39.21,1491,1387,None,Amerindian; Clinical isolate,"Clinical isolate from Amerindian resident in Aklavik, Canada",,Canada,"Canada: Aklavik village, Northwest Territories",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Clinical isolate from Amerindian resident in Aklavik, Canada",,99.5,99.4,98.2,,,Good,2014-12-08T22:11:43.424Z,2015-03-16T03:17:09.594Z
36,1078021.3,Escherichia coli O113:H21 strain FWSEC0010,negative,,1078021,Complete,FWSEC0010,O113:H21,,,MLST.Escherichia_coli_1.223,,,,2019-05-01T00:00:00Z,,PRJNA287560,SAMN08768111,GCA_005014055.1,,"CP031898,CP031899,CP031900,CP031901",,National Microbiology Laboratory,,Illumina MiSeq;Oxford Nanopore MinION,94.45x;51.16x,Unicycler;Canu v. 0.4.4.0;1.7,1,3,4,5131000,50.785305,5319,5244,None,Clinical: Human (Homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",1991,Canada,Canada,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,Mesophilic,37 C,,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:Laboratory for Foodborne Zoonoses: Public Health Agency of Canada,100,99.4,,,,Good,2019-07-14T19:16:41.004Z,2019-07-14T19:16:41.004Z
37,1078032.3,Escherichia coli O45:H2 strain FWSEC0003,negative,,1078032,Complete,FWSEC0003,O45:H2,,,MLST.Escherichia_coli_2.135,,,,2019-05-03T00:00:00Z,,PRJNA287560,SAMN08768104,GCA_005037845.2,,NJGS01000000,,National Microbiology Laboratory,,Illumina MiSeq;Oxford Nanopore MinION,100.74x;244.02x,Unicycler;Canu v. 0.4.4.0;1.7,1,2,3,5680623,50.60373,6253,6018,None,Clinical: Human (Homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2005,Canada,"Canada:Nova Scotia,Halifax",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,Mesophilic,37 C,,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,99.9,98.8,,,,Good,2019-07-14T19:23:36.427Z,2019-07-14T19:23:36.427Z
38,1086030.18,Shigella flexneri 5a str. M90T,negative,,1086030,Complete,M90T,,,,,,,,2019-04-18T00:00:00Z,,PRJNA510559,SAMN10608416,GCA_004799585.1,,"CP037923,CP037924",,Umea University,,PacBio RSII; Illumina HiSeq,155.0x,Canu v. V.1.7,1,1,2,4828909,50.665173,5428,4865,None,"Walter Reed Collection. Sansonetti, P. J., et al. (1982). ""Involvement of a plasmid in the invasive ability of Shigella flexneri."" Infect Immun 35(3): 852-860.",,9-Jul-81,USA,USA:MD,,,,,,"Human, Homo sapiens",,,dysentery,,,,,,,,,,,,,,,,Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri 5a M90T and genome-wide transcription start site determination,collected_by:Samuel Formal,99.9,97.3,,,,Good,2019-07-15T17:47:49.359Z,2019-07-15T17:47:49.359Z
39,1089456.3,Pseudomonas aeruginosa NCGM2.S1,negative,Pseudomonas aeruginosa NCGM2.S1,1089456,Complete,NCGM2.S1,,,,MLST.Pseudomonas_aeruginosa.235,,,,2011-09-30T00:00:00Z,22123763,PRJNA162173,,GCA_000284555.1,,AP012280.1,NC_017549.1,,assembly,ABI3730xl; 454,29x,GS De Novo Assembler v. 2.3,1,,1,6764661,0.661,6325,6269,Urine,Homo sapiens; urinary tract,,,Japan,Japan: Miyagi Prefecture,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,Urinary tract infection,"The MDR P. aeruginosa strain NCGM2.S1 caused an outbreak of urinary tract infection at a hospital in Miyagi Prefecture, northern Japan",,99.7,99.3,100,,,Good,2014-12-08T22:12:37.664Z,2015-03-16T03:17:09.594Z
40,1091045.3,Propionibacterium acnes ATCC 11828,positive,Propionibacterium acnes ATCC 11828,1091045,Complete,ATCC 11828,,,,,,,,2011-10-20T00:00:00Z,22156398,PRJNA73675,SAMN02602997,GCA_000231215.1,,CP003084.1,NC_017550.1,BAYGEN,,SOLiD,280x,Genomics Workbench 4.7 and the Omixon Gapped SOLiD Alignment 1.2 plug-in,1,,1,2488626,60.04,2411,2259,Abscess,subcutaneous abscess,,,,,,,,,,"Human, Homo sapiens",,,,subcutaneous abscess,,,,,gram +,,,,,,,Anaerobe,Human skin,Acne,Propionibacterium acnes is considered a skin commensal,,99.3,98.8,100,,,Good,2014-12-08T22:12:34.233Z,2015-03-16T03:17:09.594Z
41,1091046.5,Mycobacteroides abscessus subsp. bolletii BD,positive,,1091046,Complete,BD,,,,,,JCM:15297,,2018-06-09T00:00:00Z,29437099,PRJDB6557,SAMD00106553,GCA_003609715.1,,AP018436,,National Institute of Infectious Diseases,,PacBio RS II; Illumina MiSeq,38x,Canu v. 1.5,1,,1,5080450,64.05787,5047,4976,None,soil and water,isolated from soil and water,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Mycobacterium abscessus, formerly Mycobacterium chelonae subsp. abscessus, is a rapid-growing Mycobacterium sp., commonly isolated from soil and water. Recently, there was a taxonomic proposal that Mycobacterium abscessus should be divided into three subspecies such as Mycobacterium abscessus subsp. abscessus (Mycobacterium abscessus sensu stricto), Mycobacterium abscessus subsp. massiliense and Mycobacterium abscessus subsp. bolletii because of the results of whole genome sequencing analysis. Now it was renamed as Mycobacterium abscessus complex (MABC). This organism causes a chronic lung infection and also causes wound, ear and skin infections. It was also recently reported there was a potential evidence that the majority of MABC infections were acquired through transmission via fomites and aerosols and of recently emerged dominant circulating clones that have spread globally. This organism is very resistant to many commonly used antibiotics, which makes treatment difficult.",,98.6,97.2,,,,Good,2018-11-28T19:47:22.518Z,2018-11-28T19:47:22.518Z
42,1093787.3,Pseudomonas aeruginosa DK2,negative,Pseudomonas aeruginosa DK2,1093787,Complete,DK2,,,,MLST.Pseudomonas_aeruginosa.386,,,,2012-06-20T00:00:00Z,,PRJNA73815,SAMN02603895,GCA_000271365.1,,CP003149.1,NC_018080.1,Technical University of Denmark,complete,,,,1,,1,6402658,66.3,5984,5884,Lung,cystic fibrosis patient,isolated from a cystic fibrosis patient,,,,,,,,,"Human, Homo sapiens",,,cystic fibrosis,,,,,,Negative,,,,,,,,Multiple,Commensal (plant),Complete genome of Pseudomonas aeruginosa DK2 strain isolated from a cystic fibrosis patient.,,99.9,98.9,96.7,,,Good,2014-12-08T22:12:37.204Z,2015-03-16T03:17:09.594Z
43,1093790.3,Vibrio cholerae H1,negative,,1093790,Complete,H1,,,,MLST.Vibrio_cholerae.69,,,,2012-06-29T00:00:00Z,,PRJNA73829,SAMN02470784,GCF_000275645.1,,AKGH01000000,,Pacific Biosciences,,454; Illumina GAII; PacBio,421.0x,SMRT Analysis v. 1.3.1 Beta,2,,2,4089020,47.51,3772,,Stool,passed stool,,10-Oct,Haiti,Haiti,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,,,,,,,,,,Haitian Vibrio cholerae Genome Sequencing.,,99.8,99.5,100,,,Good,2016-01-17T15:29:01.873Z,2016-01-17T15:29:01.873Z
44,1095685.4,Neisseria meningitidis M7124,negative,,1095685,Complete,M7124,,,,MLST.Neisseria_spp.11,genotype:ST-11,,,2014-12-09T00:00:00Z,,PRJNA260327,SAMN03020254,GCF_000800275.1,,CP009419,NZ_CP009419.1,University of Pittsburgh,,PacBio,131x,HGAP v. 2.0,1,,1,2179483,51.73,2559,2071,None,,,Mar-00,Saudi Arabia,Saudi Arabia: Mecca,,,,,,"Human, Homo sapiens",,,Invasive meningococcal disease,,,,,,,,,,,,,,,,M7124 Neiseria meningitidis serogroup W ST-11 Hajj reference strain,collected_by:CDC,99.9,99.9,100,,,Good,2016-01-17T15:41:12.030Z,2016-01-17T15:41:12.030Z
45,1096995.4,Acinetobacter baumannii BJAB07104,negative,Acinetobacter baumannii BJAB07104,1096995,Complete,BJAB07104,,,,MLST.Acinetobacter_baumannii_2.2,,,,2013-07-09T00:00:00Z,23826102,PRJNA74421,SAMN02604244,GCA_000419385.1,,"CP003846.1,CP003907.1,CP003887.1","NC_021726.1,NC_021728.1,NC_021727.1",University of Texas at Dallas,complete,Illumina,,VELVET v. 1.0.18,1,2,3,4042229,38.9501,3854,3861,Blood,Blood,isolated from blood sample of a patient with liver cirrhosis in April 2008 and January 2007 respectively.,~2007,China,China: Beijing,,,,,,"Human, Homo sapiens",,,liver cirrhosis,,,,,,,,,,,,,,,,We have sequenced genomes of three multi-drug resistant strains of Acinetobacter baumannii from China in order to identify the sequences related to drug resistance.,,99.3,98.4,100,0.3,,Good,2014-12-08T22:09:35.014Z,2015-03-16T03:17:09.594Z
46,1096996.4,Acinetobacter baumannii BJAB0715,negative,Acinetobacter baumannii BJAB0715,1096996,Complete,BJAB0715,,,,"MLST.Acinetobacter_baumannii_1.642,MLST.Acinetobacter_baumannii_2.23",,,,2013-07-09T00:00:00Z,27458211,PRJNA74423,SAMN02604245,GCA_000419405.1,,"CP003847.1,CP003848.1","NC_021733.1,NC_021734.1",University of Texas at Dallas,complete,Illumina,,VELVET v. 1.0.18,1,1,2,4053889,38.9193,3870,3908,Cerebrospinal Fluid,CSF,isolated from cerebrospinal fluid (CSF) sample of a patient with cerebrospinal rhinorrhea in March 2007.,2007,China,China: Beijing,,,,,,"Human, Homo sapiens",,,cerebrospinal rhinorrhea,,,,Resistant,AMR Panel,,,,,,,,,,,We have sequenced genomes of three multi-drug resistant strains of Acinetobacter baumannii from China in order to identify the sequences related to drug resistance.,,99.1,98.5,100,,,Good,2014-12-08T22:09:35.036Z,2015-03-16T03:17:09.594Z
47,1096997.4,Acinetobacter baumannii BJAB0868,negative,Acinetobacter baumannii BJAB0868,1096997,Complete,BJAB0868,,,,MLST.Acinetobacter_baumannii_2.2,,,,2013-07-09T00:00:00Z,27458211,PRJNA74425,SAMN02604246,GCA_000419425.1,,"CP003849.1,CP003850.1,CP003888.1,CP003908.1","NC_021729.1,NC_021730.1,NC_021731.1,NC_021732.1",University of Texas at Dallas,complete,Illumina,,VELVET v. 1.0.18,1,3,4,4005822,38.9394,3797,3819,Abdomen,Abdominal fluid,ascites-isolated of a patient during March 2007 and April 2008,~2007,China,China: Beijing,,,,,,"Human, Homo sapiens",,,ascites,,,,Resistant,AMR Panel,,,,,,,,,,,We have sequenced genomes of three multi-drug resistant strains of Acinetobacter baumannii from China in order to identify the sequences related to drug resistance.,,99.3,98.5,100,,,Good,2014-12-08T22:09:35.060Z,2015-03-16T03:17:09.594Z
49,1112856.4,Mycoplasma pneumoniae 309,negative,Mycoplasma pneumoniae 309,1112856,Complete,,,,,MLST.Mycoplasma_pneumoniae.2,,,,2011-12-01T00:00:00Z,22328753,PRJNA85495,,GCA_000283755.1,,AP012303.1,NC_016807.1,,,,,,1,,1,817176,39.98,767,707,None,,,,Japan,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,Pneumonia,-,,99.5,99.5,100,,,Good,2014-12-08T22:12:24.413Z,2015-03-16T03:17:09.594Z
50,1122984.13,Prevotella intermedia ATCC 25611 = DSM 20706 strain ATCC 25611,negative,,1122984,Complete,ATCC 25611,,,,,,ATCC: 25611,Yes,2017-01-18T00:00:00Z,,PRJNA313956,SAMN04529094,GCF_001953955.1,,"CP019300,CP019301","NZ_CP019300.1,NZ_CP019301.1",The Forsyth Institute,,PacBio,200.0x,Celera Assembler v. June 2016; HGAP v.,2,,2,2674170,43.44,2643,2283,Lung,Empyema,,1984,USA,United States,,,,,,"Human, Homo sapiens",,,Empyema,,,,,,,,,,,C,,,,,Re-sequencing of the Prevotella intermedia type strain ATCC25611 and clinical isolate Prevotella intermedia strain-17 (January 2016) using using a PacBio RS II system (Pacific Biosciences) on a single-molecule real-time (SMRT) cell using PacBio P6-C4 chemistry.,collected_by:LV Holdeman,98.6,97.7,100,2.5,,Good,2017-03-20T05:11:44.157Z,2017-03-20T05:11:44.157Z
51,1123523.3,Staphylococcus aureus subsp. aureus 11819-97,positive,Staphylococcus aureus subsp. aureus 11819-97,1123523,Complete,11819-97,,,,MLST.Staphylococcus_aureus.80,,,,2011-12-21T00:00:00Z,,PRJNA78269,SAMN02603886,GCA_000239235.1,,"CP003193,CP003194","NC_017351.1,NC_017350.1",Statens Serum Institut,,,,,1,,1,2846546,32.88,2646,2633,Skin,skin abscess,"Danish clinical MRSA isolate, collected from a skin abscess",,Denmark,Denmark,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"""A genome from a representative of the community-associated methicillin-resistant Staphylococcus aureus ST80-IV lineage found throughout Europa, the Middle East and Northern Africa. Specifically, this is a Danish clinical MRSA isolate, 11819-97, collected from a skin abscess, representing the major phylogenetic group from this lineage in in Denmark.""",,100,100,100,,,Good,2014-12-08T22:13:23.528Z,2015-03-16T03:17:09.594Z
52,1123862.3,Klebsiella pneumoniae subsp. pneumoniae Kp13,negative,Klebsiella pneumoniae subsp. pneumoniae Kp13,1123862,Complete,Kp13,,,,MLST.Klebsiella_pneumoniae.442,, ,,2013-12-30T00:00:00Z,,PRJNA78291,SAMN02641520,GCA_000512165.1,,"CP003999.1,CP003998.1,CP004000.1,CP003997.1,CP003994.1,CP003996.1,CP003995.1","NZ_CP003999.1,NZ_CP003996.1,NZ_CP003994.1,NZ_CP003995.1,NZ_CP003997.1,NZ_CP003998.1,NZ_CP004000.1",Laborat¿¿¿¿¿¿rio Nacional de Computa¿¿¿¿¿¿¿¿¿¿o Cient¿¿¿¿¿¿fica,complete,,,,1,6,7,5739888,56.8079,5453,5736,Blood,blood,,2009,Brazil,Brazil,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,The emergence and global spread of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae are a significant threat to public health. This study aims to sequence and analyze one such isolate.,,99.6,97.7,100,0.7,,Good,2014-12-08T22:11:50.898Z,2015-03-16T03:17:09.594Z
54,1124626.4,Mycobacterium ulcerans subsp. shinshuense strain ATCC 33728,positive,,1124626,Complete,ATCC 33728,,,,,,ATCC:33728,,2016-08-27T00:00:00Z,,PRJDB5111,SAMD00057810,GCA_002356495.1,,AP017635,,National Institute of Infectious Diseases,,454; Illumina,25x,Newbler v. 2.6,1,,1,5914588,62.28,5689,,None,,,2005-01,Japan,"Japan:Tokyo, Higashimurayama",,,,,env_biome:human-associated habitat,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,We found non-pigmented clone from pigmented Mycobacteirum shinshuense after routine culture passage. We would like to evaluate M. shinshuense without the plasmid.,,99.1,97.7,98.5,5.8,,Good,2017-11-23T02:27:12.868Z,2017-11-23T02:27:12.868Z
55,1126011.4,Listeria monocytogenes 07PF0776,positive,Listeria monocytogenes 07PF0776,1126011,Complete,07PF0776,,,,MLST.Listeria_monocytogenes.4,,,,2012-04-17T00:00:00Z,22689239,PRJNA78811,SAMN02604190,GCA_000258905.1,,CP003414.1,NC_017728.1,University of Illinois at Chicago,complete,,,,1,,1,2901562,38,2845,2797,None,,,2011,USA,USA: Massachusetts,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,Yes,No,,,,,,,SOLiD Sequencing project for a cardiotropic strain of Listeria monocytogenes.,,99.9,99.3,100,,,Good,2014-12-08T22:12:00.129Z,2015-03-16T03:17:09.594Z
56,1127122.3,Helicobacter pylori XZ274,negative,Helicobacter pylori XZ274,1127122,Complete,XZ274,,,,MLST.Helicobacter_pylori.3039,,,,2012-05-14T00:00:00Z,,PRJNA79003,SAMN02603962,GCA_000262655.1,,"CP003419.1,CP003420.1","NC_017926.1,NC_017919.1",Third Military Medical University,complete,,,,1,1,2,1656544,38.6067,1811,1438,Stomach,female Tibetan gastric cancer patient's stomach,isolated from a female Tibetan gastric cancer patient's stomach in China,,China,China,,,,,,"Human, Homo sapiens",female,,,,,,,,,,,,,,,,,,The Genome Sequence of Helicobater Pylori XZ274.  HP XZ274  was isolated from a female Tibetan gastric cancer patient's stomach in China.,,99.6,97.2,100,5.4,,Good,2014-12-08T22:11:46.516Z,2015-03-16T03:17:09.594Z
57,1132508.3,Mycobacterium abscessus UC22,positive,,1132508,Complete,UC22,,,,,,,,2015-07-09T00:00:00Z,,PRJNA80959,SAMN03839812,GCF_001050395.1,,CP012044,NZ_CP012044.1,Chungnam University,,454; Illumina GAIIx; Sanger,200.69x,Newbler v. 2.6; CLC Genomics Workbench v.,1,,1,5257136,64.04,5309,5042,Lung,upper lobe fibrocavitary form of pulmonary disease,isolate from a patient with the upper lobe fibrocavitary form of pulmonary disease,2011,South Korea,South Korea: Seoul,,,,,,"Human, Homo sapiens",female,43,pulmonary disease,,,,,,,,,,,,,,,,Mycobacterium abscessus UC22 is a high virulent clinical isolate from a patient with the upper lobe fibrocavitary form of pulmonary disease.,collected_by:Samsung Medical Center,98.5,97.2,100,,,Good,2016-01-17T16:12:33.645Z,2016-01-17T16:12:33.645Z
58,1134454.3,Propionibacterium acnes HL096PA1,positive,Propionibacterium acnes HL096PA1,1134454,Complete,HL096PA1,,,,MLST.Propionibacterium_acnes.3,,,,2013-04-22T00:00:00Z,23337890,PRJNA81129,SAMN02604074,GCA_000376705.1,,"CP003293.1,CP003294.1","NC_021085.1,NC_021086.1",UCLA David Geffen School of Medicine,complete,,,,1,1,2,2549775,60.1523,2529,2249,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,,,,,,,,,,"This strain is being sequenced as a reference for the project ""Metagenomic Study of the Human Skin Microbiome Associated with Acne"". ",,99.3,98.3,100,,,Good,2014-12-08T22:12:34.806Z,2015-03-16T03:17:09.594Z
68,1134687.562,Klebsiella michiganensis strain 53828CZ,negative,,1134687,Complete,53828CZ,,,,MLST.Klebsiella_oxytoca.128,,,,2021-11-01T00:00:00Z,,PRJNA772913,SAMN22377421,GCA_020695625.1,,"CP085764,CP085765,CP085766",,Charles University in Prague,,PacBio Sequel,709x,Microbial assembly v. v.1,1,2,3,6455282,55.613605,6423,6045,Respiratory,nose swab,,2019-10,Czech Republic,Czech Republic: Prague,,,,,,Homo sapiens,,,Respiratory distress syndrome,,,,,,,,,,,,,,,,Molecular characterization of VIM-producing Enterobacterales from Czech hospitals,collected_by:Nemocnice Na Homolce,99.7,97.6,,,,Good,2021-12-24T17:52:42.426Z,2021-12-24T17:52:42.426Z
75,1138383.28,Mycobacterium paraintracellulare strain M015,positive,,1138383,Complete,M015,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,SAMD00258724,GCA_016755975.1,,AP024253,,Niigata University School of Medicine,,PacBio RS II,98x,RS_HGAP_Assembly.3 v. 2.3.0,1,,1,5588488,68.01181,5345,5281,Sputum,sputum,,2019,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,99.2,97.9,,,,Good,2021-02-01T08:07:26.339Z,2021-02-01T08:07:26.339Z
76,1150773.3,Streptococcus pyogenes JRS4,positive,,1150773,Complete,JRS4,serovar emm6,,,MLST.Streptococcus_pyogenes.37,,,,2015-06-02T00:00:00Z,,PRJNA283215,SAMN03610013,GCF_001014285.1,,CP011414,NZ_CP011414.1,Washington University School of Medicine,,454; Illumina,167,Newbler v. 2.5.3; DNASTAR SeqMan NGen,1,,1,1811968,38.63,1811,1671,None,,,1971,,,,,,,,"Human, Homo sapiens",,,Rheumatic fever-associated,,,,,,,,,,,C,,,,,We report the complete genome assemblies of the group A Streptococcus pyogenes serotype emm6 strains D471 and its streptomycin-resistant derivative JRS4. Both of these well studied laboratory strains have been extensively characterized over the past three decades and have been instrumental in the discovery of multiple aspects of streptococcal pathogenesis.,collected_by:Rockefeller University Lancefield Collection,100,99.8,100,,,Good,2016-01-17T16:03:54.402Z,2016-01-17T16:03:54.402Z
77,1155096.3,Borrelia crocidurae str. Achema,negative,Borrelia crocidurae str. Achema,1155096,Complete,,,,,,,,,2012-04-20T00:00:00Z,,PRJNA85135,SAMN02604274,GCA_000259345.1,,"CP003426.1,CP003453.1,CP003444.1,CP003434.1,CP003452.1,CP003449.1,CP003458.1,CP003445.1,CP003447.1,CP003427.1,CP003431.1,CP003433.1,CP003451.1,CP003463.1,CP003457.1,CP003430.1,CP003465.1,CP003448.1,CP003454.1,CP003455.1,CP003441.1,CP003438.1,CP003461.1,CP003435.1,CP003436.1,CP003460.1,CP003443.1,CP003437.1,CP003442.1,CP003429.1,CP003439.1,CP003440.1,CP003464.1,CP003428.1,CP003450.1,CP003432.1,CP003456.1,CP003446.1,CP003459.1,CP003462.1",,,,,,,1,38,40,1528893,26.54,1479,1470,None,,,,Senegal,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,-,,99.3,97.7,30.3,0.5,Low CheckM completeness score,Poor,2014-12-08T22:10:32.208Z,2015-03-16T03:17:09.594Z
78,1155766.14,Enterococcus faecium Aus0004,positive,Enterococcus faecium Aus0004,1155766,Complete,Aus0004,,,,MLST.Enterococcus_faecium.17,, ,,2012-03-01T00:00:00Z,,PRJNA86649,SAMN02604218,GCA_000250945.1,,"CP003351.1,CP003352.1,CP003353.1,CP003354.1","NC_017022.1,NC_017032.1,NC_017023.1,NC_017024.1",University of Melbourne,complete,,,,1,1,2,3011814,38.3424,3046,2923,Blood,the bloodstream of a patient,"isolated from the bloodstream of a patient in Melbourne, Australia in 1998",1998,Australia,Australia: Melbourne,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Vancomycin-resistant Enterococcus faecium (VRE) is one of the leading causes of nosocomial infections in healthcare facilities around the globe. VRE strain Aus0004 belongs to a common epidemic clone, multi locus sequence type 17, and was isolated from the bloodstream of a patient in Melbourne, Australia in 1998.",,98.7,97.2,100,,,Good,2014-12-08T22:11:15.995Z,2015-03-16T03:17:09.594Z
80,1163739.3,Helicobacter pylori Shi417,negative,Helicobacter pylori Shi417,1163739,Complete,Shi417,,,,MLST.Helicobacter_pylori.3046,,,,2012-04-19T00:00:00Z,,PRJNA94345,SAMN02603193,GCA_000277365.1,,CP003472.1,NC_017739.1,"Dept. Molec. Microbiology, Washington University Medical School in Saint Louis",complete,,,,1,,1,1665719,38.8,1638,1548,None,,,,Peru,Peru: Shimaa,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,Commensal,"To compare genomes of Helicobacter pylori, to study their evolution and migration patterns in different human populations.  Helicobacter pylori strain from Amerindian volunteer from remote Shimaa village in Amazon region in Peru.",,99.7,99.2,100,0.3,,Good,2014-12-08T22:11:46.287Z,2015-03-16T03:17:09.594Z
81,1163740.3,Helicobacter pylori Shi112,negative,Helicobacter pylori Shi112,1163740,Complete,Shi112,,,,MLST.Helicobacter_pylori.3044,,,,2012-04-19T00:00:00Z,,PRJNA94347,SAMN02603194,GCA_000277405.1,,CP003474.1,NC_017741.1,"Dept. Molec. Microbiology, Washington University Medical School in Saint Louis",complete,,,,1,,1,1663456,38.8,1654,1564,None,,,,Peru,Peru: Shimaa,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,Commensal,"To compare genomes of Helicobacter pylori, study their evolution and migration patterns in different human populations.  Helicobacter pylori strain from Amerindian volunteer from remote Shimaa village in Amazon region in Peru.",,99.8,99,100,,,Good,2014-12-08T22:11:46.269Z,2015-03-16T03:17:09.594Z
82,1163741.3,Helicobacter pylori Shi169,negative,Helicobacter pylori Shi169,1163741,Complete,Shi169,,,,MLST.Helicobacter_pylori.3045,,,,2012-04-19T00:00:00Z,,PRJNA94507,SAMN02603195,GCA_000277385.1,,CP003473.1,NC_017740.1,"Dept. Molec. Microbiology, Washington University Medical School in Saint Louis",complete,,,,1,,1,1616909,38.9,1604,1525,None,,,,Peru,Peru: Shimaa,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,Commensal,"To compare genomes of Helicobacter pylori, to study their evolution and migration patterns in different human populations.  Helicobacter pylori strain from Amerindian volunteer from remote Shimaa village in Amazon region in Peru.",,99.8,99.6,99.1,,,Good,2014-12-08T22:11:46.277Z,2015-03-16T03:17:09.594Z
83,1163742.3,Helicobacter pylori PeCan18,negative,Helicobacter pylori PeCan18,1163742,Complete,PeCan18,,,,MLST.Helicobacter_pylori.3028,,,,2012-04-19T00:00:00Z,,PRJNA95275,SAMN02603196,GCA_000277425.1,,CP003475.1,NC_017742.1,"Dept. Molec. Microbiology, Washington University Medical School in Saint Louis",complete,,,,1,,1,1660685,39,1633,1495,Stomach,"gastric antrum from resident of Lima, Peru","isolate from gastric antrum from resident of Lima, Peru",,Peru,Peru: Lima,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,Commensal,"To compare genomes of Helicobacter pylori, to study their evolution and migration patterns in different human populations.  Clinical isolate from gastric antrum from resident of Lima, Peru.",,99.6,99.2,100,0.6,,Good,2014-12-08T22:11:45.328Z,2015-03-16T03:17:09.594Z
84,1163743.3,Helicobacter pylori HUP-B14,negative,Helicobacter pylori HUP-B14,1163743,Complete,HUP-B14,,,,MLST.Helicobacter_pylori.3021,,,,2012-04-19T00:00:00Z,,PRJNA95277,SAMN02603197,GCA_000259235.1,,"CP003486.1,CP003487.1","NC_017733.1,NC_017734.1","Dept. Molec. Microbiology, Washington University Medical School in Saint Louis",complete,,,,1,1,2,1607584,39.0866,1597,1501,None,resident of Spain,isolate from resident of Spain,,Spain,Spain,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"To compare genomes of Helicobacter pylori, to study their evolution and migration patterns in different human populations.  Clinical isolate from resident of Spain.",,99.9,99.8,100,,,Good,2014-12-08T22:11:44.348Z,2015-03-16T03:17:09.594Z
85,1170318.3,Propionibacterium avidum 44067,positive,Propionibacterium avidum 44067,1170318,Complete,44067,,,,,,,,2013-04-17T00:00:00Z,,PRJNA157751,SAMN02603001,GCA_000367205.1,,CP005287.1,NC_021064.1,BAYGEN,complete,454; SOLiD,375,Newbler v. 2.8; CLC Genomics Workbench v.,1,,1,2526138,63.5,2362,2242,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,genome sequencing,,99.4,98.7,99.2,,,Good,2014-12-08T22:12:35.060Z,2015-03-16T03:17:09.594Z
86,1173427.6,Salmonella enterica subsp. enterica serovar Bareilly str. CFSAN000189,negative,,1173427,Complete,CFSAN000189,Bareilly,,,MLST.Salmonella_enterica.909,,,,2019-11-15T00:00:00Z,31704961,PRJNA498670,SAMN04364135,GCA_009667855.1,,"CP034177,CP034178",,USDA,,Oxford Nanopore MiniION,599.0x,Unicycler v. 10-2018,1,1,2,4806620,52.210037,4892,4663,None,,,,United Kingdom,United Kingdom,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Sequenced two of the most prominent foodborne pathogens that cause severe human illnesses worldwide, Enterohemorrhagic Escherichia coli O157:H7 and Salmonella enterica subsp. enterica serovar Bareilly with Oxford Nanopore’s MinION sequencer, and the whole genomes of both samples were assembled and polished with only a 0.1% error rate.",collected_by:PHE,97,96.3,,,,Good,2019-12-30T21:10:57.272Z,2019-12-30T21:10:57.272Z
89,1185650.4,Mycobacterium abscessus subsp. abscessus strain 936,positive,,1185650,Complete,4529,,,,,,ATCC:BEI,,2014-10-31T00:00:00Z,,PRJNA263504,SAMN03103574,GCF_000770215.1,,CP009616,NZ_CP009616.1,BEI Resources/American Type,,Illumina,150.98x,CLC Genomics Workbench v. 7.0.2,1,,1,4687494,64.33,4650,4531,Sputum,sputum,,,USA,USA: Texas,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of several mycobacterial species,passage_history:3,98.4,97.3,100,,,Good,2016-01-17T15:40:32.002Z,2016-01-17T15:40:32.002Z
90,1191061.3,Klebsiella oxytoca E718,negative,Klebsiella oxytoca E718,1191061,Complete,E718,,,,MLST.Klebsiella_oxytoca.27,,,,2012-07-09T00:00:00Z,,PRJNA167370,SAMN02603642,GCA_000276705.2,,"CP003683.1,CP003684.1","NC_018106.1,NC_021501.1,NC_018107.1",National Chung Hsing University,complete,,,,1,1,2,6450897,55.5337,6111,5909,None,patient underwent renal transplantation,"isolated in 2010, from a patient underwent renal transplantation in China then presented to a hospital in Taiwan 7 days later",2010,China,China,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,"Genomic sequencing of an NDM-1 positive antimicrobial resistance Klebsiella oxytoca strain.  A K. oxytoca clinical isolated in 2010, from a patient underwent renal transplantation in China then presented to a hospital in Taiwan 7 days later. Culture from the pelvic abscess fluid found this strain producing NDM-1 metallo beta-lactamase.",,99.6,97.8,100,1.7,,Good,2014-12-08T22:11:48.635Z,2015-03-16T03:17:09.594Z
92,1196159.3,Listeria monocytogenes serotype 4b str. 81-0558 strain 81-0558,positive,,1196159,Complete,81-0558,4b,,,MLST.Listeria_monocytogenes.1,,,,2017-06-30T00:00:00Z,,PRJNA167872,SAMN02713777,,,CP007525,,Public Health Agency of Canada,,454 Illumina,411_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2971543,37.96,2969,2911,Cerebrospinal Fluid,CSF,,1-Jun-81,Canada,Canada: Halifax,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,collected_by:Public Health Agency of Canada,99.9,99.3,100,,,Good,2017-07-23T04:19:53.169Z,2017-07-23T04:19:53.169Z
93,1196160.3,Listeria monocytogenes serotype 4b str. 81-0592 strain 81-0592,positive,,1196160,Complete,81-0592,4b,,,MLST.Listeria_monocytogenes.1,,,,2017-06-30T00:00:00Z,,PRJNA167873,SAMN02713778,,,CP007526,,Public Health Agency of Canada,,454 Illumina,328_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2975864,37.96,2976,2925,Blood,fetal blood,,1-Jul-81,Canada,Canada: Halifax,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,collected_by:Public Health Agency of Canada,99.9,99.3,100,,,Good,2017-07-23T04:20:09.943Z,2017-07-23T04:20:09.943Z
94,1196162.3,Listeria monocytogenes serotype 4b str. 10-0809 strain 10-0809,positive,,1196162,Complete,10-0809,4b,,,MLST.Listeria_monocytogenes.1,,,,2017-07-03T00:00:00Z,,PRJNA167875,SAMN07124730,,,CP007167,,Public Health Agency of Canada,,454 Illumina,328_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2975853,37.96,2976,2925,Stool,Stool,,1981,Canada,Canada: Nova Scotia,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Bureau of Microbial Hazards,99.9,99.4,100,,,Good,2017-07-23T04:21:54.173Z,2017-07-23T04:21:54.173Z
95,1196163.3,Listeria monocytogenes serotype 1/2b str. 10-0810 strain 10-0810,positive,,1196163,Complete,10-0810,1/2b,,,MLST.Listeria_monocytogenes.5,,,,2017-07-03T00:00:00Z,,PRJNA167876,SAMN07124731,,,CP007168,,Public Health Agency of Canada,,454 Illumina,461_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,3017944,37.96,3031,2962,Stool,Stool,,1996,Canada,Canada: Ontario,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Bureau of Microbial Hazards,99.9,99.4,100,,,Good,2017-07-23T04:24:09.957Z,2017-07-23T04:24:09.957Z
96,1196166.3,Listeria monocytogenes serotype 1/2a str. 10-0813 strain 10-0813,positive,,1196166,Complete,10-0813,1/2a,,,MLST.Listeria_monocytogenes.7,,,,2017-07-03T00:00:00Z,,PRJNA167879,SAMN07124734,,,CP007171,,Public Health Agency of Canada,,454 Illumina,316_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2942234,37.96,2950,2884,Blood,Blood,,2000,Canada,Canada: Manitoba,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Bureau of Microbial Hazards,100,99.7,100,,,Good,2017-07-23T04:24:44.709Z,2017-07-23T04:24:44.709Z
97,1196167.3,Listeria monocytogenes serotype 1/2a str. 10-4754 strain 10-4754,positive,,1196167,Complete,Oct-54,1/2a,,,MLST.Listeria_monocytogenes.37,,,,2017-06-30T00:00:00Z,,PRJNA167880,SAMN07124735,,,CP007197,,Public Health Agency of Canada,,454 Illumina,796_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2910922,37.98,2907,2851,Cerebrospinal Fluid,CSF,,2002,Canada,Canada: Quebec,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Laboratoire de la sante publique du Quebec,100,99.7,100,,,Good,2017-07-23T04:17:47.062Z,2017-07-23T04:17:47.062Z
98,1196169.3,Listeria monocytogenes serotype 1/2a str. 10-0933 strain 10-0933,positive,,1196169,Complete,10-0933,1/2a,,,MLST.Listeria_monocytogenes.394,,,,2017-06-30T00:00:00Z,,PRJNA167882,SAMN07124737,,,CP007199,,Public Health Agency of Canada,,454 Illumina,166_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2870277,38.02,2846,2795,Blood,Blood,,2008,Canada,Canada: Quebec,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Laboratoire de la sante publique du Quebec,100,99.7,100,,,Good,2017-07-23T04:18:59.336Z,2017-07-23T04:18:59.336Z
99,1196171.3,Listeria monocytogenes serotype 4b str. 02-1103 strain 02-1103,positive,,1196171,Complete,02-1103,4b,,,MLST.Listeria_monocytogenes.1,,,,2017-06-30T00:00:00Z,,PRJNA167884,SAMN07124739,,,CP007459,,Public Health Agency of Canada,,454 Illumina,1049_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2979105,37.95,2979,2918,Cerebrospinal Fluid,CSF,,2002,Canada,Canada: British Columbia,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:BC Centre for Disease Control Site,99.9,99.3,100,,,Good,2017-07-23T04:18:37.904Z,2017-07-23T04:18:37.904Z
100,1196172.3,Listeria monocytogenes serotype 4b str. 02-1289 strain 02-1289,positive,,1196172,Complete,02-1289,4b,,,MLST.Listeria_monocytogenes.1,,,,2017-06-30T00:00:00Z,,PRJNA167885,SAMN07124740,,,CP007460,,Public Health Agency of Canada,,454 Illumina,1086_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2979105,37.95,2979,2918,Stool,Stool,,2002,Canada,Canada: British Columbia,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:BC Centre for Disease Control Site,99.9,99.3,100,,,Good,2017-07-23T04:19:18.123Z,2017-07-23T04:19:18.123Z
101,1196174.3,Listeria monocytogenes serotype 4b str. 02-6679 strain 02-6679,positive,,1196174,Complete,Feb-79,4b,,,MLST.Listeria_monocytogenes.388,,,,2017-06-30T00:00:00Z,,PRJNA167887,SAMN02944848,,,CP008821,,Public Health Agency of Canada,,454 Illumina,1058x,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2908004,38,2873,2825,Stool,stool,,2002,Canada,Canada: Vancouver,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,collected_by:Public Health Agency of Canada,99.9,99.4,100,,,Good,2017-07-23T04:06:53.376Z,2017-07-23T04:06:53.376Z
102,1196176.3,Listeria monocytogenes serotype 1/2a str. 88-0478,positive,,1196176,Complete,88-0478,,,,,,,,2014-01-07T00:00:00Z,,PRJNA167889,,GCF_000513695.1,,CP006862,NZ_CP006862.1,Public Health Agency of Canada,,454 Illumina,883_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2994351,37.97,3027,2941,Blood,blood,,1988,Canada,Canada,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,,100,99.5,99.4,,,Good,2016-08-26T16:14:00.032Z,2016-08-26T16:14:00.032Z
