{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T08:39:28Z","timestamp":1788856768913,"version":"build-2803163510"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2015,1,1]],"date-time":"2015-01-01T00:00:00Z","timestamp":1420070400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Rationale<\/jats:title>\n                    <jats:p>HIV-associated tuberculosis remains a major health problem among the gold-mining workforce in South Africa. We postulate that high levels of recent transmission, indicated by strain clustering, are fueling the tuberculosis epidemic among gold miners.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>To combine molecular and epidemiologic data to describe Mycobacterium tuberculosis genetic diversity, estimate levels of transmission, and examine risk factors for clustering.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We conducted a cross-sectional study of culture-positive M. tuberculosis isolates in 15 gold mine shafts across three provinces in South Africa. All isolates were subject IS6110-based restriction fragment length polymorphisms, and we performed spoligotyping analysis and combined it with basic demographic and clinical information.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Measurements and Main Results<\/jats:title>\n                    <jats:p>Of the 1,602 M. tuberculosis patient isolates, 1,240 (78%) had genotyping data available for analysis. A highly diverse bacillary population was identified, comprising a total of 730 discrete genotypes. Four genotypic families (Latin American Mediterranean spoligotype family; W-Beijing; AH or X; and T1\u2013T4) accounted for over 50% of all strains. Overall, 45% (560\/1,240) of strains were genotypically clustered. The minimum estimate for recent transmission (n\u2009\u2212\u20091 method) was 32% (range, 27\u201334%). There were no individual-level risk factors for clustering, apart from borderline evidence for being non\u2013South African and having self-reported HIV infection.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The high M. tuberculosis genetic diversity and lack of risk factors for clustering are indicative of a universal risk for disease among gold miners and likely mixing with nonmining populations. Our results underscore the urgent need to intensify interventions to interrupt transmission across the entire gold-mining workforce in South Africa.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1513\/annalsats.201404-150oc","type":"journal-article","created":{"date-parts":[[2014,11,24]],"date-time":"2014-11-24T11:42:16Z","timestamp":1416829336000},"page":"12-20","source":"Crossref","is-referenced-by-count":13,"title":["Molecular Epidemiology of\n                    <i>Mycobacterium tuberculosis<\/i>\n                    among South African Gold Miners"],"prefix":"10.1093","volume":"12","author":[{"given":"Barun","family":"Mathema","sequence":"first","affiliation":[{"name":"Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York"},{"name":"Tuberculosis Center, Public Health Research Institute, Newark, New Jersey"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James J.","family":"Lewis","sequence":"additional","affiliation":[{"name":"London School of Hygiene and Tropical Medicine, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy","family":"Connors","sequence":"additional","affiliation":[{"name":"Tuberculosis Center, Public Health Research Institute, Newark, New Jersey"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Violet N.","family":"Chihota","sequence":"additional","affiliation":[{"name":"Aurum Institute, Johannesburg, South Africa, and"},{"name":"School of Public Health, University of Witwatersrand, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Shashkina","sequence":"additional","affiliation":[{"name":"Tuberculosis Center, Public Health Research Institute, Newark, New Jersey"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minty","family":"van der Meulen","sequence":"additional","affiliation":[{"name":"Aurum Institute, Johannesburg, South Africa, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward A.","family":"Graviss","sequence":"additional","affiliation":[{"name":"Houston Methodist Research Institute, Houston, Texas; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ngan P.","family":"Ha","sequence":"additional","affiliation":[{"name":"Houston Methodist Research Institute, Houston, Texas; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barry N.","family":"Kreiswirth","sequence":"additional","affiliation":[{"name":"Tuberculosis Center, Public Health Research Institute, Newark, New Jersey"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alison D.","family":"Grant","sequence":"additional","affiliation":[{"name":"London School of Hygiene and Tropical Medicine, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine L.","family":"Fielding","sequence":"additional","affiliation":[{"name":"London School of Hygiene and Tropical Medicine, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan E.","family":"Dorman","sequence":"additional","affiliation":[{"name":"Johns Hopkins University School of