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Whole genome sequencing (WGS) of <jats:italic>M. tuberculosis<\/jats:italic> is being used to infer lineages (strain-types), drug resistance mutations, and transmission patterns\u2014all informing infection control and clinical decision making. Here we analyse WGS data on 535\u00a0<jats:italic>M. tuberculosis<\/jats:italic> isolates sourced across Pakistan between years 2003 and 2020, to understand the circulating strain-types and mutations related to 12 anti-TB drugs, as well as identify transmission clusters. Most isolates belonged to lineage 3 (n\u2009=\u2009397; 74.2%) strain-types, and were MDR (n\u2009=\u2009328; 61.3%) and (pre-)XDR (n\u2009=\u2009113; 21.1%). By inferring close genomic relatedness between isolates (&lt;\u200910-SNPs difference), there was evidence of <jats:italic>M. tuberculosis<\/jats:italic> transmission, with 55 clusters formed consisting of a total of 169 isolates. Three clusters consist of <jats:italic>M. tuberculosis<\/jats:italic> that are similar to isolates found outside of Pakistan. A genome-wide association analysis comparing \u2018transmitted\u2019 and \u2018non-transmitted\u2019 isolate groups, revealed the <jats:italic>nusG<\/jats:italic> gene as most significantly associated with a potential transmissible phenotype (P\u2009=\u20095.8\u2009\u00d7\u200910<jats:sup>\u201310<\/jats:sup>). Overall, our study provides important insights into <jats:italic>M. tuberculosis<\/jats:italic> genetic diversity and transmission in Pakistan, including providing information on circulating drug resistance mutations for monitoring activities and clinical decision making. <\/jats:p>","DOI":"10.1038\/s41598-022-11795-4","type":"journal-article","created":{"date-parts":[[2022,5,11]],"date-time":"2022-05-11T10:09:32Z","timestamp":1652263772000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Characterisation of drug-resistant Mycobacterium tuberculosis mutations and transmission in Pakistan"],"prefix":"10.1038","volume":"12","author":[{"given":"Gary","family":"Napier","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anwar Sheed","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdul","family":"Jabbar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Tahir","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sajid","family":"Ali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Qasim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noor","family":"Mohammad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rumina","family":"Hasan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zahra","family":"Hasan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susana","family":"Campino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sajjad","family":"Ahmad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baharullah","family":"Khattak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon J.","family":"Waddell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taj Ali","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jody E.","family":"Phelan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taane G.","family":"Clark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,5,11]]},"reference":[{"key":"11795_CR1","unstructured":"World Health Organization (WHO). 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