103,1196177.3,Listeria monocytogenes serotype 1/2a str. 95-0093 strain 95-0093,positive,,1196177,Complete,95-0093,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167890,SAMN07124743,,,CP007019,,Public Health Agency of Canada,,454 Illumina,875_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,3000273,37.96,3031,2950,Blood,Blood,,1995,Canada,Canada: Alberta,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Provlab Alberta,100,99.5,100,,,Good,2017-07-23T04:14:52.935Z,2017-07-23T04:14:52.935Z
104,1196178.3,Listeria monocytogenes serotype 1/2a str. 98-2035 strain 98-2035,positive,,1196178,Complete,98-2035,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167891,SAMN07124744,,,CP007020,,Public Health Agency of Canada,,454 Illumina,418_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,3032209,37.96,3071,2993,Blood,Blood,,1998,Canada,Canada: Ontario,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,100,99.4,100,0.3,,Good,2017-07-23T04:15:13.843Z,2017-07-23T04:15:13.843Z
105,1196179.3,Listeria monocytogenes serotype 1/2a str. 99-6370 strain 99-6370,positive,,1196179,Complete,99-6370,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167892,SAMN07124745,,,CP007021,,Public Health Agency of Canada,,454 Illumina,758_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,3032209,37.96,3072,2993,Blood,Blood,,1999,Canada,Canada: Ontario,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,100,99.4,100,0.3,,Good,2017-07-23T04:15:26.286Z,2017-07-23T04:15:26.286Z
106,1196180.3,Listeria monocytogenes serotype 1/2a str. 02-5993 strain 02-5993,positive,,1196180,Complete,Feb-93,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167893,SAMN07124746,,,CP007007,,Public Health Agency of Canada,,454 Illumina,946_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2999248,37.97,3028,2948,Blood,Blood,,2002,Canada,Canada: Ontario,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,100,99.5,100,,,Good,2017-07-23T04:11:29.443Z,2017-07-23T04:11:29.443Z
107,1196181.4,Listeria monocytogenes serotype 1/2a str. 04-5457,positive,,1196181,Complete,Apr-57,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167894,SAMN07124747,GCA_002213565.1,,CP007008,,Public Health Agency of Canada,,454 Illumina,795_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2999326,37.97,3026,2948,Blood,Blood,,2004,Canada,Canada: Ontario,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,100,99.4,100,0.3,,Good,2017-09-29T15:34:42.137Z,2017-09-29T15:34:42.137Z
108,1196184.3,Listeria monocytogenes serotype 1/2a str. 08-6997,positive,,1196184,Complete,Aug-97,,,,,,,,2014-01-07T00:00:00Z,,PRJNA167897,,GCF_000513635.1,,CP006859,NZ_CP006859.1,Public Health Agency of Canada,,454 Illumina,722_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,3032624,37.96,3073,2991,Blood,blood,,2008,Canada,Canada,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,,100,99.4,100,0.3,,Good,2016-08-26T16:14:45.189Z,2016-08-26T16:14:45.189Z
109,1196186.3,Listeria monocytogenes serotype 1/2a str. 08-7669 strain 08-7669,positive,,1196186,Complete,Aug-69,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167899,SAMN07124750,,,CP007011,,Public Health Agency of Canada,,454 Illumina,115_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2954577,38.01,2959,2889,Blood,Blood,,2008,Canada,Canada: Saskatchewan,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,100,99.5,100,,,Good,2017-07-23T04:13:54.602Z,2017-07-23T04:13:54.602Z
110,1196189.3,Listeria monocytogenes serotype 1/2a str. 10-1046 strain 10-1046,positive,,1196189,Complete,10-1046,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167902,SAMN07124751,,,CP007017,,Public Health Agency of Canada,,454 Illumina,120_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2998206,37.97,3026,2941,Blood,Blood,,2010,Canada,Canada: Ontario,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,100,99.5,100,,,Good,2017-07-23T04:13:42.049Z,2017-07-23T04:13:42.049Z
111,1196190.3,Listeria monocytogenes serotype 1/2a str. 10-1047,positive,,1196190,Complete,10-1047,,,,,,,,2014-01-07T00:00:00Z,,PRJNA167903,,GCF_000513675.1,,CP006861,NZ_CP006861.1,Public Health Agency of Canada,,454 Illumina,378_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2998206,37.97,3028,2941,Cerebrospinal Fluid,CSF,,2010,Canada,Canada,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,,100,99.5,100,,,Good,2016-08-26T16:14:20.856Z,2016-08-26T16:14:20.856Z
112,1196191.3,Listeria monocytogenes serotype 1/2a str. 10-1321 strain 10-1321,positive,,1196191,Complete,10-1321,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167904,SAMN07124752,,,CP007018,,Public Health Agency of Canada,,454 Illumina,315_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2999326,37.97,3026,2947,Blood,Blood,,2010,Canada,Canada: Ontario,,,,,,"Human, Homo sapiens",,,Listeriosis,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,100,99.5,100,,,Good,2017-07-23T04:14:55.992Z,2017-07-23T04:14:55.992Z
117,1198627.3,Mycobacterium massiliense str. GO 06,positive,Mycobacterium massiliense str. GO 06,1198627,Complete,GO 06,,,,MLST.Mycobacterium_massiliense.4,,,,2012-07-16T00:00:00Z,22965084,PRJNA168263,,GCA_000277775.2,,CP003699.1,NC_018150.1,University of Brasilia,complete,,,,1,,1,5068807,64.2,5085,2626,Wound,wound samples of patients submitted to arthroscopic and laparoscopic surgeries had its genome sequenced,recovered from wound samples of patients submitted to arthroscopic and laparoscopic surgeries had its genome sequenced,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,Bacilli,No,No,Mesophilic,,Unknown,Aerobic,HostAssociated,Mycobacteriosis,Mycobacterium massiliense is a rapidly growing bacteria associated with opportunistic infections. A representative isolate (strain GO 06) recovered from wound samples of patients submitted to arthroscopic and laparoscopic surgeries had its genome sequenced.,,98,96.6,100,0.1,,Good,2014-12-08T22:12:07.793Z,2015-03-16T03:17:09.594Z
118,1199187.3,Mycobacterium avium subsp. paratuberculosis MAP4,positive,Mycobacterium avium subsp. paratuberculosis MAP4,1199187,Complete,MAP4,,,,,,,,2013-05-09T00:00:00Z,,PRJNA168471,SAMN02603716,GCA_000390085.1,,CP005928.1,NC_021200.1,Penn State University,complete,Sanger dideoxy sequencing; 454,18x,DNAStar Lasergene v. 11,1,,1,4829424,69.3,4603,4326,None,"humans and those associated with bovine Johne¿¿¿¿¿¿¿s disease, we characterized the complete genome sequence of strain MAP4 recovered from the breast milk of a Crohn¿¿¿¿¿¿¿s disease patient","recovered from humans and those associated with bovine Johne¿¿¿¿¿¿¿s disease, we characterized the complete genome sequence of strain MAP4 recovered from the breast milk of a Crohn¿¿¿¿¿¿¿s disease patient",,,,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,No,Yes,,,,,,,"Mycobacterium avium subspecies paratuberculosis (MAP) has been identified in some human patients with Crohn's disease. In order to identify genetic differences between MAP isolates recovered from humans and those associated with bovine Johne¿¿¿¿¿¿¿s disease, we characterized the complete genome sequence of strain MAP4 recovered from the breast milk of a Crohn¿¿¿¿¿¿¿s disease patient.",,98.7,97.7,100,,,Good,2014-12-08T22:12:06.208Z,2015-03-16T03:17:09.594Z
119,1199191.3,Legionella pneumophila subsp. pneumophila str. Thunder Bay,negative,Legionella pneumophila subsp. pneumophila str. Thunder Bay,1199191,Complete,Lp6,,,,,,,,2013-06-03T00:00:00Z,,PRJNA168333,SAMN02603729,GCA_000404245.1,,CP003730.1,NC_021350.1,Public Health Ontario,complete,,,,1,,1,3455167,38.2,3319,2998,None,38 year old male,"isolated from a 38 year old male in Northern Ontario, Canada",,Canada,Northern Ontario: Canada,,,,,,"Human, Homo sapiens",male,38,,,,,,,Negative,Bacilli,Yes,No,Unknown,,Unknown,Aerobic,Aquatic,Legionaires' disease,"Legionella pneumophila Lp6 account for the highest incidence of of non-Lp1 related Legionella infections. The genome presented here has been manually annotated and therefore provides a robust picture of a non-Lp1 clinical sample.   Strain isolated from a 38 year old male in Northern Ontario, Canada. ;missing tRNA genes",,99.5,99.3,100,,,Good,2014-12-08T22:11:55.871Z,2015-03-16T03:17:09.594Z
120,1200752.3,Escherichia coli NCCP15648,negative,,1200752,Complete,NCCP15648,,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",,,,2017-08-02T00:00:00Z,,PRJNA168631,SAMN02928551,GCA_003433275.1,,"CP009050,CP009051,CP009052,CP009053",,Yonsei University,,HiSeq2000,"1,205x",CLC Genomics workbench v. 5.1,1,3,4,5588834,50.603848,5710,5343,Stool,stool,isolated from a patient with diarrhea and has Shiga-like toxin genes and eaeA,2001,South Korea,South Korea,,,,,,"Human, Homo sapiens",,,diarrhea,,,,,,Negative,,,,Mesophilic,,,Facultative,HostAssociated,,Escherichia coli NCCP15648 was isolated from a patient with diarrhea and has Shiga-like toxin genes and eaeA. The genome sequence will be used for comparative analysis with those of other pathogenic E. coli strains.,,99.9,98.7,100,,,Good,2018-10-02T02:54:36.654Z,2018-10-02T02:54:36.654Z
122,1203599.7,Mycobacterium yongonense strain Asan 36912,positive,,1203599,Complete,Asan 36912,,,,,,,,2017-05-17T00:00:00Z,,PRJNA308264,SAMN04390158,,,CP015964,,Seoul National University College of Medicine,,,,,1,,1,5445538,68.02,5211,5156,None,,,2010-10,South Korea,South Korea: Seoul,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,Complete genome sequence of Mycobacterium yongonense MOTT-12 (Asan 36912),sample_type:isolated bacteria,99.4,98.2,100,,,Good,2017-05-30T00:40:00.889Z,2017-05-30T00:40:00.889Z
123,1205674.3,Mycobacterium canettii CIPT 140070010,positive,Mycobacterium canettii CIPT 140070010,1205674,Complete,CIPT 140070010,,,,,, ,,2012-12-19T00:00:00Z,23291586,PRJNA184389,SAMEA2271950,GCA_000328785.1,,FO203509.1,NC_019951.1,Genoscope CEA,complete,,,1,1,,1,4525948,65.5,4370,4076,Skin,Skin,human clinical isolates,2004,Djibouti,Djibouti,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"The genome sequences of four clinical isolates of tubercle bacilli with smooth colony morphology (hereafter referred to as smTB) to be deposited in the EMBL databases have been determined by using 4X Sanger shotgun, 16X Roche 454 and 50X Illumina sequencing, which has allowed together with an extensive finishing phase high quality draft sequences of the 4 genomes to be generated that were annotated and expert-curated by using the MaGe annotation platform at the Genoscope in Evry, France. The sequences are related to the Mycobacterium canettii strain (EMBL accession number PRJEA68135) recently deposited by the Sanger Institute, which is also included in this collaborative project. The genome data are of great value for reconstructing the ancestral gene pool before the clonal emergence of Mycobacterium tuberculosis and for determining the molecular events involved.",,99.5,98.9,98.9,,,Good,2014-12-08T22:12:07.306Z,2015-03-16T03:17:09.594Z
124,1205675.3,Mycobacterium canettii CIPT 140070008,positive,Mycobacterium canettii CIPT 140070008,1205675,Complete,CIPT 140070008,,,,,, ,,2012-12-19T00:00:00Z,23291586,PRJNA184401,SAMEA2272599,GCA_000328845.1,,FO203508.1,NC_019965.1,Genoscope CEA,complete,,,1,1,,1,4420197,65.53,4329,4050,Lymph Node,Lymph node,human clinical isolates,1997,Djibouti,Djibouti,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"The genome sequences of four clinical isolates of tubercle bacilli with smooth colony morphology (hereafter referred to as smTB) to be deposited in the EMBL databases have been determined by using 4X Sanger shotgun, 16X Roche 454 and 50X Illumina sequencing, which has allowed together with an extensive finishing phase high quality draft sequences of the 4 genomes to be generated that were annotated and expert-curated by using the MaGe annotation platform at the Genoscope in Evry, France. The sequences are related to the Mycobacterium canettii strain (EMBL accession number PRJEA68135) recently deposited by the Sanger Institute, which is also included in this collaborative project. The genome data are of great value for reconstructing the ancestral gene pool before the clonal emergence of Mycobacterium tuberculosis and for determining the molecular events involved.",,99.1,98.4,98.9,,,Good,2014-12-08T22:12:07.297Z,2015-03-16T03:17:09.594Z
125,1205676.3,Mycobacterium canettii CIPT 140060008,positive,Mycobacterium canettii CIPT 140060008,1205676,Complete,CIPT 140060008,,,,,, ,,2012-12-19T00:00:00Z,23291586,PRJNA184390,SAMEA2272709,GCA_000328805.1,,FO203507.1,NC_019950.1,Genoscope CEA,complete,,,1,1,,1,4432426,65.55,4309,4041,Lung,Pulmonary,human clinical isolates,1999,Djibouti,Djibouti,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"The genome sequences of four clinical isolates of tubercle bacilli with smooth colony morphology (hereafter referred to as smTB) to be deposited in the EMBL databases have been determined by using 4X Sanger shotgun, 16X Roche 454 and 50X Illumina sequencing, which has allowed together with an extensive finishing phase high quality draft sequences of the 4 genomes to be generated that were annotated and expert-curated by using the MaGe annotation platform at the Genoscope in Evry, France. The sequences are related to the Mycobacterium canettii strain (EMBL accession number PRJEA68135) recently deposited by the Sanger Institute, which is also included in this collaborative project. The genome data are of great value for reconstructing the ancestral gene pool before the clonal emergence of Mycobacterium tuberculosis and for determining the molecular events involved.",,99.6,98.7,100,,,Good,2014-12-08T22:12:07.260Z,2015-03-16T03:17:09.594Z
126,1205677.3,Mycobacterium canettii CIPT 140070017,positive,Mycobacterium canettii CIPT 140070017,1205677,Complete,CIPT 140070017,,,,,, ,,2012-12-19T00:00:00Z,23291586,PRJNA184391,SAMEA2272217,GCA_000328825.1,,FO203510.1,NC_019952.1,Genoscope CEA,complete,,,1,1,,1,4524466,65.5,4380,4091,Lymph Node,Lymph node,human clinical isolates,1997,Djibouti,Djibouti,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"The genome sequences of four clinical isolates of tubercle bacilli with smooth colony morphology (hereafter referred to as smTB) to be deposited in the EMBL databases have been determined by using 4X Sanger shotgun, 16X Roche 454 and 50X Illumina sequencing, which has allowed together with an extensive finishing phase high quality draft sequences of the 4 genomes to be generated that were annotated and expert-curated by using the MaGe annotation platform at the Genoscope in Evry, France. The sequences are related to the Mycobacterium canettii strain (EMBL accession number PRJEA68135) recently deposited by the Sanger Institute, which is also included in this collaborative project. The genome data are of great value for reconstructing the ancestral gene pool before the clonal emergence of Mycobacterium tuberculosis and for determining the molecular events involved.",,99.3,98.3,100,,,Good,2014-12-08T22:12:07.325Z,2015-03-16T03:17:09.594Z
127,1206745.3,Helicobacter cinaedi ATCC BAA-847,negative,Helicobacter cinaedi ATCC BAA-847,537971,Complete,ATCC BAA-847,,,,MLST.Helicobacter_cinaedi.19,,ATCC BAA-847,Yes,2012-07-19T00:00:00Z,23012276,PRJDB113,,GCA_000349975.1,,AP012492.1,NC_020555.1,National Center for Global Health and Medicine,complete,"ABI3730xl, Roche 454, Illumina MiSeq",20x,GS De Novo Assembler v. 2.6,1,,1,2240130,38.3,2506,2322,Stool,rectal swab,rectal swab,1980,USA,"Washington, USA",,,,,,"Human, Homo sapiens",,,,rectum,,,,,,,,,,,,,,,"Helicobacter cinaedi is one of the emerging  pathogens, which is often isolated from blood stream. We determined the whole genome sequence of the type strain of H. cinaedi, ATCC BAA-847 for the first time.",,97.3,96.3,93.2,1.9,,Good,2014-12-08T22:11:43.192Z,2015-03-16T03:17:09.594Z
128,1207470.4,Streptococcus pyogenes M1 476,positive,Streptococcus pyogenes M1 476,1207470,Complete,476,,,,MLST.Streptococcus_pyogenes.28,, ,,2012-07-14T00:00:00Z,22965090,PRJDB141,,GCA_000349925.2,,AP012491.1,NC_020540.1,National Center for Global Health and Medicine,complete,"ABI3730xl, Roche 454, Illumina MiSeq",20x,GS De Novo Assembler v. 2.6,1,,1,1831079,38.5,1929,1849,None,streptococcal toxic shock syndrome case (STSS) during pregnancy,isolated from a streptococcal toxic shock syndrome case (STSS) during pregnancy,1994,,,,,,,,"Human, Homo sapiens",female,,,,,,,,,,,,,,,,,Toxic shock syndrome,We report the completely annotated genome sequence of Streptococcus pyogens M1 476 isolated from a streptococcal toxic shock syndrome case (STSS) during pregnancy. The genome sequence will provide new insights into the underlying mechanisms to cause STSS,,99.6,97.9,100,5,,Good,2014-12-08T22:13:35.796Z,2015-03-16T03:17:09.594Z
131,1214063.4,Mycobacterium intracellulare M.i.198,positive,,1214063,Complete,M.i.198,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,SAMD00258721,GCA_016755915.1,,AP024265,,Niigata University School of Medicine,,PacBio RS II,73x,RS_HGAP_Assembly.3 v. 2.3.0,1,,1,5445552,68.04785,5355,5277,Sputum,sputum,,2005,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,98.9,96.9,,,,Good,2021-02-01T08:08:18.681Z,2021-02-01T08:08:18.681Z
132,1215088.3,Pseudomonas putida HB3267,negative,Pseudomonas putida HB3267,1215088,Complete,HB3267,,,,MLST.Pseudomonas_putida.15,,,,2012-12-19T00:00:00Z,,PRJNA171349,SAMN02604102,GCA_000325725.1,,CP003738.1,NC_019905.1,Universidad de Huelva,complete,,,1,1,,1,5875750,62.6,5321,5292,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Multi-Drug resistant,,98.9,97.4,100,,,Good,2014-12-08T22:12:39.022Z,2015-03-16T03:17:09.594Z
133,1224154.5,Vibrio cholerae O1 str. Inaba G4222,negative,,1224154,Complete,Inaba G4222,,,,MLST.Vibrio_cholerae.69,,,,2015-03-19T00:00:00Z,,PRJNA172960,SAMN02469666,GCF_000338075.1,,ANNB01000000,,CSIR,,454,11.0x,Newbler v. 2.6,2,,2,4202811,47.48,3942,3823,Stool,cholera patient stool sample,Isolated in 2001,2001,South Africa,South Africa: Gauteng,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Vibrios,Yes,,,,,,,,"Vibrio cholerae G4222 Genome Sequence. Clinical Isolate, Isolated in 2001.",,99.7,98.4,100,1.5,,Good,2016-01-17T15:30:18.962Z,2016-01-17T15:30:18.962Z
134,1224745.3,Peptoclostridium difficile BJ08,negative,,1224745,Complete,BJ08,,,,,,,,2015-05-20T00:00:00Z,,PRJNA173024,SAMN03466598,GCA_001010825.1,,CP003939,,"National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention",,Illumina,420x,SOAPdenovo v. 2.20,1,,1,4133893,28.73,3774,,None,,,2008,China,China: Beijing,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Clostridium difficile, the pathogen of Clostridium difficile infection (CDI), is a Gram-positive, spore-forming bacillus.;missing tRNA genes",sample_type:cell culture,95.5,95,96.7,0.7,,Good,2016-01-17T16:03:09.762Z,2016-01-17T16:03:09.762Z
135,1225181.3,Klebsiella pneumoniae subsp. pneumoniae KPNIH24,negative,,1225181,Complete,KPNIH24,,,,MLST.Klebsiella_pneumoniae.258,,,,2014-06-27T00:00:00Z,-,PRJNA173233,SAMN02786855,GCA_000714675.1,,"CP008797.1,CP008800.1,CP008799.1,CP008798.1","NZ_CP008797.1,NZ_CP008798.1,NZ_CP008799.1,NZ_CP008800.1",NISC,,Pacific Biosciences RS II,173x,HGAP v. 2,1,1,4,5734564,57.1176,5550,5344,Throat,throat/groin,,2012,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae.,,99.3,97.9,100,,,Good,2014-12-08T22:33:27.644Z,2015-03-16T03:17:09.594Z
136,1225197.5,Streptococcus mutans B04Sm5,positive,,1225197,Complete,B04Sm5,,,,,,,,2020-09-17T00:00:00Z,,PRJNA661123,SAMN16014813,GCA_014621675.1,,CP061071,,J. Craig Venter Institute,,Illumina MiSeq; Oxford Nanopore GridION,3000.0x,SPAdes v. 3.14.0; Flye v. 2.8-b1674;,1,,1,2011542,36.911682,1975,1880,Wound,carious lesion,,2014,USA,USA: New York City,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Whole genome sequence of B04Sm5, a reutericyclin and mutanocyclin producing strain of Streptococcus mutans",,99.9,99.4,,,,Good,2020-11-28T13:57:13.177Z,2020-11-28T13:57:13.177Z
137,1229492.3,Staphylococcus aureus 08BA02176,positive,Staphylococcus aureus 08BA02176,1229492,Complete,08BA02176,,,,MLST.Staphylococcus_aureus.398,,,,2012-09-14T00:00:00Z,,PRJNA174226,SAMN02603722,GCA_000296595.1,,CP003808.1,NC_018608.1,Public Health Agency of Canada,complete,454,,Newbler v. 1.1.03.24,1,,1,2782313,32.9,2573,2703,Skin,soft tissue infection of skin,,2008,Canada,Canada,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,The complete genome sequence of a Canadian representative LA-MRSA isolate.,,100,99.4,100,0.6,,Good,2014-12-08T22:12:57.272Z,2015-03-16T03:17:09.594Z
138,1232659.5,Haemophilus influenzae 2019,negative,,1232659,Complete,2019,,,,MLST.Haemophilus_influenzae.321,,,,2015-04-02T00:00:00Z,,PRJNA175345,SAMN03450976,GCF_000968335.1,,CP008740,NZ_CP008740.1,"The Research Institute at Nationwide Children's Hospital and The Ohio State University, Department of Microbiology and DNA Facility, The University of Iowa, Carver College of Medicine and State",,Sanger dideoxy sequencing; 454,,DNASTAR Seqman Pro v. 2010,1,,1,1969659,38.31,1972,1846,Lung,patient with chronic bronchitis,Isolate from a patient with chronic bronchitis,,,,,,,,,"Human, Homo sapiens",,,chronic bronchitis,,,,,,,,,,,,,,,,Isolate from a patient with chronic bronchitis.,,99.6,99.5,100,,,Good,2016-01-17T15:52:41.710Z,2016-01-17T15:52:41.710Z
139,1234380.3,Propionibacterium acnes C1,positive,Propionibacterium acnes C1,1234380,Complete,C1,,,,MLST.Propionibacterium_acnes.115,, ,,2012-10-03T00:00:00Z,,PRJNA175596,SAMN02604070,GCA_000302515.1,,CP003877.1,NC_018707.1,Tokyo Medical and Dental University,complete,,,,1,,1,2519002,60.1,2496,2359,None,sarcoidosis patient,isolate from sarcoidosis patient,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,Host Associated,Sarcoidosis,"Complete genome sequence of P.acnes C1, isolate from sarcoidosis patient.",,99.4,98.6,99.3,,,Good,2014-12-08T22:12:34.241Z,2015-03-16T03:17:09.594Z
140,1235829.3,Streptococcus pyogenes A20,positive,Streptococcus pyogenes A20,1235829,Complete,A20,,,,MLST.Streptococcus_pyogenes.28,,,,2012-10-22T00:00:00Z,,PRJNA175952,SAMN02603640,GCA_000307535.1,,CP003901.1,NC_018936.1,National Cheng Kung University,complete,,,1,1,,1,1837281,38.54,1834,1828,None,Necrotizing fasciitis patient,"isolated from a Necrotizing fasciitis patient in Tainan Provincial Hospital, ROC",,Taiwan,Tainan Provincial Hospital ROC,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Cocci,,,,,,,,Necrotizing faciitis,"A clinical strain was isolated from a Necrotizing fasciitis patient in Tainan Provincial Hospital, ROC.  We want to know this strain's virulence factors, and how they are regulated.",,99.7,99.4,100,,,Good,2014-12-08T22:13:35.551Z,2015-03-16T03:17:09.594Z
141,1236608.7,Moraxella catarrhalis BBH18,negative,,1236608,Complete,BBH18,,,,MLST.Moraxella_catarrhalis.128,,,,2014-01-31T00:00:00Z,20453089,PRJNA46869,SAMN02603777,GCF_000092265.1,,CP002005,NC_014147.1,Radboud University Nijmegen Medical Centre,,,,,1,,1,1863286,41.67,1933,1886,Blood,human blood,isolated from human blood and will be used for comparative analysis,,,,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Cocci,No,,Mesophilic,,,Aerobic,HostAssociated,,Moraxella catarrhalis RH4. Moraxella catarrhalis RH4 was originally isolated from human blood and will be used for comparative analysis.,,99.7,99.6,100,,,Good,2016-01-17T15:28:11.005Z,2016-01-17T15:28:11.005Z
143,1238993.3,Mycoplasma pneumoniae M129-B7,negative,Mycoplasma pneumoniae M129-B7,1238993,Complete,M129-B7,,,,MLST.Mycoplasma_pneumoniae.1,,ATCC 29342,,2013-01-04T00:00:00Z,,PRJNA176548,SAMN02604130,GCA_000331085.2,,CP003913.1,NC_020076.2,University of Alabama at Birmingham,complete,,,1,1,,1,816373,40.01,787,613,None,Homo sapiens,,,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Resequencing of M129. ATCC 29342.,,99.6,99.4,100,,,Good,2014-12-08T22:12:24.441Z,2015-03-16T03:17:09.594Z
144,1241582.3,Burkholderia thailandensis 2002721723,negative,Burkholderia thailandensis 2002721723,1241582,Complete,2002721723,,,,"MLST.Burkholderia_cepacia_complex.488,MLST.Burkholderia_pseudomallei.80",, ,,2014-02-10T00:00:00Z,,PRJNA177185,SAMN03081449,GCA_000567925.1,"SRR1609273,SRR1609274","CP004098.1,CP004097.1","NZ_CP004097.1,NZ_CP004098.1",Los Alamos National Laboratory,complete,paired end 454;  Illumina Gaii; pacBio,27X; 1128X; 58X,Newbler v. 2.6; VELVET v. 1.1.05; Allpaths,2,,2,6577133,67.5432,6425,5533,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Motile,,,,,,,,Sequencing of Burkholderia genomes.,,98.9,96,97.1,0.5,,Good,2014-12-08T22:10:43.861Z,2015-03-16T03:17:09.594Z
145,1241583.3,Burkholderia pseudomallei NCTC 13179,negative,Burkholderia pseudomallei NCTC 13179,1241583,Complete,NCTC13179,,,,MLST.Burkholderia_pseudomallei.613,, ,,2013-11-01T00:00:00Z,,PRJNA177186,SAMN02603566,GCA_000494855.1,"SRR1608120,SRR1609209,SRR1609210","CP003976.1,CP003977.1","NC_022659.1,NC_022658.1",Los Alamos National Laboratory,complete,454 (long insert PE data); Illumina GAiiX,21x; 208x; 56x,Newbler v. 2.6; Velvet v. 1.1.05; Allpaths,2,,2,7337157,67.991,7357,6085,Skin,skin ulcer,,,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Motile,,,,,,,,Sequencing of Burkholderia genomes.;many frameshifted proteins,,99.3,95.3,99.8,1.1,,Good,2014-12-08T22:10:43.168Z,2015-03-16T03:17:09.594Z
146,1241616.6,Staphylococcus aureus subsp. aureus DSM 20231,positive,,1241616,Complete,DSM 20231,,,,MLST.Staphylococcus_aureus.8,,DSM:20231,Yes,2015-06-03T00:00:00Z,,PRJNA283471,SAMN03651231,GCF_001027105.1,,"CP011526,CP011527","NZ_CP011526.1,NZ_CP011527.1",Okinawa Institute of Advanced Sciences,,PacBio,210,HGAP3 v. 2.3.0,1,1,2,2782562,32.84,2726,2734,None,Clinical,,1953,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,Genome sequencing of the type strain of Staphylococcus aureus subsp. aureus.,,100,100,100,,,Good,2016-01-17T16:07:05.172Z,2016-01-17T16:07:05.172Z
147,1243619.3,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110354,negative,,1243619,Complete,enteritidis,serovar enteritidis,,,MLST.Salmonella_enterica.11,,,,2014-04-02T00:00:00Z,24786953,PRJNA219482,SAMN02384160,GCA_000626175.1,"SRR1183736,SRR1183970",CP007175.1,NZ_CP007175.1,LFZ,,454; Illumina,>100X,MIRA v. 4,1,,1,4711160,52.2,4609,4366,None,,,2010,Canada,Canada: Alberta,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,develop molecular sub typing scheme based on whole genome sequencing data,,99.3,99,99.7,,,Good,2014-12-09T00:33:12.598Z,2015-03-16T03:17:09.594Z
148,1243621.3,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110356,negative,,1243621,Complete,enteritidis,serovar enteritidis,,,MLST.Salmonella_enterica.11,,,,2014-04-01T00:00:00Z,24786953,PRJNA219482,SAMN02384161,GCA_000623375.1,"SRR1183737,SRR1183971",CP007262.1,NZ_CP007262.1,LFZ,,454; Illumina,>100x,MIRA v. 4.0,1,,1,4682805,52.2,4586,4336,None,Human-Outbreak,,2009,Canada,Canada: Alberta,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,develop molecular sub typing scheme based on whole genome sequencing data,,99.3,99,100,,,Good,2014-12-09T00:33:14.024Z,2015-03-16T03:17:09.594Z
149,1244085.3,Klebsiella pneumoniae CG43,negative,Klebsiella pneumoniae CG43,1244085,Complete,CG43,,,,MLST.Klebsiella_pneumoniae.86,, ,,2013-10-18T00:00:00Z,,PRJNA177782,SAMN02603668,GCA_000474015.1,,CP006648.1,NC_022566.1,National Tsing Hua University,complete,Illumina; Sanger,200X,ABySS v. V,1,,1,5166857,57.6,4855,4791,Liver,liver abscess,,,Taiwan,"Taiwan: Chang-Gung Memorial Hospital, Keelung City",,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Nonmotile,,,,,,,,Complete genome sequence of Klebsiella pneumoniae CG43.  Clinical isolates from Chang-Gung Memorial Hospital.,,99.3,98.2,100,,,Good,2014-12-08T22:11:49.278Z,2015-03-16T03:17:09.594Z
150,1244111.3,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110357,negative,,1244111,Complete,enteritidis,serovar enteritidis,,,MLST.Salmonella_enterica.11,,,,2014-04-01T00:00:00Z,24786953,PRJNA219482,SAMN02384162,GCA_000623355.1,"SRR1183738,SRR1183972",CP007261.1,NZ_CP007261.1,LFZ,,454; Illumina,>100x,MIRA v. 4.0,1,,1,4678418,52.2,4578,4333,None,Human-Sporadic,,2003,Canada,Canada: Alberta,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,develop molecular sub typing scheme based on whole genome sequencing data,,99.3,99,100,,,Good,2014-12-09T00:33:14.569Z,2015-03-16T03:17:09.594Z
151,1244112.3,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110358,negative,,1244112,Complete,enteritidis,serovar enteritidis,,,MLST.Salmonella_enterica.11,,,,2014-04-01T00:00:00Z,24786953,PRJNA219482,SAMN02384163,GCA_000623335.1,"SRR1183739,SRR1183973",CP007260.1,NZ_CP007260.1,LFZ,,454; Illumina,>100x,MIRA v. 4.0,1,,1,4678687,52.2,4583,4333,None,Human-Sporadic,,2009,Canada,Canada: Alberta,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,develop molecular sub typing scheme based on whole genome sequencing data,,99.3,99,100,0.3,,Good,2014-12-09T00:33:15.138Z,2015-03-16T03:17:09.594Z
152,1244113.3,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110359,negative,,1244113,Complete,enteritidis,serovar enteritidis,,,MLST.Salmonella_enterica.11,,,,2014-04-01T00:00:00Z,24786953,PRJNA219482,SAMN02384164,GCA_000623315.1,"SRR1183740,SRR1183974",CP007259.1,NZ_CP007259.1,LFZ,,454; Illumina,>100x,MIRA v. 4.0,1,,1,4711474,52.2,4615,4371,None,Human-Sporadic,,2004,Canada,Canada: Alberta,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,develop molecular sub typing scheme based on whole genome sequencing data,,99.3,99,100,,,Good,2014-12-09T00:33:15.704Z,2015-03-16T03:17:09.594Z
153,1244118.3,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110360,negative,,1244118,Complete,enteritidis,serovar enteritidis,,,MLST.Salmonella_enterica.11,,,,2014-04-01T00:00:00Z,24786953,PRJNA219482,SAMN02384166,GCA_000623295.1,"SRR1183742,SRR1183976",CP007258.1,NZ_CP007258.1,LFZ,,454; Illumina,>100x,MIRA v. 4.0,1,,1,4678618,52.2,4579,4326,None,Human-Sporadic,,2004,Canada,Canada: Alberta,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,develop molecular sub typing scheme based on whole genome sequencing data,,99.3,99,100,,,Good,2014-12-09T00:33:16.728Z,2015-03-16T03:17:09.594Z
154,1244119.3,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110361,negative,,1244119,Complete,enteritidis,serovar enteritidis,,,MLST.Salmonella_enterica.11,,,,2014-04-01T00:00:00Z,24786953,PRJNA219482,SAMN02384167,GCA_000623275.1,"SRR1183743,SRR1183977",CP007263.1,NZ_CP007263.1,LFZ,,454; Illumina,>100x,MIRA v. 4.0,1,,1,4682911,52.2,4590,4327,None,Human-Sporadic,,2009,Canada,Canada: Alberta,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,develop molecular sub typing scheme based on whole genome sequencing data,,99.3,98.9,100,,,Good,2014-12-09T00:33:17.418Z,2015-03-16T03:17:09.594Z
155,1244120.3,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20111095,negative,,1244120,Complete,enteritidis,serovar enteritidis,,,MLST.Salmonella_enterica.11,,,,2014-04-02T00:00:00Z,24786953,PRJNA219482,SAMN02384168,GCA_000626375.1,"SRR1183744,SRR1183978",CP007254.1,NZ_CP007254.1,LFZ,,454; Illumina,>100x,MIRA v. 4.0,1,,1,4679953,52.2,4574,4330,None,Human-Outbreak,,2011,Canada,Canada: Quebec,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,develop molecular sub typing scheme based on whole genome sequencing data,,99.3,99,100,,,Good,2014-12-09T00:33:17.907Z,2015-03-16T03:17:09.594Z
156,1244529.3,Campylobacter fetus subsp. testudinum Sp3,negative,,1244529,Complete,Sp3,,,,MLST.Campylobacter_fetus.27,,,,2016-01-04T00:00:00Z,,PRJNA177181,SAMN03366410,GCF_001484645.1,,CP010953,NZ_CP010953.1,Utrecht University,,Sanger dideoxy sequencing; 454;,156x,Newbler v. 2.6,1,,1,1819051,33.11,1807,1767,None,Heterodon nasicus,isolated from human and reptiles,6-May,United Kingdom,United Kingdom: England,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing of a new C.fetus subsp. isolated from human and reptiles.,sample_type:Cell culture,99.8,99.8,100,,,Good,2016-02-01T00:34:16.235Z,2016-02-01T00:34:16.235Z
157,1247414.3,Neisseria gonorrhoeae NG-k51.05,negative,,1247414,Complete,NG-k51.05,,,,,,,,2017-01-18T00:00:00Z,,PRJNA223523,SAMN02380725,GCA_001956715.1,,"CP003974,CP003975",,RIPCM,,454; IonTorrent,23,"Newbler, Sspace v. 2.6, 03.2013",1,1,2,2236743,52.37866,2783,2203,None,male,isolated in 2005,2005,Russia,Russia: Kaluga,,,,,,"Human, Homo sapiens",,,gonorrhea,,,,,,Negative,Cocci,No,,,,,,,,"Neisseria gonorrhoeae NG-k51.05 was isolated in 2005. This is a multidrug-resistant strain and will be used to understand the prevalence, antibiotic resistance, and importance of horizontal gene transfer within this important, naturally competent organism.;many frameshifted proteins",collected_by:RIPCM,99.2,97.9,,,,Good,2018-11-28T13:37:54.470Z,2018-11-28T13:37:54.470Z
