{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T02:59:40Z","timestamp":1792205980714,"version":"4.4.0"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,1,25]],"date-time":"2019-01-25T00:00:00Z","timestamp":1548374400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100000266","name":"The Engineering and Physical Sciences Research Council","doi-asserted-by":"crossref","award":["EP\/K026003\/1"],"award-info":[{"award-number":["EP\/K026003\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000266","name":"EPSRC","doi-asserted-by":"publisher","award":["EP\/N014529\/1"],"award-info":[{"award-number":["EP\/N014529\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"EPSRC","doi-asserted-by":"publisher","award":["U54GM088558"],"award-info":[{"award-number":["U54GM088558"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,1]]},"DOI":"10.1093\/molbev\/msy242","type":"journal-article","created":{"date-parts":[[2018,12,20]],"date-time":"2018-12-20T15:14:18Z","timestamp":1545318858000},"page":"587-603","source":"Crossref","is-referenced-by-count":179,"title":["Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions"],"prefix":"10.1093","volume":"36","author":[{"given":"James","family":"Stimson","sequence":"first","affiliation":[{"name":"Department of Mathematics, Imperial College London, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Gardy","sequence":"additional","affiliation":[{"name":"British Columbia Centre for Disease Control, Communicable Disease Prevention and Control Services, Vancouver, Canada"},{"name":"School of Population and Public Health, University of British Columbia, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barun","family":"Mathema","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valeriu","family":"Crudu","sequence":"additional","affiliation":[{"name":"Phthisiopneumology Institute, Chisinau, Republic of Moldova"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ted","family":"Cohen","sequence":"additional","affiliation":[{"name":"Yale University School of Public Health, New Haven"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Colijn","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Imperial College London, London, UK"},{"name":"Department of Mathematics, Simon Fraser University, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,1,25]]},"reference":[{"issue":"10","key":"key\n\t\t\t\t2019022515503012800_msy242-B1","doi-asserted-by":"crossref","first-page":"e0164397.","DOI":"10.1371\/journal.pone.0164397","article-title":"Genomic epidemiology of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit","volume":"11","author":"Azarian","year":"2016","journal-title":"PLoS One"},{"issue":"12","key":"key\n\t\t\t\t2019022515503012800_msy242-B2","doi-asserted-by":"crossref","first-page":"827.","DOI":"10.1038\/nrg3564","article-title":"Genome dynamics during experimental evolution","volume":"14","author":"Barrick","year":"2013","journal-title":"Nat Rev Genet"},{"issue":"5","key":"key\n\t\t\t\t2019022515503012800_msy242-B3","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/j.tim.2014.01.006","article-title":"Omics approaches in food safety: fulfilling the promise?","volume":"22","author":"Bergholz","year":"2014","journal-title":"Trends Microbiol"},{"key":"key\n\t\t\t\t2019022515503012800_msy242-B4","doi-asserted-by":"crossref","first-page":"10063.","DOI":"10.1038\/ncomms10063","article-title":"Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis","volume":"6","author":"Bradley","year":"2015","journal-title":"Nat Commun"},{"issue":"10","key":"key\n\t\t\t\t2019022515503012800_msy242-B5","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1016\/S2213-2600(13)70231-5","article-title":"Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study","volume":"1","author":"Bryant","year":"2013","journal-title":"Lancet Respir Med"},{"issue":"1","key":"key\n\t\t\t\t2019022515503012800_msy242-B6","first-page":"110.","article-title":"Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data","volume":"13","author":"Bryant","year":"2013","journal-title":"BMC Microbiol"},{"key":"key\n\t\t\t\t2019022515503012800_msy242-B7","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9781139013567","volume-title":"Regression analysis of count data","author":"Cameron","year":"2013"},{"issue":"2","key":"key\n\t\t\t\t2019022515503012800_msy242-B8","doi-asserted-by":"crossref","first-page":"e1006885.","DOI":"10.1371\/journal.ppat.1006885","article-title":"When are pathogen genome sequences informative of transmission events?","volume":"14","author":"Campbell","year":"2018","journal-title":"PLoS