{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T03:44:31Z","timestamp":1792122271996,"version":"4.4.0"},"reference-count":68,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2015,9,29]],"date-time":"2015-09-29T00:00:00Z","timestamp":1443484800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosmedicine.org"],"crossmark-restriction":false},"short-container-title":["PLoS Med"],"DOI":"10.1371\/journal.pmed.1001880","type":"journal-article","created":{"date-parts":[[2015,9,29]],"date-time":"2015-09-29T13:58:51Z","timestamp":1443535131000},"page":"e1001880","update-policy":"https:\/\/doi.org\/10.1371\/journal.pmed.corrections_policy","source":"Crossref","is-referenced-by-count":266,"title":["Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal"],"prefix":"10.1371","volume":"12","author":[{"given":"Keira A.","family":"Cohen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Abeel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abigail","family":"Manson McGuire","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher A.","family":"Desjardins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanisha","family":"Munsamy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Terrance P.","family":"Shea","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruce J.","family":"Walker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nonkqubela","family":"Bantubani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deepak V.","family":"Almeida","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucia","family":"Alvarado","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sin\u00e9ad B.","family":"Chapman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nomonde R.","family":"Mvelase","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eamon Y.","family":"Duffy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael G.","family":"Fitzgerald","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pamla","family":"Govender","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharvari","family":"Gujja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanna","family":"Hamilton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clinton","family":"Howarth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey D.","family":"Larimer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kashmeel","family":"Maharaj","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew D.","family":"Pearson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margaret E.","family":"Priest","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiandong","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nesri","family":"Padayatchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacques","family":"Grosset","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah K.","family":"Young","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Wortman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koleka P.","family":"Mlisana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max R.","family":"O'Donnell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruce W.","family":"Birren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William R.","family":"Bishai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander S.","family":"Pym","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashlee M.","family":"Earl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2015,9,29]]},"reference":[{"key":"ref1","unstructured":"WHO. Global Tuberculosis Report. 2014. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.who.int\/tb\/publications\/global_report\/en\/\" xlink:type=\"simple\">http:\/\/www.who.int\/tb\/publications\/global_report\/en\/<\/ext-link>"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/S1473-3099(08)70260-3","article-title":"Extensively drug-resistant tuberculosis","volume":"9","author":"M Jassal","year":"2009","journal-title":"Lancet Infect Dis"},{"key":"ref3","unstructured":"WHO. Multidrug-resistant tuberculosis (MDR-TB) Update. 2013. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.who.int\/tb\/challenges\/mdr?MDR_TB_FactSheet.pdf\" xlink:type=\"simple\">http:\/\/www.who.int\/tb\/challenges\/mdr?MDR_TB_FactSheet.pdf<\/ext-link>"},{"key":"ref4","unstructured":"Department of Health Province of KwaZulu-Natal Annual Report 2012\/2013: Part B Performance Information. 2013. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.kznhealth.gov.za\/1213report\/partB.pdf\" xlink:type=\"simple\">http:\/\/www.kznhealth.gov.za\/1213report\/partB.pdf<\/ext-link>"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1913","DOI":"10.3201\/eid1710.100952","article-title":"Drug-Resistant tuberculosis, KwaZulu-Natal, South Africa, 2001\u20132007","volume":"17","author":"K Wallengren","year":"2011","journal-title":"Emerg Infect Dis"},{"key":"ref6","unstructured":"UNAIDS. The Gap Report: HIV estimates with uncertainty bounds 1990\u20132013. 2014. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.unaids.org\/en\/resources\/campaigns\/2014\/2014gapreport\/gapreport\" xlink:type=\"simple\">http:\/\/www.unaids.org\/en\/resources\/campaigns\/2014\/2014gapreport\/gapreport<\/ext-link>"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1016\/S0140-6736(06)69573-1","article-title":"Extensively drug-resistant tuberculosis as a cause of death in patients co-infected with tuberculosis and HIV in a rural area of South Africa","volume":"368","author":"NR Gandhi","year":"2006","journal-title":"Lancet"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1086\/522987","article-title":"Evolution of the extensively drug-resistant F15\/LAM4\/KZN strain of Mycobacterium tuberculosis in KwaZulu-Natal, South Africa","volume":"45","author":"M Pillay","year":"2007","journal-title":"Clin Infect Dis"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1093\/infdis\/jis631","article-title":"Nosocomial transmission of extensively drug-resistant tuberculosis in a rural hospital in South Africa","volume":"207","author":"NR Gandhi","year":"2013","journal-title":"J Infect Dis"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"394","DOI":"10.3201\/eid2003.131083","article-title":"Minimal Diversity of Drug-Resistant Mycobacterium tuberculosis Strains, South Africa","volume":"20","author":"NR Gandhi","year":"2014","journal-title":"Emerg Infect Dis"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1128\/JCM.05832-11","article-title":"Population structure of multi- and extensively drug-resistant Mycobacterium tuberculosis strains in South Africa","volume":"50","author":"VN Chihota","year":"2012","journal-title":"J Clin Microbiol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e17513","DOI":"10.1371\/journal.pone.0017513","article-title":"Spread of extensively drug-resistant tuberculosis in KwaZulu-Natal province, South Africa","volume":"6","author":"P Moodley","year":"2011","journal-title":"PLoS One"},{"key":"ref13","unstructured":"Tuberculosis MDR\/XDR: The Msinga Experience 2005\u20132009. 2009. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.kznhealth.gov.za\/tbmsinga.pdf\" xlink:type=\"simple\">http:\/\/www.kznhealth.gov.za\/tbmsinga.pdf<\/ext-link>"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"e70919","DOI":"10.1371\/journal.pone.0070919","article-title":"Programmatically selected multidrug-resistant strains drive the emergence of extensively drug-resistant tuberculosis in South Africa","volume":"8","author":"B M\u00fcller","year":"2013","journal-title":"PLoS One"},{"key":"ref15","first-page":"81","article-title":"Amelioration of the Deleterious Pleiotropic Effects of an Adaptive Mutation in Bacillus subtilis","volume":"48","author":"FM Cohan","year":"1994","journal-title":"Evolution (N Y)"},{"key":"ref16","first-page":"120","article-title":"Nature","author":"SJ Schrag","year":"1996","journal-title":"Nature"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1093\/genetics\/156.4.1471","article-title":"Compensatory evolution in rifampin-resistant Escherichia coli","volume":"156","author":"MG Reynolds","year":"2000","journal-title":"Genetics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1126\/science.272.5268.1641","article-title":"Compensatory ahpC gene expression in isoniazid-resistant Mycobacterium tuberculosis","volume":"272","author":"DR Sherman","year":"1996","journal-title":"Science"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1038\/ng.1038","article-title":"Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes","volume":"44","author":"I Comas","year":"2012","journal-title":"Nat Genet. Nature Publishing Group"},{"key":"ref20","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":"N Casali","year":"2014","journal-title":"Nat Genet. Nature Publishing Group"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1038\/ng.2747","article-title":"Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis","volume":"45","author":"MR Farhat","year":"2013","journal-title":"Nat Genet. Nature Publishing Group"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1038\/ng.2735","article-title":"Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance","volume":"45","author":"H Zhang","year":"2013","journal-title":"Nat Genet. Nature Publishing Group"},{"issue":"3","key":"ref23","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":"M Merker","year":"2015","journal-title":"Nat Genet"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e7778","DOI":"10.1371\/journal.pone.0007778","article-title":"Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa","volume":"4","author":"TR Ioerger","year":"2009","journal-title":"PLoS One"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1126\/science.318.5852.901a","article-title":"Tuberculosis. Few mutations divide some drug-resistant TB strains","volume":"318","author":"R Koenig","year":"2007","journal-title":"Science"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1093\/molbev\/mss075","article-title":"Bayesian phylogenetics with BEAUti and the BEAST 1.7","volume":"29","author":"AJ Drummond","year":"2012","journal-title":"Mol Biol Evol"},{"key":"ref27","unstructured":"WHO Updated interim critical concentration for first-line and second-line DST [Internet]. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.stoptb.org\/wg\/gli\/assets\/documents\/Updatedcriticalconcentrationtable_1stand2ndlinedrugspdf\" xlink:type=\"simple\">http:\/\/www.stoptb.org\/wg\/gli\/assets\/documents\/Updatedcriticalconcentrationtable_1stand2ndlinedrugspdf<\/ext-link>"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e90868","DOI":"10.1371\/journal.pone.0090868","article-title":"High rates of potentially infectious tuberculosis and multidrug-resistant tuberculosis (MDR-TB) among hospital inpatients in KwaZulu Natal, South Africa indicate risk of nosocomial transmission","volume":"9","author":"N Bantubani","year":"2014","journal-title":"PLoS One"},{"issue":"1","key":"ref29","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1097\/QAI.0000000000000221","article-title":"Adherence in the treatment of patients with extensively drug-resistant tuberculosis and HIV in South Africa: A prospective cohort study","volume":"67","author":"MR O\u2019Donnell","year":"2014","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"2188","DOI":"10.1128\/JCM.03530-14","article-title":"A novel reporter phage to detect tuberculosis and rifampicin resistance in an HIV endemic population","volume":"53","author":"MR O\u2019Donnell","year":"2015","journal-title":"J Clin Microbiol"},{"key":"ref31","first-page":"Unit 10A.2","article-title":"Genetic Manipulation of Mycobacterium tuberculosis","volume":"Chapter 10","author":"MH Larsen","year":"2007","journal-title":"Curr Protoc Microbiol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"e112963","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"},{"key":"ref33","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":"ref34","unstructured":"Picard [Internet]. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/broadinstitute.github.io\/picard\" xlink:type=\"simple\">http:\/\/broadinstitute.github.io\/picard<\/ext-link>"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","article-title":"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models","volume":"22","author":"A Stamatakis","year":"2006","journal-title":"Bioinformatics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"2869","DOI":"10.1073\/pnas.0511240103","article-title":"Variable host-pathogen compatibility in Mycobacterium tuberculosis","volume":"103","author":"S Gagneux","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1016\/j.meegid.2012.02.004","article-title":"SITVITWEB\u2014a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology","volume":"12","author":"C Demay","year":"2012","journal-title":"Infect Genet Evol"},{"key":"ref38","first-page":"226","article-title":"Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96)","author":"M Ester","year":"1996"},{"key":"ref39","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":"TM Walker","year":"2013","journal-title":"Lancet Infect Dis. Elsevier Ltd"},{"key":"ref40","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":"TM Walker","year":"2014","journal-title":"Lancet Respir Med"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7554\/eLife.05166","article-title":"Large scale population-based whole genome sequencing of Mycobacterium tuberculosis provides insights into transmission in a high prevalence area","volume":"4","author":"J Guerra-Assun\u00e7\u00e3o","year":"2015","journal-title":"Elife"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v007.i10","article-title":"zt: a software tool for simple and partial Mantel tests","volume":"7","author":"E Bonnet","year":"2002","journal-title":"J Stat Softw"},{"key":"ref43","author":"JW Inman","year":"1835"},{"key":"ref44","unstructured":"Swofford DL. PAUP: Phylogenetic Analysis Using Parsimony, Version 3.1 Computer program distributed by the Illinois Natural History Survey, Champaign, Illinois. 1991."},{"key":"ref45","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":"CB Ford","year":"2013","journal-title":"Nat Genet"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/1471-2334-13-110","article-title":"Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data","volume":"13","author":"JM Bryant","year":"2013","journal-title":"BMC Infect Dis"},{"key":"ref47","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":"A Roetzer","year":"2013","journal-title":"PLoS Med"},{"key":"ref48","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":"CB Ford","year":"2011","journal-title":"Nat Genet"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/S1473-3099(07)70108-1","article-title":"Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development","volume":"7","author":"S Gagneux","year":"2007","journal-title":"Lancet Infect Dis"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"e311","DOI":"10.1371\/journal.pbio.0060311","article-title":"High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography","volume":"6","author":"R Hershberg","year":"2008","journal-title":"PLoS Biol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"4812","DOI":"10.1038\/ncomms5812","article-title":"A robust SNP barcode for typing Mycobacterium tuberculosis complex strains","volume":"5","author":"F Coll","year":"2014","journal-title":"Nat Commun"},{"key":"ref52","unstructured":"South Africa KwaZulu-Natal location map [Internet]. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/commons.wikimedia.org\/wiki\/File:South_Africa_KwaZulu-Natal_location_map.svg\" xlink:type=\"simple\">https:\/\/commons.wikimedia.org\/wiki\/File:South_Africa_KwaZulu-Natal_location_map.svg<\/ext-link>"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"2100","DOI":"10.1016\/S0140-6736(10)60359-9","article-title":"Global tuberculosis drug development pipeline: the need and the reality","volume":"375","author":"Z Ma","year":"2010","journal-title":"Lancet. Elsevier Ltd"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1111\/mmi.12520","article-title":"Fitness costs of rifampicin resistance in Mycobacterium tuberculosis are amplified under conditions of nutrient starvation and compensated by mutation in the \u03b2\u2032 subunit of RNA polymerase","volume":"91","author":"T Song","year":"2014","journal-title":"Mol Microbiol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1128\/AAC.01541-12","article-title":"Putative compensatory mutations in the rpoc gene of rifampin-resistant mycobacterium tuberculosis are associated with ongoing transmission","volume":"57","author":"M De Vos","year":"2013","journal-title":"Antimicrob Agents Chemother"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1038\/ng.2743","article-title":"Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-\u03b2-D-arabinose biosynthetic and utilization pathway genes","volume":"45","author":"H Safi","year":"2013","journal-title":"Nat Genet. Nature Publishing Group"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"87S","DOI":"10.1183\/09031936.02.00309102","article-title":"Tuberculosis therapy: past, present and future","volume":"20","author":"MD Iseman","year":"2002","journal-title":"Eur Respir J"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"e30593","DOI":"10.1371\/journal.pone.0030593","article-title":"Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints","volume":"7","author":"CRE McEvoy","year":"2012","journal-title":"PLoS One"},{"key":"ref59","first-page":"1","article-title":"Genomic Epidemiology of Multidrug-resistant Mycobacterium tuberculosis During Transcontinental Spread","author":"M Coscolla","year":"2015","journal-title":"J Infect Dis"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1056\/NEJMoa0907847","article-title":"Rapid molecular detection of tuberculosis and rifampin resistance","volume":"363","author":"CC Boehme","year":"2010","journal-title":"N Engl J Med"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1086\/595689","article-title":"Clinical characteristics and treatment outcomes of patients with isoniazid-monoresistant tuberculosis","volume":"48","author":"A Cattamanchi","year":"2009","journal-title":"Clin Infect Dis"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"e84197","DOI":"10.1371\/journal.pone.0084197","article-title":"Do we need to detect isoniazid resistance in addition to rifampicin resistance in diagnostic tests for tuberculosis?","volume":"9","author":"CM Denkinger","year":"2014","journal-title":"PLoS One"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1186\/1471-2334-14-442","article-title":"Effects of introducing Xpert MTB\/RIF test on multi-drug resistant tuberculosis diagnosis in KwaZulu-Natal South Africa","volume":"14","author":"NR Dlamini-Mvelase","year":"2014","journal-title":"BMC Infect Dis"},{"key":"ref64","first-page":"180ra49","article-title":"Community-wide isoniazid preventive therapy drives drug-resistant tuberculosis: a model-based analysis","volume":"5","author":"HL Mills","year":"2013","journal-title":"Sci Transl Med"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"7042","DOI":"10.1073\/pnas.0600349103","article-title":"Beneficial and perverse effects of isoniazid preventive therapy for latent tuberculosis infection in HIV-tuberculosis coinfected populations","volume":"103","author":"T Cohen","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1056\/NEJMoa1214289","article-title":"A Trial of Mass Isoniazid Preventive Therapy for Tuberculosis Control","volume":"370","author":"GJ Churchyard","year":"2014","journal-title":"N Engl J Med"},{"key":"ref67","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":"V Eldholm","year":"2015","journal-title":"Nat Commun. Nature Publishing Group"},{"key":"ref68","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":"M Merker","year":"2015","journal-title":"Nat Genet. Nature Publishing Group"}],"container-title":["PLOS Medicine"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pmed.1001880","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,22]],"date-time":"2022-05-22T08:25:19Z","timestamp":1653207919000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pmed.1001880"}},"subtitle":[],"editor":[{"given":"John Z","family":"Metcalfe","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2015,9,29]]},"references-count":68,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2015,9,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pmed.1001880","relation":{},"ISSN":["1549-1676"],"issn-type":[{"value":"1549-1676","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,9,29]]}}}