158,1248902.3,Escherichia coli O145:H28 str. RM13514,negative,Escherichia coli O145:H28 str. RM13514,1248902,Complete,RM13514,serovar s,,,MLST.Escherichia_coli_1.32,, ,,2014-01-14T00:00:00Z,24410921,PRJNA178648,SAMN02641383,GCA_000520035.1,,"CP006027.1,CP006029.1,CP006028.1","NZ_CP006027.1,NZ_CP006028.1,NZ_CP006029.1","""USDA, ARS, WRRC, PSM""",complete,454; Illumina; PacBio,,Newbler v. v2.3; Velvet v. v1.0.13;,1,2,3,5737294,50.6743,5979,5776,Stool,feces; clinical sample,,,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,Nonsporulating,Mesophilic,37C,Mesophilic,Facultative,Multiple,Enteric,"""Recently there has been an increase in outbreaks associated with non-O157 Shiga-toxin producing Escherichia coli (STEC), most commonly associated with the serotypes O26, O45, O103, O111, O121, and O145. Escherichia coli O145:H28 str. RM13514 was a clinical isolate and linked to the 2010 multi-state outbreak of E. coli O145 infection associated with consumption of shredded romaine lettuce in US.""",,99.7,99,100,,,Good,2014-12-08T22:11:32.227Z,2015-03-16T03:17:09.594Z
159,1248915.3,Escherichia coli O145:H28 str. RM13516,negative,Escherichia coli O145:H28 str. RM13516,1248915,Complete,RM13516,serovar s,,,MLST.Escherichia_coli_1.6130,, ,,2014-01-14T00:00:00Z,24410921,PRJNA178650,SAMN02641384,GCA_000520055.1,,"CP006262.1,CP006264.1,CP006263.1","NZ_CP006262.1,NZ_CP006263.1,NZ_CP006264.1","""USDA, ARS, WRRC, PSM""",complete,454; Illumina; PacBio,,Newbler v. v2.3; Velvet v. v1.0.13;,1,2,3,5559008,50.5948,5667,5513,Stool,feces,isolated from a patient in Belgium during a 2007 outbreak of STEC infection associated with consumption of ice cream produced in a farm,2007,Belgium,Belgium,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,Nonsporulating,Mesophilic,37C,Mesophilic,Facultative,Multiple,Enteric,"""Recently there has been an increase in outbreaks associated with non-O157 Shiga-toxin producing Escherichia coli (STECs), most commonly associated with the serotypes O26, O45, O103, O111, O121, and O145. Escherichia coli O145:H28 str. RM13516 was isolated from a patient in Belgium during a 2007 outbreak of STEC infection associated with consumption of ice cream produced in a farm.""",,99.4,98.8,100,,,Good,2014-12-08T22:11:32.238Z,2015-03-16T03:17:09.594Z
160,1249468.3,Burkholderia pseudomallei NCTC 13178,negative,Burkholderia pseudomallei NCTC 13178,1249468,Complete,NCTC13178,,,,MLST.Burkholderia_pseudomallei.286,,NCTC 13178,,2013-12-26T00:00:00Z,,PRJNA178668,SAMN02641521,GCA_000511895.1,"SRR1608117,SRR1608118,SRR1608119","CP004001.1,CP004002.1","NZ_CP004001.1,NZ_CP004002.1",Los Alamos National Laboratory,complete,454 LMP; Illumina GAiiX; PacBio RS,21x; 450x; 63x,Newbler v. 2.6; Velvet 1.1.05; AllPaths v.,2,,2,7391364,67.9365,7371,6084,Brain,post mortem brain,,,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Motile,,,,,,,,"Whole genome sequence of Burkholderia pseudomallei NCTC13178, funded by US Department of Homeland Security (DHS).",,99.2,95.7,100,,,Good,2014-12-08T22:10:43.143Z,2015-03-16T03:17:09.594Z
161,1249469.3,Burkholderia pseudomallei MSHR1328,negative,,1249469,Complete,MSHR1328,,,,MLST.Burkholderia_pseudomallei.259,,,,2015-06-19T00:00:00Z,,PRJNA178669,SAMN03455786,GCF_000970935.1,,APNR01000000,,Los Alamos National Laboratory,,Illumina HiSeq; 454; PacBio,987.0x,Newbler v. 2.6; Velvet v. 1.1.05; AllPaths,2,,2,7154488,68.1,7270,5871,Sputum,sputum,,2001,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,,,,,,,,"Whole genome sequence of Burkholderia pseudomallei MSHR1328, funded by US Department of Homeland Security (DHS).",,99.2,95.6,100,0.3,,Good,2016-01-17T15:53:19.477Z,2016-01-17T15:53:19.477Z
162,1249470.6,Burkholderia pseudomallei MSHR1079,negative,,1249470,Complete,MSHR1079,,,,MLST.Burkholderia_pseudomallei.111,,,,2015-06-19T00:00:00Z,,PRJNA178670,SAMN03203247,GCF_000970955.1,,"CM003194,CM003195",,Los Alamos National Laboratory,,454; Illumina HiSeq; PacBio,299.0x,Newbler v. 2.6; Velvet v. 1.1.05;,2,,2,7354275,67.98,7443,6046,Lymph Node,lymph node,,2001,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,,,,,,,,"Whole genome sequence of Burkholderia pseudomallei MSHR1079, funded by US Department of Homeland Security (DHS).",sample_type:Microbial isolate culture,99,95.4,100,,,Good,2016-07-04T20:54:01.075Z,2016-07-04T20:54:01.075Z
163,1249475.3,Burkholderia pseudomallei MSHR840,negative,,1249475,Complete,MSHR840,,,,MLST.Burkholderia_pseudomallei.257,,,,2015-06-02T00:00:00Z,25931592,PRJNA238264,SAMN03068727,GCF_000959185.1,"SRR1614027,SRR1614028,SRR1614030","CP009474,CP009473","NZ_CP009474.1,NZ_CP009473.1",Los Alamos National Laboratory,,Illumina; PacBio; 454,661x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,2,,2,7129813,68.12,7175,5830,Brain,Human Brain Tissue,,1999,Australia,Australia: Ipswitch,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,,,,,,,,Genome sequencing of Burkholderia pseudomallei MSHR840,,99.2,96,100,0.9,,Good,2016-01-17T15:50:15.096Z,2016-01-17T15:50:15.096Z
164,1249615.4,Mycobacterium tuberculosis K,positive,,1249615,Complete,K,,,,,,,,2014-06-05T00:00:00Z,-,PRJNA178919,SAMN02803802,GCA_000698475.1,,CP007803.1,NZ_CP007803.1,Seoul National University,,Santer; Illumina MiSeq,570.51x,Phred/Phrap/Consed; CLC Genomics Workbench,1,,1,4385518,65.6,4298,4145,None,human-associated habitat,,1998,South Korea,South Korea,,,,,,"Human, Homo sapiens",,,,,,,,,,Bacilli,No,No,,,,,,,Mycobacterium tuberculosis K. Sequencing of clinical isolate in Korea. This strain is sequenced for comparative genomic studies.,,99.6,98.9,100,,,Good,2014-12-09T00:45:13.826Z,2015-03-16T03:17:09.594Z
165,1249650.3,Ehrlichia chaffeensis str. West Paces,negative,,1249650,Complete,West Paces,,,,,,,,2014-04-17T00:00:00Z,-,PRJNA178990,SAMN02367293,GCA_000632965.1,,CP007480.1,NZ_CP007480.1,IGS,,PacBio,17.01X,HGAP v. 1.4,1,,1,1170935,30.1,968,962,Blood,blood,,2000,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing and Comparison of Genomes and Transcriptome Profiles of Human Ehrlichiosis Agents.,,99.5,98.8,100,,,Good,2014-12-08T22:35:19.431Z,2015-03-16T03:17:09.594Z
166,1249651.3,Ehrlichia chaffeensis str. Heartland,negative,,1249651,Complete,Heartland,,,,,,,,2014-04-17T00:00:00Z,-,PRJNA178991,SAMN02203185,GCA_000632815.1,,CP007473.1,NZ_CP007473.1,IGS,,PacBio,13.21X,HGAP v. 1.4,1,,1,1172721,30.1,975,970,None,,,1999,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing and Comparison of Genomes and Transcriptome Profiles of Human Ehrlichiosis Agents.,,99.4,98.7,100,,,Good,2014-12-08T22:35:19.963Z,2015-03-16T03:17:09.594Z
167,1249652.3,Ehrlichia chaffeensis str. Jax,negative,,1249652,Complete,Jax,,,,,,,,2014-04-17T00:00:00Z,-,PRJNA178992,SAMN02364462,GCA_000632865.1,,CP007475.1,NZ_CP007475.1,IGS,,PacBio,34X,HGAP v. 1.4,1,,1,1176890,30.1,992,989,None,,,1997,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing and Comparison of Genomes and Transcriptome Profiles of Human Ehrlichiosis Agents.,,99.6,99,100,,,Good,2014-12-08T22:35:20.495Z,2015-03-16T03:17:09.594Z
168,1249653.3,Ehrlichia chaffeensis str. Liberty,negative,,1249653,Complete,Liberty,,,,,,,,2014-04-17T00:00:00Z,-,PRJNA178993,SAMN02364461,GCA_000632885.1,,CP007476.1,NZ_CP007476.1,IGS,,PacBio,18.97X,HGAP v. 1.4,1,,1,1176202,30.1,991,989,None,,,1998,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing and Comparison of Genomes and Transcriptome Profiles of Human Ehrlichiosis Agents.,,99.6,99,100,,,Good,2014-12-08T22:35:21.500Z,2015-03-16T03:17:09.594Z
169,1249654.3,Ehrlichia chaffeensis str. Osceola,negative,,1249654,Complete,Osceola,,,,,,,,2014-04-17T00:00:00Z,-,PRJNA178994,SAMN02364994,GCA_000632905.1,,CP007477.1,NZ_CP007477.1,IGS,,PacBio,14.11X,HGAP v. 1.4,1,,1,1175197,30.1,987,988,None,,,1997,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing and Comparison of Genomes and Transcriptome Profiles of Human Ehrlichiosis Agents.,,99.5,98.8,100,,,Good,2014-12-08T22:35:21.939Z,2015-03-16T03:17:09.594Z
170,1249655.3,Ehrlichia chaffeensis str. Saint Vincent,negative,,1249655,Complete,Saint Vincent,,,,,,,,2014-04-17T00:00:00Z,-,PRJNA178995,SAMN02364995,GCA_000632925.1,,CP007478.1,NZ_CP007478.1,IGS,,PacBio,14.88X,HGAP v. 1.4,1,,1,1173884,30.1,980,973,None,,,1996,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing and Comparison of Genomes and Transcriptome Profiles of Human Ehrlichiosis Agents.,,99.5,98.8,100,,,Good,2014-12-08T22:35:22.394Z,2015-03-16T03:17:09.594Z
171,1249656.3,Ehrlichia chaffeensis str. Wakulla,negative,,1249656,Complete,Wakulla,,,,,,,,2014-04-17T00:00:00Z,-,PRJNA178996,SAMN02367298,GCA_000632945.1,,CP007479.1,NZ_CP007479.1,IGS,,PacBio,19.05X,HGAP v. 1.4,1,,1,1174357,30.1,984,980,None,,,1997,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing and Comparison of Genomes and Transcriptome Profiles of Human Ehrlichiosis Agents.,,99.6,99,100,,,Good,2014-12-08T22:35:23.270Z,2015-03-16T03:17:09.594Z
172,1249658.4,Burkholderia pseudomallei PB08298010,negative,,1249658,Complete,PB08298010,,,,MLST.Burkholderia_pseudomallei.426,,,,2015-06-02T00:00:00Z,25931592,PRJNA238269,SAMN03023795,GCF_000959345.1,"SRR1614031,SRR1614032,SRR1614033","CP009551,CP009550","NZ_CP009551.1,NZ_CP009550.1",Los Alamos National Laboratory,,Illumina; PacBio; 454,530x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,2,,2,7375551,67.91,7423,6003,None,Human Clinical,,2008,USA,USA: Arizona,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,,,,,,,,Genome sequencing of Burkholderia pseudomallei PB08298010,,99.2,96,100,1.3,,Good,2016-01-17T15:50:18.126Z,2016-01-17T15:50:18.126Z
173,1249659.3,Burkholderia pseudomallei MSHR520,negative,Burkholderia pseudomallei MSHR520,1249659,Complete,MSHR520,,,,MLST.Burkholderia_pseudomallei.36,, ,,2014-03-03T00:00:00Z,,PRJNA178699,SAMN03081457,GCA_000583835.1,"SRR1609227,SRR1609228,SRR1609229","CP004369.1,CP004368.1","NZ_CP004368.1,NZ_CP004369.1",Los Alamos National Laboratory,complete,paired end 454; Illumina Gaii; pacBio,29x; 408x; 98x,Newbler v. 2.6; VELVET v. 1.1.05; Allpaths,2,,2,7450511,67.891,7436,6113,Blood,blood,,1998,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Motile,,,,,,,,"""Whole genome sequence of Burkholderia pseudomallei MSHR520, funded by US Department of Homeland Security (DHS).""",,99.2,95.3,100,0.4,,Good,2014-12-08T22:10:43.070Z,2015-03-16T03:17:09.594Z
174,1249663.3,Burkholderia thailandensis H0587,negative,Burkholderia thailandensis H0587,1249663,Complete,H0587,,,,"MLST.Burkholderia_cepacia_complex.544,MLST.Burkholderia_pseudomallei.101",, ,,2014-02-10T00:00:00Z,,PRJNA178703,SAMN03081448,GCA_000567905.1,"SRR1609240,SRR1609248,SRR1609249","CP004090.1,CP004089.1","NZ_CP004089.1,NZ_CP004090.1",Los Alamos National Laboratory,complete,paired end 454; Illumina Gaii; pacBio,29X; 466X; 77X,Newbler v. 2.6; VELVET v. 1.1.05; Allpaths,2,,2,6768375,67.7476,6527,5629,Wound,pleural wound,,1997,USA,USA: LA,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Motile,,,,,,,,"""Whole genome sequence of Burkholderia thailandensis H0587, 2002721121, funded by US Department of Homeland Security (DHS).""",,99,96.1,100,0.5,,Good,2014-12-08T22:10:43.924Z,2015-03-16T03:17:09.594Z
176,1260222.3,Chlamydia trachomatis IU824,negative,Chlamydia trachomatis IU824,1260222,Complete,IU824,,,,MLST.Chlamydiales_spp.12,, ,,2013-03-15T00:00:00Z,,PRJEB193712,SAMEA2272106,GCA_000348845.1,,"HF562298.1,HF562299.1","NC_020511.1,NC_020551.1",z,complete,,,,1,1,2,1050524,41.2636,994,897,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Two C. trachomatis isolates from cases of repeated treatment failure were previously characterised as being resistant to tetracycline. However, genome sequencing of these isolates did not reveal any known tetracycline-resistance genes or mutations that may confer resistance. Moreover, tetracycline resistance assays showed tetracycline sensitive phenotypes for both isolates. We therefore conclude that the previously findings can be explained by well-known difficulties in assaying C. trachomatis for antibiotic resistance.",,99.7,99.6,100,,,Good,2014-12-08T22:10:53.960Z,2015-03-16T03:17:09.594Z
177,1260223.3,Chlamydia trachomatis IU888,negative,Chlamydia trachomatis IU888,1260223,Complete,IU888,,,,MLST.Chlamydiales_spp.12,, ,,2013-03-15T00:00:00Z,,PRJEB627,SAMEA2272485,GCA_000348825.1,,"HF562300.1,HF562301.1","NC_020512.1,NC_020513.1",z,complete,,,,1,1,2,1050524,41.2636,990,897,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Two C. trachomatis isolates from cases of repeated treatment failure were previously characterised as being resistant to tetracycline. However, genome sequencing of these isolates did not reveal any known tetracycline-resistance genes or mutations that may confer resistance. Moreover, tetracycline resistance assays showed tetracycline sensitive phenotypes for both isolates. We therefore conclude that the previously findings can be explained by well-known difficulties in assaying C. trachomatis for antibiotic resistance.",,99.7,99.6,100,,,Good,2014-12-08T22:10:53.972Z,2015-03-16T03:17:09.594Z
178,1262462.5,Yersinia enterocolitica (type O:5) str. YE53/03,negative,,1262462,Complete,YE53/03,serovar s,,,MLST.Yersinia_spp.3,,,,2014-01-06T00:00:00Z,,PRJEB661,,GCF_000968115.1,,HF571988,NZ_HF571988.1,WTSI,,,,,1,,1,4940199,47.3,4795,4365,Stool,bio-serotype 2A and was isolated from human faecal matter,is from bio-serotype 2A and was isolated from human faecal matter,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Yersinia enterocolitica is an important food-borne pathogen causing gastroenteritis in humans. It is also frequently found in animals. The species is currently divided into 6 different bio-serotypes, which have different pathogenic potential and differ also in prevalence around the world. This strain was sequenced for comparative analysis of all bio-serotypes. This strain is from bio-serotype 2A and was isolated from human faecal matter.",,100,98.7,100,,,Good,2016-01-17T15:52:38.193Z,2016-01-17T15:52:38.193Z
179,1262464.3,Yersinia enterocolitica (type O:9) str. YE56/03,negative,,1262464,Complete,YE56/03,serovar s,,,MLST.Yersinia_spp.12,,,,2014-05-12T00:00:00Z,24753568,PRJEB663,SAMEA3146262,GCF_001050755.1,,CAQE01000000,,WTSI,,,,,,,1,4564695,46.95,4366,3917,Stool,human faecal matter,isolated from human faecal matter,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Yersinia enterocolitica is an important food-borne pathogen causing gastroenteritis in humans. It is also frequently found in animals. The species is currently divided into 6 different bio-serotypes, which have different pathogenic potential and differ also in prevalence around the world. This strain was sequenced for comparative analysis of all bio-serotypes. This strain is of bio-serotype O:2 and was isolated from human faecal matter.",,99.5,98.5,100,,,Good,2016-01-17T16:12:39.859Z,2016-01-17T16:12:39.859Z
180,1262466.3,Yersinia enterocolitica (type O:3) str. YE12/03,negative,,1262466,Complete,YE12/03,serovar s,,,,,,,2014-05-12T00:00:00Z,24753568,PRJEB665,SAMEA3146322,GCF_001050795.1,,CAQG01000000,,WTSI,,,,,,,1,4528241,47,4362,3893,Stool,bio-serotype O:3 and was isolated from human faecal matter,is from bio-serotype O:3 and was isolated from human faecal matter,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Yersinia enterocolitica is an important food-borne pathogen causing gastroenteritis in humans. It is also frequently found in animals. The species is currently divided into 6 different bio-serotypes, which have different pathogenic potential and differ also in prevalence around the world. This strain was sequenced for comparative analysis of all bio-serotypes. This strain is from bio-serotype O:3 and was isolated from human faecal matter.",,99.6,97.6,100,,,Good,2016-01-17T16:12:40.530Z,2016-01-17T16:12:40.530Z
181,1262467.6,Yersinia enterocolitica (type O:2) str. YE3094/96,negative,,1262467,Complete,YE3094/96,serovar s,,,MLST.Yersinia_spp.13,,,,2014-05-12T00:00:00Z,24753568,PRJEB666,SAMEA3146323,GCF_001050815.1,,CAQH01000000,,WTSI,,,,,,,1,4666303,46.96,4716,4051,None,animal isolate,derived from an animal isolate,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Yersinia enterocolitica is an important food-borne pathogen causing gastroenteritis in humans. It is also frequently found in animals. The species is currently divided into 6 different bio-serotypes, which have different pathogenic potential and differ also in prevalence around the world. This strain was sequenced for comparative analysis of all bio-serotypes. This strain is of bio-serotype O:2a,2b,3 and is derived from an animal isolate.",,99.5,97.6,100,,,Good,2016-01-17T16:12:40.890Z,2016-01-17T16:12:40.890Z
182,1262525.3,Mycobacterium tuberculosis PanR0201,positive,Mycobacterium tuberculosis PanR0201,1262525,Complete,PanR0201,,,,,,,,2013-08-02T00:00:00Z,,PRJNA182109,SAMN02471069,GCA_000442945.1,,CM002049.1,-,Texas A&M University,WGS,Illumina GAIIx,68.0x,in-house software v. 11/13/2012,1,,1,4402571,65.5,4352,,None,clinical isolate,isolate from Panama,,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR isolate from Panama.,,99.6,99.3,100,,,Good,2014-12-08T22:12:14.876Z,2015-03-16T03:17:09.594Z
183,1262526.3,Mycobacterium tuberculosis PanR0802,positive,Mycobacterium tuberculosis PanR0802,1262526,Complete,PanR0802,,,,,,,,2013-08-02T00:00:00Z,,PRJNA182111,SAMN02471108,GCA_000442965.1,,CM002050.1,-,Texas A&M University,WGS,Illumina GAIIx,72.0x,in-house software v. 11/13/2012,1,,1,4408178,65.6,4339,,None,clinical isolate,isolate from Panama,,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR isolate from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.347Z,2015-03-16T03:17:09.594Z
184,1262529.3,Mycobacterium tuberculosis PanR1005,positive,Mycobacterium tuberculosis PanR1005,1262529,Complete,PanR1005,,,,,,,,2013-08-01T00:00:00Z,,PRJNA182112,SAMN02471042,GCA_000443005.1,,CM002051.1,-,Texas A&M University,WGS,Illumina GAIIx,73.0x,in-house software v. 11/13/2012,1,,1,4408147,65.6,4322,,None,clinical isolate,isolate from Panama,,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR isolate from Panama.,,99.3,99.1,100,,,Good,2014-12-08T22:12:15.449Z,2015-03-16T03:17:09.594Z
185,1263756.3,Mycoplasma pneumoniae 54089,negative,,1263756,Complete,54089,,,,MLST.Mycoplasma_pneumoniae.20,,,,2015-08-21T00:00:00Z,26275904,PRJNA182263,SAMN03284387,GCF_001272755.1,,CP010542,NZ_CP010542.1,University of Alabama at Birmingham,,Illumina MiSeq,at least 300x,ABySS v. 1.3.7,1,,1,816565,40.01,782,704,Throat,throat,,2009,USA,USA:AL,,,,,,"Human, Homo sapiens",,,pneumonia,,,,,,,,,,,,,,,Mycoplasma pneumonia,WGS of Mycoplasma pneumoniae strain 5408.,collected_by:Unknown,99.9,99.9,100,,,Good,2016-01-17T17:03:59.340Z,2016-01-17T17:03:59.340Z
186,1263757.3,Mycoplasma pneumoniae 54524,negative,,1263757,Complete,54524,,,,MLST.Mycoplasma_pneumoniae.20,,,,2015-08-21T00:00:00Z,26275904,PRJNA182264,SAMN03284388,GCF_001272775.1,,CP010543,NZ_CP010543.1,University of Alabama at Birmingham,,Illumina MiSeq,at least 300x,ABySS v. 1.3.7,1,,1,816583,40.01,784,705,Throat,throat,,2009,USA,USA:AL,,,,,,"Human, Homo sapiens",,,pneumonia,,,,,,,,,,,,,,,Mycoplasma pneumonia,WGS of Mycoplasma pneumoniae strain 54524.,collected_by:Unknown,99.9,99.9,100,,,Good,2016-01-17T17:03:59.743Z,2016-01-17T17:03:59.743Z
187,1263758.3,Mycoplasma pneumoniae 51494,negative,,1263758,Complete,51494,,,,MLST.Mycoplasma_pneumoniae.20,,,,2015-08-21T00:00:00Z,26275904,PRJNA182270,SAMN03284386,GCF_001272735.1,,CP010541,NZ_CP010541.1,University of Alabama at Birmingham,,Illumina MiSeq,at least 300x,ABySS v. 1.3.7,1,,1,816404,40.01,781,703,Throat,throat,isolated from CSF,2006,USA,USA:CO,,,,,,"Human, Homo sapiens",,,pneumonia,,,,,,,,,,,,,,,Mycoplasma pneumonia,"WGS of Mycoplasma pneumoniae strain 51494, isolated from CSF.",collected_by:Unknown,99.9,99.9,100,,,Good,2016-01-17T17:03:58.961Z,2016-01-17T17:03:58.961Z
188,1263760.3,Mycoplasma pneumoniae 85138,negative,,1263760,Complete,85138,,,,,,,,2015-08-21T00:00:00Z,26275904,PRJNA182272,SAMN03284391,GCF_001272815.1,,CP010545,NZ_CP010545.1,University of Alabama at Birmingham,,Illumina MiSeq,at least 300x,ABySS v. 1.3.7,1,,1,816402,40.01,783,706,Respiratory,Respiratory specimen,isolate from China,1985,China,China,,,,,,"Human, Homo sapiens",,,pneumonia,,,,,,,,,,,,,,,Mycoplasma pneumonia,"WGS of Mycoplasma pneumoniae strain 85138, isolate from China.",collected_by:Unknown,99.9,99.9,100,,,Good,2016-01-17T17:04:00.560Z,2016-01-17T17:04:00.560Z
189,1263761.3,Mycoplasma pneumoniae 39443,negative,,1263761,Complete,39443,,,,MLST.Mycoplasma_pneumoniae.2,,,,2015-08-21T00:00:00Z,26275904,PRJNA182273,SAMN03284385,GCF_001272715.1,,CP010540,NZ_CP010540.1,University of Alabama at Birmingham,,Illumina MiSeq,at least 300x,ABySS v. 1.3.7,1,,1,817184,39.98,785,706,Throat,throat,,1999,USA,USA:AL,,,,,,"Human, Homo sapiens",,,pneumonia,,,,,,,,,,,,,,,Mycoplasma pneumonia,"WGS of Mycoplasma pneumoniae strain 39443, clinical isolate 1999.",collected_by:Unknown,99.9,99.9,100,,,Good,2016-01-17T17:03:58.562Z,2016-01-17T17:03:58.562Z
190,1263762.3,Mycoplasma pneumoniae 85084,negative,,1263762,Complete,85084,,,,,,,,2015-08-21T00:00:00Z,26275904,PRJNA182274,SAMN03284389,GCF_001272795.1,,CP010544,NZ_CP010544.1,University of Alabama at Birmingham,,Illumina MiSeq,at least 300x,ABySS v. 1.3.7,1,,1,816404,40.01,784,708,Throat,throat,isolate from China,1985,China,China,,,,,,"Human, Homo sapiens",,,pneumonia,,,,,,,,,,,,,,,Mycoplasma pneumonia,"WGS of Mycoplasma pneumoniae strain 85084, isolate from China.",collected_by:Unknown,99.9,99.9,100,,,Good,2016-01-17T17:04:00.136Z,2016-01-17T17:04:00.136Z
191,1263763.3,Mycoplasma pneumoniae M1139,negative,,1263763,Complete,M1139,,,,MLST.Mycoplasma_pneumoniae.4,,,,2015-08-21T00:00:00Z,26275904,PRJNA182275,SAMN03284392,GCF_001272855.1,,CP010547,NZ_CP010547.1,University of Alabama at Birmingham,,Illumina MiSeq,at least 300x,ABySS v. 1.3.7,1,,1,817045,39.98,790,709,Respiratory,Respiratory specimen,isolate from England,1981,United Kingdom,United Kingdom: England,,,,,,"Human, Homo sapiens",,,pneumonia,,,,,,,,,,,,,,,Mycoplasma pneumonia,"WGS of Mycoplasma pneumoniae strain M1139, isolate from England.",collected_by:Unknown,99.9,99.9,100,,,Good,2016-01-17T17:04:01.281Z,2016-01-17T17:04:01.281Z
192,1263835.4,Mycoplasma pneumoniae MAC,negative,,1263835,Complete,MAC,,,,MLST.Mycoplasma_pneumoniae.2,,ATCC:15492,,2015-08-21T00:00:00Z,26275904,PRJNA182261,SAMN03284394,GCF_001272915.1,,CP010550,NZ_CP010550.1,University of Alabama at Birmingham,,Illumina MiSeq,at least 300x,ABySS v. 1.3.7,1,,1,817156,39.98,789,703,Lung,Human lung disease,,1944,USA,USA:CA,,,,,,"Human, Homo sapiens",,,pneumonia,,,,,,,,,,,,,,,,MAC,collected_by:Unknown,99.9,99.9,100,,,Good,2016-01-17T17:04:02.300Z,2016-01-17T17:04:02.300Z
194,1263871.1,Klebsiella pneumoniae ATCC BAA-2146,negative,,1263871,Complete,ATCC BAA-2146,,,,MLST.Klebsiella_pneumoniae.11,,ATCC:BAA-2146,,2014-06-13T00:00:00Z,24905728,PRJNA183901,SAMN02152539,GCF_000364385.2,"SRR1185120,SRR931757",APNN01000000,,Sandia National Laboratories,,Illumina MiSeq; Pacific Biosystems,85X (Illumina),Newbler GS De Novo Assembler v. 2.8,1,4,5,5781127,56.97,5824,5653,Urine,urine,isolated in the U.S,2010,USA,United States,,,,,,"Human, Homo sapiens",,,urinary tract infection,,,,,,Negative,Bacilli,No,,Mesophilic,37C,,Aerobic,HostAssociated,nosocomial infections,"First Klebsiella strain isolated in the U.S. to be reported as a ""superbug"", i.e., positive for the NDM1 antibiotic resistance gene.",collected_by:CDC,99.5,97.6,100,,,Good,2016-01-17T15:30:26.813Z,2016-01-17T15:30:26.813Z
195,1266446.3,Mycobacterium tuberculosis PanR0704,positive,Mycobacterium tuberculosis PanR0704,1266446,Complete,PanR0704,,,,,,,,2013-08-02T00:00:00Z,,PRJNA181126,SAMN02471068,GCA_000442795.1,,CM002048.1,-,Texas A&M University,WGS,Illumina GAIIx,85.1x,in-house software v. 11/13/2012,1,,1,4398504,65.6,4332,,None,clinical isolate,isolate from Panama,,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR isolate from Panama.,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.310Z,2015-03-16T03:17:09.594Z
196,1267000.5,Mycoplasma hominis ATCC 27545,negative,,1267000,Complete,LBD-4,,,,,,ATCC:27545,,2014-10-22T00:00:00Z,,PRJNA264054,SAMN03112835,GCF_000767725.1,,CP009652,NZ_CP009652.1,University of Missouri - Columbia,,PacBio,714 x,HGAP v. 2.0,1,,1,715165,26.94,590,563,Blood,blood,isolated from a human patient with septicemia,1965,USA,USA: Maryland,,,,,,"Human, Homo sapiens",,,septicemia,,,,,,Negative,,No,,Mesophilic,,,Aerobic,HostAssociated,Septicemia,"Genome Sequencing of Mycoplasma hominis LBD-4, isolated from a human patient with septicemia.",biomaterial_provider:ATCC:27545;identified_by:immunofluorescence,96.6,96.4,96.6,,,Good,2016-01-17T15:40:30.175Z,2016-01-17T15:40:30.175Z
197,1267754.3,Corynebacterium urealyticum DSM 7111,positive,Corynebacterium urealyticum DSM 7111,1267754,Complete,DSM 7111,,,,,,DSM 7111,,2013-02-06T00:00:00Z,,PRJNA183484,SAMN02603063,GCA_000338095.1,,CP004085.1,NC_020230.1,Center for Biotechnology,complete,"454 Genome Sequencer FLX System, Ion",59X,Newbler v. 2.6; G4All v. 1.0.5,1,,1,2316065,64.2,1977,1935,Kidney,ectopic kidney of a 9-year-old patient,isolated from a 9-year-old male with ectopic kidney,,Germany,Germany,,,,,,"Human, Homo sapiens",male,9,,,,,,,Positive,Coccobacilli,No,,Mesophilic,37C,,Aerobic,HostAssociated,Urinary tract infection,"Corynebacterium urealyticum is a member of normal human skin and mucosal flora. This organism, however, can colonize the urinary tract causing infections.  Corynebacterium urealyticum DSM 7111 (Strain no. 3) was isolated from a 9-year-old male with ectopic kidney.",,96.5,96.1,99.1,,,Good,2014-12-08T22:11:04.541Z,2015-03-16T03:17:09.594Z
842,1280938.3,Pseudomonas aeruginosa B136-33,negative,Pseudomonas aeruginosa B136-33,1280938,Complete,B136-33,,,,MLST.Pseudomonas_aeruginosa.1024,,,,2013-04-09T00:00:00Z,,PRJNA185969,SAMN02603669,GCA_000359505.1,,CP004061.1,NC_020912.1,National Tsing Hua University,complete,Sanger dideoxy sequencing; 454; Illumina;,,"ABySS v. July, 2011; Roche Newbler",1,,1,6421010,66.4,5952,5828,Stool,infant with community-acquired diarrhea,isolate from an infant with community-acquired diarrhea,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Characterization of a Psedomonas aeruginosa isolate from an infant with community-acquired diarrhea.,,97.8,96.7,99.1,0.6,,Good,2014-12-08T22:12:36.399Z,2015-03-16T03:17:09.594Z
843,1280940.3,Mycoplasma pneumoniae M2592,negative,,1280940,Complete,M2592,,,,MLST.Mycoplasma_pneumoniae.2,,,,2015-08-21T00:00:00Z,26275904,PRJNA186010,SAMN03284393,GCF_001272895.1,,CP010549,NZ_CP010549.1,University of Alabama at Birmingham,,Illumina MiSeq,at least 300x,ABySS v. 1.3.7,1,,1,817198,39.98,786,704,Respiratory,Respiratory specimen,isolated in 1982,1982,United Kingdom,United Kingdom: England,,,,,,"Human, Homo sapiens",,,pneumonia,,,,,,,,,,,,,,,Mycoplasma pneumonia,"WGS of Mycoplasma pneumoniae strain M2592, respiratory specimen from England isolated in 1982.",collected_by:Unknown,99.8,99.8,100,,,Good,2016-01-17T17:04:01.991Z,2016-01-17T17:04:01.991Z
924,1284663.3,Lactobacillus plantarum ZJ316,positive,Lactobacillus plantarum ZJ316,1284663,Complete,ZJ316,,,,,, ,,2013-02-06T00:00:00Z,,PRJNA186807,SAMN02604341,GCA_000338115.2,,CP004082.1,NC_020229.1,Zhejiang Gongshang University,complete,Illumina,,SOAPdenovo v. 1.05,1,,1,3203964,44.6,3122,3159,Stool,healthy newborn fecal sample; feces,"isolated from health infant fecal samples, has many probiotic properties, such as significant improvement of pig growth and pork quality, and antimicrobial activity against various pathogens in vitro, such as Micrococcus luteus, Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Salmonella enterica, Listeria monocytogenes, and others",,,,,,,,,"Human, Homo sapiens",,infant,healthy,,,,,,Positive,Bacilli,No,No,,,,,,,"The genome sequence gives us a basis to further elucidate the functional mechanisms of its probiotic properties. And it also can provide the information compared with other related species.  Lactobacillus plantarum strain ZJ316, originally isolated from health infant fecal samples, has many probiotic properties, such as significant improvement of pig growth and pork quality, and antimicrobial activity against various pathogens in vitro, such as Micrococcus luteus, Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Salmonella enterica, Listeria monocytogenes, and others.",,97.6,95.9,100,,,Good,2014-12-08T22:11:54.242Z,2015-03-16T03:17:09.594Z
925,1287066.3,Enterococcus faecalis DENG1,positive,Enterococcus faecalis DENG1,1287066,Complete,DENG1,,,,MLST.Enterococcus_faecalis.191,, ,,2014-02-05T00:00:00Z,,PRJNA187445,SAMN03081447,GCA_000550745.1,,CP004081.1,NZ_CP004081.1,The Affiliated Shenzhen Nanshan Hospital of Guangdong Medical College,complete,,,,1,,1,2961043,37.5,2893,2884,Sputum,sputum,sputum of 54-year-old male with acute myelocytic leukemia complicate by severe pneumonia,,,,,,,,,"Human, Homo sapiens",Male,54,acute myelocytic leukemia complicated by severe pneumonia,,,,,,,,,,,,,,,,"""Linezolid is an important antibiotic to treat the enterococcus infection, however, the characteristic of complete genome of linezolid-resistant enterococcus fecalis is rarely reported. Thus this report described the complete genome of a linezolid-resistant enterococcus fecalis from the clinical sample.""",,99.8,99.1,100,,,Good,2014-12-08T22:11:13.526Z,2015-03-16T03:17:09.594Z
926,1290427.3,Rickettsia prowazekii str. NMRC Madrid E,negative,Rickettsia prowazekii str. NMRC Madrid E,1290427,Complete,NMRC Madrid E,,,,,,,,2013-04-11T00:00:00Z,,PRJNA188523,SAMN01983875,GCA_000363905.1,,CP004888.1,NC_020992.1,Naval Medical Research Center,complete,454 Titanium,145X,Newbler v. 2.3,1,,1,1111520,29,926,938,None,,,1941,Spain,Spain: Madrid,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Coccobacilli,,,,,,,,,"Rickettsia prowazekii is the causative agent of epidemic typhus. The classic vector of R. prowazekii is the human body louse, but there are also sporadic cases of R. prowazekii that may involve transmission from either flying squirrels or their lice/fleas. Comparison of human and flying squirrel isolates should aid our understanding of the biology of R. prowazekii in flying squirrels and the possible relationship to sporadic R. prowazekii infection of humans.",,99.9,98.6,100,,,Good,2014-12-08T22:12:44.344Z,2015-03-16T03:17:09.594Z
927,1290428.3,Rickettsia prowazekii str. Breinl,negative,Rickettsia prowazekii str. Breinl,1290428,Complete,Breinl,,,,,,,,2013-04-11T00:00:00Z,,PRJNA188530,SAMN01983876,GCA_000367405.1,,CP004889.1,NC_020993.1,Naval Medical Research Center,complete,454 Titanium,108X,Newbler v. 2.3,1,,1,1109301,29,914,920,None,,,1920,Poland,Poland: Warsaw,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Coccobacilli,,,,,,,,,"Rickettsia prowazekii is the causative agent of epidemic typhus. The classic vector of R. prowazekii is the human body louse, but there are also sporadic cases of R. prowazekii that may involve transmission from either flying squirrels or their lice/fleas. Comparison of human and flying squirrel isolates should aid our understanding of the biology of R. prowazekii in flying squirrels and the possible relationship to sporadic R. prowazekii infection of humans.",,99.8,99.5,100,,,Good,2014-12-08T22:12:44.256Z,2015-03-16T03:17:09.594Z
930,1295140.4,Haemophilus influenzae CGSHiCZ412602,negative,,1295140,Complete,CGSHiCZ412602,,,,MLST.Haemophilus_influenzae.712,,,,2014-06-05T00:00:00Z,-,PRJNA189674,SAMN02800345,GCA_000698365.1,,CP007805.1,NZ_CP007805.1,Center for Genomic Science,,Pacific Biosciences RSII,,RS_HGAP_Assembly.2 v. 2.1.1,1,,1,1811802,38.1,1731,1723,Ear,"middle ear fluid, child",,,Czech Republic,Czech Republic,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,No,,,,,,,,"Otitis media, middle ear fluid, child.",,99.5,99.2,100,,,Good,2014-12-09T00:33:26.624Z,2015-03-16T03:17:09.594Z
