{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T14:33:45Z","timestamp":1781274825013,"version":"3.54.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T00:00:00Z","timestamp":1759968000000},"content-version":"vor","delay-in-days":36,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000272","name":"National Institute for Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018336","name":"Health Protection Research Unit","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100018336","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Healthcare Associated Infections and Antimicrobial Resistance"},{"DOI":"10.13039\/501100000769","name":"Oxford University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000769","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UK Health Security Agency","award":["NIHR200915"],"award-info":[{"award-number":["NIHR200915"]}]},{"name":"Oxford Biomedical Research Centre"},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/T008784\/1"],"award-info":[{"award-number":["BB\/T008784\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100030827","name":"NHS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100030827","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UKHSA"},{"DOI":"10.13039\/501100000276","name":"Department of Health and Social Care","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000276","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>WGS has become a key tool for diagnosing Mycobacterium tuberculosis infections, but discrepancies between genotypic and phenotypic drug susceptibility testing can hinder effective treatment and surveillance. This study investigated the impact of resistant subpopulations and compensatory mutations in WGS-based rifampicin resistance prediction.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Based on a dataset of 35\u200a538 clinical M. tuberculosis samples, the sensitivity and specificity of resistance classification were evaluated with and without considering subpopulations and compensatory mutations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>By lowering the fraction of reads required to identify a resistance-associated variant in a sample from 0.90 to 0.05, the sensitivity increased significantly from 94.3% to 96.4% without a significant impact on specificity. Allowing compensatory mutations to predict resistance further lowered the false negative rate. Finally, we found that samples with resistant subpopulations were less likely to be compensated than homogeneous resistant samples. Further analysis of these samples revealed distinct clusters with differing amounts of within-sample diversity, pointing towards different mechanisms of resistance acquisition, such as within-host evolution and secondary infections.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our results indicate that a substantial fraction of false negative calls in WGS-based rifampicin resistance prediction can be explained by masked resistant subpopulations. The genetic diversity within the heterogeneous samples is consistent with at least 28% of the rifampicin resistance arising from secondary infections.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jacamr\/dlaf175","type":"journal-article","created":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T11:38:58Z","timestamp":1758022738000},"source":"Crossref","is-referenced-by-count":5,"title":["Subpopulations in clinical samples of\n                    <i>M. tuberculosis<\/i>\n                    can give rise to rifampicin resistance and shed light on how resistance is acquired"],"prefix":"10.1093","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5167-9840","authenticated-orcid":false,"given":"Viktoria M","family":"Brunner","sequence":"first","affiliation":[{"name":"Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0912-4483","authenticated-orcid":false,"given":"Philip W","family":"Fowler","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]},{"name":"National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital , Oxford ,","place":["UK"]},{"name":"Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford , Oxford ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,10,9]]},"reference":[{"key":"2025120807214540700_dlaf175-B1","author":"World Health Organization"},{"key":"2025120807214540700_dlaf175-B2","author":"World Health Organization"},{"key":"2025120807214540700_dlaf175-B3","doi-asserted-by":"publisher","first-page":"4236","DOI":"10.1038\/srep04236","article-title":"Dramatic reduction of culture time of Mycobacterium tuberculosis","volume":"4","author":"Ghodbane","year":"2014","journal-title":"Sci Rep"},{"key":"2025120807214540700_dlaf175-B4","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/S2213-2600(15)00466-X","article-title":"Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study","volume":"4","author":"Pankhurst","year":"2016","journal-title":"Lancet Resp Med"},{"key":"2025120807214540700_dlaf175-B5","doi-asserted-by":"publisher","first-page":"2635","DOI":"10.1128\/JCM.00521-07","article-title":"Evaluation of the GenoType MTBDRplus assay for rifampin and isoniazid susceptibility testing of Mycobacterium tuberculosis strains and clinical specimens","volume":"45","author":"Hillemann","year":"2007","journal-title":"J Clin Micro"},{"key":"2025120807214540700_dlaf175-B6","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.cmi.2016.09.008","article-title":"Whole genome sequencing of Mycobacterium tuberculosis for detection of drug resistance: a systematic review","volume":"23","author":"Papaventsis","year":"2017","journal-title":"Clin Microbiol Infect"},{"key":"2025120807214540700_dlaf175-B7","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1038\/s41579-019-0214-5","article-title":"Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues","volume":"17","author":"Meehan","year":"2019","journal-title":"Nat Rev Microbiol"},{"key":"2025120807214540700_dlaf175-B8","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/S1473-3099(23)00498-X","article-title":"Emergence of bedaquiline-resistant tuberculosis and of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis strains with rpoB Ile491Phe mutation not detected by Xpert MTB\/RIF in Mozambique: a retrospective observational study","volume":"24","author":"Barilar","year":"2024","journal-title":"Lancet Infect Dis"},{"key":"2025120807214540700_dlaf175-B9","volume-title":"Catalogue of Mutations in Mycobacterium tuberculosis complex and Their Association with Drug Resistance,","author":"World Health Organization","year":"2023","edition":"2nd edn. 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