{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T10:34:29Z","timestamp":1776508469186,"version":"3.51.2"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T00:00:00Z","timestamp":1750118400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100000002","name":"US National Institutes of Health, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI147681"],"award-info":[{"award-number":["R01AI147681"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"US National Institutes of Health, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["K01AI182503"],"award-info":[{"award-number":["K01AI182503"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Whole genome sequence data can generate insights about Mycobacterium tuberculosis (Mtb) transmission. We used whole genome sequencing and linked epidemiology data from a recent randomized trial to characterize Mtb relatedness across 3 geographically distinct South African sites.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We sequenced culture isolates from participants with culture-positive tuberculosis in the Kharituwe study, which evaluated household contact investigation strategies in 1 urban and 2 rural sites. We adapted a previous bioinformatic pipeline to clean, extract, and filter Mtb reads; perform reference alignment; calculate single-nucleotide polymorphism (SNP) distances between isolates; and group isolates into clusters linked by recent transmission based on 3 SNP-based cutoffs. Sequence data were linked to individual data on demographics and risk factors. We analyzed clustering across and within study sites and used log-binomial regression to assess characteristics associated with clustering.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>At a cutoff of 12 SNPs, 213 of 714 sequenced isolates passing quality control filters were clustered. While only 3 of 45 pairs included participants from different sites, the majority of clusters with \u22654 participants included representation from at least 2 sites. Expanding to a 20-SNP cutoff revealed a large cluster containing 10% of isolates, with urban\/rural representation mirroring that of all the isolates (61% urban, 39% rural). Participants from the urban site, TB household contacts, and participants reporting a history of incarceration were more likely to be in a cluster.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Observed clustering and strain diversity across sites indicate the presence of multiple ongoing and geographically dispersed outbreaks in this setting.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/infdis\/jiaf326","type":"journal-article","created":{"date-parts":[[2025,6,27]],"date-time":"2025-06-27T09:02:17Z","timestamp":1751014937000},"page":"870-881","source":"Crossref","is-referenced-by-count":3,"title":["Molecular Epidemiology of <i>Mycobacterium tuberculosis<\/i> Across 3 Distinct Geographic Sites in South Africa"],"prefix":"10.1093","volume":"232","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3214-3228","authenticated-orcid":false,"given":"Theresa 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