931,1295765.3,Mycobacterium tuberculosis TKK_02_0049,positive,,1295765,Complete,TKK_02_0049,,,,,,,,2014-04-30T00:00:00Z,,PRJNA190973,SAMN01925659,GCF_000659665.1,"SRR847789,SRR924226",JMAL01000000,,Broad Institute,,Illumina,141.0x,allpaths v. R46813,,,1,4401928,65.61,4302,4004,None,Bodily fluid,,9-Sep-11,South Africa,"South Africa: King George V Hospital, Durban",,,,,,"Human, Homo sapiens",,,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,,,,TB-ARC - KRITH,,99.8,99.3,100,,,Good,2016-01-17T15:35:01.031Z,2016-01-17T15:35:01.031Z
934,1296536.96,Enterobacter hormaechei subsp. xiangfangensis strain Ec61,negative,,1296536,Complete,Ec61,,,,MLST.Enterobacter_cloacae.451,,,,2020-10-26T00:00:00Z,,PRJNA630224,SAMN14828832,GCA_014931695.1,,"CP053103,CP053104,CP053105,CP053106",,Universidade Federal de Sao Paulo,,Illumina MiSeq; Oxford Nanopore MiniION,120.0x,Unicycler v. v0.4.0,1,3,4,5123505,55.16132,5045,4840,Respiratory,Transtracheal aspirate,,5-Jan-14,Brazil,Brazil: Sao Paulo,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Investigation of Antimicrobial Resistance Genes in Enterobacterales,sample_type:Pure culture one microbial species,99.6,98.3,,,,Good,2021-01-02T05:43:50.902Z,2021-01-02T05:43:50.902Z
935,1299325.4,Mycobacterium abscessus subsp. bolletii 103,positive,,1299325,Complete,103,,,,MLST.Mycobacterium_abscessus.5,,,,2014-09-26T00:00:00Z,-,PRJNA260405,SAMN03067425,GCA_000758385.1,,CP009407.1,NZ_CP009407.1,BEI Resources/American Type,,Illumina,138.06,CLC Genomics Workbench v. 7.0.2,1,,1,5051394,64.14,5007,4867,Sputum,sputum,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,,,,,,,,Whole genome sequencing of several maycobacterial species,,98.2,97.1,100,,,Good,2015-03-12T13:41:25.223Z,2015-03-16T03:17:09.594Z
936,1299326.5,Mycobacterium kansasii 662,positive,,1299326,Complete,662,,,,,,BEI<USA>:NR-44268,,2015-07-28T00:00:00Z,,PRJNA260705,SAMN03067433,GCF_000831265.1,,CP009481,,BEI Resources/American Type,,Illumina,107.6,CLC Genomics Workbench v. 7.0.2,1,,1,6383492,66.23,6026,4933,Sputum,Sputum,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of several maycobacterial species,,99.2,97.6,98.5,5.1,,Good,2016-01-17T15:43:15.500Z,2016-01-17T15:43:15.500Z
937,1299328.5,Mycobacterium kansasii 824,positive,,1299328,Complete,824,,,,,,BEI<USA>:NR-44269,,2014-09-26T00:00:00Z,,PRJNA260831,SAMN03067434,GCF_000831305.1,,CP009483,NZ_CP009483.1,BEI Resources/American Type,,Illumina,70.49x,CLC Genomics Workbench v. 7.0.2,1,,1,6402301,66.22,6066,4955,Sputum,Sputum,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Mycobacterium kansasii 824,isolate:824,99.2,97.5,100,5,,Good,2016-01-17T15:43:15.823Z,2016-01-17T15:43:15.823Z
938,1299329.4,Mycobacterium avium subsp. avium 2285 (S) 2285 (S),positive,,1299329,Complete,2285 (S),,,,,,,,2014-09-26T00:00:00Z,-,PRJNA260408,SAMN03067429,GCA_000831285.1,,CP009482.1,NZ_CP009482.1,BEI Resources/American Type,,Illumina,89.3,CLC Genomics Workbench v. 7.0.2,1,,1,5197664,69.15,4947,4620,Sputum,sputum,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,,,,,,,,Whole genome sequencing of several maycobacterial species,,98.4,97.7,100,,,Good,2015-03-12T13:41:25.547Z,2015-03-16T03:17:09.594Z
939,1299330.4,Mycobacterium avium subsp. avium 2285 (R) 2285 (R),positive,,1299330,Complete,2285 (R),,,,,,,,2014-09-26T00:00:00Z,-,PRJNA260407,SAMN03067428,GCA_000758285.1,,CP009493.1,NZ_CP009493.1,BEI Resources/American Type,,Illumina,87.04,CLC Genomics Workbench v. 7.0.2,1,,1,5169415,69.15,4931,4618,None,"Deposited to BEI by Dr. Diane Ordway,Colorado State University",,,,,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,,,,,,,,Whole genome sequencing of several maycobacterial species,,98.4,97.5,100,,,Good,2015-03-12T13:41:25.868Z,2015-03-16T03:17:09.594Z
940,1299331.5,Mycobacterium intracellulare 1956,positive,,1299331,Complete,1956,,,,,,BEI<USA>:NR-44267,,2014-10-20T00:00:00Z,,PRJNA260706,SAMN03067432,GCF_000767485.1,,CP009499,NZ_CP009499.1,BEI Resources/American Type,,Illumina,121.41,CLC Genomics Workbench v. 7.0.2,1,,1,5183048,68.35,4938,4664,Sputum,Sputum,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of several maycobacterial species,,99.1,98.4,99.1,,,Good,2016-01-17T15:40:29.041Z,2016-01-17T15:40:29.041Z
947,1303024.3,Mycobacterium abscessus subsp. bolletii 50594,positive,Mycobacterium abscessus subsp. bolletii 50594,1303024,Complete,50594,,,,,,,,2013-05-22T00:00:00Z,,PRJNA191917,SAMN02603852,GCA_000445035.1,,"CP004374.1,CP004376.1,CP004375.1","NC_021282.1,NC_021279.1,NC_021278.1",Seoul National University College of Medicine,complete,GS FLX Titanium,76x,Newbler v. 2.7,1,2,3,5270527,64.176,5371,5185,None,,,,South Korea,South Korea,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,CurvedShaped,No,No,,,,,,,Complete genome sequencing of M. massiliense Type II strain.,,98.1,96.8,100,,,Good,2014-12-08T22:12:05.582Z,2015-03-16T03:17:09.594Z
958,1305738.8,Mycobacterium orygis strain MUHC/MB/EPTB/Orygis/51145,positive,,1305738,Complete,MUHC/MB/EPTB/Orygis/51145,,,,,,,,2020-11-06T00:00:00Z,,PRJNA672657,SAMN16564840,GCA_015265495.1,,CP063804,,Mc Gill University Health Centre,,PacBio Sequel,13.0x,Canu v. 2.0,1,,1,4352172,65.620316,4280,3988,Cerebrospinal Fluid,Cerebospinal fluid,"is from human highlight the need for implementation programmes, policies and research to achieve better public health outcomes and to combat this zoonoses",23-Sep-97,Canada,Canada: Quebec,,,,,,"Human, Homo sapiens",not collected,,Tuberculosis,,,host_disease_outcome:Chronic disease;host_disease_stage:extrapulmonary TB,,,,,,,,,,,,,"Mycobacterium orygis (M. orygis) a newly described MTBC member is known to cause infection in wide range of hosts including animals and humans (Van Ingen 2012). Identification of M. orygis from human highlight the need for implementation programmes, policies and research to achieve better public health outcomes and to combat this zoonoses. Considering this, we sequenced the complete genome of M. orygis for the first time, which in future will aid in understanding the genetic features and epidemiology of this human and veterinary pathogen.",collected_by:Laboratoire de Sante Publique du Quebec;passage_history:3,99.4,98.2,,,,Good,2020-11-30T12:59:45.073Z,2020-11-30T12:59:45.073Z
959,1305849.3,Enterococcus faecium Aus0085,positive,Enterococcus faecium Aus0085,1305849,Complete,Aus0085,,,,MLST.Enterococcus_faecium.203,,,,2013-08-06T00:00:00Z,,PRJNA193299,SAMN02604219,GCA_000444405.1,,"CP006620.1,CP006622.1,CP006624.1,CP006621.1,CP006625.1,CP006623.1,CP006626.1","NC_021994.1,NC_021995.1,NC_021989.1,NC_021987.1,NC_021996.1,NC_021988.1,NC_021990.1",University Of Melbourne,complete,454,40X,Newbler v. 2.8,1,6,7,3239275,37.947,3374,3221,Blood,the bloodstream of a patient,"isolated Aus0085, isolated from the bloodstream of a patient in Melbourne, Australia in 2009",2009,Australia,Australia: Melbourne,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Cocci,Nonmotile,Nonsporulating,,,,,,,"Complete genome sequence for the ST203 E. faecium isolated Aus0085, isolated from the bloodstream of a patient in Melbourne, Australia in 2009.",,98.4,96.7,100,,,Good,2014-12-08T22:11:16.004Z,2015-03-16T03:17:09.594Z
960,1306417.5,Burkholderia pseudomallei MSHR5858,negative,,1306417,Complete,MSHR5858,,,,MLST.Burkholderia_pseudomallei.562,,,,2015-03-11T00:00:00Z,25414490,PRJNA244526,SAMN02902606,GCF_000755945.1,,"CP008891,CP008892","NZ_CP008891.1,NZ_CP008892.1",Los Alamos National Laboratory,,Illumina; PacBio,535x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,2,,2,7072128,68.25,7118,5760,Sputum,sputum,,1/1/11,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Genome sequencing of Burkholderia pseudomallei MSHR5858,biomaterial_provider:USAMRIID,99.1,96.1,100,,,Good,2016-01-17T15:40:04.481Z,2016-01-17T15:40:04.481Z
961,1306419.4,Burkholderia pseudomallei HBPUB10303a,negative,,1306419,Complete,HBPUB10303a,,,,MLST.Burkholderia_pseudomallei.48,,,,2014-12-01T00:00:00Z,25414490,PRJNA244524,SAMN02902612,GCF_000755905.1,,"CP008894,CP008893","NZ_CP008894.1,NZ_CP008893.1",Los Alamos National Laboratory,,Illumina; 454; PacBio,409x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,2,,2,7178176,68.16,7203,5822,Respiratory,tracheal suction,,1/5/11,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Genome sequencing of Burkholderia pseudomallei HBPUB10303a,biomaterial_provider:USAMRIID,99.2,95.9,100,,,Good,2016-01-17T15:40:03.794Z,2016-01-17T15:40:03.794Z
962,1306420.5,Burkholderia pseudomallei MSHR5848,negative,,1306420,Complete,MSHR5848,,,,MLST.Burkholderia_pseudomallei.553,,,,2014-12-01T00:00:00Z,25414490,PRJNA244424,SAMN02902465,GCF_000755965.1,,"CP008909,CP008910","NZ_CP008909.1,NZ_CP008910.1",Los Alamos National Laboratory,,Illumina; 454; PacBio,193x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,2,,2,7290434,68.04,7350,5975,Sputum,sputum,,1/1/11,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Genome sequencing of Burkholderia pseudomallei MSHR5848,biomaterial_provider:USAMRIID,99.2,96,100,,,Good,2016-01-17T15:40:04.830Z,2016-01-17T15:40:04.830Z
963,1306421.4,Burkholderia pseudomallei MSHR5855,negative,,1306421,Complete,MSHR5855,,,,MLST.Burkholderia_pseudomallei.553,,,,2014-09-18T00:00:00Z,25414490,PRJNA244422,SAMN02866394,GCA_000756065.1,,"CP008783.1,CP008784.1","NZ_CP008784.1,NZ_CP008783.1",Los Alamos National Laboratory,,Illumina; 454; PacBio,474x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,2,,2,7297804,68.0218,7136,5981,Sputum,sputum,,2011,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Genome sequencing of Burkholderia pseudomallei MSHR5855,,99.3,96.1,100,,,Good,2014-12-08T22:36:17.542Z,2015-03-16T03:17:09.594Z
977,1307427.5,Fusobacterium nucleatum subsp. vincentii ChDC F8 strain KCOM 1231,negative,,1307427,Complete,KCOM 1231,,,,,,,,2015-09-22T00:00:00Z,,PRJNA270144,SAMN03263151,GCA_001296125.1,,CP012714,,Chosun University,,Illumina HiSeq,1331.0x,AllPaths_LG v. 47944; SSPACE v. 2.3.1;,1,,1,2038535,27.08,1879,1826,Mouth,subgingival dental plaque,,3/1/05,South Korea,South Korea: Gwangju,,,,,"env_biome:subgingival dental plaque,periodontitis","Human, Homo sapiens",,,,,,,,,Negative,Fusobacteria,No,,,37C,,Anaerobic,HostAssociated,,Analyzing virulence factors of Fusobacterium nucleatum subsp. vincentii KCOM 1231;missing tRNA genes,,99.9,99.9,100,,,Good,2016-01-17T17:10:28.329Z,2016-01-17T17:10:28.329Z
978,1307428.4,Fusobacterium nucleatum subsp. nucleatum ChDC F316 strain KCOM 1322,negative,,1307428,Complete,KCOM 1322,,,,,,,,2015-09-22T00:00:00Z,,PRJNA270149,SAMN03263583,GCF_001296165.1,,CP012716,NZ_CP012716.1,Chosun University,,Illumina HiSeq,1331.0x,AllPaths_LG v. 47944; SSPACE v. 2.3.1;,1,,1,2227266,27.14,2148,2014,Mouth,"Subgingival dental plaque, periodontitis",,3/1/05,South Korea,South Korea: Gwangju,,,,,"env_biome:subgingival dental plaque, periodontitis","Human, Homo sapiens",,,,,,,,,Negative,Fusobacteria,No,,,37C,,Anaerobic,HostAssociated,,Analyzing virulence factors of Fusobacterium nucleatum subsp. nucleatum KCOM 1322,,99.9,99.6,100,2.7,,Good,2016-01-17T17:10:29.072Z,2016-01-17T17:10:29.072Z
979,1307442.5,Fusobacterium hwasookii ChDC F174,negative,,1307442,Complete,ChDC F174,,,,,,KCOM:1256,,2015-12-02T00:00:00Z,,PRJNA270134,SAMN03263088,GCF_001455145.1,,"CP013331,CP013332,CP013333","NZ_CP013331.1,NZ_CP013332.1,NZ_CP013333.1",Chosun University,,Illumina HiSeq,1331.0x,AllPaths_LG v. 47944; SSPACE v. 2.3.1;,1,2,3,2531722,27.11,2360,2294,Mouth,subgingival dental plaque,,3/1/05,South Korea,South Korea: Gwangju,,,,,env_biome:gingivitis,"Human, Homo sapiens",,,,,,,,,Negative,Fusobacteria,No,,,37C,,Anaerobic,HostAssociated,,Analyzing virulence factors of Fusobacterium nucleatum subsp. hwasookii KCOM 1256,,99.4,99,100,0.5,,Good,2016-01-30T11:19:31.991Z,2016-01-30T11:19:31.991Z
980,1307443.5,Fusobacterium hwasookii ChDC F206,negative,,1307443,Complete,ChDC F206,,,,,,KCOM:1258,,2015-12-02T00:00:00Z,,PRJNA270138,SAMN03263145,GCF_001455085.1,,"CP013336,CP013337","NZ_CP013336.1,NZ_CP013337.1",Chosun University,,Illumina HiSeq,1331.0x,AllPaths_LG v. 47944; SSPACE v. 2.3.1;,1,1,2,2430523,27.24,2361,2289,Mouth,subgingival plaque,,3/1/05,South Korea,South Korea: Gwangju,,,,,env_biome:gingivitis,"Human, Homo sapiens",,,,,,,,,Negative,Fusobacteria,No,,,37C,,Anaerobic,HostAssociated,,Analyzing virulence factors of Fusobacterium nucleatum subsp. hwasookii KCOM 1258,,99.6,99.1,100,,,Good,2016-01-30T11:16:35.604Z,2016-01-30T11:16:35.604Z
981,1307444.5,Fusobacterium hwasookii ChDC F300,negative,,1307444,Complete,ChDC F300,,,,,,KCOM:1268,,2015-12-02T00:00:00Z,,PRJNA270142,SAMN03263150,GCF_001455105.1,,"CP013334,CP013335","NZ_CP013334.1,NZ_CP013335.1",Chosun University,,Illumina HiSeq,1331.0x,AllPaths_LG v. 47944; SSPACE v. 2.3.1;,1,1,2,2527063,27.12,2466,2383,Mouth,subgingival dental plaque,,3/1/05,South Korea,South Korea: Gwangju,,,,,env_biome:dental plaque,"Human, Homo sapiens",,,,,,,,,Negative,Fusobacteria,No,,,37C,,Anaerobic,HostAssociated,,Analyzing virulence factors of Fusobacterium nucleatum subsp. hwasookii KCOM 1268,,99.3,98.9,100,0.5,,Good,2016-01-30T11:18:08.139Z,2016-01-30T11:18:08.139Z
982,1308539.8,Klebsiella pneumoniae subsp. pneumoniae ATCC 43816,negative,,1308539,Complete,ATCC 43816,,,,MLST.Klebsiella_pneumoniae.493,,ATCC:43816,,2020-12-15T00:00:00Z,,PRJNA675363,SAMN16705163,GCA_016071735.1,,CP064352,,University of Pittsburgh,,PacBio Sequel,443.0x,Flye v. 2.8,1,,1,5362708,57.379967,5247,5040,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,,Completed genome sequence of Klebsiella pneumoniae strain 43816,,99.7,98.1,,,,Good,2021-01-01T19:48:49.744Z,2021-01-01T19:48:49.744Z
1051,1311573.5,Helicobacter pylori UM032,negative,Helicobacter pylori UM032,1311573,Complete,UM032,,,,,,,,2013-05-14T00:00:00Z,,PRJNA196982,SAMN02230257,GCA_000392455.3,,CP005490.1,NC_021215.1,University of Malaya,complete,Pacific Biosciences,20X,SMRT de novo v. CLR,1,,1,1599933,38.8,1678,1571,None,biospy sample from patient,,,Malaysia,Malaysia: KL,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Spirilla,Yes,No,,,,,,,Helicobacter pylori UM032.,,99.8,98.4,100,5.5,,Good,2014-12-08T22:11:46.364Z,2015-03-16T03:17:09.594Z
1361,1316254.3,Veillonella parvula HSIVP1,negative,Veillonella parvula HSIVP1,1316254,Complete,HSIVP1,,,,,,,,2013-08-19T00:00:00Z,,PRJNA196131,SAMN02471223,GCA_000448705.1,,CM002135.1,-,Top Institute Food and Nutrition (TIFN),WGS,454; Illumina HiSeq,476.0x,Celera Assembler v. 6.1; SSPACE v. 1.1,1,,1,2177985,38.5,2026,2014,Stool,ileostomy effluent evening sample obtained from a 79 year-old male ileostomist plated on Veillonella selective agar,,2010,Netherlands,Netherlands,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,,,,,,,,HostAssociated,,"Specific aspects of the environmental interaction-potential and the metabolic capacity of small-intestinal bacterial strains was investigated through analysis of their genome sequences. Furthermore, the genomes enabled the comparison with related strains from other niches, allowing the identification of genetic targets for strain-specific PCR-based detection in intestinal samples from different individuals.;many frameshifted proteins",,99.8,97.7,100,1.9,,Good,2014-12-08T22:13:43.918Z,2015-03-16T03:17:09.594Z
1362,1316408.3,Streptococcus sp. HSISM1,positive,Streptococcus sp. HSISM1,1316408,Complete,HSISM1,,,,,,,,2013-08-19T00:00:00Z,,PRJNA196120,SAMN02471220,GCA_000448565.1,,CM002128.1,-,Top Institute Food and Nutrition (TIFN),WGS,454; Illumina HiSeq,472.0x,Celera Assembler v. 6.1; SSPACE v. 1.1,1,,1,2334592,41.4,2261,2226,Stool,ileostomy effluent evening sample obtained from a 79 year-old male ileostomist plated on Mitis-salivarius agar,,2010,Netherlands,Netherlands,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,,,,,,,,HostAssociated,,"Specific aspects of the environmental interaction-potential and the metabolic capacity of small-intestinal Streptococcus strains was investigated through analysis of their genome sequences. Furthermore, the genomes enabled the comparison with other streptococci from other niches, allowing the identification of genetic targets for strain-specific PCR-based detection in intestinal samples from different individuals.;many frameshifted proteins",,98.8,96.9,97.3,7.4,,Good,2014-12-08T22:13:36.987Z,2015-03-16T03:17:09.594Z
1363,1316409.3,Streptococcus sp. HSISB1,positive,Streptococcus sp. HSISB1,1316409,Complete,HSISB1,,,,,,,,2013-08-19T00:00:00Z,,PRJNA196122,SAMN02471222,GCA_000448625.1,,CM002131.1,-,Top Institute Food and Nutrition (TIFN),WGS,454; Illumina HiSeq,602.0x,Celera Assembler v. 6.1; SSPACE v. 1.1,1,,1,1906877,37.2,2173,2160,Stool,ileostomy effluent evening sample obtained from a 79 year-old male ileostomist plated on Mitis-salivarius agar,,2010,Netherlands,Netherlands,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,,,,,,,,HostAssociated,,"Specific aspects of the environmental interaction-potential and the metabolic capacity of small-intestinal Streptococcus strains was investigated through analysis of their genome sequences. Furthermore, the genomes enabled the comparison with other streptococci from other niches, allowing the identification of genetic targets for strain-specific PCR-based detection in intestinal samples from different individuals.;many frameshifted proteins",,99.2,92.2,98.1,18.6,High CheckM contamination score,Poor,2014-12-08T22:13:36.977Z,2015-03-16T03:17:09.594Z
1364,1316410.3,Streptococcus sp. HSISS1,positive,Streptococcus sp. HSISS1,1316410,Complete,HSISS1,,,,,,,,2013-08-19T00:00:00Z,,PRJNA196124,SAMN02471216,GCA_000448645.1,,CM002132.1,-,Top Institute Food and Nutrition (TIFN),WGS,454; Illumina HiSeq,496.0x,Celera Assembler v. 6.1; SSPACE v. 1.1,1,,1,2128142,40.1,1961,1939,Stool,ileostomy effluent evening sample obtained from a 79 year-old male ileostomist plated on Mitis-salivarius agar,,2010,Netherlands,Netherlands,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,,,,,,,,HostAssociated,,"Specific aspects of the environmental interaction-potential and the metabolic capacity of small-intestinal Streptococcus strains was investigated through analysis of their genome sequences. Furthermore, the genomes enabled the comparison with other streptococci from other niches, allowing the identification of genetic targets for strain-specific PCR-based detection in intestinal samples from different individuals.;many frameshifted proteins",,99.3,97.9,99.3,4,,Good,2014-12-08T22:13:36.999Z,2015-03-16T03:17:09.594Z
1365,1316411.3,Streptococcus sp. HSISS2,positive,Streptococcus sp. HSISS2,1316411,Complete,HSISS2,,,,,,,,2013-08-19T00:00:00Z,,PRJNA196125,SAMN02471217,GCA_000448665.1,,CM002133.1,-,Top Institute Food and Nutrition (TIFN),WGS,454; Illumina HiSeq,551.0x,Celera Assembler v. 6.1; SSPACE v. 1.1,1,,1,2360910,39.8,2294,2247,Stool,ileostomy effluent evening sample obtained from a 79 year-old male ileostomist plated on Mitis-salivarius agar,,2010,Netherlands,Netherlands,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,,,,,,,,HostAssociated,,"Specific aspects of the environmental interaction-potential and the metabolic capacity of small-intestinal Streptococcus strains was investigated through analysis of their genome sequences. Furthermore, the genomes enabled the comparison with other streptococci from other niches, allowing the identification of genetic targets for strain-specific PCR-based detection in intestinal samples from different individuals.;many frameshifted proteins",,97.2,92.2,94.7,14.3,High CheckM contamination score,Poor,2014-12-08T22:13:37.009Z,2015-03-16T03:17:09.594Z
1366,1316412.3,Streptococcus sp. HSISS3,positive,Streptococcus sp. HSISS3,1316412,Complete,HSISS3,,,,,,,,2013-08-19T00:00:00Z,,PRJNA196126,SAMN02471218,GCA_000448605.1,,CM002130.1,-,Top Institute Food and Nutrition (TIFN),WGS,454; Illumina HiSeq,540.0x,Celera Assembler v. 6.1; SSPACE v. 1.1,1,,1,2399857,39.3,2273,2230,Stool,ileostomy effluent evening sample obtained from a 79 year-old male ileostomist plated on Mitis-salivarius agar,,2010,Netherlands,Netherlands,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,,,,,,,,HostAssociated,,"Specific aspects of the environmental interaction-potential and the metabolic capacity of small-intestinal Streptococcus strains was investigated through analysis of their genome sequences. Furthermore, the genomes enabled the comparison with other streptococci from other niches, allowing the identification of genetic targets for strain-specific PCR-based detection in intestinal samples from different individuals.;many frameshifted proteins",,99,97,98.6,7.3,,Good,2014-12-08T22:13:37.020Z,2015-03-16T03:17:09.594Z
1367,1316413.3,Streptococcus sp. HSISS4,positive,Streptococcus sp. HSISS4,1304,Complete,HSISS4,,,,,,,,2013-08-19T00:00:00Z,,PRJNA196127,SAMN02471219,GCA_000448685.1,"SRR2895389,SRR2904399,SRR2905722",CM002134.1,-,Top Institute Food and Nutrition (TIFN),WGS,454; Illumina HiSeq,557.0x,Celera Assembler v. 6.1; SSPACE v. 1.1,1,,1,2207810,40.2,2126,2091,Stool,ileostomy effluent evening sample obtained from a 79 year-old male ileostomist plated on Mitis-salivarius agar,,2010,Netherlands,Netherlands,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,,,,,,,,HostAssociated,,"Specific aspects of the environmental interaction-potential and the metabolic capacity of small-intestinal Streptococcus strains was investigated through analysis of their genome sequences. Furthermore, the genomes enabled the comparison with other streptococci from other niches, allowing the identification of genetic targets for strain-specific PCR-based detection in intestinal samples from different individuals.",,96.7,92.7,92.8,12.7,High CheckM contamination score,Poor,2014-12-08T22:13:37.029Z,2015-03-16T03:17:09.594Z
1368,1316414.3,Enterococcus sp. HSIEG1,positive,Enterococcus sp. HSIEG1,1316414,Complete,HSIEG1,,,,MLST.Enterococcus_faecium.755,,,,2013-08-19T00:00:00Z,,PRJNA196128,SAMN02471221,GCA_000448585.1,,CM002129.1,-,Top Institute Food and Nutrition (TIFN),WGS,454; Illumina HiSeq,306.0x,Celera Assembler v. 6.1; SSPACE v. 1.1,1,,1,3447851,40.5,3900,3901,Stool,ileostomy effluent evening sample obtained from a 79 year-old male ileostomist plated on Veillonella selective agar,,2010,Netherlands,The netherlands,,,,,,"Human, Homo sapiens",male,79,ileostomist,,,,,,Positive,,,,,,,,Host Associated,,"Specific aspects of the environmental interaction-potential and the metabolic capacity of small-intestinal bacterial strains was investigated through analysis of their genome sequences. Furthermore, the genomes enabled the comparison with related strains from other niches, allowing the identification of genetic targets for strain-specific PCR-based detection in intestinal samples from different individuals.;many frameshifted proteins",,98.8,91.1,98.8,21,High CheckM contamination score,Poor,2014-12-08T22:11:18.222Z,2015-03-16T03:17:09.594Z
1370,1321369.3,Staphylococcus aureus Bmb9393,positive,Staphylococcus aureus Bmb9393,1321369,Complete,Bmb9393,,,,MLST.Staphylococcus_aureus.239,,,,2013-07-05T00:00:00Z,,PRJNA196937,SAMN02603524,GCA_000418345.1,,"CP005288.1,CP005289.1","NC_021670.1,NC_021657.1",LNCC,complete,454 GS FLX Titanium,25x,Newbler v. 2.5.3; Celera software v.7,1,1,2,2983456,32.8966,2831,2653,Blood,patient with blood stream infection,"isolated from a patient with blood stream infection in a hospital located in Rio de Janeiro, Brazil in 1993",1993,Brazil,Brazil: Rio de Janeiro,,,,,,"Human, Homo sapiens",,,blood stream infection,,,,,,,,,,,,,,,,"Staphylococcus aureus sp. aureus strain BMB9393 belonging to the lineage ST239-SCCmecIII was isolated from a patient with blood stream infection in a hospital located in Rio de Janeiro, Brazil in 1993. Has superior ability to accumulate ica-independent biofilm and adhere and invade human airway cells. Widely found in Brazilian hospitals associated with different infectious diseases mainly pneumonia, bacteremia, and surgical-site infections",,100,99.7,100,,,Good,2014-12-08T22:12:57.827Z,2015-03-16T03:17:09.594Z
1371,1321939.6,Helicobacter pylori UM037,negative,Helicobacter pylori UM037,1321939,Complete,UM037,,,,,,,,2013-05-14T00:00:00Z,,PRJNA196985,,GCA_000392515.3,,CP005492.1,NC_021217.1,University of Malaya,complete,Pacific Biosciences,20X,SMRT de novo v. CLR,1,,1,1694406,38.9,1752,1637,None,biospy sample from patient,,,Malaysia,Malaysia: KL,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Spirilla,Yes,No,,,,,,,Helicobacter pylori UM037.,,99.5,98.5,100,2.9,,Good,2014-12-08T22:11:46.381Z,2015-03-16T03:17:09.594Z
1372,1321940.5,Helicobacter pylori UM066,negative,Helicobacter pylori UM066,1321940,Complete,UM066,,,,MLST.Helicobacter_pylori.2185,,,,2013-05-14T00:00:00Z,,PRJNA196986,,GCA_000392535.3,,CP005493.1,NC_021218.1,University of Malaya,complete,Pacific Biosciences,20X,SMRT de novo v. CLR,1,,1,1658730,38.6,1698,1595,None,biospy sample from patient,,,Malaysia,Malaysia: KL,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Helicobacter pylori UM066.,,99.7,98.2,100,2.3,,Good,2014-12-08T22:11:46.423Z,2015-03-16T03:17:09.594Z
1375,1328325.3,Klebsiella pneumoniae subsp. pneumoniae KPR0928,negative,,1328325,Complete,KPR0928,,,,MLST.Klebsiella_pneumoniae.258,,,,2014-07-02T00:00:00Z,-,PRJNA198784,SAMN02786856,GCA_000717515.1,,"CP008831.1,CP008832.1,CP008833.1","NZ_CP008831.1,NZ_CP008832.1,NZ_CP008833.1",NISC,,Pacific Biosciences RS II,170x,HGAP v. 2,1,1,3,5436785,57.3174,5237,5055,Sputum,sputum,,2012,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae.,,99.6,98.3,100,,,Good,2014-12-08T22:38:19.406Z,2015-03-16T03:17:09.594Z
1376,1333849.3,Enterobacter cloacae ECR091,negative,,1333849,Complete,ECR091,,,,MLST.Enterobacter_cloacae.97,,,,2014-09-09T00:00:00Z,-,PRJNA202892,SAMN02713646,GCA_000750275.1,,"CP008905.1,CP008908.1,CP008906.1,CP008907.1","NZ_CP008905.1,NZ_CP008906.1,NZ_CP008907.1,NZ_CP008908.1",NISC,,Pacific Biosciences RS II,120x,HGAP v. 2,1,1,4,4959888,54.7421,4589,4451,Urine,urine,,2012,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of Enterobacter cloacae.,,99.3,97.9,100,0.3,,Good,2014-12-08T22:39:01.455Z,2015-03-16T03:17:09.594Z
1377,1333850.3,Enterobacter cloacae ECNIH2,negative,,1333850,Complete,ECNIH2,,,,,,,,2014-07-09T00:00:00Z,-,PRJNA202893,SAMN02713682,GCA_000724505.1,,"CP008823.1,CP008824.1,CP008825.1,CP008826.1","NZ_CP008823.1,NZ_CP008824.1,NZ_CP008825.1,NZ_CP008826.1",NISC,,Pacific Biosciences RS II,109x,HGAP v. 2,1,1,4,5502685,54.8216,5212,5091,None,sink drain,,2012,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of Enterobacter cloacae.,,99.5,98.3,100,0.9,,Good,2014-12-08T22:39:01.969Z,2015-03-16T03:17:09.594Z
1378,1333851.3,Enterobacter cloacae ECNIH3,negative,,1333851,Complete,ECNIH3,,,,MLST.Enterobacter_cloacae.97,,,,2014-09-09T00:00:00Z,-,PRJNA202894,SAMN02713683,GCA_000750225.1,,"CP008897.1,CP008901.1,CP008898.1,CP008900.1,CP008899.1","NZ_CP008897.1,NZ_CP008898.1,NZ_CP008899.1,NZ_CP008900.1,NZ_CP008901.1",NISC,,Pacific Biosciences RS II,170x,HGAP v. 2,1,1,5,5061388,54.5891,4695,4559,Respiratory,tracheal aspirate,,2011,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of Enterobacter cloacae.,,99.4,97.7,100,,,Good,2014-12-08T22:39:03.003Z,2015-03-16T03:17:09.594Z
1379,1333852.3,Klebsiella oxytoca KONIH1,negative,,1333852,Complete,KONIH1,,,,MLST.Klebsiella_oxytoca.202,,,,2014-06-27T00:00:00Z,-,PRJNA202895,SAMN02786843,GCA_000714655.1,,"CP008788.1,CP008790.1,CP008789.1,CP008791.1","NZ_CP008788.1,NZ_CP008789.1,NZ_CP008790.1,NZ_CP008791.1",NISC,,Pacific Biosciences RS II,136x,HGAP v. 2,1,1,4,6684898,55.6381,6374,6155,Stool,perirectal swab,,2012,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of Klebsiella oxytoca.,,99.7,98.2,100,,,Good,2014-12-08T22:39:03.482Z,2015-03-16T03:17:09.594Z
1380,1335307.3,Burkholderia pseudomallei MSHR305,negative,Burkholderia pseudomallei MSHR305,1335307,Complete,MSHR305,,,,MLST.Burkholderia_pseudomallei.36,,,,2013-07-24T00:00:00Z,23969058,PRJNA203336,SAMN02603568,GCA_000439695.1,"SRR1609230,SRR1609231,SRR1609232","CP006469.1,CP006470.1","NC_021877.1,NC_021884.1",Los Alamos National Laboratory,complete,Illumina HiSeq (std and LMP) & PacBio RS,306X; 77X,Newbler v. 2.6; Velvet v. 1.2.08;,2,,2,7428072,67.8908,7382,6105,Brain,autopsy brain sample,,1994,Australia,Australia: Northern Territory,,,,,,"Human, Homo sapiens",,,fatal encephalomyelitis,,,,,,Negative,Rod-shaped,Motile,,,,,,,Melioidosis,Improved High Quality Draft Genome of Burkholderia pseudomallei MSHR305.,,99.2,95.6,100,0.4,,Good,2014-12-08T22:10:43.007Z,2015-03-16T03:17:09.594Z
1390,1338032.3,Vibrio parahaemolyticus O1:K33 str. CDC_K4557,negative,,1338032,Complete,CDC _K4557,,,,MLST.Vibrio_parahaemolyticus.799,,,,2013-07-16T00:00:00Z,-,PRJNA203445,SAMN02179884,GCA_000430425.1,,"CP006008.1,CP006007.1","NC_021848.1,NC_021822.1",University of California at Davis,,PacBio RS,100x,HGAP v. 1.4,2,,2,5138575,45.3352,4606,4579,None,oyster,,2007,USA,USA: LA,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",,99.7,99.1,100,,,Good,2014-12-08T22:39:09.926Z,2015-03-16T03:17:09.594Z
1391,1338034.3,Vibrio parahaemolyticus O1:Kuk str. FDA_R31,negative,,1338034,Complete,FDA_R31,,,,MLST.Vibrio_parahaemolyticus.23,,,,2013-07-16T00:00:00Z,-,PRJNA203445,SAMN02179882,GCA_000430405.1,,"CP006005.1,CP006004.1","NC_021821.1,NC_021847.1",University of California at Davis,,PacBio RS,100x,HGAP v. 1.4,2,,2,5223562,45.3287,4760,4731,Stool,stool,,19-Sep-06,USA,USA: LA,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",,99.7,99,100,0.4,,Good,2014-12-08T22:39:10.382Z,2015-03-16T03:17:09.594Z
1392,1338035.3,Campylobacter jejuni 32488,negative,,1338035,Complete,,,,,,,,,2013-07-16T00:00:00Z,-,PRJNA203445,SAMN02179883,GCA_000430385.1,,CP006006.1,NC_021834.1,University of California at Davis,,PacBio RS,100x,HGAP v. 1.4,1,,1,1702398,30.5,1766,1689,None,,,4-Jan,USA,USA: NY,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",,99.9,99.9,100,,,Good,2014-12-08T22:39:10.865Z,2015-03-16T03:17:09.594Z
1393,1340842.3,Campylobacter jejuni subsp. jejuni str. RM3420,negative,,1340842,Complete,RM3420,HS:19,,,MLST.Campylobacter_jejuni.22,,,,2016-10-18T00:00:00Z,,PRJNA206197,SAMN05830826,GCF_001767215.1,,CP017456,NZ_CP017456.1,USDA ARS,,454; Illumina,122x,Newbler v. 2.3; Geneious v. 9.1,1,,1,1666780,30.56,1727,1626,None,hospital,,1980,Canada,Canada: Toronto,,,,,,"Human, Homo sapiens",,,enteritis,,,,,,Negative,,,,,,,,,,"The food-borne pathogens Campylobacter jejuni (Cj) and C. coli (Cc) produce capsular polysaccharides (CPS) that are the major antigenic determinants of the classical Penner serotyping system that distinguishes these Campylobacters into 65 groups. In order to examine the genomic diversity of Cj and Cc, and to identify DNA signatures for the development of faster and cheaper typing assays, we have determined the draft genome sequences of 38 Cj and 18 Cc strains representing 56 different Penner serotypes.","collected_by:M. A. Karmali, The Hospital for Sick Children, Toronto",99.9,99.9,100,,,Good,2016-11-17T07:42:40.558Z,2016-11-17T07:42:40.558Z
1394,1340851.3,Pseudomonas aeruginosa RP73,negative,Pseudomonas aeruginosa RP73,1340851,Complete,RP73,,,,MLST.Pseudomonas_aeruginosa.198,,,,2013-06-24T00:00:00Z,,PRJNA206088,SAMN02603771,GCA_000414035.1,,CP006245.1,NC_021577.1,"San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Diseases, Milano, Italy",complete,454,50X,Newbler-gsAssembler module v.  2.5.3;,1,,1,6342034,66.5,5940,5762,Lung,patient with Cystic Fibrosis,isolate from a patient with Cystic Fibrosis,,,,,,,,,"Human, Homo sapiens",,,Cystic Fibrosis,,,,,,,,,,,,,,,,"Complete genome sequence of Pseudomonas aeruginosa RP73, a persistent isolate from a patient with Cystic Fibrosis.",,99.6,99.1,99.7,,,Good,2014-12-08T22:12:37.904Z,2015-03-16T03:17:09.594Z
1395,1341656.4,Francisella tularensis subsp. tularensis str. SCHU S4 substr. NR-28534,negative,,1341656,Complete,SCHU S4,,,,,,,,2015-05-12T00:00:00Z,,PRJNA270247,SAMN03264783,GCF_000978785.2,"SRR1714339,SRR1714340,SRR1714341","CP010446,CP010447","NZ_CP010446.2,NZ_CP010447.1",Lovelace Respiratory Research Institute,,PacBio,448.41x,Celera Assembler v. 1.105,1,1,2,1888434,32.3,2109,2094,None,,,1941,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Animal Model Development,,99.9,99.3,100,2.4,,Good,2016-01-17T15:54:40.775Z,2016-01-17T15:54:40.775Z
