{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,11]],"date-time":"2026-10-11T13:42:05Z","timestamp":1791726125617,"version":"4.3.4"},"reference-count":31,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T00:00:00Z","timestamp":1752537600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"H2020 European Research Council","doi-asserted-by":"publisher","award":["Grant agreement ID: 883582"],"award-info":[{"award-number":["Grant agreement ID: 883582"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:sec id=\"sec020\">\n<jats:title>Introduction<\/jats:title>\n<jats:p>Resistance to bedaquiline \u2013 a novel, promising medication against tuberculosis (TB), is already emerging, and uncertainties regarding the role of the different resistance-conferring mutations complicate the development of molecular diagnostic tools for detecting resistance. Mutations in the three genes <jats:italic>atpE, pepQ, and Rv0678<\/jats:italic> have been associated with increased minimum inhibitory concentrations (MICs) to bedaquiline in <jats:italic>Mycobacterium tuberculosis<\/jats:italic> (Mtb). Here, we studied the effect of known and novel mutations in these genes on the phenotypic susceptibility to bedaquiline in Mtb isolates from patients with drug-resistant TB in the country of Georgia.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec021\">\n<jats:title>Methods<\/jats:title>\n<jats:p>We used retrospective Mtb isolates (2011\u20132019) with whole-genome sequencing data, and prospectively collected diagnostic isolates with phenotypic resistance (2019\u20132022) to bedaquiline at the Georgian National Reference Laboratory. We determined bedaquiline MIC values using the Sensititre<jats:sup>TM<\/jats:sup> MYCOTB MIC plate. MIC of 0.12 \u03bcg\/mL was defined as borderline and MIC\u2009\u2265\u20090.25 \u03bcg\/mL as a resistant isolate. A phylogeny was inferred to assess the likely role of the identified variants in bedaquiline resistance, while taking into consideration population structure of the strains analyzed.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec022\">\n<jats:title>Results<\/jats:title>\n<jats:p>We analyzed a total of 69 Mtb isolates and identified 61 mutations across the three target genes. Seventeen (27.8%) of these variants were associated with borderline (0.12 \u03bcg\/mL) or resistant (\u22650.25 \u03bcg\/mL) MICs to bedaquiline. In addition to six previously described bedaquiline resistance-conferring mutations in <jats:italic>atpE<\/jats:italic> and <jats:italic>Rv0678<\/jats:italic>, we identified two novel variants in <jats:italic>Rv0678<\/jats:italic> (Leu95Ser and Ile108fs) likely involved in bedaquiline resistance. We found a Tyr92Cys mutation in <jats:italic>Rv0678<\/jats:italic> in two epidemiologically linked isolates, which likely emerged as a consequence of previous exposure to clofazimine.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec023\">\n<jats:title>Conclusion<\/jats:title>\n<jats:p>Consistent with previous reports, our study confirms that mutations in <jats:italic>Rv0678<\/jats:italic> are the most frequent cause of bedaquiline resistance in Georgia, in addition to an increasing clinical relevance of mutations in <jats:italic>atpE<\/jats:italic>, while the role of <jats:italic>pepQ<\/jats:italic> mutations remains to be defined.<\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pone.0326794","type":"journal-article","created":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T17:36:36Z","timestamp":1752600996000},"page":"e0326794","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Linking genetic and phenotypic bedaquiline resistance in Mycobacterium tuberculosis strains from Georgia"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1227-1900","authenticated-orcid":true,"given":"Nino","family":"Maghradze","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chlo\u00e9","family":"Loiseau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Galo Adrian","family":"Goig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nino","family":"Bablishvili","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Levan","family":"Jugheli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonia","family":"Borrell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nestani","family":"Tukvadze","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7188-4996","authenticated-orcid":true,"given":"Russell Ryan","family":"Kempker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zaza","family":"Avaliani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7783-9048","authenticated-orcid":true,"given":"Sebastien","family":"Gagneux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,7,15]]},"reference":[{"issue":"5707","key":"pone.0326794.ref001","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1126\/science.1106753","article-title":"A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis","volume":"307","author":"K Andries","year":"2005","journal-title":"Science"},{"key":"pone.0326794.ref002","doi-asserted-by":"crossref","first-page":"106336","DOI":"10.1016\/j.phrs.2022.106336","article-title":"Bedaquiline and Linezolid improve anti-TB treatment outcome in drug-resistant TB patients with HIV: A systematic review and meta-analysis","volume":"182","author":"Y Wu","year":"2022","journal-title":"Pharmacol Res"},{"key":"pone.0326794.ref003","first-page":"54","volume-title":"The use of bedaquiline in the treatment of multidrug-resistant tuberculosis: interim policy guidance [Internet","author":"World Health Organization","year":"2013"},{"issue":"3","key":"pone.0326794.ref004","first-page":"684","article-title":"Unexpected high prevalence of resistance-associated Rv0678 variants in MDR-TB patients without documented prior use of clofazimine or bedaquiline","volume":"72","author":"C Villellas","year":"2017","journal-title":"J Antimicrob Chemother"},{"issue":"11","key":"pone.0326794.ref005","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.01304-20","article-title":"Characterization of genomic variants associated with resistance to bedaquiline and delamanid in naive Mycobacterium tuberculosis clinical strains","volume":"58","author":"S Battaglia","year":"2020","journal-title":"J Clin Microbiol"},{"key":"pone.0326794.ref006","article-title":"Frequent acquisition of bedaquiline resistance by epidemic extensively drug-resistant Mycobacterium tuberculosis strains in Russia during long-term treatment","author":"I Mokrousov","year":"2020","journal-title":"Clin Microbiol Infect [Internet]."},{"key":"pone.0326794.ref007","author":"GA Goig","year":"2024"},{"issue":"4","key":"pone.0326794.ref008","article-title":"Re-Understanding the Mechanisms of Action of the Anti-Mycobacterial Drug Bedaquiline. 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