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Maio","year":"2017","journal-title":"Genetics"},{"key":"ref24","unstructured":"Agency for Healthcare Research and Quality (AHRQ). Project CLEAR (Changing Lives by Eradicating Antibiotic Resistance) Trial; 2018. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/clinicaltrials.gov\/ct2\/show\/NCT01209234\" xlink:type=\"simple\">https:\/\/clinicaltrials.gov\/ct2\/show\/NCT01209234<\/ext-link>. Last accessed 08-23-2018."},{"key":"ref25","first-page":"158","article-title":"Research in Computational Molecular Biology","author":"S Nurk","year":"2013"},{"issue":"14","key":"ref26","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"11","key":"ref27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement","volume":"9","author":"BJ Walker","year":"2014","journal-title":"PLOS ONE"},{"issue":"3","key":"ref28","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"NJ Croucher","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"ref29","first-page":"1","article-title":"Bacterial Population Genetics in Infectious Disease","author":"MH Schierup","year":"2010"},{"issue":"8","key":"ref30","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1111\/j.1461-0248.2011.01640.x","article-title":"Statistical inference for stochastic simulation models\u2013theory and application","volume":"14","author":"F Hartig","year":"2011","journal-title":"Ecology Letters"},{"issue":"6","key":"ref31","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1007\/s11222-011-9288-2","article-title":"Approximate Bayesian computational methods","volume":"22","author":"JM Marin","year":"2012","journal-title":"Statistics and Computing"},{"issue":"1","key":"ref32","doi-asserted-by":"crossref","first-page":"e17","DOI":"10.1371\/journal.pmed.0050017","article-title":"Key role for clumping factor B in Staphylococcus aureus nasal colonization of humans","volume":"5","author":"HF Wertheim","year":"2008","journal-title":"PLoS medicine"},{"key":"ref33","article-title":"Pattern Recognition and Machine Learning (Information Science and Statistics)","author":"CM Bishop","year":"2006"},{"key":"ref34","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-4145-2","article-title":"Monte Carlo Statistical Methods","author":"CP Robert","year":"2004"},{"issue":"3","key":"ref35","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"NJ Croucher","year":"2014","journal-title":"Nucleic acids research"},{"issue":"2","key":"ref36","doi-asserted-by":"crossref","first-page":"e1004041","DOI":"10.1371\/journal.pcbi.1004041","article-title":"ClonalFrameML: efficient inference of recombination in whole bacterial genomes","volume":"11","author":"X Didelot","year":"2015","journal-title":"PLoS computational biology"},{"issue":"5","key":"ref37","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1093\/molbev\/msx066","article-title":"Efficient inference of recent and ancestral recombination within bacterial populations","volume":"34","author":"R Mostowy","year":"2017","journal-title":"Molecular biology and evolution"},{"key":"ref38","unstructured":"Stimson J, Gardy JL, Mathema B, Crudu V, Cohen T, Colijn C. Beyond the SNP threshold: identifying outbreak clusters using inferred transmissions; 2018. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.biorxiv.org\/content\/early\/2018\/12\/03\/319707\" xlink:type=\"simple\">https:\/\/www.biorxiv.org\/content\/early\/2018\/12\/03\/319707<\/ext-link>."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006534","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,5,2]],"date-time":"2019-05-02T00:00:00Z","timestamp":1556755200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006534","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T10:31:32Z","timestamp":1663324292000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006534"}},"subtitle":[],"editor":[{"given":"Peter M","family":"Kasson","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,4,22]]},"references-count":38,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2019,4,22]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006534","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/429464","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4,22]]}}}