1396,1343064.4,Staphylococcus aureus subsp. aureus ST772-MRSA-V strain DAR4145,positive,,1343064,Complete,DAR4145,,,,MLST.Staphylococcus_aureus.772,,,,2015-01-20T00:00:00Z,,PRJNA270689,SAMN03268345,GCF_000828035.1,,CP010526,NZ_CP010526.1,Menzies School of Health Research,,PacBio SMRT,287x,HGAP v. 2.2,1,,1,2860508,32.85,2686,2642,Blood,Blood Sample,,2009,India,India: Mumbai,,,,,,"Human, Homo sapiens",,,Methicillin-Resistant Staphylococcus aureus,,,,,,,,,,,,,,,,"Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of hospital-associated infection, but there is growing awareness of the emergence of multidrug-resistant lineages in community settings around the world. One such lineage is ST772-MRSA-V, which has disseminated widely and is increasingly prevalent in India. We sequenced the complete genome of DAR4145, a strain of the ST772-MRSA-V lineage from India, and investigate its genomic characteristics in regards to antibiotic resistance and virulence factors.","collected_by:D. Ashley Robinson, Anand Manoharan",100,99.6,100,,,Good,2016-01-17T15:43:07.052Z,2016-01-17T15:43:07.052Z
1397,1344043.3,Mycobacterium tuberculosis PanR0203,positive,Mycobacterium tuberculosis PanR0203,1344043,Complete,PanR0203,,,,,,,,2013-08-02T00:00:00Z,,PRJNA207751,SAMN02471063,GCA_000443305.1,,CM002052.1,-,Texas A&M University,WGS,Illumina GAIIx,81.0x,in house software v. 10/18/2012,1,,1,4397671,65.6,4318,,None,clinical isolate,,,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.4,100,,,Good,2014-12-08T22:12:14.894Z,2015-03-16T03:17:09.594Z
1398,1344044.3,Mycobacterium tuberculosis PanR0205,positive,Mycobacterium tuberculosis PanR0205,1344044,Complete,PanR0205,,,,,,,,2013-08-02T00:00:00Z,,PRJNA207752,SAMN02471103,GCA_000443325.1,,CM002053.1,-,Texas A&M University,WGS,Illumina GAIIx,75.0x,in house software v. 10/18/2012,1,,1,4408813,65.5,4332,,None,clinical isolate,,,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:14.903Z,2015-03-16T03:17:09.594Z
1399,1344045.3,Mycobacterium tuberculosis PanR0206,positive,Mycobacterium tuberculosis PanR0206,1344045,Complete,PanR0206,,,,,,,,2013-08-02T00:00:00Z,,PRJNA207753,SAMN02471113,GCA_000443345.1,,CM002054.1,-,Texas A&M University,WGS,Illumina GAIIx,134.0x,in-house software v. 10/18/2012,1,,1,4404319,65.6,4334,,None,clinical isolate,,,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.3,100,,,Good,2014-12-08T22:12:14.912Z,2015-03-16T03:17:09.594Z
1400,1344046.3,Mycobacterium tuberculosis PanR0207,positive,Mycobacterium tuberculosis PanR0207,1344046,Complete,PanR0207,,,,,,,,2013-08-02T00:00:00Z,,PRJNA207754,SAMN02471065,GCA_000443425.1,,CM002056.1,-,Texas A&M University,WGS,Illumina GAIIx,144.0x,in-house software v. 10/18/2012,1,,1,4398802,65.6,4333,,None,clinical isolate,,,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:14.920Z,2015-03-16T03:17:09.594Z
1401,1344047.3,Mycobacterium tuberculosis PanR0208,positive,Mycobacterium tuberculosis PanR0208,1344047,Complete,PanR0208,,,,,,,,2013-08-02T00:00:00Z,,PRJNA207755,SAMN02471064,GCA_000443365.1,,CM002055.1,-,Texas A&M University,WGS,Illumina GAIIx,69.0x,in-house software v. 10/18/2012,1,,1,4393994,65.4,4311,,None,clinical isolate,,,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.3,100,,,Good,2014-12-08T22:12:14.929Z,2015-03-16T03:17:09.594Z
1402,1344048.3,Mycobacterium tuberculosis PanR0209,positive,Mycobacterium tuberculosis PanR0209,1344048,Complete,PanR0209,,,,,,,,2013-08-02T00:00:00Z,,PRJNA207756,SAMN02471079,GCA_000443405.1,,CM002057.1,-,Texas A&M University,WGS,Illumina GAIIx,59.0x,in-house software v. 10/18/2012,1,,1,4408133,65.6,4362,,None,clinical isolate,,,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:14.937Z,2015-03-16T03:17:09.594Z
1403,1346765.3,Mycobacterium tuberculosis PanR0412,positive,Mycobacterium tuberculosis PanR0412,1346765,Complete,PanR0412,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208605,SAMN02471067,GCA_000443445.1,,CM002058.1,-,Texas A&M University,WGS,Illumina GAIIx,47.0x,in-house software v. 10/18/2012,1,,1,4393218,65.5,4333,,None,clinical isolate,,2004,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.159Z,2015-03-16T03:17:09.594Z
1404,1346766.3,Mycobacterium tuberculosis PanR0411,positive,Mycobacterium tuberculosis PanR0411,1346766,Complete,PanR0411,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208604,SAMN02471104,GCA_000443485.1,,CM002060.1,-,Texas A&M University,WGS,Illumina GAIIx,73.0x,in-house software v. 10/18/2012,1,,1,4404586,65.6,4353,,None,clinical isolate,,2004,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.150Z,2015-03-16T03:17:09.594Z
1405,1346767.3,Mycobacterium tuberculosis PanR0410,positive,Mycobacterium tuberculosis PanR0410,1346767,Complete,PanR0410,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208603,SAMN02471081,GCA_000443465.1,,CM002059.1,-,Texas A&M University,WGS,Illumina GAIIx,67.0x,in-house software v. 10/18/2012,1,,1,4404835,65.6,4337,,None,clinical isolate,,2004,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.140Z,2015-03-16T03:17:09.594Z
1406,1346768.3,Mycobacterium tuberculosis PanR0409,positive,Mycobacterium tuberculosis PanR0409,1346768,Complete,PanR0409,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208602,SAMN02471070,GCA_000443505.1,,CM002061.1,-,Texas A&M University,WGS,Illumina GAIIx,69.0x,in-house software v. 10/18/2012,1,,1,4402591,65.6,4326,,None,clinical isolate,,2004,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.4,100,,,Good,2014-12-08T22:12:15.130Z,2015-03-16T03:17:09.594Z
1407,1346770.3,Mycobacterium tuberculosis PanR0407,positive,Mycobacterium tuberculosis PanR0407,1346770,Complete,PanR0407,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208600,SAMN02471043,GCA_000443525.1,,CM002062.1,-,Texas A&M University,WGS,Illumina GAIIx,37.0x,in-house software v. 10/18/2012,1,,1,4405148,65.3,4302,,None,clinical isolate,,2004,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,98.7,98.4,97.8,,,Good,2014-12-08T22:12:15.120Z,2015-03-16T03:17:09.594Z
1408,1346771.3,Mycobacterium tuberculosis PanR0405,positive,Mycobacterium tuberculosis PanR0405,1346771,Complete,PanR0405,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208599,SAMN02471044,GCA_000443545.1,,CM002063.1,-,Texas A&M University,WGS,Illumina GAIIx,138.0x,in-house software v. 10/18/2012,1,,1,4403568,65.6,4368,,None,clinical isolate,,2004,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.111Z,2015-03-16T03:17:09.594Z
1409,1346772.3,Mycobacterium tuberculosis PanR0404,positive,Mycobacterium tuberculosis PanR0404,1346772,Complete,PanR0404,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208598,SAMN02471093,GCA_000443575.1,,CM002064.1,-,Texas A&M University,WGS,Illumina GAIIx,71.0x,in-house software v. 10/18/2012,1,,1,4404247,65.4,4344,,None,clinical isolate,,2004,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.102Z,2015-03-16T03:17:09.594Z
1410,1346773.3,Mycobacterium tuberculosis PanR0403,positive,Mycobacterium tuberculosis PanR0403,1346773,Complete,PanR0403,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208597,SAMN02471082,GCA_000443595.1,,CM002065.1,-,Texas A&M University,WGS,Illumina GAIIx,68.0x,in-house software v. 10/18/2012,1,,1,4400856,65.6,4316,,None,clinical isolate,,2004,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.5,100,,,Good,2014-12-08T22:12:15.092Z,2015-03-16T03:17:09.594Z
1411,1346774.3,Mycobacterium tuberculosis PanR0402,positive,Mycobacterium tuberculosis PanR0402,1346774,Complete,PanR0402,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208596,SAMN02471045,GCA_000443615.1,,CM002066.1,-,Texas A&M University,WGS,Illumina GAIIx,64.0x,in-house software v. 10/18/2012,1,,1,4412421,65.5,4364,,None,clinical isolate,,2004,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.5,100,,,Good,2014-12-08T22:12:15.083Z,2015-03-16T03:17:09.594Z
1412,1346775.3,Mycobacterium tuberculosis PanR0401,positive,Mycobacterium tuberculosis PanR0401,1346775,Complete,PanR0401,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208595,SAMN02471071,GCA_000443635.1,,CM002067.1,-,Texas A&M University,WGS,Illumina GAIIx,44.0x,in-house software v. 10/18/2012,1,,1,4407862,65.4,4342,,None,clinical isolate,,2004,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.3,99.2,100,,,Good,2014-12-08T22:12:15.074Z,2015-03-16T03:17:09.594Z
1413,1346776.3,Mycobacterium tuberculosis PanR0317,positive,Mycobacterium tuberculosis PanR0317,1346776,Complete,PanR0317,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208585,SAMN02471083,GCA_000443655.1,,CM002068.1,-,Texas A&M University,WGS,Illumina GAIIx,27.0x,in-house software v. 10/18/2012,1,,1,4392448,65.4,4302,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.3,99,98.9,,,Good,2014-12-08T22:12:15.064Z,2015-03-16T03:17:09.594Z
1414,1346777.3,Mycobacterium tuberculosis PanR0316,positive,Mycobacterium tuberculosis PanR0316,1346777,Complete,PanR0316,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208584,SAMN02471066,GCA_000443675.1,,CM002069.1,-,Texas A&M University,WGS,Illumina GAIIx,76.0x,in-house software v. 10/18/2012,1,,1,4394000,65.6,4326,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.053Z,2015-03-16T03:17:09.594Z
1415,1346778.3,Mycobacterium tuberculosis PanR0315,positive,Mycobacterium tuberculosis PanR0315,1346778,Complete,PanR0315,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208583,SAMN02471046,GCA_000443695.1,,CM002070.1,-,Texas A&M University,WGS,Illumina GAIIx,42.0x,in-house software v. 10/18/2012,1,,1,4403042,65.4,4332,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.2,99,100,,,Good,2014-12-08T22:12:15.042Z,2015-03-16T03:17:09.594Z
1416,1346779.3,Mycobacterium tuberculosis PanR0314,positive,Mycobacterium tuberculosis PanR0314,1346779,Complete,PanR0314,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208582,SAMN02471109,GCA_000443715.1,,CM002073.1,-,Texas A&M University,WGS,Illumina GAIIx,81.0x,in-house software v. 10/18/2012,1,,1,4392414,65.6,4349,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.031Z,2015-03-16T03:17:09.594Z
1417,1346780.3,Mycobacterium tuberculosis PanR0313,positive,Mycobacterium tuberculosis PanR0313,1346780,Complete,PanR0313,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208581,SAMN02471105,GCA_000443795.1,,CM002072.1,-,Texas A&M University,WGS,Illumina GAIIx,78.0x,in-house software v. 10/18/2012,1,,1,4401613,65.6,4345,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.021Z,2015-03-16T03:17:09.594Z
1418,1346781.3,Mycobacterium tuberculosis PanR0311,positive,Mycobacterium tuberculosis PanR0311,1346781,Complete,PanR0311,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208580,SAMN02471084,GCA_000443935.1,,CM002080.1,-,Texas A&M University,WGS,Illumina GAIIx,35.0x,in-house software v. 10/18/2012,1,,1,4404380,65.4,4327,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.1,98.9,100,,,Good,2014-12-08T22:12:15.011Z,2015-03-16T03:17:09.594Z
1419,1346782.3,Mycobacterium tuberculosis PanR0309,positive,Mycobacterium tuberculosis PanR0309,1346782,Complete,PanR0309,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208579,SAMN02471091,GCA_000443755.1,,CM002071.1,-,Texas A&M University,WGS,Illumina GAIIx,146.0x,in-house software v. 10/18/2012,1,,1,4390137,65.6,4308,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.002Z,2015-03-16T03:17:09.594Z
1420,1346783.3,Mycobacterium tuberculosis PanR0308,positive,Mycobacterium tuberculosis PanR0308,1346783,Complete,PanR0308,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208578,SAMN02471047,GCA_000443815.1,,CM002076.1,-,Texas A&M University,WGS,Illumina GAIIx,130.0x,in-house software v. 10/18/2012,1,,1,4391527,65.6,4336,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.3,100,,,Good,2014-12-08T22:12:14.994Z,2015-03-16T03:17:09.594Z
1421,1346784.3,Mycobacterium tuberculosis PanR0307,positive,Mycobacterium tuberculosis PanR0307,1346784,Complete,PanR0307,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208577,SAMN02471080,GCA_000443835.1,,CM002077.1,-,Texas A&M University,WGS,Illumina GAIIx,111.0x,in-house software v. 10/18/2012,1,,1,4403994,65.5,4340,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.3,100,,,Good,2014-12-08T22:12:14.984Z,2015-03-16T03:17:09.594Z
1422,1346785.3,Mycobacterium tuberculosis PanR0306,positive,Mycobacterium tuberculosis PanR0306,1346785,Complete,PanR0306,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208576,SAMN02471048,GCA_000443855.1,,CM002079.1,-,Texas A&M University,WGS,Illumina GAIIx,49.0x,in-house software v. 1,1,,1,4402981,65.4,4332,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.4,99.1,100,,,Good,2014-12-08T22:12:14.974Z,2015-03-16T03:17:09.594Z
1423,1346786.3,Mycobacterium tuberculosis PanR0305,positive,Mycobacterium tuberculosis PanR0305,1346786,Complete,PanR0305,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208575,SAMN02471092,GCA_000443915.1,,CM002078.1,-,Texas A&M University,WGS,Illumina GAIIx,46.0x,in house software v. 10/18/2012,1,,1,4386956,65.6,4322,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.3,100,,,Good,2014-12-08T22:12:14.964Z,2015-03-16T03:17:09.594Z
1424,1346787.3,Mycobacterium tuberculosis PanR0304,positive,Mycobacterium tuberculosis PanR0304,1346787,Complete,PanR0304,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208574,SAMN02471110,GCA_000443875.1,,CM002074.1,-,Texas A&M University,WGS,Illumina GAIIx,43.0x,in-house software v. 10/18/2012,1,,1,4397923,65.4,4320,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.4,99.2,100,,,Good,2014-12-08T22:12:14.956Z,2015-03-16T03:17:09.594Z
1425,1346788.3,Mycobacterium tuberculosis PanR0301,positive,Mycobacterium tuberculosis PanR0301,1346788,Complete,PanR0301,,,,,,,,2013-08-02T00:00:00Z,,PRJNA208573,SAMN02471049,GCA_000443895.1,,CM002075.1,-,Texas A&M University,WGS,Illumina GAIIx,85.0x,in-house software v. 10/18/2012,1,,1,4395537,65.5,4307,,None,clinical isolate,,2003,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama,,99.6,99.3,100,,,Good,2014-12-08T22:12:14.946Z,2015-03-16T03:17:09.594Z
1426,1348662.3,Corynebacterium argentoratense DSM 44202,positive,Corynebacterium argentoratense DSM 44202,1348662,Complete,DSM 44202,,,,,,CIP 104296,Yes,2013-08-27T00:00:00Z,8590681,PRJNA209048,SAMN02603032,GCA_000590555.1,,CP006365.1,NC_022198.1,Bielefeld University,complete,Illumina,131.55,Newbler v. 2.8,1,,1,2031902,58.9,1913,1875,Throat,throat culture,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Rod-shaped,Nonmotile,Nonsporulating,Mesophilic,37 C,Unknown,Unknown,Host Associated,,"Complete genome sequence of Corynebacterium argentoratense IBS B10697 (= CIP 104296, DSM 44202).Sequencing of this genome is part of an ongoing effort to provide genome sequences for all Corynebacterium type strains",,97,96.6,99.2,0.3,,Good,2014-12-08T22:11:03.115Z,2015-03-16T03:17:09.594Z
1428,1349827.3,Campylobacter jejuni subsp. jejuni M129,negative,,1349827,Complete,M129,,,,,,,,2016-11-03T00:00:00Z,,PRJNA209349,SAMN02990965,GCF_001865595.1,,"CP007749,CP007750","NZ_CP007749.1,NZ_CP007750.1",University of Arizona,,454,59x,Newbler v. 2.6; Geneious v. 5.6,1,1,2,1801315,30.26,1888,1881,Stool,Clinical,"isolated from a human feces from a clinical case at University Medical Center (UMC) at the University of Arizona, and is motile and highly invasive in vitro",1990,USA,USA:Tucson,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,CurvedShaped,Yes,,Thermophilic,42C,,Microaerophilic,HostAssociated,Human Gastroenteritis,"This strain was originally isolated from a human feces from a clinical case at University Medical Center (UMC) at the University of Arizona, and is motile and highly invasive in vitro.",collected_by:Dr. Lynn Joens,99.5,99,100,0.6,,Good,2016-11-19T08:42:58.917Z,2016-11-19T08:42:58.917Z
1616,1352355.3,Pseudomonas aeruginosa c7447m,negative,Pseudomonas aeruginosa c7447m,1352355,Complete,c7447m,,,,MLST.Pseudomonas_aeruginosa.2589,, ,,2013-09-16T00:00:00Z,24115552,PRJNA209859,SAMN02603588,GCA_000468935.1,,CP006728.1,-,Marshall University School of Medicine,complete,Illumina GAIIX,224X,Illumina Pipeline v. SCS 2.8.0;,1,,1,6262305,66.5,5805,5657,Lung,patient with a chronic lung infection with P,isolate from a patient with a chronic lung infection with P. aeruginosa,,,,,,,,,"Human, Homo sapiens",,,chronic lung infection with P. aeruginosa,,,,,,Negative,Bacilli,Yes,No,Mesophilic,37C,Unknown,Facultative,HostAssociated,,Mucoid isolate from a patient with a chronic lung infection with P. aeruginosa.,,99.7,99.6,100,,,Good,2014-12-08T22:12:38.118Z,2015-03-16T03:17:09.594Z
1617,1352356.3,Helicobacter pylori SouthAfrica20,negative,Helicobacter pylori SouthAfrica20,1352356,Complete,SouthAfrica20,,,,,,,,2013-08-21T00:00:00Z,,PRJNA209860,SAMN02604293,GCA_000590775.1,,CP006691.1,NC_022130.1,Vanderbilt University School of Medicine,complete,454,25x,GS De Novo Assemble v. Jan 2011,1,,1,1622903,38.6,1704,1704,Stomach,stomach,,,South Africa,South Africa,,,,,,"Human, Homo sapiens",,,,stomach,,,,,,,,,,,,,,,For comparative analysis;many frameshifted proteins,,99.7,97.3,100,3.7,,Good,2014-12-08T22:11:46.305Z,2015-03-16T03:17:09.594Z
1618,1352570.3,Mycobacterium tuberculosis PanR0501,positive,Mycobacterium tuberculosis PanR0501,1352570,Complete,PanR0501,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210047,SAMN02471050,GCA_000445245.1,,CM002127.1,-,Texas A&M University,WGS,Illumina GAIIx,74.0x,in-house software v. 10/18/2012,1,,1,4407393,65.5,4348,,None,clinical isolate,,2005,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.168Z,2015-03-16T03:17:09.594Z
1619,1352571.3,Mycobacterium tuberculosis PanR0503,positive,Mycobacterium tuberculosis PanR0503,1352571,Complete,PanR0503,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210048,SAMN02471074,GCA_000445265.1,,CM002126.1,-,Texas A&M University,WGS,Illumina GAIIx,29.0x,in-house software v. 10/18/2012,1,,1,4386949,65.4,4323,,None,clinical isolate,,2005,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.178Z,2015-03-16T03:17:09.594Z
1620,1352572.3,Mycobacterium tuberculosis PanR0505,positive,Mycobacterium tuberculosis PanR0505,1352572,Complete,PanR0505,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210049,SAMN02471058,GCA_000445285.1,,CM002125.1,-,Texas A&M University,WGS,Illumina GAIIx,69.0x,in-house software v. 10/18/2012,1,,1,4407883,65.4,4348,,None,clinical isolate,,2005,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.188Z,2015-03-16T03:17:09.594Z
1621,1352573.3,Mycobacterium tuberculosis PanR0601,positive,Mycobacterium tuberculosis PanR0601,1352573,Complete,PanR0601,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210050,SAMN02471075,GCA_000445305.1,,CM002124.1,-,Texas A&M University,WGS,Illumina GAIIx,38.0x,in-house software v. 10/18/2012,1,,1,4388875,65.2,4277,,None,clinical isolate,,2006,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,97.7,97.5,97.8,,,Good,2014-12-08T22:12:15.197Z,2015-03-16T03:17:09.594Z
1622,1352574.3,Mycobacterium tuberculosis PanR0602,positive,Mycobacterium tuberculosis PanR0602,1352574,Complete,PanR0602,,,,,,,,2013-08-05T00:00:00Z,,PRJNA210051,SAMN02471059,GCA_000445325.1,,CM002122.1,-,Texas A&M University,WGS,Illumina GAIIx,73.0x,in-house software v. 10/18/2012,1,,1,4406449,65.6,4351,,None,clinical isolate,,2006,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.207Z,2015-03-16T03:17:09.594Z
1623,1352575.3,Mycobacterium tuberculosis PanR0603,positive,Mycobacterium tuberculosis PanR0603,1352575,Complete,PanR0603,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210052,SAMN02471094,GCA_000445345.1,,CM002121.1,-,Texas A&M University,WGS,Illumina GAIIx,56.0x,in-house software v. 10/18/2012,1,,1,4408055,65.4,4327,,None,clinical isolate,,2006,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.4,99.3,100,,,Good,2014-12-08T22:12:15.216Z,2015-03-16T03:17:09.594Z
1624,1352576.3,Mycobacterium tuberculosis PanR0604,positive,Mycobacterium tuberculosis PanR0604,1352576,Complete,PanR0604,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210053,SAMN02471051,GCA_000445365.1,,CM002120.1,-,Texas A&M University,WGS,Illumina GAIIx,23.0x,in-house software v. 10/18/2012,1,,1,4388029,65.5,4316,,None,clinical isolate,,2006,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.226Z,2015-03-16T03:17:09.594Z
1625,1352577.3,Mycobacterium tuberculosis PanR0605,positive,Mycobacterium tuberculosis PanR0605,1352577,Complete,PanR0605,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210054,SAMN02471060,GCA_000445515.1,,CM002123.1,-,Texas A&M University,WGS,Illumina GAIIx,67.0x,in-house software v. 10/18/2012,1,,1,4405197,65.6,4322,,None,clinical isolate,,2006,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.1,100,,,Good,2014-12-08T22:12:15.236Z,2015-03-16T03:17:09.594Z
1626,1352578.3,Mycobacterium tuberculosis PanR0606,positive,Mycobacterium tuberculosis PanR0606,1352578,Complete,PanR0606,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210055,SAMN02471100,GCA_000445535.1,,CM002119.1,-,Texas A&M University,WGS,Illumina GAIIx,79.0x,in-house software v. 10/18/2012,1,,1,4408738,65.6,4327,,None,clinical isolate,,2006,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.245Z,2015-03-16T03:17:09.594Z
1627,1352579.3,Mycobacterium tuberculosis PanR0607,positive,Mycobacterium tuberculosis PanR0607,1352579,Complete,PanR0607,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210056,SAMN02471061,GCA_000445555.1,,CM002114.1,-,Texas A&M University,WGS,Illumina GAIIx,118.0x,in-house software v. 10/18/2012,1,,1,4405199,65.6,4345,,None,clinical isolate,,2006,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.255Z,2015-03-16T03:17:09.594Z
1628,1352580.3,Mycobacterium tuberculosis PanR0609,positive,Mycobacterium tuberculosis PanR0609,1352580,Complete,PanR0609,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210057,SAMN02471052,GCA_000445575.1,,CM002116.1,-,Texas A&M University,WGS,Illumina GAIIx,102.0x,in-house software v. 10/18/2012,1,,1,4405944,65.6,4337,,None,clinical isolate,,2006,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.264Z,2015-03-16T03:17:09.594Z
1629,1352581.3,Mycobacterium tuberculosis PanR0610,positive,Mycobacterium tuberculosis PanR0610,1352581,Complete,PanR0610,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210058,SAMN02471076,GCA_000445595.1,,CM002118.1,-,Texas A&M University,WGS,Illumina GAIIx,79.0x,in-house software v. 10/18/2012,1,,1,4402491,65.5,4352,,None,clinical isolate,,2006,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.273Z,2015-03-16T03:17:09.594Z
1630,1352582.3,Mycobacterium tuberculosis PanR0611,positive,Mycobacterium tuberculosis PanR0611,1352582,Complete,PanR0611,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210059,SAMN02471111,GCA_000445615.1,,CM002115.1,-,Texas A&M University,WGS,Illumina GAIIx,87.0x,in-house software v. 10/18/2012,1,,1,4398105,65.5,4321,,None,clinical isolate,,2006,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.282Z,2015-03-16T03:17:09.594Z
1631,1352583.3,Mycobacterium tuberculosis PanR0702,positive,Mycobacterium tuberculosis PanR0702,1352583,Complete,PanR0702,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210060,SAMN02471095,GCA_000445635.1,,CM002117.1,-,Texas A&M University,WGS,Illumina GAIIx,58.0x,in-house software v. 10/18/2012,1,,1,4406983,65.5,4345,,None,clinical isolate,,2007,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.292Z,2015-03-16T03:17:09.594Z
1632,1352584.3,Mycobacterium tuberculosis PanR0703,positive,Mycobacterium tuberculosis PanR0703,1352584,Complete,PanR0703,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210061,SAMN02471101,GCA_000445655.1,,CM002113.1,-,Texas A&M University,WGS,Illumina GAIIx,70.0x,in-house software v. 10/18/2012,1,,1,4398277,65.6,4336,,None,clinical isolate,,2007,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.4,100,,,Good,2014-12-08T22:12:15.300Z,2015-03-16T03:17:09.594Z
1633,1352585.3,Mycobacterium tuberculosis PanR0707,positive,Mycobacterium tuberculosis PanR0707,1352585,Complete,PanR0707,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210062,SAMN02471112,GCA_000445675.1,,CM002111.1,-,Texas A&M University,WGS,Illumina GAIIx,90.0x,in-house software v. 10/18/2012,1,,1,4405806,65.5,4334,,None,clinical isolate,,2007,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.319Z,2015-03-16T03:17:09.594Z
1634,1352586.3,Mycobacterium tuberculosis PanR0708,positive,Mycobacterium tuberculosis PanR0708,1352586,Complete,PanR0708,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210063,SAMN02471102,GCA_000445695.1,,CM002109.1,-,Texas A&M University,WGS,Illumina GAIIx,75.0x,in-house software v. 10/18/2012,1,,1,4399724,65.6,4338,,None,clinical isolate,,2007,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.4,100,,,Good,2014-12-08T22:12:15.328Z,2015-03-16T03:17:09.594Z
1635,1352587.3,Mycobacterium tuberculosis PanR0801,positive,Mycobacterium tuberculosis PanR0801,1352587,Complete,PanR0801,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210064,SAMN02471096,GCA_000445715.1,,CM002112.1,-,Texas A&M University,WGS,Illumina GAIIx,73.0x,in-house software v. 10/18/2012,1,,1,4400549,65.6,4327,,None,clinical isolate,,2008,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.4,100,,,Good,2014-12-08T22:12:15.337Z,2015-03-16T03:17:09.594Z
1636,1352588.3,Mycobacterium tuberculosis PanR0803,positive,Mycobacterium tuberculosis PanR0803,1352588,Complete,PanR0803,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210065,SAMN02471062,GCA_000445735.1,,CM002108.1,-,Texas A&M University,WGS,Illumina GAIIx,116.0x,in-house software v. 10/18/2012,1,,1,4406371,65.6,4343,,None,clinical isolate,,2008,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.356Z,2015-03-16T03:17:09.594Z
1637,1352589.3,Mycobacterium tuberculosis PanR0804,positive,Mycobacterium tuberculosis PanR0804,1352589,Complete,PanR0804,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210066,SAMN02471053,GCA_000445755.1,,CM002110.1,-,Texas A&M University,WGS,Illumina GAIIx,104.0x,in-house software v. 10/18/2012,1,,1,4402266,65.5,4322,,None,clinical isolate,,2008,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.366Z,2015-03-16T03:17:09.594Z
1638,1352590.3,Mycobacterium tuberculosis PanR0805,positive,Mycobacterium tuberculosis PanR0805,1352590,Complete,PanR0805,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210067,SAMN02471054,GCA_000445775.1,,CM002107.1,-,Texas A&M University,WGS,Illumina GAIIx,39.0x,in-house software v. 10/18/2012,1,,1,4394016,65.4,4312,,None,clinical isolate,,2008,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.3,99.1,100,,,Good,2014-12-08T22:12:15.376Z,2015-03-16T03:17:09.594Z
1639,1352591.3,Mycobacterium tuberculosis PanR0902,positive,Mycobacterium tuberculosis PanR0902,1352591,Complete,PanR0902,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210068,SAMN02471077,GCA_000445795.1,,CM002106.1,-,Texas A&M University,WGS,Illumina GAIIx,49.0x,in-house software v. 10/18/2012,1,,1,4392209,65.4,4324,,None,clinical isolate,,2009,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.385Z,2015-03-16T03:17:09.594Z
1640,1352592.3,Mycobacterium tuberculosis PanR0903,positive,Mycobacterium tuberculosis PanR0903,1352592,Complete,PanR0903,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210069,SAMN02471097,GCA_000445815.1,,CM002105.1,-,Texas A&M University,WGS,Illumina GAIIx,98.0x,in-house software v. 10/18/2012,1,,1,4402661,65.6,4339,,None,clinical isolate,,2009,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.4,100,,,Good,2014-12-08T22:12:15.394Z,2015-03-16T03:17:09.594Z
1641,1352593.3,Mycobacterium tuberculosis PanR0904,positive,Mycobacterium tuberculosis PanR0904,1352593,Complete,PanR0904,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210070,SAMN02471078,GCA_000445835.1,,CM002104.1,-,Texas A&M University,WGS,Illumina GAIIx,107.0x,in-house software v. 10/18/2012,1,,1,4407151,65.6,4360,,None,clinical isolate,,2009,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.404Z,2015-03-16T03:17:09.594Z
1642,1352594.3,Mycobacterium tuberculosis PanR0906,positive,Mycobacterium tuberculosis PanR0906,1352594,Complete,PanR0906,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210071,SAMN02471073,GCA_000445855.1,,CM002102.1,-,Texas A&M University,WGS,Illumina GAIIx,101.0x,in-house software v. 10/18/2012,1,,1,4399991,65.6,4335,,None,clinical isolate,,2009,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.4,100,,,Good,2014-12-08T22:12:15.413Z,2015-03-16T03:17:09.594Z
1643,1352595.3,Mycobacterium tuberculosis PanR0907,positive,Mycobacterium tuberculosis PanR0907,1352595,Complete,PanR0907,,,,,,,,2013-08-05T00:00:00Z,23884993,PRJNA210072,SAMN02471098,GCA_000445875.1,,CM002103.1,-,Texas A&M University,WGS,Illumina GAIIx,84.0x,in-house software v. 10/18/2012,1,,1,4400321,65.6,4335,,None,clinical isolate,,2009,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.3,100,,,Good,2014-12-08T22:12:15.422Z,2015-03-16T03:17:09.594Z
1644,1352596.3,Mycobacterium tuberculosis PanR0908,positive,Mycobacterium tuberculosis PanR0908,1352596,Complete,PanR0908,,,,,,,,2013-08-05T00:00:00Z,,PRJNA210073,SAMN02471055,GCA_000445895.1,,CM002101.1,-,Texas A&M University,WGS,Illumina GAIIx,45.0x,in-house software v. 10/18/2012,1,,1,4400052,65.5,4349,,None,clinical isolate,,2009,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.4,100,,,Good,2014-12-08T22:12:15.431Z,2015-03-16T03:17:09.594Z
1645,1352597.3,Mycobacterium tuberculosis PanR0909,positive,Mycobacterium tuberculosis PanR0909,1352597,Complete,PanR0909,,,,,,,,2013-08-05T00:00:00Z,,PRJNA210074,SAMN02471056,GCA_000445915.1,,CM002100.1,-,Texas A&M University,WGS,Illumina GAIIx,136.0x,in-house software v. 10/18/2012,1,,1,4408002,65.5,4353,,None,clinical isolate,,2009,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.5,99.3,100,,,Good,2014-12-08T22:12:15.440Z,2015-03-16T03:17:09.594Z
1646,1352598.3,Mycobacterium tuberculosis PanR1006,positive,Mycobacterium tuberculosis PanR1006,1352598,Complete,PanR1006,,,,,,,,2013-08-05T00:00:00Z,,PRJNA210075,SAMN02471099,GCA_000445975.1,,CM002097.1,-,Texas A&M University,WGS,Illumina GAIIx,64.0x,in-house software v. 10/18/2012,1,,1,4409116,65.5,4343,,None,clinical isolate,,2010,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.4,100,,,Good,2014-12-08T22:12:15.458Z,2015-03-16T03:17:09.594Z
1647,1352599.3,Mycobacterium tuberculosis PanR1007,positive,Mycobacterium tuberculosis PanR1007,1352599,Complete,PanR1007,,,,,,,,2013-08-05T00:00:00Z,,PRJNA210076,SAMN02471072,GCA_000445935.1,,CM002098.1,-,Texas A&M University,WGS,Illumina GAIIx,98.0x,in-house software v. 10/18/2012,1,,1,4398360,65.6,4280,,None,clinical isolate,,2010,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.4,100,,,Good,2014-12-08T22:12:15.467Z,2015-03-16T03:17:09.594Z
1648,1352600.3,Mycobacterium tuberculosis PanR1101,positive,Mycobacterium tuberculosis PanR1101,1352600,Complete,PanR1101,,,,,,,,2013-08-05T00:00:00Z,,PRJNA210077,SAMN02471057,GCA_000445955.1,,CM002099.1,-,Texas A&M University,WGS,Illumina GAIIx,76.0x,in-house software v. 10/18/2012,1,,1,4369690,65.5,4332,,None,clinical isolate,,2011,Panama,Panama,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,MDR-TB from Panama.,,99.6,99.4,100,,,Good,2014-12-08T22:12:15.476Z,2015-03-16T03:17:09.594Z
1656,1355100.3,Escherichia coli JJ1886,negative,Escherichia coli JJ1886,1355100,Complete,JJ1886,,,,MLST.Escherichia_coli_1.131,, ,,2013-10-29T00:00:00Z,24309736,PRJNA218163,SAMN02603887,GCA_000493755.1,,"CP006784.1,CP006789.1,CP006785.1,CP006788.1,CP006786.1,CP006787.1","NC_022648.1,NC_022651.1,NC_022661.1,NC_022650.1,NC_022649.1,NC_022662.1",Statens Serum Institut,complete,454; Illumina; PacBio,50x,MIRA v. 3.9.9; ABySS v. 1.3.4; PBJelly v.,1,4,6,5308284,50.7667,5323,5049,None,Patient,,2007,USA,United States,,,,,,"Human, Homo sapiens",,,fatal urosepsis,,,,,,Negative,Bacilli,Motile,Nonsporulating,Mesophilic,37C,Unknown,Facultative,Multiple,Urosepsis,Complete Genome of the Epidemic and Highly Virulent CTX-M-15-Producing H30-Rx Subclone of Escherichia coli ST131.,,99.8,98.3,100,,,Good,2014-12-08T22:11:27.555Z,2015-03-16T03:17:09.594Z
1657,1355101.3,Escherichia coli JJ1887,negative,,1355101,Complete,JJ1887,,,,MLST.Escherichia_coli_1.131,,,,2016-03-17T00:00:00Z,,PRJNA311313,SAMN04481707,GCF_001593565.1,,"CP014316,CP014317,CP014318,CP014319,CP014321,CP014320","NZ_CP014316.1,NZ_CP014317.1,NZ_CP014318.1,NZ_CP014319.1,NZ_CP014321.1,NZ_CP014320.1",Translational Genomics Research Institute,,PacBio,118X,HGAP v. 3,1,5,6,5331521,50.8,5540,5273,None,,is from a nearly identical strain,2007,USA,United States,,,,,,"Human, Homo sapiens",,,D014552,,,,,,,,,,,C,,,,,"We report the complete genome sequence, including five plasmid sequences, of Escherichia coli ST131 isolate JJ1887. The isolate was obtained in 2007 in the United States from a patient with recurrent urinary tract infections, whose caregiver died from urosepsis from a nearly identical strain.",collected_by:not applicable,99.9,98.1,100,0.4,,Good,2016-04-27T17:05:48.674Z,2016-04-27T17:05:48.674Z