Pathog"},{"issue":"10","key":"key\n\t\t\t\t2019022515503012800_msy242-B9","doi-asserted-by":"crossref","first-page":"e1002137.","DOI":"10.1371\/journal.pmed.1002137","article-title":"Whole genome sequence analysis of a large isoniazid-resistant tuberculosis outbreak in London: a retrospective observational study","volume":"13","author":"Casali","year":"2016","journal-title":"PLoS Med"},{"issue":"3","key":"key\n\t\t\t\t2019022515503012800_msy242-B10","doi-asserted-by":"crossref","first-page":"279.","DOI":"10.1038\/ng.2878","article-title":"Evolution and transmission of drug-resistant tuberculosis in a Russian population","volume":"46","author":"Casali","year":"2014","journal-title":"Nat Genet"},{"issue":"12","key":"key\n\t\t\t\t2019022515503012800_msy242-B11","doi-asserted-by":"crossref","first-page":"e83012.","DOI":"10.1371\/journal.pone.0083012","article-title":"Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing","volume":"8","author":"Clark","year":"2013","journal-title":"PLoS One"},{"issue":"3","key":"key\n\t\t\t\t2019022515503012800_msy242-B12","doi-asserted-by":"crossref","first-page":"e91024.","DOI":"10.1371\/journal.pone.0091024","article-title":"Whole genome sequencing of Mycobacterium tuberculosis reveals slow growth and low mutation rates during latent infections in humans","volume":"9","author":"Colangeli","year":"2014","journal-title":"PLoS One"},{"issue":"45","key":"key\n\t\t\t\t2019022515503012800_msy242-B13","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1098\/rsif.2009.0284","article-title":"Resolving the impact of waiting time distributions on the persistence of measles","volume":"7","author":"Conlan","year":"2010","journal-title":"J R Soc Interface"},{"issue":"3","key":"key\n\t\t\t\t2019022515503012800_msy242-B14","first-page":"e000029.","article-title":"Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157: H7 strains causing severe human disease in the UK","volume":"1","author":"Dallman","year":"2015","journal-title":"Microb Genom"},{"issue":"4","key":"key\n\t\t\t\t2019022515503012800_msy242-B15","first-page":"997","article-title":"Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks","volume":"34","author":"Didelot","year":"2017","journal-title":"Mol Biol Evol"},{"issue":"7","key":"key\n\t\t\t\t2019022515503012800_msy242-B16","doi-asserted-by":"crossref","first-page":"1869","DOI":"10.1093\/molbev\/msu121","article-title":"Bayesian inference of infectious disease transmission from whole-genome sequence data","volume":"31","author":"Didelot","year":"2014","journal-title":"Mol Biol Evol"},{"issue":"4","key":"key\n\t\t\t\t2019022515503012800_msy242-B17","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1016\/j.jhin.2016.02.022","article-title":"Monitoring the spread of meticillin-resistant Staphylococcus aureus in The Netherlands from a reference laboratory perspective","volume":"93","author":"Donker","year":"2016","journal-title":"J Hosp Infect"},{"key":"key\n\t\t\t\t2019022515503012800_msy242-B18","doi-asserted-by":"crossref","first-page":"7119.","DOI":"10.1038\/ncomms8119","article-title":"Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain","volume":"6","author":"Eldholm","year":"2015","journal-title":"Nat Commun"},{"issue":"11","key":"key\n\t\t\t\t2019022515503012800_msy242-B19","doi-asserted-by":"crossref","first-page":"490.","DOI":"10.1186\/s13059-014-0490-3","article-title":"Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient","volume":"15","author":"Eldholm","year":"2014","journal-title":"Genome Biol"},{"issue":"6","key":"key\n\t\t\t\t2019022515503012800_msy242-B20","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1128\/JCM.00025-15","article-title":"PhyResSE: a web tool delineating Mycobacterium tuberculosis antibiotic resistance and lineage from whole-genome sequencing data","volume":"53","author":"Feuerriegel","year":"2015","journal-title":"J Clin Microbiol"},{"issue":"11","key":"key\n\t\t\t\t2019022515503012800_msy242-B21","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1093\/aje\/kwg251","article-title":"The interval between successive cases of an infectious disease","volume":"158","author":"Fine","year":"2003","journal-title":"Am J Epidemiol"},{"issue":"5","key":"key\n\t\t\t\t2019022515503012800_msy242-B22","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1038\/ng.811","article-title":"Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection","volume":"43","author":"Ford","year":"2011","journal-title":"Nat Genet"},{"issue":"7","key":"key\n\t\t\t\t2019022515503012800_msy242-B23","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1038\/ng.2656","article-title":"Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis","volume":"45","author":"Ford","year":"2013","journal-title":"Nat