{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T11:23:26Z","timestamp":1785583406640,"version":"3.56.0"},"reference-count":47,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2022,8,5]],"date-time":"2022-08-05T00:00:00Z","timestamp":1659657600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:sec id=\"sec001\">\n<jats:title>Background<\/jats:title>\n<jats:p>Ethiopia is one of the high multidrug-resistant tuberculosis (MDR-TB) burden countries. However, phenotypic drug susceptibility testing can take several weeks due to the slow growth of <jats:italic>Mycobacterium tuberculosis<\/jats:italic> complex (MTBC) strains. In this study, we assessed the performance of a Sanger sequencing approach to predict resistance against five anti-tuberculosis drugs and the pattern of resistance mediating mutations.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec002\">\n<jats:title>Methods<\/jats:title>\n<jats:p>We enrolled 226 MTBC culture-positive MDR-TB suspects and collected sputum specimens and socio-demographic and TB related data from each suspect between June 2015 and December 2016 in Addis Ababa, Ethiopia. Phenotypic drug susceptibility testing (pDST) for rifampicin, isoniazid, pyrazinamide, ethambutol, and streptomycin using BACTEC MGIT 960 was compared with the results of a Sanger sequencing analysis of seven resistance determining regions in the genes <jats:italic>rpoB<\/jats:italic>, <jats:italic>katG<\/jats:italic>, <jats:italic>fabG-inhA<\/jats:italic>, <jats:italic>pncA<\/jats:italic>, <jats:italic>embB<\/jats:italic>, <jats:italic>rpsL<\/jats:italic>, <jats:italic>and rrs<\/jats:italic>.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec003\">\n<jats:title>Result<\/jats:title>\n<jats:p>DNA isolation for Sanger sequencing was successfully extracted from 92.5% (209\/226) of the MTBC positive cultures, and the remaining 7.5% (17\/226) <jats:italic>strains<\/jats:italic> were excluded from the final analysis. Based on pDST results, drug resistance proportions were as follows: isoniazid: 109\/209 (52.2%), streptomycin: 93\/209 (44.5%), rifampicin: 88\/209 (42.1%), ethambutol: 74\/209 (35.4%), and pyrazinamide: 69\/209 (33.0%). Resistance against isoniazid was mainly mediated by the mutation <jats:italic>katG<\/jats:italic> S315T (97\/209, 46.4%) and resistance against rifampicin by <jats:italic>rpoB<\/jats:italic> S531L (58\/209, 27.8%). The dominating resistance-conferring mutations for ethambutol, streptomycin, and pyrazinamide affected codon 306 in <jats:italic>embB<\/jats:italic> (48\/209, 21.1%), codon 88 in <jats:italic>rpsL<\/jats:italic> (43\/209, 20.6%), and codon 65 in <jats:italic>pncA<\/jats:italic> (19\/209, 9.1%), respectively. We observed a high agreement between phenotypic and genotypic DST, such as 89.9% (at 95% confidence interval [CI], 84.2%\u201395.8%) for isoniazid, 95.5% (95% CI, 91.2%\u201399.8%) for rifampicin, 98.6% (95% CI, 95.9\u2013100%) for ethambutol, 91.3% (95% CI, 84.6\u201398.1%) for pyrazinamide and 57.0% (95% CI, 46.9%\u201367.1%) for streptomycin.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec004\">\n<jats:title>Conclusion<\/jats:title>\n<jats:p>We detected canonical mutations implicated in resistance to rifampicin, isoniazid, pyrazinamide, ethambutol, and streptomycin. High agreement with phenotypic DST results for all drugs renders Sanger sequencing promising to be performed as a complementary measure to routine phenotypic DST in Ethiopia. Sanger sequencing directly from sputum may accelerate accurate clinical decision-making in the future.<\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pone.0271508","type":"journal-article","created":{"date-parts":[[2022,8,5]],"date-time":"2022-08-05T17:38:56Z","timestamp":1659721136000},"page":"e0271508","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":10,"title":["Prediction of drug resistance by Sanger sequencing of Mycobacterium tuberculosis complex strains isolated from multidrug resistant tuberculosis suspect patients in Ethiopia"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4719-4709","authenticated-orcid":true,"given":"Eyob 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Adam","family":"Shuaib","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1633-8623","authenticated-orcid":true,"given":"Desalegn","family":"Addise","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Belay","family":"Tessema","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Niemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,8,5]]},"reference":[{"key":"pone.0271508.ref001","author":"World Health Organization","year":"2019"},{"issue":"1","key":"pone.0271508.ref002","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s40794-018-0065-5","article-title":"Epidemiology of multidrug-resistant tuberculosis (MDR-TB) in Ethiopia: a systematic review and meta-analysis of the 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