1658,1356855.3,Pseudomonas aeruginosa DK1 strain DK1,negative,,1356855,Complete,DK1,,,,MLST.Pseudomonas_aeruginosa.387,,,,2015-11-03T00:00:00Z,,PRJEB9823,SAMEA3484633,,,LN870292,,DTU Systems Biology,,,,,1,,1,6212531,66.57,5813,5640,Sputum,sputum,,1997,Denmark,Denmark,,,,,,"Human, Homo sapiens",,,,,,,Susceptible,Computational Prediction,,,,,,,,,,,"Pseudomonas aeruginosa is an important opportunistic pathogen associated with chronic pulmonary infections and mortality in cystic fibrosis (CF) patients. Here, we present the complete genome sequence of stable mucoid P. aeruginosa strain DK1-NH57388A, a CF isolate which has previously been used to establish chronic lung infections in an animal model.",,99.9,99.7,100,,,Good,2017-07-23T07:40:40.496Z,2017-07-23T07:40:40.496Z
1659,1357994.3,Campylobacter jejuni subsp. jejuni 00-2425,negative,Campylobacter jejuni subsp. jejuni 00-2425,1357994,Complete,00-2425,,,,,, ,,2013-09-16T00:00:00Z,,PRJNA211797,SAMN02603723,GCA_000468915.2,,CP006729.1,NC_022362.1,Public Health Agency of Canada,complete,"Illumina MiSeq, ABI 3730",48X,Velvet optimizer v. 1.1208,1,,1,1718980,30.5,1800,1714,Stool,stool sample,,2000,Canada,Canada,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Motile,Nonsporulating,Thermophilic,42C,,Microaerophilic,,,"We are investigating the effect of the presence of the C. jejuni CJIE1 prophage on protein expression. To do so, we are comparing protein expression in natural variants of the organism with and without the prophage. It is necessary to detect and deal with any differences in gene content.",,100,99.9,100,,,Good,2014-12-08T22:10:46.576Z,2015-03-16T03:17:09.594Z
1660,1358410.3,Campylobacter coli 15-537360,negative,Campylobacter coli 15-537360,1358410,Complete,15-537360,,,,,, ,,2013-11-01T00:00:00Z,24336384,PRJNA211871,SAMN02603390,GCA_000494775.1,,"CP006702.1,CP006703.1","NC_022660.1,NC_022656.1",Institute of Food Research,complete,Sanger dideoxy sequencing; Illumina,,CLC Genomics Workbench v. 6.0; DNASTAR,1,1,2,1685020,31.3688,1723,1621,Stomach,42-year old female,,2001,,,,,,,,"Human, Homo sapiens",Female,42,gastroenteritis,,,,,,Negative,,Motile,,,,,,,,Complete genome of Campylobacter coli clinical isolate 15-537360.,,99.8,99.7,100,,,Good,2014-12-08T22:10:45.540Z,2015-03-16T03:17:09.594Z
1661,1359155.3,Anaplasma phagocytophilum str. ApWI1,negative,,1359155,Complete,ApWI1,,,,MLST.Anaplasma_phagocytophilum.64,,,,2015-03-27T00:00:00Z,,PRJNA212467,SAMN02666742,GCF_000964945.1,"SRR1178887,SRR1178888,SRR1178889",LAOF01000000,,IGS,,PacBio,19.46x,HGAP2 v. Unknown,,,1,1497074,41.64,1627,1551,None,,,,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"This project is focused on improving our understanding of vector borne diseases caused by bacteria in the order Rickettsiales by obtaining further diverse genomes from the Anaplasma, Ehrlichia, Orientia, Rickettsia, and Neoehrlichia genera. The analysis is expected to elucidate the molecular mechanisms of host tropism, immune response, and pathogenicity/virulence as reflected in the isolates selected for sequencing.",,99.7,97.6,100,2.2,,Good,2016-01-17T15:51:48.291Z,2016-01-17T15:51:48.291Z
1662,1359159.3,Anaplasma phagocytophilum str. HGE2,negative,,1359159,Complete,HGE2,,,,MLST.Anaplasma_phagocytophilum.64,,,,2015-03-27T00:00:00Z,,PRJNA212466,SAMN02665693,GCF_000964935.1,,LAOE01000000,,IGS,,PacBio,13.40x,HGAP2 v. Unknown,,,1,1482055,41.65,1604,1511,None,,,,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"This project is focused on improving our understanding of vector borne diseases caused by bacteria in the order Rickettsiales by obtaining further diverse genomes from the Anaplasma, Ehrlichia, Orientia, Rickettsia, and Neoehrlichia genera. The analysis is expected to elucidate the molecular mechanisms of host tropism, immune response, and pathogenicity/virulence as reflected in the isolates selected for sequencing.",,99.9,98.3,100,0.3,,Good,2016-01-17T15:51:47.970Z,2016-01-17T15:51:47.970Z
1663,1359162.3,Anaplasma phagocytophilum str. Webster,negative,,1359162,Complete,Webster,,,,MLST.Anaplasma_phagocytophilum.64,,,,2015-03-27T00:00:00Z,,PRJNA212447,SAMN02666091,GCF_000964685.1,,LANS01000000,,IGS,,PacBio,Unknown,HGAP3 v. Unknown,,,1,1479407,41.64,1616,1533,None,,,,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"This project is focused on improving our understanding of vector borne diseases caused by bacteria in the order Rickettsiales by obtaining further diverse genomes from the Anaplasma, Ehrlichia, Orientia, Rickettsia, and Neoehrlichia genera. The analysis is expected to elucidate the molecular mechanisms of host tropism, immune response, and pathogenicity/virulence as reflected in the isolates selected for sequencing.",,99.9,98.4,100,,,Good,2016-01-17T15:51:43.841Z,2016-01-17T15:51:43.841Z
1664,1380767.3,Campylobacter jejuni subsp. jejuni 00-2426,negative,Campylobacter jejuni subsp. jejuni 00-2426,1380767,Complete,00-2426,,,,,,,,2013-09-12T00:00:00Z,,PRJNA213841,SAMN02603724,GCA_000466105.2,,CP006708.1,NC_022352.1,Public Health Agency of Canada,complete,Illumina MiSeq,,Velvet optimizer velvet v. 1.1208,1,,1,1615143,30.4,1708,1686,Stool,stool sample,,2000,Canada,Canada,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Curved-shaped,Motile,Nonsporulating,Thermophilic,42 C,NonHalophilic,Microaerophilic,Multiple,,"We are investigating the effect of the presence of the C. jejuni CJIE1 prophage on protein expression. To do so, we are comparing protein expression in natural variants of the organism with and without the prophage. It is necessary to detect and deal with any differences in gene content.",,100,99.9,100,,,Good,2014-12-08T22:10:46.593Z,2015-03-16T03:17:09.594Z
1665,1380768.3,Campylobacter jejuni subsp. jejuni 00-2538,negative,Campylobacter jejuni subsp. jejuni 00-2538,1380768,Complete,00-2538,,,,,,,,2013-09-12T00:00:00Z,,PRJNA213842,SAMN02603725,GCA_000466065.2,,CP006707.1,NC_022351.1,Public Health Agency of Canada,complete,Illumina MiSeq,,Velvet optimizer velvet v. 1.1208,1,,1,1664792,30.5,1768,1713,Stool,stool sample,,2000,Canada,Canada,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Curved-shaped,Motile,Nonsporulating,Thermophilic,42 C,NonHalophilic,Microaerophilic,Multiple,Diarrhea,"We are investigating the effect of the presence of the C. jejuni CJIE1 prophage on protein expression. To do so, we are comparing protein expression in natural variants of the organism with and without the prophage. It is necessary to detect and deal with any differences in gene content.",,100,99.9,100,,,Good,2014-12-08T22:10:46.608Z,2015-03-16T03:17:09.594Z
1666,1380908.3,Klebsiella pneumoniae JM45,negative,Klebsiella pneumoniae JM45,1380908,Complete,JM45,,,,MLST.Klebsiella_pneumoniae.11,,,,2013-08-12T00:00:00Z,,PRJNA213804,SAMN02603607,GCA_000445405.1,,"CP006656.1,CP006657.1,CP006658.1","NC_022082.1,NC_022078.1,NC_022083.1","Microbiology Laboratory, Hangzhou Yuhang Hospital of Traditional Chinese Medicine, Hangzhou, PR China",complete,454,30X,Newbler v. 2.7,1,2,3,5603174,57.2405,5508,5141,None,72-year-old male with cerebral infarction after colon carcinoma resection,"isolated another carbapenem-resistant K. pneumoniae strain and then performed bacteriological experiments, PCR and whole-genome sequencing",2010,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Infections caused by K. pneumoniae are discovered throughout the world. This organism is a major cause of urinary tract infection and an important source of nosocomial infection. To date, the spread of multidrug-resistant, even pandrug-resistant, K. pneumoniae has developed into a serious clinical threat. Furthermore, carbapenemases production has recently emerged as an important mechanism for carbapenems resistance. Disturbingly, more and more novel carbapenemases and their variants were continuously discovered. In 2011, we also reported a carbapenem-resistant strain of K. pneumoniae which carried a KPC-2 variant4. In 2010, we isolated another carbapenem-resistant K. pneumoniae strain and then performed bacteriological experiments, PCR and whole-genome sequencing. The genomic sequence data provided us the cause of the carbapenem resistance of this strain.K. pneumoniae JM45 was an isolate from the blood of a 72-year-old male with cerebral infarction after colon carcinoma resection hospitalized in the intensive care unit, the Second Affiliated Hospital of ZheJiang University School of Medcine on April 7, 2010. Species identification was carried out by using Vitek Gram-negative identification cards (bioM¿¿¿¿¿rieux, Marcy l¿¿¿¿¿¿¿Etoile, France) and by 16S rDNA and gyrA sequencing for BLAST searches on Genbank. The minimum inhibitory concentrations(MICs) were determined by Etest (AB bioMe¿¿¿¿rieux, Solna, Sweden) with the results interpreted according to Clinical and Laboratory Standards Institute(CLSI) guidelines. For rapid detection of the presence of AmpC-derepressed, extended-spectrum ¿¿¿¿¿-lactamases(ESBL) and metallo-¿¿¿¿¿-lactamases(MBL), a new system (Cica-Beta-Test, Kanto Chemical, Japan) was utilized. The Modified Hodge Test was carried out to detect carbapenemases.We isolated a pandrug-resistant K. pneumoniae strain from the blood of a patient with cerbral infarction after colon carcinoma resection in the intensive care unit. According to Cica-Beta-Test and Modified Hodge Test, it was considered to harbor various kinds of ¿¿¿¿¿-lactamases including carbapenemase. However, we only detected four class A ¿¿¿¿¿-lactamase genes with no carbapenemase genes by PCR unexpectedly. To explain the inconsistency of these results, we subsequently conducted whole-genome sequencing for K. pneumoniae JM45. As a result, we also detected four homologous class A ¿¿¿¿¿-lactamase genes, and in addition, discovered two novel genes encoding metallo-¿¿¿¿¿-lactamase domain protein locating on the chromosome simultaneously. This is the first report of two non-cassette-mediated metallo-¿¿¿¿¿-lactamase domain protein sequences for carbapenem resistance in the same strain. We will carry out further research on these two novel genes by cloning and expression analysis followed by enzyme kinetics analysis.",,99.2,96.7,99.3,1.9,,Good,2014-12-08T22:11:49.455Z,2015-03-16T03:17:09.594Z
1667,1382920.3,Helicobacter pylori oki102,negative,,1382920,Complete,Oki102,,,,,,,,2014-03-25T00:00:00Z,24744331,PRJNA215147,SAMN03081488,GCA_000600045.1,,CP006820.1,NZ_CP006820.1,Okinawa Institute of Advanced Sciences,,PacBio,489x,HGAP v. 2.0,1,,1,1633212,38.8,1634,1478,None,patient,"isolated from a patient in Okinawa, Japan who had gastric atrophy",,Japan,Japan: Okinawa,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Constructing a high quality complete genome sequence of Helicobacter pylori Oki102 to perform comparative genomic analyses in a high resolution manner. This strain was originally isolated from a patient in Okinawa, Japan who had gastric atrophy.",,99.9,99.6,100,0.3,,Good,2014-12-08T22:40:53.842Z,2015-03-16T03:17:09.594Z
1668,1382921.3,Helicobacter pylori oki112,negative,,1382921,Complete,Oki112,,,,,,,,2014-03-25T00:00:00Z,24744331,PRJNA215148,SAMN03081489,GCA_000600085.1,,CP006821.1,NZ_CP006821.1,Okinawa Institute of Advanced Sciences,,PacBio,328x,HGAP v. 2.0,1,,1,1637925,38.8,1636,1477,None,patient,"isolated from a patient in Okinawa, Japan who had gastric atrophy",,Japan,Japan: Okinawa,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Constructing a high quality complete genome sequence of Helicobacter pylori Oki112 to perform comparative genomic analyses in a high resolution manner. This strain was originally isolated from a patient in Okinawa, Japan who had gastric atrophy.",,99.9,99.6,100,0.2,,Good,2014-12-08T22:40:54.441Z,2015-03-16T03:17:09.594Z
1669,1382922.3,Helicobacter pylori oki128,negative,,1382922,Complete,Oki128,,,,,,,,2014-03-25T00:00:00Z,24744331,PRJNA215150,SAMN03081490,GCA_000600125.1,,CP006822.1,NZ_CP006822.1,Okinawa Institute of Advanced Sciences,,PacBio,261x,HGAP v. 2.0,1,,1,1553826,39,1575,1393,None,patient,"isolated from a patient in Okinawa, Japan who had gastric atrophy",,Japan,Japan: Okinawa,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Constructing a high quality complete genome sequence of Helicobacter pylori Oki128 to perform comparative genomic analyses in a high resolution manner. This strain was originally isolated from a patient in Okinawa, Japan who had gastric atrophy.",,99.7,99.4,99.7,0.3,,Good,2014-12-08T22:40:55Z,2015-03-16T03:17:09.594Z
1670,1382923.3,Helicobacter pylori oki154,negative,,1382923,Complete,Oki154,,,,,,,,2014-03-25T00:00:00Z,24744331,PRJNA215152,SAMN03081491,GCA_000600145.1,,CP006823.1,NZ_CP006823.1,Okinawa Institute of Advanced Sciences,,PacBio,822x,HGAP v. 2.0,1,,1,1599700,38.8,1625,1439,None,patient,"isolated from a patient in Okinawa, Japan who had duodenal ulcer",,Japan,Japan: Okinawa,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Constructing a high quality complete genome sequence of Helicobacter pylori Oki154 to perform comparative genomic analyses in a high resolution manner. This strain was originally isolated from a patient in Okinawa, Japan who had duodenal ulcer.",,99.7,99.3,99.7,0.9,,Good,2014-12-08T22:40:55.896Z,2015-03-16T03:17:09.594Z
1671,1382924.3,Helicobacter pylori oki422,negative,,1382924,Complete,Oki422,,,,,,,,2014-03-25T00:00:00Z,24744331,PRJNA215149,SAMN03081492,GCA_000600165.1,,CP006824.1,NZ_CP006824.1,Okinawa Institute of Advanced Sciences,,PacBio,432x,HGAP v. 2.0,1,,1,1634852,38.8,1645,1468,None,patient,"isolated from a patient in Okinawa, Japan who had gastric atrophy",,Japan,Japan: Okinawa,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Constructing a high quality complete genome sequence of Helicobacter pylori Oki422 to perform comparative genomic analyses in a high resolution manner. This strain was originally isolated from a patient in Okinawa, Japan who had gastric atrophy.",,99.9,99.6,100,0.3,,Good,2014-12-08T22:40:56.871Z,2015-03-16T03:17:09.594Z
1672,1382925.3,Helicobacter pylori oki673,negative,,1382925,Complete,Oki673,,,,,,,,2014-03-25T00:00:00Z,24744331,PRJNA215154,SAMN03081493,GCA_000600185.1,,CP006825.1,NZ_CP006825.1,Okinawa Institute of Advanced Sciences,,PacBio,193x,HGAP v. 2.0,1,,1,1595058,38.8,1621,1437,None,patient,"isolated from a patient in Okinawa, Japan who had gastric ulcer",,Japan,Japan: Okinawa,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Constructing a high quality complete genome sequence of Helicobacter pylori Oki673 to perform comparative genomic analyses in a high resolution manner. This strain was originally isolated from a patient in Okinawa, Japan who had gastric ulcer.",,99.7,99.3,99.7,,,Good,2014-12-08T22:40:57.330Z,2015-03-16T03:17:09.594Z
1673,1382926.3,Helicobacter pylori oki828,negative,,1382926,Complete,Oki828,,,,,,,,2014-03-25T00:00:00Z,24744331,PRJNA215153,SAMN03081494,GCA_000600205.1,,CP006826.1,NZ_CP006826.1,Okinawa Institute of Advanced Sciences,,PacBio,434x,HGAP v. 2.0,1,,1,1600345,38.8,1627,1445,None,patient,"isolated from a patient in Okinawa, Japan who had duodenal ulcer",,Japan,Japan: Okinawa,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Constructing a high quality complete genome sequence of Helicobacter pylori Oki828 to perform comparative genomic analyses in a high resolution manner. This strain was originally isolated from a patient in Okinawa, Japan who had duodenal ulcer.",,99.7,99,99.7,0.6,,Good,2014-12-08T22:40:57.959Z,2015-03-16T03:17:09.594Z
1674,1382927.3,Helicobacter pylori oki898,negative,,1382927,Complete,Oki898,,,,,,,,2014-03-25T00:00:00Z,24744331,PRJNA215151,SAMN03081495,GCA_000600225.1,,CP006827.1,NZ_CP006827.1,Okinawa Institute of Advanced Sciences,,PacBio,613x,HGAP v. 2.0,1,,1,1634875,38.8,1613,1488,None,patient,"isolated from a patient in Okinawa, Japan who had duodenal ulcer",,Japan,Japan: Okinawa,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Constructing a high quality complete genome sequence of Helicobacter pylori Oki898 to perform comparative genomic analyses in a high resolution manner. This strain was originally isolated from a patient in Okinawa, Japan who had duodenal ulcer.",,99.9,99.4,100,,,Good,2014-12-08T22:40:58.420Z,2015-03-16T03:17:09.594Z
1675,1383068.3,Campylobacter jejuni subsp. jejuni 00-2544,negative,Campylobacter jejuni subsp. jejuni 00-2544,1383068,Complete,00-2544,,,,,,,,2013-09-12T00:00:00Z,,PRJNA214465,SAMN02603726,GCA_000466075.2,,"CP006709.1,CP006710.1","NC_022353.1,NC_022354.1",Public Health Agency of Canada,complete,Illumina MiSeq,,Velvet optimizer velvet v. 1.1208,1,1,2,1710056,30.3726,1830,1763,Stool,stool sample,,2000,Canada,Canada,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Curved-shaped,Motile,Nonsporulating,Thermophilic,42 C,NonHalophilic,Microaerophilic,Multiple,Diarrhea,"We are investigating the effect of the presence of the C. jejuni CJIE1 prophage on protein expression. To do so, we are comparing protein expression in natural variants of the organism with and without the prophage. It is necessary to detect and deal with any differences in gene content.",,99.9,99.8,100,,,Good,2014-12-08T22:10:46.619Z,2015-03-16T03:17:09.594Z
1676,1385930.3,Burkholderia dolosa PC543,negative,,1385930,Complete,PC543,,,,MLST.Burkholderia_cepacia_complex.472,,LMG:19468,,2014-01-06T00:00:00Z,,PRJNA214965,SAMN02470544,GCF_000497165.1,,AWRY01000000,,McMaster University,,Illumina HiSeq,40.0x,IBDA v. May-2013,3,,3,6297968,67.04,6527,5739,Respiratory,airway from a patient with cystic fibrosis,,,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,,Unknown,,,Aerobic,Multiple,,Genome sequencing of cystic fibrosis airways isolate Burkholderia dolosa PC543 (LMG 19468),,99.4,95.6,99.3,1.4,,Good,2016-01-17T15:33:50.594Z,2016-01-17T15:33:50.594Z
1677,1386087.3,Neisseria meningitidis LNP21362,negative,,1386087,Complete,LNP21362,,,,,,,,2015-01-07T00:00:00Z,-,PRJNA215160,SAMN03201679,GCA_000816165.1,,CP006869.1,NZ_CP006869.1,Institut Pasteur,,Illumina; PacBio,,HGAP 2.0 v. Sept. 2013,1,,1,2139957,51.82,2689,1945,None,patient,,2009,France,France,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Cocci,No,,,,,,,,Hyper-endemic French isolate,,98.7,98.2,98.8,1.8,,Good,2015-03-12T13:42:56.980Z,2015-03-16T03:17:09.594Z
1679,1386968.3,Francisella tularensis subsp. novicida PA10-7858,negative,,1386968,Complete,PA10-7858,,,,,,,,2016-11-03T00:00:00Z,,PRJNA215224,SAMN05449121,GCF_001865695.1,,CP016635,NZ_CP016635.1,Los Alamos National Laboratory,,454; Illumina,38.2x; 339x,Newbler v. 2.6; VELVET v. 1.1.05,1,,1,1978958,32.36,1932,1921,Blood,blood sample,,,USA,USA: Pennsylvania,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"This finished genome sequence was annotated by the automated RAST service (http://rast.nmpdr.org/) with limited manual inspection and clean-up. Source DNA and bacteria available from: Jeannine Petersen, Division of Vector-Borne Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado 80521, nzp0@cdc.gov. Contacts: Jean F. Challacombe (jchalla@lanl.gov), Cheryl R. Kuske (kuske@lanl.gov)",,99.6,99.4,100,,,Good,2016-11-19T09:02:55.906Z,2016-11-19T09:02:55.906Z
1685,1391726.3,Helicobacter pylori 26695-1,negative,,1391726,Complete,26695-1,,,,MLST.Helicobacter_pylori.181,,,,2015-01-21T00:00:00Z,-,PRJNA270700,SAMN03268385,GCA_000826985.1,,CP010435.1,NZ_CP010435.1,Oita University,,Illumina HiSeq,680.0x,CLC NGS Cell v. April-2011,1,,1,1667638,38.87,1677,1543,Stomach,Human stomach biopsy,,5-Jan,USA,USA: Texas,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,This strain was sequenced as a wild type to compare with artificially induced drug resistant strains.,,99.8,99.4,100,,,Good,2015-03-12T13:43:05.366Z,2015-03-16T03:17:09.594Z
1689,1392476.3,Staphylococcus aureus subsp. aureus 6850,positive,Staphylococcus aureus subsp. aureus 6850,1392476,Complete,6850,,,,MLST.Staphylococcus_aureus.50,,,,2013-08-30T00:00:00Z,,PRJNA216988,SAMN02604264,GCA_000462955.1,,CP006706.1,NC_022222.1,University of Wuerzburg,complete,454 GS-FLX; Sanger,,Newbler v. 2.0.00.20 FLX,1,,1,2736560,32.8,2571,2429,None,patient with a complicated S,"derived from a patient with a complicated S. aureus bacteremia, associated with osteomyelitis and septic arthritis",,,,,,,,,"Human, Homo sapiens",,,"complicated S. aureus bacteremia, associated with osteomyelitis and septic arthritis",,,,,,,,,,,,,,,,"Staphylococcus aureus 6850 is a highly cytotoxic and clinically virulent methicillin-sensitive strain, originally derived from a patient with a complicated S. aureus bacteremia, associated with osteomyelitis and septic arthritis.",,100,99.9,100,1.2,,Good,2014-12-08T22:13:23.969Z,2015-03-16T03:17:09.594Z
1690,1392499.4,Klebsiella pneumoniae subsp. pneumoniae 1158,negative,,1392499,Complete,1158,serovar K2,,,MLST.Klebsiella_pneumoniae.65,,,,2015-01-06T00:00:00Z,-,PRJNA217288,SAMN03097203,GCA_000814805.1,,CP006722.1,NZ_CP006722.1,National Chung Hsing University,,454 GS Junior; Illumina Miseq; Sanger ABI,18X; 213X,CLC genomic workbench v. 5.5,1,,1,5341039,57.23,4983,4989,None,,,2-Apr,Taiwan,Taiwan,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Complete sequencing of a serotype K2 Klebsiella pneumoniae strain in Taiwan.,,99,97.5,100,0.3,,Good,2015-03-12T13:43:06.829Z,2015-03-16T03:17:09.594Z
1691,1395589.3,Leptospira interrogans serovar Linhai str. 56609,negative,,1395589,Complete,56609,Linhai,,,"MLST.Leptospira_spp.92,MLST.Leptospira_spp_2.224",,,,2015-03-04T00:00:00Z,25776677,PRJNA217894,SAMN03375751,GCF_000941035.1,,"CP006723,CP006724,CP006725,CP006726,CP006727","NZ_CP006723.1,NZ_CP006724.1,NZ_CP006725.1,NZ_CP006726.1,NZ_CP006727.1","Department of Medical Microbiology and Parasitology, Institutes of Medical Science, Shanghai Jiao Tong University School of Medicine",,454,29.5x,Newbler v. 2.3,2,3,5,4915652,35.05,4886,4141,None,patient,isolated from a patient in Linhai Zhejiang providence 1954,,China,Linhai Zhejiang,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Leptospira interrogans serovar Linhai strain 56609 was first isolated from a patient in Linhai Zhejiang providence 1954.,,99.3,98.3,100,2.7,,Good,2016-01-17T15:45:57.331Z,2016-01-17T15:45:57.331Z
1703,1403335.5,Porphyromonas gingivalis 381,negative,,1403335,Complete,381,,,,MLST.Porphyromonas_gingivalis.96,,,,2015-10-14T00:00:00Z,,PRJNA276132,SAMN03656156,GCF_001314265.1,,CP012889,NZ_CP012889.1,University of Florida,,454 GS20 shotgun and paired-end reads,49.50x,Velvet v. 0.7.63 and Newbler v. 2.3,1,,1,2378872,48.36,2258,1968,Mouth,subgingival plaque,,1975,USA,"USA: Boston, MA, Forsyth Dental Center",,,,,env_biome:oral cavity of periodontitis patient,"Human, Homo sapiens",,,Chronic periodontitis,,,,,,Negative,Bacilli,No,,Mesophilic,37,,Anaerobic,HostAssociated,Periodontitis,"This study was performed to elucidate the genetic backgrounds responsible for phenotypic differences among 4 strains of P. gingivalis, and compare them with other, currently available genomic sequences to provide a clearer understanding of virulence phenotypes of this bacterium.",,99.9,99.6,100,,,Good,2016-01-17T17:15:19.873Z,2016-01-17T17:15:19.873Z
1704,1403336.3,Porphyromonas gingivalis AJW4,negative,,1403336,Complete,AJW4,,,,,,,,2015-08-26T00:00:00Z,,PRJNA276132,SAMN03372093,GCF_001274615.1,,CP011996,NZ_CP011996.1,University of Florida,,454; Sanger,59.53x,Velvet v. 0.7.63; Newbler v. 2.3,1,,1,2372492,48.27,2280,2002,Mouth,Subgingival plaque,,1988,USA,"USA: Buffalo, NY, State University of New York",,,,,"env_biome:Oral cavity, periodontitis patient","Human, Homo sapiens",,,,,,,,,Negative,Bacilli,No,,Mesophilic,37,,Anaerobic,HostAssociated,Periodontitis,"This study was performed to elucidate the genetic backgrounds responsible for phenotypic differences among 4 strains of P. gingivalis, and compare them with other, currently available genomic sequences to provide a clearer understanding of virulence phenotypes of this bacterium.",,99.9,99.6,100,,,Good,2016-01-17T17:04:21.312Z,2016-01-17T17:04:21.312Z
1705,1403338.3,Porphyromonas gingivalis A7A1-28,negative,,1403338,Complete,A7A1-28,,,,MLST.Porphyromonas_gingivalis.1,,,,2015-11-17T00:00:00Z,,PRJNA276132,SAMN03653671,GCF_001444325.1,,CP013131,,University of Florida,,454; Sanger,94.40x,Velvet v. 0.7.63; Newbler v. 2.3,1,,1,2249024,48.58,2160,1841,Mouth,Tooth abscess,,1987,USA,"USA: Buffalo, NY, State University of New York",,,,,"env_biome:Oral cavity, periodontitis patient with non-insulin dependent diabetes","Human, Homo sapiens",,,,,,,,,Negative,Bacilli,No,,Mesophilic,37,,Anaerobic,HostAssociated,Periodontitis,"This study was performed to elucidate the genetic backgrounds responsible for phenotypic differences among 4 strains of P. gingivalis, and compare them with other, currently available genomic sequences to provide a clearer understanding of virulence phenotypes of this bacterium.;many frameshifted proteins",sample_type:Subgingival plaque,99.8,99,100,0.3,,Good,2016-01-17T17:48:11.907Z,2016-01-17T17:48:11.907Z
1706,1407059.3,Pseudomonas aeruginosa PA38182,negative,,1407059,Complete,PA38182,serovar O12,,,,,,,2014-01-23T00:00:00Z,-,PRJEB4573,SAMEA3138907,GCA_000531435.1,,HG530068.1,NZ_HG530068.1,BUGS,,,,,1,,1,7586152,64.9,7206,7279,None,"the sewer and an historical isolate, suggesting that the ST111 strain has been endemic","isolate from the sewer and an historical isolate, suggesting that the ST111 strain has been endemic in the hospital for many years",,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"A series of extensively drug-resistant (XDR) isolates of Pseudomonas aeruginosa from two outbreaks in UK hospitals were characterized by whole genome sequencing (WGS). Although these isolates were resistant to antibiotics other than colistin, we confirmed that they are still sensitive to disinfectants. The sequencing confirmed that isolates in the larger outbreak were serotype O12 and further revealed that they belonged to the ST111 sequence type which is a major epidemic strain of P. aeruginosa throughout Europe. As this is the first reported sequence of an ST111 strain, the genome was examined in depth, focusing particularly on antibiotic resistance and potential virulence genes, and on the reported regions of genome plasticity. High degrees of sequence similarity were discovered between outbreak isolates collected from recently infected patients, sinks, an isolate from the sewer and an historical isolate, suggesting that the ST111 strain has been endemic in the hospital for many years. The ability to translate easily from outbreak investigation to detailed genome biology using the same data demonstrates the flexibility of WGS application in a clinical setting.;many frameshifted proteins",,98.8,91.1,100,11.1,High CheckM contamination score,Poor,2014-12-08T22:42:01.328Z,2015-03-16T03:17:09.594Z
1707,1407462.3,Helicobacter pylori BM012A,negative,Helicobacter pylori BM012A,1407462,Complete,BM012A,,,,MLST.Helicobacter_pylori.849,, ,,2013-11-22T00:00:00Z,24340004,PRJNA224090,SAMN02376623,GCA_000498315.1,,CP006888.1,NC_022886.1,Pennsylvania State University,complete,454 Roche FLX Titanium,83x,Newbler v. 2.6,1,,1,1660425,38.9,1697,1571,Stomach,antral gastric biopsy specimens,antral gastric biopsy specimens were taken from human volunteers during gastroendoscopy,,Australia,"Australia: Sir Charles Gairdner Hospital, Nedlands, Western Australia",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,Host Associated,,analysis of genomic changes following naturally occurring bacterial transmission between spouses,,99.9,99.4,100,,,Good,2014-12-08T22:11:43.472Z,2015-03-16T03:17:09.594Z
1708,1407463.3,Helicobacter pylori BM012S,negative,Helicobacter pylori BM012S,1407463,Complete,BM012S,,,,MLST.Helicobacter_pylori.849,, ,,2013-11-22T00:00:00Z,24340004,PRJNA229079,SAMN02376624,GCA_000498335.1,,CP006889.1,NC_022911.1,Pennsylvania State University,complete,454 Roche FLX Titanium,136x,Newbler v. 2.8,1,,1,1660469,38.9,1701,1573,Stomach,antral gastric biopsy specimens,antral gastric biopsy specimens were taken from human volunteers during gastroendoscopy,,Australia,"Australia: Sir Charles Gairdner Hospital, Nedlands, Western Australia",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,Host Associated,,derived strain after naturally occurring transmission between adults,,99.9,99.5,100,0.3,,Good,2014-12-08T22:11:43.481Z,2015-03-16T03:17:09.594Z
1710,1408268.58,Corynebacterium ulcerans FRC58,positive,,1408268,Complete,FRC58,,,,,,,,2015-06-26T00:00:00Z,24407640,PRJNA222503,SAMN02471303,GCF_000499805.2,,AYTI01000000,NZ_CP011913.1,Federal University of Para,,Ion Torrent,800x,Newbler v. 2.9; CONTIGuator 2,1,,1,2542597,53.3,2412,2361,Lung,bronchitis secretion from patient in hospital,,10-Jul,France,France: Troyes,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,No,,Mesophilic,,,Unknown,HostAssociated,"Pharyngitis, pneumonia, granulomatous pulmonary nodules, skin ulcers and diphtheria","Recently Corynebacterium ulcerans has been considered distinct from C. diphtheriea. She is capable of causing infectious processes in humans and animals, sometimes fatal. In humans, have been a growing number of cases of different infectious diseases who had no previous contacts with domestic or wild animals or food derivatives. Besides the frames of diphtheria, the micro-organism can cause pharyngitis, pneumonia, lung nodules, granulomatous and skin ulcers. Besides producing toxin antigenically homologous to the diphtheria toxin, the C. ulcerans also produces phospholipase D, which are considered the main virulence factors of this bacterium",,98.7,98,100,,,Good,2016-01-17T15:33:52.773Z,2016-01-17T15:33:52.773Z
1711,1408283.5,Clostridium botulinum CDC_1436,positive,,1408283,Complete,CDC_1436,serovar A2b5,,,MLST.Clostridium_botulinum.7,,,,2015-01-14T00:00:00Z,-,PRJNA222585,SAMN03222820,GCA_000817935.1,,"CP006908.1,CP006909.1","NZ_CP006908.1,NZ_CP006909.1",Los Alamos National Laboratory,,454; Illuminus,25x; 275x,Newbler v. 2.3-PreRelease 6/30/09; Velvet,1,1,2,4365669,28,4281,4206,Stool,infant stool,,1977,USA,USA: Utah,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,Yes,Yes,,,,,,,"Finished genome sequence of C. botulinum CDC_1436, serotype A2b5",,99.3,98.7,100,1.3,,Good,2015-03-12T13:43:48.408Z,2015-03-16T03:17:09.594Z
1712,1412451.3,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110223,negative,,1412451,Complete,enteritidis,serovar enteritidis,,,MLST.Salmonella_enterica.11,,,,2014-04-01T00:00:00Z,24786953,PRJNA219482,SAMN02384165,GCA_000623175.1,"SRR1183741,SRR1183975",CP007266.1,-,LFZ,,454; Illumina,,MIRA v. 4.0,1,,1,4771577,52.2,4713,4429,None,Human- mung bean-Outbreak,,2005,Canada,Canada: Ontario,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,develop molecular sub typing scheme based on whole genome sequencing data,,99.3,98.5,100,0.5,,Good,2014-12-09T00:34:00.418Z,2015-03-16T03:17:09.594Z
1713,1412452.3,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19992322,negative,,1412452,Complete,enteritidis,serovar enteritidis,,,MLST.Salmonella_enterica.11,,,,2014-04-01T00:00:00Z,24786953,PRJNA219482,SAMN02384169,GCA_000623455.1,SRR1183745,CP007291.1,-,LFZ,,Illumina,,MIRA v. 4.0,1,,1,4685855,52.1,4599,4327,Stool,Human-Stool,,1998,Canada,Canada: Quebec,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,develop molecular sub typing scheme based on whole genome sequencing data,,99.2,98.5,100,,,Good,2014-12-09T00:34:00.910Z,2015-03-16T03:17:09.594Z
1714,1412592.3,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121175,negative,,1412592,Complete,enteritidis,serovar enteritidis,,,MLST.Salmonella_enterica.11,,,,2014-04-01T00:00:00Z,24786953,PRJNA219482,SAMN02384313,GCA_000623055.2,SRR1183889,CP007269.2,NZ_CP007269.1,LFZ,,Illumina,>70X,MIRA v. 4.0,1,,1,4679953,52.2,4574,4367,None,chick paper,,2010,Canada,Canada: Ontario,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,,,,,,,,,develop molecular sub typing scheme based on whole genome sequencing data,,99.3,99,100,,,Good,2014-12-09T00:35:33.230Z,2015-03-16T03:17:09.594Z