Genet"},{"key":"key\n\t\t\t\t2019022515503012800_msy242-B24","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9781139626514","volume-title":"Stochastic processes: theory for applications","author":"Gallagher","year":"2013"},{"issue":"7","key":"key\n\t\t\t\t2019022515503012800_msy242-B25","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1093\/infdis\/jiu574","article-title":"Relapse or reinfection with tuberculosis: a whole genome sequencing approach in a large population-based cohort with high HIV prevalence and active follow-up","volume":"211","author":"Guerra-Assun\u00e7\u00e3o","year":"2015","journal-title":"J Infect Dis"},{"key":"key\n\t\t\t\t2019022515503012800_msy242-B26","first-page":"1","article-title":"Genotyping and whole-genome sequencing to identify tuberculosis transmission to pediatric patients in British Columbia, Canada, 2005\u20132014","volume":"40","author":"Guthrie","year":"2018","journal-title":"J Infect Dis"},{"issue":"12","key":"key\n\t\t\t\t2019022515503012800_msy242-B27","doi-asserted-by":"crossref","first-page":"e1004613.","DOI":"10.1371\/journal.pcbi.1004613","article-title":"Epidemic reconstruction in a phylogenetics framework: transmission trees as partitions of the node set","volume":"11","author":"Hall","year":"2015","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"key\n\t\t\t\t2019022515503012800_msy242-B28","doi-asserted-by":"crossref","first-page":"287","DOI":"10.20506\/rst.35.1.2433","article-title":"Using genomics data to reconstruct transmission trees during disease outbreaks","volume":"35","author":"Hall","year":"2016","journal-title":"Rev Sci Tech"},{"issue":"1","key":"key\n\t\t\t\t2019022515503012800_msy242-B29","doi-asserted-by":"crossref","first-page":"21.","DOI":"10.1186\/s12916-016-0566-x","article-title":"Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review","volume":"14","author":"Hatherell","year":"2016","journal-title":"BMC Med"},{"key":"key\n\t\t\t\t2019022515503012800_msy242-B30","author":"Jombart","year":"2017"},{"issue":"1","key":"key\n\t\t\t\t2019022515503012800_msy242-B31","doi-asserted-by":"crossref","first-page":"15.","DOI":"10.1186\/1476-072X-12-15","article-title":"Using statistical methods and genotyping to detect tuberculosis outbreaks","volume":"12","author":"Kammerer","year":"2013","journal-title":"Int J Health Geogr"},{"issue":"4","key":"key\n\t\t\t\t2019022515503012800_msy242-B32","doi-asserted-by":"crossref","first-page":"e00398","DOI":"10.1128\/mBio.00398-13","article-title":"Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti","volume":"4","author":"Katz","year":"2013","journal-title":"MBio"},{"key":"key\n\t\t\t\t2019022515503012800_msy242-B33","author":"Kendall","year":"2016"},{"issue":"6","key":"key\n\t\t\t\t2019022515503012800_msy242-B34","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1016\/j.cmi.2016.03.014","article-title":"Whole genome analysis of Mycobacterium tuberculosis isolates from recurrent episodes of tuberculosis, Finland, 1995\u20132013","volume":"22","author":"Korhonen","year":"2016","journal-title":"Clin Microbiol Infect"},{"issue":"1","key":"key\n\t\t\t\t2019022515503012800_msy242-B35","doi-asserted-by":"crossref","first-page":"35.","DOI":"10.1186\/1745-6150-4-35","article-title":"Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria","volume":"4","author":"Kuo","year":"2009","journal-title":"Biol Direct"},{"issue":"12","key":"key\n\t\t\t\t2019022515503012800_msy242-B36","doi-asserted-by":"crossref","first-page":"1905","DOI":"10.1093\/infdis\/jiv011","article-title":"Reemergence and amplification of tuberculosis in the Canadian Arctic","volume":"211","author":"Lee","year":"2015","journal-title":"J Infect Dis"},{"issue":"7","key":"key\n\t\t\t\t2019022515503012800_msy242-B37","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1016\/j.ijmm.2016.05.017","article-title":"Substantial molecular evolution and mutation rates in prolonged latent Mycobacterium tuberculosis infection in humans","volume":"306","author":"Lillebaek","year":"2016","journal-title":"Int J Med Microbiol"},{"issue":"5","key":"key\n\t\t\t\t2019022515503012800_msy242-B38","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1016\/j.jmva.2006.11.013","article-title":"Comparing clusterings \u2013 an information based distance","volume":"98","author":"Meil\u0103","year":"2007","journal-title":"J Multivar Anal"},{"issue":"3","key":"key\n\t\t\t\t2019022515503012800_msy242-B39","doi-asserted-by":"crossref","first-page":"242.","DOI":"10.1038\/ng.3195","article-title":"Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage","volume":"47","author":"Merker","year":"2015","journal-title":"Nat