Medicine, Baltimore, Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gavin J.","family":"Churchyard","sequence":"additional","affiliation":[{"name":"London School of Hygiene and Tropical Medicine, London, United Kingdom"},{"name":"Aurum Institute, Johannesburg, South Africa, and"},{"name":"School of Public Health, University of Witwatersrand, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,1,1]]},"reference":[{"key":"2026012303410920700_bib1","volume-title":"Global tuberculosis control: a short update to the 2009 report","author":"World Health Organization (WHO)","year":"2009"},{"key":"2026012303410920700_bib2","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1001\/archinte.163.9.1009","article-title":"The growing burden of tuberculosis: global trends and interactions with the HIV epidemic","volume":"163","author":"Corbett","year":"2003","journal-title":"Arch Intern Med"},{"key":"2026012303410920700_bib3","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1164\/rccm.200806-846OC","article-title":"HIV infection does not affect active case finding of tuberculosis in South African gold miners","volume":"180","author":"Lewis","year":"2009","journal-title":"Am J Respir Crit Care Med"},{"key":"2026012303410920700_bib4","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1097\/00002030-200012010-00016","article-title":"HIV infection and silicosis: the impact of two potent risk factors on the incidence of mycobacterial disease in South African miners","volume":"14","author":"Corbett","year":"2000","journal-title":"AIDS"},{"key":"2026012303410920700_bib5","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1086\/339540","article-title":"Morbidity and mortality in South African gold miners: impact of untreated disease due to human immunodeficiency virus","volume":"34","author":"Corbett","year":"2002","journal-title":"Clin Infect Dis"},{"key":"2026012303410920700_bib6","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1097\/QAD.0b013e3283097cfa","article-title":"Effects of duration of HIV infection and secondary tuberculosis transmission on tuberculosis incidence in the South African gold mines","volume":"22","author":"Glynn","year":"2008","journal-title":"AIDS"},{"key":"2026012303410920700_bib7","doi-asserted-by":"crossref","first-page":"2321","DOI":"10.1001\/jama.282.24.2321","article-title":"Identification of a W variant outbreak of Mycobacterium tuberculosis via population-based molecular epidemiology","volume":"282","author":"Bifani","year":"1999","journal-title":"JAMA"},{"key":"2026012303410920700_bib8","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1093\/clinids\/24.1.35","article-title":"Retrospective detection of laboratory cross-contamination of Mycobacterium tuberculosis cultures with use of DNA fingerprint analysis","volume":"24","author":"Braden","year":"1997","journal-title":"Clin Infect Dis"},{"key":"2026012303410920700_bib9","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1086\/339345","article-title":"Identification and evolution of an IS6110 low-copy-number Mycobacterium tuberculosis cluster","volume":"185","author":"Mathema","year":"2002","journal-title":"J Infect Dis"},{"key":"2026012303410920700_bib10","doi-asserted-by":"crossref","first-page":"e1000034","DOI":"10.1371\/journal.ppat.1000034","article-title":"The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis","volume":"4","author":"Caws","year":"2008","journal-title":"PLoS Pathog"},{"key":"2026012303410920700_bib11","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1016\/S0140-6736(00)02730-6","article-title":"Tuberculosis control and molecular epidemiology in a South African gold-mining community","volume":"356","author":"Godfrey-Faussett","year":"2000","journal-title":"Lancet"},{"key":"2026012303410920700_bib12","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1086\/605930","article-title":"Molecular epidemiology of Mycobacterium tuberculosis in a South African community with high HIV prevalence","volume":"200","author":"Middelkoop","year":"2009","journal-title":"J Infect Dis"},{"key":"2026012303410920700_bib13","doi-asserted-by":"crossref","first-page":"1687","DOI":"10.1016\/S0140-6736(01)06712-5","article-title":"HIV-1 and recurrence, relapse, and reinfection of tuberculosis after cure: a cohort study in South African mineworkers","volume":"358","author":"Sonnenberg","year":"2001","journal-title":"Lancet"},{"key":"2026012303410920700_bib14","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1128\/JCM.42.2.891-894.2004","article-title":"Genotypic and phenotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from rural districts of the Western Cape Province of South Africa","volume":"42","author":"Streicher","year":"2004","journal-title":"J Clin Microbiol"},{"key":"2026012303410920700_bib15","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1056\/NEJM199910143411602","article-title":"Exogenous reinfection as a cause of recurrent tuberculosis after curative treatment","volume":"341","author":"van Rie","year":"1999","journal-title":"N Engl J Med"},{"key":"2026012303410920700_bib16","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":"Churchyard","year":"2014","journal-title":"N