1715,1413216.3,Acinetobacter baumannii AB07,negative,Acinetobacter baumannii PKAB07,1413216,Complete,AB07,,,,MLST.Acinetobacter_baumannii_1.195,, ,,2014-02-24T00:00:00Z,24652977,PRJNA224967,,GCA_000576535.1,,"CP006963.1,CP006964.1",-,Pondicherry University,complete,Illumina GAII,10.0x,Velvet v. 1.2.08; ABySS v. 1.3.5; A5,1,1,2,4242611,39.2898,3890,3821,Wound,wound infection of a hospitalized patient,,,India,India: Pondicherry,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Multidrug resistant clinical isolate causing nosocomial infections,,98.2,92.2,98.4,4.6,,Good,2014-12-08T22:09:32.117Z,2015-03-16T03:17:09.594Z
1716,1415775.6,Clostridium baratii str. Sullivan,positive,,1415775,Complete,Sullivan,,,,,,,,2014-12-04T00:00:00Z,-,PRJNA225788,SAMN03222823,GCA_000789395.1,,"CP006905.1,CP006906.1","NZ_CP006905.1,NZ_CP006906.1",Los Alamos National Laboratory,,454; Illumina,44.7x; 321.4x,Newbler v. 2.3; Velvet v. 1.0.13; Parallel,1,1,2,3338630,28.25,3175,3169,Stool,adult stool,,2007,USA,USA: New York,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,Yes,,,,,,,Complete genome sequence of Clostridium baratii Sullivan,,97,95,100,,,Good,2015-03-12T13:43:55.778Z,2015-03-16T03:17:09.594Z
1718,1420012.3,Klebsiella pneumoniae 30660/NJST258_1,negative,Klebsiella pneumoniae 30660/NJST258_1,1420012,Complete,30660/NJST258_1,,,,MLST.Klebsiella_pneumoniae.258,, ,,2014-03-19T00:00:00Z,24639510,PRJNA226698,SAMN03081502,GCA_000598005.1,,"CP006923.1,CP006924.1,CP006927.1,CP006928.1,CP006925.1,CP006926.1","NZ_CP006923.1,NZ_CP006927.1,NZ_CP006926.1,NZ_CP006925.1,NZ_CP006928.1,NZ_CP006924.1",Igenbio Inc,complete,,,,1,5,6,5540936,57.146,5385,5799,Urine,urinary tract infection,,2010,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Towards an understanding of the success of the pandemic ST258 carbapenem-resistant Klebsiella pneumoniae strain,,99.3,97.9,96.9,0.1,,Good,2014-12-08T22:11:48.788Z,2015-03-16T03:17:09.594Z
1719,1420013.3,Klebsiella pneumoniae 30684/NJST258_2,negative,Klebsiella pneumoniae 30684/NJST258_2,1420013,Complete,30684/NJST258_2,,,,MLST.Klebsiella_pneumoniae.258,, ,,2014-03-19T00:00:00Z,24639510,PRJNA226699,SAMN03081501,GCA_000597905.1,,"CP006918.1,CP006919.1,CP006921.1,CP006922.1","NZ_CP006918.1,NZ_CP006919.1,NZ_CP006922.1,NZ_CP006921.1",Igenbio Inc,complete,,,,1,3,4,5417216,57.4316,5233,5591,Urine,urinary tract infection,,2010,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Towards an understanding of the success of the pandemic ST258 carbapenem-resistant Klebsiella pneumoniae strain,,99.5,97.9,100,0.4,,Good,2014-12-08T22:11:48.797Z,2015-03-16T03:17:09.594Z
1720,1420885.6,Vibrio cholerae MS6,negative,,1420885,Complete,MS6,,,,MLST.Vibrio_cholerae.75,,,,2014-06-17T00:00:00Z,24887199,PRJDB1528,-,GCA_000829215.1,,"AP014525.1,AP014524.1","NZ_AP014525.1,NZ_AP014524.1","Research Institute for Microbial Diseases, Osaka University",,454 GS FLX; ABI 3130xl; Illumina,24.5x,GS De Novo Assembler v. 2.6,2,,2,4030944,47.49,3638,3752,Stool,"diarrheal patient, and was named MS6","isolate from a diarrheal patient, and was named MS6",,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Vibrio cholerae are found in the aquatic environment in different parts of the world. They are facultatively anaerobic, asporogenous, motile, curved or straight gram-negative rods. More than 200 serogroups of V. cholerae have been recognized to date, but only serogroups O1 and O139 are known to cause cholera in humans of epidemic and pandemic proportions. We obtained a V. cholerae O1 El Tor isolate from a diarrheal patient, and was named MS6. Multilocus sequence typing analysis revealed that strain MS6 was most closely related to the US Gulf Coast clone; however, two housekeeping genes of MS6 exhibit novel sequence types. This analysis represents an important step toward the understanding of the evolutional history and of the genetic basis underlying pathogenicity in cholera organism.",,99.7,99.6,100,,,Good,2015-03-12T13:43:58.097Z,2015-03-16T03:17:09.594Z
1722,1427342.3,Pseudomonas aeruginosa SCV20265,negative,Pseudomonas aeruginosa SCV20265,1427342,Complete,SCV20265,,,,MLST.Pseudomonas_aeruginosa.299,, ,,2013-12-18T00:00:00Z,,PRJNA229445,SAMN02415141,GCA_000510305.1,,CP006931.1,NC_023149.1,Helmholtz Center for Infection Research,complete,PacBio; Illumina GAIIx,135x,HGAP SMRTPortal v. 2.0.1,1,,1,6725183,66.3,6312,6299,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,,Yes,,,,,,HostAssociated,Cystic fibrosis,Complete genome sequence of highly adherent P.aeruginosa small-colony variant SCV20265,,99.6,99,100,,,Good,2014-12-08T22:12:37.932Z,2015-03-16T03:17:09.594Z
1723,1427374.3,Streptococcus agalactiae CNCTC 10/84,positive,,1427374,Complete,CNCTC 10/84,,,,MLST.Streptococcus_agalactiae.26,,NCTC 10,,2014-11-14T00:00:00Z,25540350,PRJNA229124,SAMN03178022,GCA_000782855.1,,CP006910.1,NZ_CP006910.1,IGS,,Illumina,90x,Celera Assembler v. 7.0,1,,1,2013842,35.44,1965,1944,None,,,1977,USA,"USA: Atlanta, GA",,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,This is a genome sequencing project for Streptococcus agaiactiae CNCTC 10/84,,99.6,99.5,100,,,Good,2015-03-12T13:44:08.046Z,2015-03-16T03:17:09.594Z
1725,1431450.3,Helicobacter pylori PMSS1 strain PMSS1,negative,,1431450,Complete,PMSS1,,,Type I cagPAI positive,MLST.Helicobacter_pylori.31,,,,2017-02-10T00:00:00Z,,PRJNA306775,SAMN04362855,GCF_001991095.1,,"CP018823,CP018824","NZ_CP018823.1,NZ_CP018824.1","University of California, Davis",,"PacBio, HiSeq",>500x,SMRT Analysis pipeline (HGAP & QUIVER) v.,1,1,2,1624538,39.01,1605,1462,Stomach,Stomach,,1994,Australia,Australia: Sydney,,,,,,"Human, Homo sapiens",,,Duodenal ulcer,,,host_description:Greek immigrant with family history of peptic ulcer disease,,,,,,,Mesophilic,37 C,,Microaerophilic,HostAssociated,Duodenal ulcer,"Characterization of the genome for H. pylori PMSS1, which is commonly used in animal models of infection",collected_by:Adrian Lee,99.7,99.5,100,,,Good,2017-03-20T07:38:25.209Z,2017-03-20T07:38:25.209Z
1729,1435046.4,Shigella flexneri G1663,negative,,1435046,Complete,G1663,,,,,,,,2015-06-08T00:00:00Z,,PRJNA231092,SAMN02440121,GCF_001021855.1,,"CP007037,CP007038","NZ_CP007037.1,NZ_CP007038.1",TEDA Institute of Biological and Biotechnology,,Illumina GAIIx; 454,120x,Velvet v. 1.2.01,1,1,2,4817311,50.7,5370,4578,Stool,stool sample,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,To construct evolutionary tree,,99.6,97.8,99.6,,,Good,2016-01-17T16:05:36.895Z,2016-01-17T16:05:36.895Z
1730,1435985.3,Burkholderia pseudomallei MSHR435,negative,,1435985,Complete,MSHR435,,,,MLST.Burkholderia_pseudomallei.126,,,,2014-11-12T00:00:00Z,,PRJNA231480,SAMN02999478,GCF_000775165.1,,JRFP01000000,,Los Alamos National Laboratory,,454; Illumina; PacBio,314.0x,Newbler v. 2.6; Velvet v. 1.1.05;,2,,2,7133242,67.92,7337,6051,None,clinical isolate,,,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,,,,,,,,Genome sequencing of Burkholderia pseudomallei MSHR435,,96,92.1,94.4,2.1,,Good,2016-01-17T15:40:45.540Z,2016-01-17T15:40:45.540Z
1731,1435994.3,Burkholderia pseudomallei MSHR2243,negative,,1435994,Complete,MSHR2243,,,,MLST.Burkholderia_pseudomallei.132,,,,2014-10-31T00:00:00Z,-,PRJNA231528,SAMN03004264,GCA_000770415.1,"SRR2874411,SRR2874412,SRR2896944","CP009270.1,CP009269.1","NZ_CP009270.1,NZ_CP009269.1",Los Alamos National Laboratory,,Illumina; 454,331x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,2,,2,7145194,68.22,6933,5801,None,clinical isolate,,,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,No,,,,,,,Genome sequencing of Burkholderia pseudomallei MSHR2243,,99.3,95.7,100,,,Good,2015-03-12T13:44:57.793Z,2015-03-16T03:17:09.594Z
1732,1437000.3,Burkholderia pseudomallei MSHR1153,negative,,1437000,Complete,MSHR1153,,,,MLST.Burkholderia_pseudomallei.117,,,,2014-10-31T00:00:00Z,-,PRJNA231860,SAMN03008919,GCA_000770435.1,"SRR2875412,SRR2875413,SRR2875414","CP009271.1,CP009272.1","NZ_CP009271.1,NZ_CP009272.1",Los Alamos National Laboratory,,Illumina; 454; PacBio,269x,Newbler v. 2.6; Velvet v. 1.2.01; Allpaths,2,,2,7312903,68.06,7103,5951,None,clinical isolate,,,Australia,Australia,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Yes,No,,,,,,,Genome sequencing of Burkholderia pseudomallei MSHR1153,,99.2,95.6,100,0.2,,Good,2015-03-12T13:45:01.946Z,2015-03-16T03:17:09.594Z
1733,1437007.3,Streptococcus pyogenes STAB902,positive,,1437007,Complete,STAB902,,,,MLST.Streptococcus_pyogenes.406,,,,2014-07-22T00:00:00Z,-,PRJNA231895,SAMN03081524,GCA_000732425.1,,CP007041.1,NZ_CP007041.1,nicolas.soriano@univ-rennes1.fr,,Illumina; PCR+Sanger,130,CLC Genomics workbench v. 6.5.1,1,,1,1892124,38.5,1925,1809,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,S. pyogenes non-invasive M3 strain,,99.7,99.5,100,,,Good,2014-12-08T22:57:13.933Z,2015-03-16T03:17:09.594Z
1734,1437008.3,Streptococcus pyogenes STAB1102,positive,,1437008,Complete,STAB1102,,,,MLST.Streptococcus_pyogenes.5,,,,2014-07-22T00:00:00Z,-,PRJNA231786,SAMN03081522,GCA_000732345.1,,CP007023.1,-,Service Bacteriologie CHU Pontchaillou,,Illumina,"2,400x",CLC Genomics workbench v. 6.5.1,1,,1,1709442,38.6,1624,1582,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Cocci,No,No,,,,,HostAssociated,,"Genome sequence of streptococcus pyogenes strain STAB1102 (emm83), a human pathogen associated with skin tissue infection in Brittany.",,99.6,99.3,100,,,Good,2014-12-09T00:45:55.359Z,2015-03-16T03:17:09.594Z
1735,1437873.4,Pseudomonas aeruginosa PA99,negative,,1437873,Complete,PA99,,,,MLST.Pseudomonas_aeruginosa.964,,,,2019-11-04T00:00:00Z,,PRJNA560136,SAMN12569252,GCA_009498355.1,,CP042967,,Chiang Mai University,,PacBio RSII,176.0x,HGAP v. 3,1,,1,6946480,65.93629,7428,6608,Sputum,sputum,,2016,Thailand,Thailand: Chiang Mai,,,,,,"Human, Homo sapiens",,,unspecified,,,,Resistant,Computational Prediction,,,,,,,,,,,Genome characterization of XDR Pseudomonas aeruginosa,collected_by:MNCMH,99,89.7,,,,Good,2019-11-25T13:42:19.090Z,2019-11-25T13:42:19.090Z
1736,1440052.3,Escherichia albertii KF1,negative,Escherichia albertii KF1,1440052,Complete,KF1,,,,MLST.Escherichia_coli_1.4638,, ,,2013-12-30T00:00:00Z,,PRJNA232181,SAMN02641387,GCA_000512125.1,,CP007025.1,NZ_CP007025.1,"Department of Microbiology, Medical University of Bialystok",complete,454; Illumina; IonTorrent,75x,MaSuRCA v. 2.1.0,1,,1,4701875,49.7,4690,4422,Stool,5 Bangladeshi children with diarrhea,isolated from 5 Bangladeshi children with diarrhea,,Bangladesh,Bangladesh,,,,,,"Human, Homo sapiens",,,,,,,,,Negative,Bacilli,Nonmotile,,,,,,,,"Escherichia albertii is a new emerging enetric pathogen that has been associated with infections in humans and birds.E. albertii was first isolated from 5 Bangladeshi children with diarrhea. These isolates were initially identified as Hafnia alvei, but further analysis showed that they were more closely related to Escherichia coli and Shigella flexneri, and subsequently reclassified as E. albertii in 2003. E. albertii produces intimin, a virulence factor characteristic for enteropathogenic (EPEC) and enterohemorrhagic E. coli (EHEC) strains. However, its pathogenic potential is currently unknown and it is unclear how common is this new species in food and clinical samples. In addition, its identification is difficult because of the lack of biochemical tests, and exclusively based on molecular methods (e.g. PCR).The project will provide a platform to identify new genes that may contribute to this pathogen's virulence or markers usefull in reliable identification of E. albertii strains. Moreover, it can expand our knowledge about genomic variability, plasticity and mechanisms of evolution of enteropathogenic Escherichia spp. strains.",,99.4,97.3,97,,,Good,2014-12-08T22:11:18.855Z,2015-03-16T03:17:09.594Z
1737,1440772.3,Streptococcus pyogenes STAB901,positive,,1440772,Complete,STAB901,serovar M44,,,MLST.Streptococcus_pyogenes.178,,,,2014-07-22T00:00:00Z,-,PRJNA232121,SAMN03081523,GCA_000732385.1,,CP007024.1,-,"Bacteriology Service, CHU Pontchaillou Rennes, France",,454,30x,CLC Genomics workbench v. 6.5.1,1,,1,1795609,38.5,2029,1358,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Cocci,,,,,,,,,Invasive and epidemic strain of serotype M44 group A streptococcus;many frameshifted proteins,,99.5,94.8,100,10.7,High CheckM contamination score,Poor,2014-12-09T00:36:06.190Z,2015-03-16T03:17:09.594Z
1738,1441379.3,Mycoplasma pneumoniae M29,negative,,1441379,Complete,M29,,,,MLST.Mycoplasma_pneumoniae.3,,,,2014-07-28T00:00:00Z,-,PRJNA232505,SAMN02582400,GCA_000733995.1,,CP008895.1,NZ_CP008895.1,National Natural Science Foundaton of China,,Illumina HiSeq,10000.0x,SOAPdenovo v. 1.05,1,,1,857799,39.9,815,,Throat,throat swab,"isolated in Outpatient Department of Beijingfriendship Hospital, affiliated to Capital Medical University, Beijing, and was kept in Beijing Tropical Medicine Research Institute",2005,China,"China: Beijing, Beijingfriendship Hospital",,,,,,"Human, Homo sapiens",,,,,,,,,,,Yes,No,,,,,,,"Mycoplasma pneumoniae M29 was isolated in Outpatient Department of Beijingfriendship Hospital, affiliated to Capital Medical University, Beijing, and was kept in Beijing Tropical Medicine Research Institute. It has no mutation at domain ⅴof 23S rRAN, and is sensitive to macrolide antibiotics.",,99.5,98.3,100,6.7,,Good,2014-12-09T00:45:56.424Z,2015-03-16T03:17:09.594Z
1739,1452727.3,Bacillus anthracis str. Turkey32,positive,,1452727,Complete,Turkey32,,,,MLST.Bacillus_cereus.1,,,,2015-02-05T00:00:00Z,-,PRJNA236040,SAMN03010432,GCA_000833275.1,"SRR2155541,SRR2155542","CP009315.1,CP009316.1,CP009314.1","NZ_CP009315.1,NZ_CP009316.1,NZ_CP009314.1",Los Alamos National Laboratory,,Illumina; 454,324x,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,1,2,3,5505298,35.24,5856,5711,Skin,skin,,20-Oct-91,Turkey,Turkey: Yozgat,,,,,,"Human, Homo sapiens",,,,,,,,,Positive,Bacilli,,Yes,,,,,,,Genome sequencing of Bacillus anthracis Turkey32,,100,99.3,100,0.6,,Good,2015-03-12T13:45:31.848Z,2015-03-16T03:17:09.594Z
1740,1454640.3,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1878,negative,,1454640,Complete,H2662-08-1997,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2016-04-19T00:00:00Z,,PRJNA236709,SAMN02716865,GCF_001623825.1,,"CP014979,CP014980",,USDA-ARS-USMARC,,PacBio RS II C3 P5,152.44,Celera v. 7.0,,1,2,4985715,52.14,5133,4740,None,,,Aug-97,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Salmonella comparative genomics,collected_by:CDC,99.8,99,100,,,Good,2016-04-28T13:19:37.159Z,2016-04-28T13:19:37.159Z
1741,1454641.3,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1908,negative,,1454641,Complete,CDC 2010K-1587,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2016-04-19T00:00:00Z,,PRJNA236710,SAMN02716879,GCF_001623645.1,,"CP014965,CP014966","NZ_CP014965.1,NZ_CP014966.1",USDA-ARS-USMARC,,PacBio RS II C3 P5,122.88,Celera v. 7.0,,1,2,5008298,52.12,5132,4755,Stool,stool,,6-Jun,USA,USA: BIFSCo Region 8,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Salmonella comparative genomics,collected_by:CDC,99.8,99.3,100,,,Good,2016-04-28T13:11:58.563Z,2016-04-28T13:11:58.563Z
1742,1454642.3,Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2011K-0870,negative,,1454642,Complete,CDC 2011K-0870,,,,MLST.Salmonella_enterica.19,,,,2015-04-20T00:00:00Z,,PRJNA236711,SAMN02712200,GCF_000973645.1,,CP007523,NZ_CP007523.1,USDA-ARS-USMARC,,PacBio RS II C3 P5,complete: 22 X coverage : reads >= 8000,Celera Assembler v. 8.1,1,,1,4769471,52.23,4735,4623,Stool,stool,,27-Feb-11,USA,USA: BIFSCo Region 7,,,,,env_biome:human-associated habitat,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Salmonella comparative genomics,,99.8,99.4,100,,,Good,2016-01-17T15:53:59.532Z,2016-01-17T15:53:59.532Z
1743,1454643.3,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1910,negative,,1454643,Complete,CDC 2011K-1702,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2016-04-19T00:00:00Z,,PRJNA236712,SAMN02716880,GCF_001623685.1,,"CP014967,CP014968","NZ_CP014967.1,NZ_CP014968.1",USDA-ARS-USMARC,,PacBio RS II C3 P5,134.63,Celera v. 7.0,,1,2,5000337,52.13,5141,4745,Urine,urine,,11-Jul,USA,USA: BIFSCo Region 7,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Salmonella comparative genomics,collected_by:CDC,99.8,99.2,100,,,Good,2016-04-28T13:12:44.979Z,2016-04-28T13:12:44.979Z
1744,1454644.3,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1906,negative,,1454644,Complete,CDC 2009K-1640,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2016-04-19T00:00:00Z,,PRJNA236713,SAMN02716877,GCF_001623805.1,,"CP014975,CP014976","NZ_CP014975.1,NZ_CP014976.1",USDA-ARS-USMARC,,PacBio RS II C3 P5,88.13,Celera v. 7.0,,1,2,5027726,52.13,5172,4786,None,,,2009,USA,USA: BIFSCo Region 2,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Salmonella comparative genomics,collected_by:CDC,99.8,99.4,100,,,Good,2016-04-28T13:19:33.105Z,2016-04-28T13:19:33.105Z
1745,1454645.3,Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2009K-2059,negative,,1454645,Complete,CDC 2009K-2059,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2016-04-19T00:00:00Z,,PRJNA236714,SAMN02716878,GCF_001623775.1,,CP014983,NZ_CP014983.1,USDA-ARS-USMARC,,PacBio RS II C3 P5,147.03,Celera v. 7.0,,,1,4823793,52.18,4884,4536,Stool,stool,,9-Oct,USA,USA: BIFSCo Region 2,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Salmonella comparative genomics,collected_by:CDC,99.8,99.4,100,,,Good,2016-04-28T13:16:04.300Z,2016-04-28T13:16:04.300Z
1746,1455315.5,Acinetobacter baumannii LAC-4,negative,,1455315,Complete,LAC-4,,,,"MLST.Acinetobacter_baumannii_1.447,MLST.Acinetobacter_baumannii_2.10",,,,2015-03-11T00:00:00Z,25728466,PRJNA242902,SAMN02709859,GCF_000786735.1,,"CP007712,CP007713,CP007714","NZ_CP007712.1,NZ_CP007713.1,NZ_CP007714.1","California State University, Los Angeles",,Roche 454 FLX+; Illumina Hiseq2000;,43.5x; 255.6x; 408x,GS De Novo Assembler v. unknown,1,2,3,3968436,39,3826,3806,None,unavailable,,1/2/97,USA,"USA: Los Angeles County, California",,,,,,"Human, Homo sapiens",,,unavailable,,,,,,Negative,Coccobacilli,No,,Mesophilic,37C,,Aerobic,HostAssociated,Bacterial infection,The goals of this project are to identify virulence factor genes and to understand the mechanisms of pathogenesis and resistance,collected_by:Public Health Laboratory,98.8,98.2,98.4,1,,Good,2016-01-17T15:41:06.592Z,2016-01-17T15:41:06.592Z
1756,1463164.204,Klebsiella quasipneumoniae subsp. similipneumoniae strain 07A044T,negative,,1463164,Complete,07A044T,,,,MLST.Klebsiella_pneumoniae.1215,,,,2021-10-19T00:00:00Z,,PRJNA768294,SAMN22024805,GCA_020525685.1,,"CP084787,CP084788",,Monash University,,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5189735,58.128365,5031,4915,Blood,blood,,1997,,Germany,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",99.6,99,,,,Good,2021-12-24T12:03:57.874Z,2021-12-24T12:03:57.874Z
1773,1463165.82,Klebsiella quasipneumoniae strain L22,negative,,1463165,Complete,L22,K1,,,MLST.Klebsiella_pneumoniae.367,,,,2018-09-04T00:00:00Z,,PRJNA482505,SAMN09708445,GCA_003443835.1,,"CP031257,CP031258,CP031259,CP031260,CP031261,CP031262",,Peking University People 's Hospital,,PacBio,106.0x,HGAP v. SMRT Link v5.1.0,1,5,6,5631032,57.198166,5545,,Lung,bronchoalveolar lavage fluid,,9/2/14,China,China,,,,,,"Human, Homo sapiens",male,70y,pneumoniae,,,host_disease_outcome:death,,,,,,,,,,,,,research Klebsiella quasipneumoniae Genome,collected_by:Yatao Guo,99,97.5,100,0.7,,Good,2018-10-02T05:40:57.427Z,2018-10-02T05:40:57.427Z
1928,1507806.5,Campylobacter fetus subsp. testudinum strain 772,negative,,1507806,Complete,772,,,,MLST.Campylobacter_fetus.17,,,,2018-03-07T00:00:00Z,,PRJNA436182,SAMN08618845,GCA_002973655.1,,CP027287,,Guangzhou Center for Disease Control and Prevention,,Illumina HiSeq,1547.0x,SOAPdenovo v. v2.04,1,,1,1863540,33.13334,1875,1815,Abdomen,ascites,,4/1/15,China,China: Guangzhou,,,,,,"Human, Homo sapiens",,,Peritonitis,,,,,,,,,,,,,,,,"C. fetus subsp testudinum strain 772, complete genome",collected_by:Panyu central hospital,99.6,99.6,100,,,Good,2018-05-26T04:26:23.063Z,2018-05-26T04:26:23.063Z
1941,1530123.79,Acinetobacter seifertii strain AS9,negative,,1530123,Complete,AS9,,,,"MLST.Acinetobacter_baumannii_2.553,MLST.Acinetobacter_baumannii_1.262",,,,2020-09-24T00:00:00Z,,PRJNA662665,SAMN16092213,GCA_014723155.1,,"CP061681,CP061682",,Taipei Veterans General Hospital,,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,1,2,4084907,38.628075,3904,3785,Blood,blood,,2010/2017,Taiwan,Taiwan,,,,,,"Human, Homo sapiens",,,bloodstream infection,,,,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:TVGH,99.3,97.9,,,,Good,2020-11-28T21:54:05.296Z,2020-11-28T21:54:05.296Z
1946,1563222.9,Citrobacter pasteurii strain UMH17,negative,,1563222,Complete,UMH17,,,,MLST.Citrobacter_freundii.128,,,,2018-10-17T00:00:00Z,30087402,PRJNA412823,SAMN07729549,,,CP024676,,University of Michigan,,PacBio,213x,HGAP v. 2,1,,1,4654874,51.89728,4540,4469,None,,,13-Oct,USA,USA: Michigan,,,,,,"Human, Homo sapiens",,,bacteremia,,,,,,,,,,,,,,,,"The goal of this study was to identify bacterial genes that contribute to the survival and fitness of an opportunistic pathogen, Citrobacter freundii, during bacteremia. Bacterial isolates were obtained from University of Michigan Hospital System patients with Citrobacter bloodstream infections and the genomic sequences of each were determined de novo. From these isolates, a single C. freundii strain was selected for use in INSeq experiments to identify fitness genes in a murine model of bacteremia.",collected_by:University of Michigan,99.2,97.9,,,,Good,2018-11-29T02:27:58.454Z,2018-11-29T02:27:58.454Z
2080,1617964.3,Shigella flexneri 4c strain 1205,negative,,1617964,Complete,1205,,,,,,,,2016-03-03T00:00:00Z,,PRJNA288251,SAMN03797408,GCF_001579965.1,,"CP012140,CP012141,CP012142,CP012143",,Hangzhou Centrer for Disease Control amd Prevention,,PacBio,100x,HS HGAP v. 2,1,3,4,5196066,50.42,5947,5122,None,,,2012,China,China,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,genome sequence,sample_type:cell culture,99.4,97.2,100,,,Good,2016-03-18T11:07:24.124Z,2016-03-18T11:07:24.124Z
2082,1620419.123,Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CFSAN067216,negative,,1620419,Complete,CFSAN067216,Typhimurium var. 5-,,,MLST.Salmonella_enterica.19,,,,2018-12-31T00:00:00Z,,PRJNA215355,SAMN08274661,GCA_003986675.1,,"CP028318,CP028319",,FDA/CFSAN,,PacBio,481.0x,HGAP v. 3.0,1,1,2,4978420,52.14283,5234,5034,None,,,2010,USA,USA:PA,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Listeria monocytogenes Database: isolates from the Food and Drug Administration, Center for Food Safety and Applied Nutrition",collected_by:Dudley Lab/Penn State/PADOH,99.8,99,,,,Good,2019-01-31T23:19:23.549Z,2019-01-31T23:19:23.549Z
2154,1639133.23,Citrobacter portucalensis strain IOMTU157,negative,,1639133,Complete,IOMTU157,,,,MLST.Citrobacter_freundii.15,,,,2020-01-28T00:00:00Z,,PRJDB9230,SAMD00201481,GCA_010319905.1,,AP022378,,"Department of Microbiology, Juntendo University Graduate School of Medicine",,Illuminia MiSeq; Oxford nanopore MinION,62x,Unicycler v. 0.4.8,1,,1,4987090,52.067577,4868,4687,None,,,2012,Nepal,Nepal:Kathmandu,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Highly drug-resistant Citrobacter spp. clinical isolates were detected in medical settings in Nepal. These isolates harbored genes encoding carbapenem- and aminoglycoside-resistant factors.,,96.1,94.7,,,,Good,2020-03-26T18:59:09.043Z,2020-03-26T18:59:09.043Z
2156,1648923.37,Bacillus paralicheniformis strain Bac84,positive,,1648923,Complete,Bac84,,,,,,,,2018-03-12T00:00:00Z,,PRJNA412146,SAMN07701716,GCA_002993925.1,,CP023665,,King Abdullah University of Science and Technology,,PacBio,273X,Celera Assembler v. 2.3.0.140935.p5,1,,1,4376831,45.841774,4611,,None,Red Sea lagoons-Microbial mat,"isolated from the Red Sea, specifically three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS) collected from Rabigh harbor lagoon (39°0′35",2012-04,Saudi Arabia,Saudi Arabia:Rabigh harbor lagoon,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"We sequenced genomes isolated from the Red Sea, specifically three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS) collected from Rabigh harbor lagoon (39°0′35.762′′ E, 22°45′5.582′′ N) and Al-Kharrar lagoon (38°54′39.638′′ E, 22°54′50.251′′ N) in Saudi Arabia. MN mud was sampled from the coastal lagoon of the Red Sea alongside mangrove tree. MM was sampled approximately 7.5 m away from the coastal lagoon. BS refers to sediments with no contact with lagoon water at high tide.",sample_type:cell culture,99.8,99.5,100,,,Good,2018-05-31T01:06:48.374Z,2018-05-31T01:06:48.374Z
2165,1667327.52,Klebsiella quasipneumoniae subsp. quasipneumoniae strain 01A030T,negative,,1667327,Complete,01A030T,,,,MLST.Klebsiella_pneumoniae.1528,,,,2021-10-19T00:00:00Z,,PRJNA768294,SAMN22024800,GCA_020525925.1,,"CP084876,CP084877",,Monash University,,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5507230,58.001953,5391,5169,Blood,blood,,1997,,Austria,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",99.8,98.6,,,,Good,2021-12-24T12:04:07.801Z,2021-12-24T12:04:07.801Z
2169,1686392.3,Enterobacter sp. MGH120,negative,,1686392,Complete,MGH120,,,,MLST.Enterobacter_cloacae.79,,,,2015-07-21T00:00:00Z,,PRJNA271899,SAMN03280184,GCF_001037725.1,"SRR2127462,SRR2127492,SRR2135077,SRR2135149",LETH01000000,,Broad Institute,,Illumina,134.0x,allpaths v. R48559,,,1,4607622,55.51,4331,4228,None,,,2014,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing of Carbapenem resistant bacteria Genome sequencing,,99.5,98.4,100,,,Good,2016-01-17T16:09:58.196Z,2016-01-17T16:09:58.196Z
2170,1686396.3,Enterobacter sp. BIDMC93,negative,,1686396,Complete,BIDMC93,,,,MLST.Enterobacter_cloacae.677,,,,2015-07-21T00:00:00Z,,PRJNA271899,SAMN03280188,GCF_001037805.1,"SRR2127654,SRR2127796,SRR2131448,SRR2135242",LETL01000000,,Broad Institute,,Illumina,135.0x,allpaths v. R48559,,,1,4701014,55.52,4369,4273,None,,,2013,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Sequencing of Carbapenem resistant bacteria Genome sequencing,,99.5,98.6,100,,,Good,2016-01-17T16:09:59.796Z,2016-01-17T16:09:59.796Z
2174,1697043.4,Bordetella sp. H567,negative,,1697043,Complete,H567,,,,,,,,2016-08-12T00:00:00Z,,PRJNA287884,SAMN03940794,GCF_001704295.1,"SRR5070890,SRR5070985",CP012334,NZ_CP012334.1,Centers for Disease Control and Prevention,,PacBio RSII; Illumina HiSeq,184x,HGAP v. 3,1,,1,5532470,66.12,5072,4630,None,,,2010,USA,USA: CA,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to characterize genomes of Bordetella species other than B. pertussis. Members of the genus Bordetella cause respiratory and opportunistic infection in a variety of hosts. These data are being made available to facilitate comparative analyses for the study of this important group of bacterial pathogens.,,97.9,94.6,97.1,4.3,,Good,2016-09-11T19:48:45.244Z,2016-09-11T19:48:45.244Z
2201,1759399.3,Streptococcus sp. A12,positive,,1759399,Complete,A12,,,,,,,,2016-03-11T00:00:00Z,26826230,PRJNA302800,SAMN04287214,GCF_001587175.1,SRR2984661,CP013651,NZ_CP013651.1,University of Florida,,PacBio,100,HGAP.3 v. 1,1,,1,1874337,42.21,1799,1730,Mouth,supragingival plaque from caries-free child,isolated from a human plaque sample capable of inhibiting Streptococcus mutans,2013,USA,USA: Florida,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,C,,,,,A highly arginolytic strain of Streptococci that was isolated from a human plaque sample capable of inhibiting Streptococcus mutans.,sample_type:whole organism,99.2,98.7,98.3,0.5,,Good,2016-03-18T15:36:06.381Z,2016-03-18T15:36:06.381Z
2669,1806053.29,Corynebacterium diphtheriae bv. mitis strain PC0646,positive,,1806053,Complete,PC0646,,,,,,,,2020-09-30T00:00:00Z,,PRJNA541849,SAMN11811052,GCA_014826095.1,,CP040557,,"Divison of Bacterial Diseases, Centers for Disease Control",,PacBio RSII; Illumina MiSeq,316x,HGAP v. 3,1,,1,2386265,53.513,2386,2242,Wound,Wound,"recovered from clinical specimens, most notably C. diphtheriae from human respiratory, blood, or cutaneous infection",2018,USA,USA: WA,,,,,,"Human, Homo sapiens",,,diphtheria,,,,,,,,,,,,,,,,"The Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention characterizes isolates of Corynebacterium species recovered from clinical specimens, most notably C. diphtheriae from human respiratory, blood, or cutaneous infection. However, collection does include some isolates from other sources. Isolates of C. diphtheriae and C. ulcerans have been tested for the presence and expression of diphtheria toxin. These data are made available to facilitate genomic study of these pathogens.",,99.9,99,,,,Good,2020-11-29T01:19:59.868Z,2020-11-29T01:19:59.868Z
2675,1812934.3,Enterobacter cloacae complex 'Hoffmann cluster III' strain DSM 14563,negative,,1812934,Complete,DSM 14563,,,,MLST.Enterobacter_cloacae.816,,DSM:14563,,2016-09-16T00:00:00Z,,PRJNA259658,SAMN05581748,GCF_001729745.1,SRR4045259,"CP017186,CP017187","NZ_CP017186.1,NZ_CP017187.1",JCVI,,PacBio,15.31x,HGAP v. 3.0.0,1,1,2,4678566,55.33,4443,4323,None,,,,Germany,Germany,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Carbapenem resistance in Enterobacteriacae is increasingly due to the presence of the KPC beta-lactamase, which can be transferred on several different plasmids. The project is designed to better understand the spread of the blaKPC gene and the genetic backgrounds in which it is carried.",,99.6,98.9,100,,,Good,2016-11-16T11:25:28.680Z,2016-11-16T11:25:28.680Z
2682,1812935.7,Enterobacter cloacae complex 'Hoffmann cluster IV' strain DSM 16690,negative,,1812935,Complete,DSM 16690,,,,MLST.Enterobacter_cloacae.905,,DSM:16690,,2016-09-16T00:00:00Z,,PRJNA259658,SAMN05581750,GCF_001729805.1,SRR4045261,"CP017184,CP017185","NZ_CP017184.1,NZ_CP017185.1",JCVI,,PacBio,13.1x,HGAP v. 3.0.0,1,1,2,4899997,56.04,4665,4489,None,,,,Germany,Germany,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Carbapenem resistance in Enterobacteriacae is increasingly due to the presence of the KPC beta-lactamase, which can be transferred on several different plasmids. The project is designed to better understand the spread of the blaKPC gene and the genetic backgrounds in which it is carried.",,99.5,98.3,100,,,Good,2016-11-16T11:35:16.810Z,2016-11-16T11:35:16.810Z
2685,1839798.3,Bacillus sp. FDAARGOS_235 strain FDAARGOS_235,positive,,1839798,Complete,FDAARGOS_235,,,,,,FDA:FDAARGOS_235,,2017-03-29T00:00:00Z,,PRJNA231221,SAMN04875572,,,"CP020437,CP020434,CP020436,CP020435",,US Food and Drug Administration,,PacBio,14.0110509265725x,HGAP v. 3,1,3,4,5608141,35.28,6019,5799,Blood,Blood,,15-Sep-14,USA,USA:DC,,,,,,"Human, Homo sapiens",male,4Y,CVL infection,,,,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:Children's National Hospital,99.7,98.1,100,1.2,,Good,2017-05-28T05:09:15.552Z,2017-05-28T05:09:15.552Z
2688,1920110.3,Citrobacter sp. CFNIH10,negative,,1920110,Complete,CFNIH10,,,,MLST.Citrobacter_freundii.299,,,,2018-02-06T00:00:00Z,,PRJNA430813,SAMN06040393,GCA_002934585.1,,"CP026216,CP026212,CP026215,CP026214,CP026211,CP026210,CP026213",,NIH,,PacBio RSII,253x,HGAP v. 2.3,1,6,7,5738233,52.989502,5999,5817,None,patients and hospital environment,isolated from patients and hospital environment,2016,USA,United States,,,,,env_biome:wastewater/sludge,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Carbapenem Resistant Enterobacteriaceae strains including Klebsiella, Escherichia, Enterobacter, Citrobacter and Pantoea species isolated from patients and hospital environment.",,99.2,97.6,99.7,,,Good,2018-05-25T23:56:16.845Z,2018-05-25T23:56:16.845Z