Genet"},{"issue":"19","key":"key\n\t\t\t\t2019022515503012800_msy242-B40","doi-asserted-by":"crossref","first-page":"6575","DOI":"10.1128\/JB.186.19.6575-6585.2004","article-title":"Genome-wide molecular clock and horizontal gene transfer in bacterial evolution","volume":"186","author":"Novichkov","year":"2004","journal-title":"J Bacteriol"},{"issue":"4","key":"key\n\t\t\t\t2019022515503012800_msy242-B41","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1128\/JCM.03235-14","article-title":"Delineating community outbreaks of Salmonella enterica serovar Typhimurium by use of whole-genome sequencing: insights into genomic variability within an outbreak","volume":"53","author":"Octavia","year":"2015","journal-title":"J Clin Microbiol"},{"issue":"2","key":"key\n\t\t\t\t2019022515503012800_msy242-B42","doi-asserted-by":"crossref","first-page":"vew031.","DOI":"10.1093\/ve\/vew031","article-title":"Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks","volume":"2","author":"Poon","year":"2016","journal-title":"Virus Evol"},{"issue":"2","key":"key\n\t\t\t\t2019022515503012800_msy242-B43","doi-asserted-by":"crossref","first-page":"e1001387.","DOI":"10.1371\/journal.pmed.1001387","article-title":"Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study","volume":"10","author":"Roetzer","year":"2013","journal-title":"PLoS Med"},{"issue":"4","key":"key\n\t\t\t\t2019022515503012800_msy242-B44","doi-asserted-by":"crossref","first-page":"592.","DOI":"10.1093\/bioinformatics\/btq706","article-title":"phangorn: phylogenetic analysis in R","volume":"27","author":"Schliep","year":"2011","journal-title":"Bioinformatics"},{"issue":"2","key":"key\n\t\t\t\t2019022515503012800_msy242-B45","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/S1473-3099(12)70277-3","article-title":"Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study","volume":"13","author":"Walker","year":"2013","journal-title":"Lancet Infect Dis"},{"issue":"4","key":"key\n\t\t\t\t2019022515503012800_msy242-B46","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/S2213-2600(14)70027-X","article-title":"Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007\u201312, with whole pathogen genome sequences: an observational study","volume":"2","author":"Walker","year":"2014","journal-title":"Lancet Respir Med"},{"issue":"1609","key":"key\n\t\t\t\t2019022515503012800_msy242-B47","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1098\/rspb.2006.3754","article-title":"How generation intervals shape the relationship between growth rates and reproductive numbers","volume":"274","author":"Wallinga","year":"2007","journal-title":"Proc R Soc Lond B Biol Sci"},{"issue":"3","key":"key\n\t\t\t\t2019022515503012800_msy242-B48","doi-asserted-by":"crossref","first-page":"e1003549.","DOI":"10.1371\/journal.pcbi.1003549","article-title":"Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data","volume":"10","author":"Worby","year":"2014","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"key\n\t\t\t\t2019022515503012800_msy242-B49","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/S1473-3099(16)30418-2","article-title":"Transmission of multidrug-resistant Mycobacterium tuberculosis in Shanghai, China: a retrospective observational study using whole-genome sequencing and epidemiological investigation","volume":"17","author":"Yang","year":"2017","journal-title":"Lancet Infect Dis"},{"issue":"7","key":"key\n\t\t\t\t2019022515503012800_msy242-B50","doi-asserted-by":"crossref","first-page":"e69875.","DOI":"10.1371\/journal.pone.0069875","article-title":"Finding evidence for local transmission of contagious disease in molecular epidemiological datasets","volume":"8","author":"Ypma","year":"2013","journal-title":"PLoS One"}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/mbe\/article-pdf\/36\/3\/587\/27980635\/msy242.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,11,12]],"date-time":"2019-11-12T16:15:08Z","timestamp":1573575308000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article\/36\/3\/587\/5300248"}},"subtitle":[],"editor":[{"given":"Thomas","family":"Leitner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,1,25]]},"references-count":50,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2019,1,25]]},"published-print":{"date-parts":[[2019,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msy242","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/319707","asserted-by":"object"}]},"ISSN":["0737-4038","1537-1719"],"issn-type":[{"value":"0737-4038","type":"print"},{"value":"1537-1719","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,3]]},"published":{"date-parts":[[2019,1,25]]}}}