Engl J Med"},{"key":"2026012303410920700_bib17","first-page":"1024","article-title":"Liquid vs. solid culture for tuberculosis: performance and cost in a resource-constrained setting","volume":"14","author":"Chihota","year":"2010","journal-title":"Int J Tuberc Lung Dis"},{"key":"2026012303410920700_bib18","volume-title":"Public health mycobacteriology: a guide for the level III laboratory","author":"Kent","year":"1985"},{"key":"2026012303410920700_bib19","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1128\/jcm.31.2.406-409.1993","article-title":"Strain identification of Mycobacterium tuberculosis DNA by DNA fingerprinting: recommendations for a standardized methodology","volume":"31","author":"van Embden","year":"1993","journal-title":"J Clin Microbiol"},{"key":"2026012303410920700_bib20","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/1471-2180-6-23","article-title":"Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology","volume":"6","author":"Brudey","year":"2006","journal-title":"BMC Microbiol"},{"key":"2026012303410920700_bib21","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1128\/jcm.35.4.907-914.1997","article-title":"Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology","volume":"35","author":"Kamerbeek","year":"1997","journal-title":"J Clin Microbiol"},{"key":"2026012303410920700_bib22","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1086\/498574","article-title":"Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites","volume":"193","author":"Gutacker","year":"2006","journal-title":"J Infect Dis"},{"key":"2026012303410920700_bib23","doi-asserted-by":"crossref","first-page":"1703","DOI":"10.1056\/NEJM199406163302402","article-title":"The epidemiology of tuberculosis in San Francisco: a population-based study using conventional and molecular methods","volume":"330","author":"Small","year":"1994","journal-title":"N Engl J Med"},{"key":"2026012303410920700_bib24","first-page":"1001","article-title":"Historic and recent events contribute to the disease dynamics of Beijing-like Mycobacterium tuberculosis isolates in a high incidence region","volume":"6","author":"Richardson","year":"2002","journal-title":"Int J Tuberc Lung Dis"},{"key":"2026012303410920700_bib25","first-page":"311","article-title":"Predominance of a single genotype of Mycobacterium tuberculosis in regions of Southern Africa","volume":"11","author":"Chihota","year":"2007","journal-title":"Int J Tuberc Lung Dis"},{"key":"2026012303410920700_bib26","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":"Gandhi","year":"2013","journal-title":"J Infect Dis"},{"key":"2026012303410920700_bib27","first-page":"99","article-title":"Genotypic diversity of extensively drug-resistant tuberculosis (XDR-TB) in South Africa","volume":"12","author":"Mlambo","year":"2008","journal-title":"Int J Tuberc Lung Dis"},{"key":"2026012303410920700_bib28","doi-asserted-by":"crossref","first-page":"5779","DOI":"10.1128\/JCM.43.11.5779-5781.2005","article-title":"Distribution of strain families of Mycobacterium tuberculosis causing pulmonary and extrapulmonary disease in hospitalized children in Cape Town, South Africa","volume":"43","author":"Nicol","year":"2005","journal-title":"J Clin Microbiol"},{"key":"2026012303410920700_bib29","doi-asserted-by":"crossref","first-page":"5774","DOI":"10.1128\/JCM.42.12.5774-5782.2004","article-title":"Clonal expansion of a globally disseminated lineage of Mycobacterium tuberculosis with low IS6110 copy numbers","volume":"42","author":"Warren","year":"2004","journal-title":"J Clin Microbiol"},{"key":"2026012303410920700_bib30","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.3201\/eid1407.060468","article-title":"Determinants of cluster size in large, population-based molecular epidemiology study of tuberculosis, northern Malawi","volume":"14","author":"Glynn","year":"2008","journal-title":"Emerg Infect Dis"},{"key":"2026012303410920700_bib31","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1093\/ije\/dyh021","article-title":"Transmission of tuberculosis in a high incidence urban community in South Africa","volume":"33","author":"Verver","year":"2004","journal-title":"Int J Epidemiol"},{"key":"2026012303410920700_bib32","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1002\/ajim.20716","article-title":"Oscillating migration and the epidemics of silicosis, tuberculosis, and HIV infection in South African gold miners","volume":"53","author":"Rees","year":"2010","journal-title":"Am J Ind Med"},{"key":"2026012303410920700_bib33","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":"Pillay","year":"2007","journal-title":"Clin Infect Dis"},{"key":"2026012303410920700_bib34","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/j.tube.2007.05.010","article-title":"The role of IS6110 in the evolution of Mycobacterium tuberculosis","volume":"87","author":"McEvoy","year":"2007","journal-title":"Tuberculosis (Edinb)"},{"key":"2026012303410920700_bib35","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.tube.2008.09.003","article-title":"Changing Mycobacterium tuberculosis population highlights clade-specific pathogenic