{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T18:10:56Z","timestamp":1787508656051,"version":"build-2736575974"},"reference-count":36,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2017,3,16]],"date-time":"2017-03-16T00:00:00Z","timestamp":1489622400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI119145"],"award-info":[{"award-number":["R01AI119145"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute of Allergy and Infectious Diseases (US)","award":["F30AI122673"],"award-info":[{"award-number":["F30AI122673"]}]},{"DOI":"10.13039\/100009429","name":"NRSA","doi-asserted-by":"crossref","award":["5 T32 AI 7647-13"],"award-info":[{"award-number":["5 T32 AI 7647-13"]}],"id":[{"id":"10.13039\/100009429","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0170449","type":"journal-article","created":{"date-parts":[[2017,3,16]],"date-time":"2017-03-16T13:30:22Z","timestamp":1489671022000},"page":"e0170449","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient"],"prefix":"10.1371","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5240-9604","authenticated-orcid":true,"given":"Ali","family":"Bashir","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver","family":"Attie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitchell","family":"Sullivan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Sebra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kavindra V.","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deena","family":"Altman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theodore","family":"Pak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayeeta","family":"Dutta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kieran","family":"Chacko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth","family":"Webster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martha","family":"Lewis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camille","family":"Hamula","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristin W.","family":"Delli Carpini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara E.","family":"Murray","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Kasarskis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harm","family":"van Bakel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shirish","family":"Huprikar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2017,3,16]]},"reference":[{"issue":"Suppl 4","key":"ref1","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1111\/ajt.12095","article-title":"Donor-derived infections in solid organ transplantation","volume":"13","author":"MG Ison","year":"2013","journal-title":"Am J Transplant"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/nbt.2288","article-title":"A hybrid approach for the automated finishing of bacterial genomes","volume":"30","author":"A Bashir","year":"2012","journal-title":"Nat Biotechnol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1038\/nbt.2280","article-title":"Hybrid error correction and de novo assembly of single-molecule sequencing reads","volume":"30","author":"S Koren","year":"2012","journal-title":"Nat Biotechnol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/nmeth.2474","article-title":"Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data","volume":"10","author":"C-S Chin","year":"2013","journal-title":"Nat Methods"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1056\/NEJMoa1106920","article-title":"Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany","volume":"365","author":"DA Rasko","year":"2011","journal-title":"N Engl J Med"},{"key":"ref6","article-title":"Transmission of Methicillin-Resistant Staphylococcus aureus via Deceased Donor Liver Transplantation Confirmed by Whole Genome Sequencing","author":"DR Altman","year":"2014","journal-title":"Am J Transplant"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"2059","DOI":"10.1128\/JCM.28.9.2059-2063.1990","article-title":"Comparison of genomic DNAs of different enterococcal isolates using restriction endonucleases with infrequent recognition sites","volume":"28","author":"BE Murray","year":"1990","journal-title":"J Clin Microbiol"},{"key":"ref8","doi-asserted-by":"crossref","unstructured":"Delcher AL, Salzberg SL, Phillippy AM. Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinformatics. 2003;Chapter 10: Unit 10.3.","DOI":"10.1002\/0471250953.bi1003s00"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref10","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013; Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/arxiv.org\/abs\/1303.3997\" xlink:type=\"simple\">http:\/\/arxiv.org\/abs\/1303.3997<\/ext-link>"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"H Li","year":"2011","journal-title":"Bioinformatics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"A Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1186\/s13059-015-0849-0","article-title":"Circlator: automated circularization of genome assemblies using long sequencing reads","volume":"16","author":"M Hunt","year":"2015","journal-title":"Genome Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"T Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"3348","DOI":"10.1128\/AAC.00419-13","article-title":"The comprehensive antibiotic resistance database","volume":"57","author":"AG McArthur","year":"2013","journal-title":"Antimicrob Agents Chemother"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1186\/s13059-014-0524-x","article-title":"The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes","volume":"15","author":"TJ Treangen","year":"2014","journal-title":"Genome Biol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2334","DOI":"10.1128\/JB.00259-12","article-title":"Comparative analysis of the first complete Enterococcus faecium genome","volume":"194","author":"MMC Lam","year":"2012","journal-title":"J Bacteriol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2665","DOI":"10.1534\/genetics.105.048975","article-title":"A simple and robust statistical test for detecting the presence of recombination","volume":"172","author":"TC Bruen","year":"2006","journal-title":"Genetics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation","volume":"30","author":"T Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"AJ Page","year":"2015","journal-title":"Bioinformatics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: Multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"ACE Darling","year":"2004","journal-title":"Genome Res"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"2233","DOI":"10.1128\/JCM.33.9.2233-2239.1995","article-title":"Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing","volume":"33","author":"FC Tenover","year":"1995","journal-title":"J Clin Microbiol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.jhin.2011.04.016","article-title":"Changes in vancomycin-resistant Enterococcus faecium causing outbreaks in Brazil","volume":"79","author":"IC V Palazzo","year":"2011","journal-title":"J Hosp Infect"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1186\/1471-2180-13-291","article-title":"Molecular analysis and distribution of multidrug-resistant Enterococcus faecium isolates belonging to clonal complex 17 in a tertiary care center in Mexico City","volume":"13","author":"SA Ochoa","year":"2013","journal-title":"BMC Microbiol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1093\/jac\/dkt054","article-title":"Molecular epidemiology of vancomycin-resistant enterococcal bacteraemia: Results from the canadian nosocomial infection surveillance program, 1999\u20132009","volume":"68","author":"M McCracken","year":"2013","journal-title":"J Antimicrob Chemother"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s10096-009-0847-9","article-title":"A newly described vancomycin-resistant ST412 Enterococcus faecium predominant in Greek hospitals","volume":"29","author":"A Damani","year":"2010","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/j.diagmicrobio.2012.07.012","article-title":"Genetic features and molecular epidemiology of Enterococcus faecium isolated in two university hospitals in Brazil","volume":"74","author":"LPP da Silva","year":"2012","journal-title":"Diagn Microbiol Infect Dis"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"e60589","DOI":"10.1371\/journal.pone.0060589","article-title":"Microevolutionary events involving narrow host plasmids influences local fixation of vancomycin-resistance in Enterococcus populations","volume":"8","author":"AR Freitas","year":"2013","journal-title":"PLoS One"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1128\/AAC.39.2.362","article-title":"Heterogeneity of the vanA gene cluster in clinical isolates of enterococci from the northeastern United States","volume":"39","author":"S Handwerger","year":"1995","journal-title":"Antimicrob Agents Chemother"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1570","DOI":"10.1093\/jac\/dkq192","article-title":"Tn1546 structures and multilocus sequence typing of vanA-containing enterococci of animal, human and food origin","volume":"65","author":"M L\u00f3pez","year":"2010","journal-title":"J Antimicrob Chemother"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/0196-6553(88)90053-3","article-title":"CDC definitions for nosocomial infections, 1988","volume":"16","author":"JS Garner","year":"1988","journal-title":"Am J Infect Control"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"2446","DOI":"10.1128\/AAC.39.11.2446","article-title":"Identification of chromosomal mobile element conferring high-level vancomycin resistance in Enterococcus faecium","volume":"39","author":"S Handwerger","year":"1995","journal-title":"Antimicrob Agents Chemother"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1963","DOI":"10.1128\/JCM.40.6.1963-1971.2002","article-title":"Multilocus sequence typing scheme for Enterococcus faecium","volume":"40","author":"WL Homan","year":"2002","journal-title":"J Clin Microbiol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1471-2180-7-30","article-title":"Assessing the reliability of eBURST using simulated populations with known ancestry","volume":"7","author":"KME Turner","year":"2007","journal-title":"BMC Microbiol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"R118","DOI":"10.1186\/gb-2012-13-12-r118","article-title":"Microevolutionary analysis of Clostridium difficile genomes to investigate transmission","volume":"13","author":"X Didelot","year":"2012","journal-title":"Genome Biol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0170449","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,3]],"date-time":"2020-10-03T20:36:33Z","timestamp":1601757393000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0170449"}},"subtitle":[],"editor":[{"given":"Ulrich","family":"N\u00fcbel","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,3,16]]},"references-count":36,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2017,3,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0170449","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,3,16]]}}}