2690,1935181.3,Shigella flexneri 1c strain Y394,negative,,1935181,Complete,Y394,1c,,,,,,,2017-10-04T00:00:00Z,28899344,PRJNA382451,SAMN06706581,GCA_002442995.1,,CP020753,,Australian National University,,PacBio; Illumina MiSeq,203.0x,HGAP3.3 SMRT Pipeline v. 2.3.0; Pilon v.,1,,1,4584634,50.91,5175,4822,Stool,Human stool sample,,1988,Bangladesh,Bangladesh: Matlab,,,,,,"Human, Homo sapiens",,,Shigellosis,,,,,,,,,,,,,,,,"Shigella species cause bacillary dysentery – a severe form of diarrhoea, characterized by acute colonic and rectal mucosal inflammation leading to fever, abdominal cramps and bloody mucoid stools. Out of four species of Shigella, S. flexneri is the most prevalent enteric pathogen in developing countries. Shigella is transmitted through faecal-oral route and can cause gastrointestinal infection via an exceptionally low infectious dose (as many as 10 bacteria). S. flexneri is classified into different serotypes based on the O-antigen structure of its lipopolysaccharide. The serotype conversion is mediated by bacteriophages and plasmids carrying genes that modify the O-antigen. The S. flexneri serotype 1c is a novel serotype, which has now been found to be prevalent in many developing countries. However, little is known about its virulence signatures and evolution. Here, we provide the unique features of this serotype through the whole genome sequencing and bioinformatics tools. We also identified it as a highly adaptive pathogen with unique O-antigen modification possibly mediated by three different bacteriophages during its evolution. Furthermore, this serotype possesses several hypothetical genes and putative bacteriophage regions that will guide future investigation to identify novel genes involved in pathogen’s virulence and its survival in the host environment.;many frameshifted proteins",collected_by:Nils I. A. Carlin,99.6,97.5,99.6,,,Good,2017-11-23T02:52:19.805Z,2017-11-23T02:52:19.805Z
2700,1962118.4,Mycobacterium abscessus subsp. massiliense strain FLAC047,positive,,1962118,Complete,FLAC047,,,,,,,,2017-05-15T00:00:00Z,,PRJNA315990,SAMN06859124,,,CP021122,,University of Michigan Medical School,,Illumina,150X,SPAdes v. 3.5.0,1,,1,4936470,64.25,4924,4851,None,,,2015,USA,United States,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of M. abscessus complex isolates.,collected_by:Lindsay J. Caverly,98.5,97.4,100,,,Good,2017-05-29T19:52:42.903Z,2017-05-29T19:52:42.903Z
2831,1977852.3,Bordetella sp. J329,negative,,1977852,Complete,J329,,,,,,,,2019-01-09T00:00:00Z,,PRJNA287884,SAMN06350661,GCA_004006215.1,,CP021250,,Centers for Disease Control and Prevention,,PacBio RSII; Illumina MiSeq,157x,HGAP v. 3,1,,1,3925525,62.284,3727,3429,None,,,2015,USA,USA: GA,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to characterize genomes of Bordetella species other than B. pertussis. Members of the genus Bordetella cause respiratory and opportunistic infection in a variety of hosts. These data are being made available to facilitate comparative analyses for the study of this important group of bacterial pathogens.,,95.6,93.8,,,,Good,2019-02-01T04:38:24.971Z,2019-02-01T04:38:24.971Z
2842,2026186.18,Bacillus paranthracis strain NCCP 15910,positive,,2026186,Complete,NCCP 15910,,,,MLST.Bacillus_cereus.994,,NCCP:15910,,2020-01-15T00:00:00Z,,PRJNA556101,SAMN12340779,GCA_009884335.1,,"CP041981,CP041980",,Korea Centers for Disease Control & Prevention (KCDC),,IonTorrent; PacBio,207.0x,SPAdes v. 3.1,1,1,2,5507895,35.40349,6090,5589,Stool,stool,,5/20/13,South Korea,South Korea: Seoul,,,,,,"Human, Homo sapiens",,,diarrhea,,,,,,,,,,,,,,,,A clinical isolate of the genus Bacillus,collected_by:Korea National Institute of Health,97.9,94.9,,,,Good,2020-02-01T15:58:05.936Z,2020-02-01T15:58:05.936Z
2843,2026187.8,Bacillus pacificus strain NCCP 15909,positive,,2026187,Complete,NCCP 15909,,,,MLST.Bacillus_cereus.1032,,NCCP:15909,,2020-01-15T00:00:00Z,,PRJNA556100,SAMN12340734,GCA_009884315.1,,"CP041979,CP041978,CP041977",,Korea Centers for Disease Control & Prevention (KCDC),,PacBio; IonTorrent,243.0x,SPAdes v. 3.1,1,2,3,5463271,35.450447,6078,5558,Stool,stool,,3/13/13,South Korea,South Korea: Seoul,,,,,,"Human, Homo sapiens",,,diarrhea,,,,,,,,,,,,,,,,A clinical isolate of the genus Bacillus,collected_by:Korea National Institute of Health,97.9,94.8,,,,Good,2020-02-07T13:50:54.571Z,2020-02-07T13:50:54.571Z
2847,2026240.33,Klebsiella quasivariicola strain 08A119,negative,,2026240,Complete,08A119,,,,MLST.Klebsiella_pneumoniae.1214,,,,2021-10-19T00:00:00Z,,PRJNA768294,SAMN22024810,GCA_020525665.1,,"CP084768,CP084769",,Monash University,,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5869016,56.822468,5862,5570,Blood,blood,,1997,,Germany,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",99.6,98.2,,,,Good,2021-12-24T12:04:04.323Z,2021-12-24T12:04:04.323Z
2857,2027919.315,Enterobacter cloacae complex sp. strain ECL60,negative,,2027919,Complete,ECL60,,,,,,,,2021-09-15T00:00:00Z,,PRJNA757181,SAMN20825299,GCA_019998725.1,,"CP083234,CP083235,CP083236",,Yongchuan Hospital of Chongqing Medical University,,Oxford Nanopore PromethION,500.0x,canu v. 1.6,1,2,3,4954601,54.794724,4826,4650,Blood,blood,,9/22/17,China,"China: Jiamusi, Heilongjiang Province",,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"Carbapenem-resistant Enterobacteriaceae (CRE) has been considered a serious global threat, the objectives of our study were the following: (i) to describe the prevalence of clinical CRE isolates, (ii) to identify the mechanisms and clonal relatedness among these CRE strains, (iii) to examine the genetic context of IMP-4.",sample_type:Pure culture,99.6,98.5,,,,Good,2021-12-24T00:49:45.676Z,2021-12-24T00:49:45.676Z
2861,2048778.3,Escherichia coli O178:H19 strain 2012C-4431,negative,,2048778,Complete,2012C-4431,O178:H19,,STEC,MLST.Escherichia_coli_2.537,,,,2017-11-02T00:00:00Z,,PRJNA218110,SAMN04851096,GCA_002741595.1,,"CP024289,CP024290,CP024291,CP024292",,CDC,,PacBio,430.0x,HGAP v. 3,1,3,4,5307783,50.76,5316,,Stool,stool,,10/18/12,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,collected_by:EDLB-CDC,99.8,98.7,100,,,Good,2017-11-24T17:08:58.323Z,2017-11-24T17:08:58.323Z
2863,2058152.49,Klebsiella grimontii strain 5512.56,negative,,2058152,Complete,5512.56,,,,MLST.Klebsiella_oxytoca.16,,,,2021-04-08T00:00:00Z,,PRJNA689715,SAMN17215154,GCA_017863935.1,,"CP067391,CP067390,CP067389,CP067384,CP067388,CP067387,CP067386,CP067385",,University of Bern,,Illumina NovaSeq; Oxford Nanopore MinION,262.28x,Unicycler v. 0.4.8,1,7,8,6193468,55.697018,6101,5770,None,Not defined,,2014-09,Switzerland,Switzerland,,,,,,Homo sapiens,,,Not defined,,,,,,,,,,,,,,,,"Whole genome sequencing and characterization of two multidrug-resistant K. grimontii strains possessing blaVIM-1 and blaVIM-1 together with mcr-9, respectively.","collected_by:Institute for Infectious Diseases, University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",99.6,97.4,,,,Good,2021-04-25T14:54:23.331Z,2021-04-25T14:54:23.331Z
2865,2067421.3,Escherichia coli O25:H4 strain 18044,negative,,2067421,Complete,18044,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,,,2020-12-22T00:00:00Z,32866241,PRJDB9114,SAMD00199041,GCA_016756455.1,,"AP022326,AP022327,AP022328,AP022329,AP022330,AP022331",,Fukuoka Institute of Health and Environmental Sciences,,Sequel; GridION X5; MiSeq,56x,Unicycler v. 0.4.4,1,5,6,5256311,50.861755,5285,4988,None,persons infected with HNoV,derived from persons infected with HNoV,2018,Japan,Japan,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"The proportion of Enterobacteriaceae such as Escherichia coli increases in human gut microbiota after infection with norovirus (HNoV). This shows that HNoV-infected persons are susceptible to Enterobacteriaceae. When a HNoV-infected person is further infected with Enterobacteriaceae possessing strong pathogenicity and/or showing multiple antimicrobial-resistances, health condition of the person may be worse. Aims of this project are to evaluate pathogenicity and antimicrobial resistance of Enterobacteriaceae which derived from persons infected with HNoV.",,99.9,98.9,,,,Good,2021-02-01T08:03:16.445Z,2021-02-01T08:03:16.445Z
2868,2072463.9,Escherichia coli O78 strain 3,negative,,2072463,Complete,3,O78,,,MLST.Escherichia_coli_1.57,,,,2021-10-03T00:00:00Z,,PRJNA765063,SAMN21542538,GCA_020217445.1,,"CP084096,CP084097",,The First Hospital of Jilin University,,Illumina HiSeq 4000 platform,99.92x,SOAPdenovo v. July-2020,1,1,2,5360188,50.65537,5341,5021,Sputum,sputum,,5/5/16,China,China:Jilin Province,,,,,,Homo sapiens,,,pneumonia,,,,,,,,,,,,,,,,To find the relevant gene for biofilms information,collected_by:Zhimin Guo,99.9,99.2,,,,Good,2021-10-31T06:58:21.906Z,2021-10-31T06:58:21.906Z
2869,2077147.3,Citrobacter freundii complex sp. CFNIH3,negative,,2077147,Complete,CFNIH3,,,,MLST.Citrobacter_freundii.110,,,,2018-01-29T00:00:00Z,,PRJNA430813,SAMN03455982,GCA_002903215.1,,"CP026235,CP026237,CP026236",,NIH,,PacBio RSII,215x,HGAP v. 2.3,1,2,3,5634842,51.874233,5755,5561,None,patients and hospital environment,isolated from patients and hospital environment,2014,USA,United States,,,,,env_biome:waste water,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Carbapenem Resistant Enterobacteriaceae strains including Klebsiella, Escherichia, Enterobacter, Citrobacter and Pantoea species isolated from patients and hospital environment.",,99.3,96.5,100,0.3,,Good,2018-05-25T20:31:40.101Z,2018-05-25T20:31:40.101Z
2870,2077148.3,Citrobacter freundii complex sp. CFNIH4,negative,,2077148,Complete,CFNIH4,,,,MLST.Citrobacter_freundii.167,,,,2018-02-06T00:00:00Z,,PRJNA430813,SAMN03455986,GCA_002934505.1,,"CP026231,CP026233,CP026234,CP026232",,NIH,,PacBio RSII,200x,HGAP v. 2.3,1,3,4,5629494,51.75078,5883,5724,None,patients and hospital environment,isolated from patients and hospital environment,2014,USA,United States,,,,,env_biome:waste water,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Carbapenem Resistant Enterobacteriaceae strains including Klebsiella, Escherichia, Enterobacter, Citrobacter and Pantoea species isolated from patients and hospital environment.",,99,97.3,100,,,Good,2018-05-25T23:54:30.428Z,2018-05-25T23:54:30.428Z
2871,2077149.3,Citrobacter freundii complex sp. CFNIH9,negative,,2077149,Complete,CFNIH9,,,,MLST.Citrobacter_freundii.166,,,,2018-01-29T00:00:00Z,,PRJNA430813,SAMN04287052,GCA_002903305.1,,"CP026238,CP026240,CP026241,CP026242,CP026239",,NIH,,PacBio RSII,205x,canu v. 1.3,1,4,5,5688355,51.608135,5884,5741,None,patients and hospital environment,isolated from patients and hospital environment,2015,USA,United States,,,,,env_biome:waste water,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Carbapenem Resistant Enterobacteriaceae strains including Klebsiella, Escherichia, Enterobacter, Citrobacter and Pantoea species isolated from patients and hospital environment.",,99.3,97.9,100,0.3,,Good,2018-05-25T20:32:16.833Z,2018-05-25T20:32:16.833Z
3135,2126982.6,Escherichia coli O18:H1 strain CFSAN067215,negative,,2126982,Complete,CFSAN067215,,,,"MLST.Escherichia_coli_1.73,MLST.Escherichia_coli_2.4",,,,2019-04-11T00:00:00Z,,PRJNA230969,SAMN08737532,GCA_004771135.1,,"CP028320,CP028321,CP028322,CP028323",,FDA/CFSAN,,PacBio,405.0x,HGAP v. 3.0,1,3,4,5242835,50.63415,5484,5362,None,,,2000,USA,USA:CA,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured E. coli as part of the US Food and Drug Administration surveillance project for the rapid detection of foodborne contamination events.,collected_by:Dudley Lab/Penn State,99.9,98.8,,,,Good,2019-07-14T17:54:05.102Z,2019-07-14T17:54:05.102Z
3153,2259134.3,Sutterella sp. 6FBBBH3,negative,,2494234,Complete,6FBBBH3,,,,,,JCM:32470,,2018-10-10T00:00:00Z,,PRJDB7182,SAMD00129657,GCA_003609995.1,,AP018786,,"Microbe Division/ Japan Collection of Microorganisms, RIKEN BioResource Research Center",,PacBio RSII,Unknown,HGAP v. 3.0,1,,1,2725161,62.83915,2363,2113,Stool,fecal sample of a healthy Japanese man,isolated from a fecal sample of a healthy Japanese man,2/28/17,,,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,"Strain 6FBBBH3, which is an obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative cocci, was isolated from a fecal sample of a healthy Japanese man. Strain 6FBBBH3 was affiliated to the genus Sutterella, with highest similarity to S. stercoricanis CCUG 47620T (97.1 %), followed by S. parvirubra YIT 11816T (96.6 %) and S. wadsworthensis WAL 7877 (95.2 %). We analyzed the draft genome sequence of strain 6FBBBH3.",,96.6,95.5,,,,Good,2018-11-28T19:45:25.592Z,2018-11-28T19:45:25.592Z
3155,2420308.3,Streptococcus sp. FDAARGOS_520 strain Not applicable,positive,,2420308,Complete,Not applicable,,,,MLST.Streptococcus_agalactiae.28,,FDA:FDAARGOS_520,,2018-11-21T00:00:00Z,,PRJNA231221,SAMN10163214,GCA_003812685.1,,CP033810,,US Food and Drug Administration,,Pacbio; Illumina,29.71x,Canu v. 1.4,1,,1,2099619,35.48644,2150,2106,Sputum,sputum,,3/8/16,,,,,,,,"Human, Homo sapiens",female,22Y,Cystic fibrosis,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,100,99.8,,,,Good,2018-11-30T03:11:06.872Z,2018-11-30T03:11:06.872Z
3156,2420309.3,Streptococcus sp. FDAARGOS_521 strain Not applicable,positive,,2420309,Complete,Not applicable,,,,MLST.Streptococcus_agalactiae.19,,FDA:FDAARGOS_521,,2018-11-21T00:00:00Z,,PRJNA231221,SAMN10163215,GCA_003812465.1,,CP033809,,US Food and Drug Administration,,Pacbio; Illumina,29.53x,Canu v. 1.4,1,,1,2157002,35.62106,2260,2198,Vagina,Miscellaneous vagina,,1/7/16,,,,,,,,"Human, Homo sapiens",female,19Y,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,100,99.6,,,,Good,2018-11-30T03:05:02.664Z,2018-11-30T03:05:02.664Z
3157,2420310.3,Streptococcus sp. FDAARGOS_522 strain Not applicable,positive,,2420310,Complete,Not applicable,,,,MLST.Streptococcus_agalactiae.1,,FDA:FDAARGOS_522,,2018-11-21T00:00:00Z,,PRJNA231221,SAMN10163216,GCA_003812445.1,,CP033808,,US Food and Drug Administration,,Pacbio; Illumina,30.46x,Canu v. 1.2,1,,1,2101126,35.525906,2148,2099,Vagina,Miscellaneous vagina,,2/7/16,,,,,,,,"Human, Homo sapiens",female,19Y,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,100,99.8,,,,Good,2018-11-30T03:09:24.920Z,2018-11-30T03:09:24.920Z
3158,2420313.3,Enterococcus sp. FDAARGOS_553 strain Not applicable,positive,,2420313,Complete,Not applicable,,,,MLST.Enterococcus_faecium.755,,FDA:FDAARGOS_553,,2018-11-21T00:00:00Z,,PRJNA231221,SAMN10163246,GCA_003812305.1,,"CP033740,CP033739,CP033741",,US Food and Drug Administration,,Pacbio; Illumina,121.10x,Canu v. 1.4,1,2,3,3283483,40.41507,3324,3114,None,,,,,,,,,,,"Human, Homo sapiens",,,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:University of North Carolina,99.3,97.9,,,,Good,2018-11-30T03:08:09.268Z,2018-11-30T03:08:09.268Z
3184,2489010.6,Klebsiella africana strain 200023,negative,,2489010,Complete,200023,,,,,,,,2021-10-19T00:00:00Z,,PRJNA768294,SAMN22024779,GCA_020526085.1,,"CP084874,CP084875",,Monash University,,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5443802,56.696957,5334,5120,Stool,feces,,2016,,Senegal,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",99.8,98.5,,,,Good,2021-12-24T12:10:55.486Z,2021-12-24T12:10:55.486Z
3185,2500132.3,Enterobacter sp. N18-03635,negative,,2500132,Complete,N18-03635,,,,MLST.Enterobacter_cloacae.261,,,,2019-01-09T00:00:00Z,,PRJNA511479,SAMN10638715,GCA_004006055.1,,"CP034769,CP034768",,Public Health Agency of Canada,,Illumina NextSeq; Oxford Nanopore MiniION,20.0x,Unicycler v. 0.4.6.0,1,1,2,4687155,55.625065,4516,4411,Stool,rectal swab,,,Canada,Canada,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Carbapenemase-producing organisms isolated in Canada,collected_by:not collected,99.4,98.8,,,,Good,2019-02-01T04:38:18.470Z,2019-02-01T04:38:18.470Z
3186,2545800.3,Pseudomonas sp. FDAARGOS_761 strain Not applicable,negative,,2545800,Complete,Not applicable,,,,MLST.Pseudomonas_aeruginosa.971,,FDA:FDAARGOS_761,,2020-06-15T00:00:00Z,,PRJNA231221,SAMN11056476,GCA_013343155.1,,CP054572,,US Food and Drug Administration,,Pacbio; Illumina,616.89x,"SMRT v. 2.3.0, HGAP v. 3",1,,1,6384852,66.415596,6009,5847,Stool,healthy biopsy tissue taken from the rectum,,,USA,USA:VA,,,,,,"Human, Homo sapiens",male,59Y,,,,host_description:Not applicable,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),96.9,96.1,,,,Good,2020-07-01T15:34:48.487Z,2020-07-01T15:34:48.487Z
3187,2572075.3,Campylobacter sp. CFSAN093257,negative,,197,Complete,CFSAN093257,,,,,,,,2020-04-27T00:00:00Z,,PRJNA258022,SAMN11487379,GCA_012889875.1,,CP040616,,FDA/CFSAN,,"Oxford Nanopore GridION, Illumina MiSeq",76x,SPAdes; CANU v. SPAdes v3.1.1; Canu v1.7,1,,1,1720666,30.4689,1817,1754,None,,,1/3/18,Chile,Chile,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Campylobacter from FDA-CFSAN (Center for Food Safety and Applied Nutrition) for surveillance of foodborne pathogens.,"collected_by:Carlos Blondel lab, Universidad Autonoma",99,98.9,,,,Good,2020-06-03T21:28:39.028Z,2020-06-03T21:28:39.028Z
3188,2572089.3,TM7 phylum sp. oral taxon 952 strain TM7x,negative,,2572089,Complete,TM7x,,,,,,,,2019-05-23T00:00:00Z,,PRJNA282954,SAMN11483332,GCA_005697395.1,,CP040011,,The Forsyth Institute,,PacBio Sequel,776x,HGAP v. 4,1,,1,705178,44.451614,721,701,Mouth,human oral cavity UCLA1,,13-May,USA,"USA: Los Angeles, California",,,100 m,,,"Human, Homo sapiens",male,42,,,,,,,,,,,,C,,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02152;collected_by:Forsyth Institute;lab_host:Actinomyces odontolyticus strain XH001",,,,,,Good,2019-07-21T01:48:53.673Z,2019-07-21T01:48:53.673Z
3192,2576376.3,Streptococcus sp. 1643,positive,,2576376,Complete,1643,,,,,,,,2019-06-11T00:00:00Z,,PRJNA542100,SAMN06040852,GCA_006228325.1,,CP040231,,The University of Texas at Dallas,,Illumina HiSeq; PacBio RSII,100.0x,Unicycler v. 0.4.7,1,,1,1898954,41.23349,1913,1882,None,Infective endocarditits,,1999/2003,USA,USA,,,,,,"Human, Homo sapiens",,,,,,,,,,,,,,,,,,,Whole genome sequencing associated with phosphatidylcholine biosynthesis in Mitis Group Streptococci,sample_type:Hospital Isolate,,,,,,Good,2019-07-21T02:11:59.281Z,2019-07-21T02:11:59.281Z
3195,2590157.5,Klebsiella variicola subsp. variicola strain 01A065,negative,,2590157,Complete,01A065,,,,,,,,2021-10-19T00:00:00Z,,PRJNA768294,SAMN22024812,GCA_020525605.1,,CP084766,,Monash University,,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,,1,5467687,57.56573,5332,5162,Blood,blood,,1997,,Austria,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",99.9,98.7,,,,Good,2021-10-31T16:14:01.045Z,2021-10-31T16:14:01.045Z
3196,2592065.4,Escherichia coli O1:H42 strain CLSC36,negative,,2592065,Complete,CLSC36,O1:H42,,UPEC,MLST.Escherichia_coli_1.648,,,,2019-07-09T00:00:00Z,,PRJNA551561,SAMN12158196,GCA_006777045.1,,"CP041300,CP041299",,McGill University,,PacBio,138.0x,HGAP v. May-2015; Celera Assembler v.,1,1,2,5278774,50.42186,5293,4992,Urine,urine from healthy adult with cystitis,,9/26/05,Canada,Canada: Montreal,,,,,,"Human, Homo sapiens",,,cystitis,,,,,,,,,,,,,,,,This strain was sequenced as part of a study that investigated the activity of the outer membrane protease OmpT among uropathogenic Escherichia coli clinical isolates. Healthy adult with cystitis,collected_by:Student health services McGill University,99.6,98.4,,,,Good,2019-09-30T16:44:45.900Z,2019-09-30T16:44:45.900Z
3214,2666100.4,Neisseria brasiliensis strain N.177.16,negative,,2666100,Complete,N.177.16,,,,,genotype:Capsule group B,,,2019-11-19T00:00:00Z,,PRJNA588397,SAMN13243042,GCA_009671065.1,,CP046027,,University of Pittsburgh,,Oxford Nanopore MiniION,80x,SPAdes v. 3.6,1,,1,2617510,49.228695,2828,2532,Wound,ulcer exudate,,2016-02,Brazil,Brazil: Parana State.,,,,,,"Human, Homo sapiens",female,74,Wound infection,,,host_description:Leprosy (Hansen's disease);host_health_state:poor,,,,,,,,,,,,,Isolates from two human cases of Neisseria brasiliensis carrying N. meningitidis capsule genes,"collected_by:Claudio Sacchi Institute Adolfo Lutz, Brazil",96.6,96.1,,,,Good,2019-12-30T22:47:03.842Z,2019-12-30T22:47:03.842Z
3217,2697517.3,Escherichia coli O84:H7 strain Trh52,negative,,2697517,Complete,Trh52,O84:H7,,EPEC/ExPEC,MLST.Escherichia_coli_1.28,genotype:ST28,,,2021-02-03T00:00:00Z,,PRJNA593384,SAMN13782172,GCA_016803935.1,,"CP047600,CP047601",,Norwegian University of Life Sciences,,Oxford Nanopore MiniION; Illumina MiSeq,27.7x,Unicycler v. 0.4.7.0,1,1,2,4926859,50.58391,4863,4617,Stool,feces,,2002,Norway,Norway: Trondelag,,,,,,Homo sapiens,,<5,Diarrhea,,,,,,,,,,,,,,,,Sequencing of enteropathogenic Escherichia coli clinical isolates,"collected_by:Department of Medical Microbiology, St. Olavs Hospital",100,99.6,,,,Good,2021-02-27T17:36:49.399Z,2021-02-27T17:36:49.399Z
3254,2807624.3,Staphylococcus sp. SM9054,positive,,2807624,Complete,SM9054,,,,MLST.Staphylococcus_aureus.97,,,,2021-02-22T00:00:00Z,,PRJNA698720,SAMN17734770,GCA_016917335.1,,CP070306,,Korea University,,PacBio Sequel,100.0x,FALCON-Unzip v. 0.5,1,,1,2836077,32.83472,2780,2739,None,,,2020-11,South Korea,South Korea,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Complete genome of Staphylococcus sp. SM9094,sample_type:whole organism,100,99.7,,,,Good,2021-03-27T18:56:20.916Z,2021-03-27T18:56:20.916Z
3255,2807625.3,Staphylococcus sp. SM3655,positive,,2807625,Complete,SM3655,,,,MLST.Staphylococcus_aureus.97,,,,2021-02-22T00:00:00Z,,PRJNA698719,SAMN17734769,GCA_016917315.1,,CP070305,,Korea University,,PacBio Sequel,100.0x,FALCON-Unzip v. 0.5,1,,1,2836293,32.835217,2780,2739,None,,,2020-12,South Korea,South Korea,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Complete genome of Staphylococcus sp. SM3655,sample_type:whole organism,100,99.7,,,,Good,2021-03-27T18:55:32.517Z,2021-03-27T18:55:32.517Z
3261,2810404.4,Escherichia coli O7:H4 strain MIN14,negative,,2810404,Complete,MIN14,O7:H4,,,"MLST.Escherichia_coli_1.93,MLST.Escherichia_coli_2.83",genotype:ST-93,,,2021-03-23T00:00:00Z,,PRJNA700422,SAMN17831486,GCA_017570585.1,,"CP069646,CP069647,CP069648,CP069649,CP069651,CP069652,CP069653,CP069654,CP069655,CP069656,CP069650",,Medical University of Bialystok,,Illumina MiSeq; Oxford Nanopore MinION,100x,Unicycler hybrid assembly v. v0.4.8-beta,1,10,11,5032262,50.624413,5124,4783,Respiratory,upper respiratory tract,,7/21/16,Poland,Poland: Bialystok,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Genome and mobilome structures of extraintestinal E. coli strains isolated in Poland,,99.9,98.8,,,,Good,2021-03-29T20:45:20.877Z,2021-03-29T20:45:20.877Z
3262,2810405.4,Escherichia coli O89m:H10 strain MIN12,negative,,2810405,Complete,MIN12,O89m:H10,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",genotype:ST-10,,,2021-03-23T00:00:00Z,,PRJNA700422,SAMN17831485,GCA_017570605.1,,"CP069657,CP069658,CP069659,CP069660,CP069662,CP069663,CP069664,CP069665,CP069661",,Medical University of Bialystok,,Illumina MiSeq; Oxford Nanopore MinION,484x,Unicycler hybrid assembly v. v0.4.8-beta,1,8,9,5274803,50.791298,5402,5018,Wound,wound,,5/5/18,Poland,Poland: Bialystok,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Genome and mobilome structures of extraintestinal E. coli strains isolated in Poland,,99.9,99.3,,,,Good,2021-03-29T20:40:45.930Z,2021-03-29T20:40:45.930Z
3263,2810406.4,Escherichia coli O89m:H9 strain MIN11,negative,,2810406,Complete,MIN11,O89m:H9,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.10",genotype:ST-10,,,2021-03-23T00:00:00Z,,PRJNA700422,SAMN17831484,GCA_017570625.1,,"CP069666,CP069667,CP069668,CP069670,CP069671,CP069672,CP069673,CP069674,CP069675,CP069676,CP069669",,Medical University of Bialystok,,Illumina MiSeq; Oxford Nanopore MinION,100x,Unicycler hybrid assembly v. v0.4.8-beta,1,10,11,4988215,50.413765,5016,4688,Respiratory,lower respiratory tract,,3/29/18,Poland,Poland: Bialystok,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Genome and mobilome structures of extraintestinal E. coli strains isolated in Poland,,99.5,99,,,,Good,2021-03-29T20:45:10.509Z,2021-03-29T20:45:10.509Z
3264,2810407.4,Escherichia coli O126:H45 strain MIN10,negative,,2810407,Complete,MIN10,O126:H45,,,"MLST.Escherichia_coli_1.162,MLST.Escherichia_coli_2.355",genotype:ST-162,,,2021-03-23T00:00:00Z,,PRJNA700422,SAMN17831483,GCA_017570645.1,,"CP069677,CP069678,CP069679,CP069681,CP069680",,Medical University of Bialystok,,Illumina MiSeq; Oxford Nanopore MinION,260x,Unicycler hybrid assembly v. v0.4.8-beta,1,4,5,5402822,50.560966,5496,5171,Respiratory,upper respiratory tract,,3/13/18,Poland,Poland: Bialystok,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Genome and mobilome structures of extraintestinal E. coli strains isolated in Poland,,99.9,99,,,,Good,2021-03-29T20:44:54.494Z,2021-03-29T20:44:54.494Z
3265,2810408.4,Escherichia coli O176:H45 strain MIN9,negative,,2810408,Complete,MIN9,O176:H45,,,,genotype:ST-6856,,,2021-03-23T00:00:00Z,,PRJNA700422,SAMN17831482,GCA_017570665.1,,"CP069682,CP069683,CP069684,CP069686,CP069687,CP069688,CP069689,CP069690,CP069691,CP069685",,Medical University of Bialystok,,Illumina MiSeq; Oxford Nanopore MinION,100x,Unicycler hybrid assembly v. v0.4.8-beta,1,9,10,5032799,50.551075,5126,4789,Wound,wound,,3/5/18,Poland,Poland: Bialystok,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Genome and mobilome structures of extraintestinal E. coli strains isolated in Poland,,99.9,98.7,,,,Good,2021-03-29T20:45:24.823Z,2021-03-29T20:45:24.823Z
3266,2810409.4,Escherichia coli H20 strain MIN6,negative,,2810409,Complete,MIN6,H20,,,"MLST.Escherichia_coli_1.533,MLST.Escherichia_coli_2.310",genotype:ST-553,,,2021-03-23T00:00:00Z,,PRJNA700422,SAMN17831481,GCA_017570685.1,,"CP069692,CP069693,CP069694,CP069696,CP069697,CP069698,CP069699,CP069700,CP069695",,Medical University of Bialystok,,Illumina MiSeq; Oxford Nanopore MinION,446x,Unicycler hybrid assembly v. v0.4.8-beta,1,8,9,5186956,50.59108,5268,4909,Wound,wound,,9/6/17,Poland,Poland: Bialystok,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Genome and mobilome structures of extraintestinal E. coli strains isolated in Poland,,99.8,98.3,,,,Good,2021-03-29T20:45:16.550Z,2021-03-29T20:45:16.550Z
3316,2829835.3,Klebsiella sp. P1954,negative,,2829835,Complete,P1954,,,,MLST.Klebsiella_pneumoniae.15,,,,2021-04-29T00:00:00Z,,PRJNA722138,SAMN18746132,GCA_018199955.1,,"CP073373,CP073374,CP073375,CP073376",,Institute of Environmental Microbiology,,Oxford Nanopore,257.2x,CANU v. 1.5,1,3,4,5650766,57.129246,5578,5368,None,,,8/27/19,China,"China: Fuzhou, Fujian",,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,klebsiella isolated from hospital,sample_type:strain,99.6,98.2,,,,Good,2021-06-02T18:04:16.145Z,2021-06-02T18:04:16.145Z
3317,2829836.3,Klebsiella sp. P1927,negative,,2829836,Complete,P1927,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-04-29T00:00:00Z,,PRJNA722143,SAMN18746170,GCA_018204675.1,,"CP073377,CP073378,CP073379,CP073380",,Institute of Environmental Microbiology,,Oxford Nanopore,295.5x,Canu v. 1.5,1,3,4,6172359,56.608276,6366,6081,None,,,8/27/19,China,"China: Fuzhou, Fujian",,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Klebsiella isolated from hospital confers extremly high multi-antibiotics resistance,sample_type:strain,99.7,98.2,,,,Good,2021-06-02T18:04:11.468Z,2021-06-02T18:04:11.468Z
3328,2838237.5,Leptospira sp. severe_002,negative,,2838237,Complete,severe_002,,,,MLST.Leptospira_spp.49,,,,2021-10-25T00:00:00Z,34638178,PRJNA716760,SAMN18451304,GCA_020544525.1,,"CP075692,CP075693",,Chulalongkorn University,,Illumina MiSeq,69.19x,SPAdes v. 3.13.0,2,,2,5523351,37.523502,5793,,None,"2 patietns, one with mild and another with severe symptoms, were inlcuded","isolated from 2 patietns, one with mild and another with severe symptoms, were inlcuded in this study",7/2/12,,Thailand,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"Leptospirosis is a zoonotic disease, caused by spirochetes from the genus Leptospira. In Thailand, Leptospira interrogans is a major cause of leptospirosis. Leptospirosis patients present with the wide range of clinical manifestations from asymptomatic, mild infections to severe illness involving organ failures. For better understanding the difference between Leptopira isolates causing mild and severe leptospirosis, illumina sequencing was used to sequence genomic DNA in both serotype. DNA of Leptospira isolated from 2 patietns, one with mild and another with severe symptoms, were inlcuded in this study. The paired-end reads were removed adapters and trimmed with Q30 score using Trimmomatic. Trimmed reads were constructed to contigs and scaffolds using Spades. Cross-contamination of scaffolds was evaluated by ContEst16s. Prokka tool for bacterial annotation was used to annotate sequences from both Leptospira isolates. Predicted amino acid sequences from Prokka were searched to EggNOG and David gene ontology database for finding gene ontology. In addition, Leptospira from mild and severe patients annotated that passed the criteria e-value < 10e-5 from blastp against virulence factor database were used to analysis with venn diagram. From this study, we found 13 and 12 genes that unique in the isolates from mild and severe patietns, respectively. The 12 genes in the severe isolate might be virulence factor genes that affect disease severity. However, these genes should be validated in further study.",sample_type:culture,99,97.6,,,,Good,2021-12-24T12:53:08.616Z,2021-12-24T12:53:08.616Z
3331,2838238.5,Leptospira sp. mild_001,negative,,2838238,Complete,mild_001,,,,,,,,2021-10-25T00:00:00Z,34638178,PRJNA716760,SAMN18451303,GCA_020544505.1,,"CP075694,CP075695",,Chulalongkorn University,,Illumina MiSeq,174.64x,SPAdes v. 3.13.0,2,,2,5060276,35.059456,5132,,None,"2 patietns, one with mild and another with severe symptoms, were inlcuded","isolated from 2 patietns, one with mild and another with severe symptoms, were inlcuded in this study",7/2/12,,Thailand,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"Leptospirosis is a zoonotic disease, caused by spirochetes from the genus Leptospira. In Thailand, Leptospira interrogans is a major cause of leptospirosis. Leptospirosis patients present with the wide range of clinical manifestations from asymptomatic, mild infections to severe illness involving organ failures. For better understanding the difference between Leptopira isolates causing mild and severe leptospirosis, illumina sequencing was used to sequence genomic DNA in both serotype. DNA of Leptospira isolated from 2 patietns, one with mild and another with severe symptoms, were inlcuded in this study. The paired-end reads were removed adapters and trimmed with Q30 score using Trimmomatic. Trimmed reads were constructed to contigs and scaffolds using Spades. Cross-contamination of scaffolds was evaluated by ContEst16s. Prokka tool for bacterial annotation was used to annotate sequences from both Leptospira isolates. Predicted amino acid sequences from Prokka were searched to EggNOG and David gene ontology database for finding gene ontology. In addition, Leptospira from mild and severe patients annotated that passed the criteria e-value < 10e-5 from blastp against virulence factor database were used to analysis with venn diagram. From this study, we found 13 and 12 genes that unique in the isolates from mild and severe patietns, respectively. The 12 genes in the severe isolate might be virulence factor genes that affect disease severity. However, these genes should be validated in further study.",sample_type:culture,99.4,99,,,,Good,2021-12-24T12:53:01.096Z,2021-12-24T12:53:01.096Z
3410,2848143.3,Escherichia coli O85:H1 strain 03-3638,negative,,2848143,Complete,Mar-38,O85:H1,,STEC,MLST.Escherichia_coli_1.706,,,,2021-06-22T00:00:00Z,,PRJNA735700,SAMN19011648,GCA_018986775.1,,"CP076714,CP076715,CP076716,CP076717",,Health Canada,,Illumina MiSeq/NextSeq and Oxford,61x (Illumina)/x,Unicycler (normal mode) using PE Illumina,1,3,4,5163097,50.494915,5184,4907,None,,,2003,Canada,Canada,,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,Characterization of shiga toxin (stx) genes in E. coli including novel stx variants/subtypes,collected_by:Health Canada - Bureau of Microbial Hazards,100,99.2,,,,Good,2021-06-26T10:52:44.740Z,2021-06-26T10:52:44.740Z
3771,2876028.6,Enterobacter cloacae complex sp. ECL352,negative,,2876028,Complete,ECL352,,,,MLST.Enterobacter_cloacae.25,,,,2021-09-25T00:00:00Z,,PRJNA757181,SAMN21399027,GCA_020149545.1,,"CP083709,CP083710,CP083711,CP083712,CP083713,CP083714",,Yongchuan Hospital of Chongqing Medical University,,Oxford Nanopore PromethION,550.0x,canu v. 1.6,1,5,6,4958769,55.75757,4932,4801,Sputum,sputum,,9/24/20,China,"China:Yongchuan District, Chongqing",,,,,,Homo sapiens,,,,,,,,,,,,,,,,,,,"Carbapenem-resistant Enterobacteriaceae (CRE) has been considered a serious global threat, the objectives of our study were the following: (i) to describe the prevalence of clinical CRE isolates, (ii) to identify the mechanisms and clonal relatedness among these CRE strains, (iii) to examine the genetic context of IMP-4.",sample_type:pure culture,99.6,98.2,,,,Good,2021-12-24T04:12:05.221Z,2021-12-24T04:12:05.221Z