characteristics","volume":"89","author":"van der Spuy","year":"2009","journal-title":"Tuberculosis (Edinb)"},{"key":"2026012303410920700_bib36","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1128\/JCM.42.2.769-772.2004","article-title":"Molecular characteristics and global spread of Mycobacterium tuberculosis with a Western Cape F11 genotype","volume":"42","author":"Victor","year":"2004","journal-title":"J Clin Microbiol"},{"key":"2026012303410920700_bib37","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/S0966-842X(01)02277-6","article-title":"Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains","volume":"10","author":"Bifani","year":"2002","journal-title":"Trends Microbiol"},{"key":"2026012303410920700_bib38","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.1086\/592575","article-title":"Recent and rapid emergence of W-Beijing strains of Mycobacterium tuberculosis in Cape Town, South Africa","volume":"47","author":"Cowley","year":"2008","journal-title":"Clin Infect Dis"},{"key":"2026012303410920700_bib39","first-page":"195","article-title":"Spread of an emerging Mycobacterium tuberculosis drug-resistant strain in the Western Cape of South Africa","volume":"11","author":"Victor","year":"2007","journal-title":"Int J Tuberc Lung Dis"},{"key":"2026012303410920700_bib40","doi-asserted-by":"crossref","first-page":"e19548","DOI":"10.1371\/journal.pone.0019548","article-title":"Transmission pattern of drug-resistant tuberculosis and its implication for tuberculosis control in eastern rural China","volume":"6","author":"Hu","year":"2011","journal-title":"PLoS ONE"},{"key":"2026012303410920700_bib41","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1093\/aje\/155.6.565","article-title":"Methodological problems in the molecular epidemiology of tuberculosis","volume":"155","author":"Murray","year":"2002","journal-title":"Am J Epidemiol"},{"key":"2026012303410920700_bib42","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1017\/S095026880100499X","article-title":"The effect of age and study duration on the relationship between \u2018clustering\u2019 of DNA fingerprint patterns and the proportion of tuberculosis disease attributable to recent transmission","volume":"126","author":"Vynnycky","year":"2001","journal-title":"Epidemiol Infect"},{"key":"2026012303410920700_bib43","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1128\/CMR.00061-05","article-title":"Molecular epidemiology of tuberculosis: current insights","volume":"19","author":"Mathema","year":"2006","journal-title":"Clin Microbiol Rev"},{"key":"2026012303410920700_bib44","article-title":"Community-wide isoniazid preventive therapy among gold miners in South Africa: the Thibela TB study","author":"Chihota","year":"2012"},{"key":"2026012303410920700_bib45","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1017\/S0950268806007278","article-title":"Molecular epidemiology of tuberculosis after declining incidence, New York City, 2001-2003","volume":"135","author":"Driver","year":"2007","journal-title":"Epidemiol Infect"},{"key":"2026012303410920700_bib46","doi-asserted-by":"crossref","first-page":"524","DOI":"10.2105\/AJPH.2009.175646","article-title":"Mining and risk of tuberculosis in sub-Saharan Africa","volume":"101","author":"Stuckler","year":"2011","journal-title":"Am J Public Health"},{"key":"2026012303410920700_bib47","doi-asserted-by":"crossref","first-page":"967","DOI":"10.5588\/ijtld.11.0122","article-title":"Trends in drug-resistant tuberculosis in a gold-mining workforce in South Africa, 2002-2008","volume":"16","author":"van Halsema","year":"2012","journal-title":"Int J Tuberc Lung Dis"},{"key":"2026012303410920700_bib48","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1056\/NEJMe1105555","article-title":"What is thwarting tuberculosis prevention in high-burden settings?","volume":"365","author":"Nardell","year":"2011","journal-title":"N Engl J Med"},{"key":"2026012303410920700_bib49","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1056\/NEJMoa1003176","article-title":"Whole-genome sequencing and social-network analysis of a tuberculosis outbreak","volume":"364","author":"Gardy","year":"2011","journal-title":"N Engl J Med"}],"container-title":["Annals of the American Thoracic Society"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/annalsats\/article-pdf\/12\/1\/12\/66548523\/annalsats_12_1_12.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/annalsats\/article-pdf\/12\/1\/12\/66548523\/annalsats_12_1_12.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T08:41:28Z","timestamp":1769157688000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/annalsats\/article\/12\/1\/12\/8429472"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,1,1]]},"references-count":49,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2015,1,1]]},"published-print":{"date-parts":[[2015,1,1]]}},"URL":"https:\/\/doi.org\/10.1513\/annalsats.201404-150oc","relation":{},"ISSN":["2329-6933","2325-6621"],"issn-type":[{"value":"2329-6933","type":"print"},{"value":"2325-6621","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2015,1]]},"published":{"date-parts":[[2015,1,1]]}}}