{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T01:51:26Z","timestamp":1774317086860,"version":"3.50.1"},"reference-count":30,"publisher":"AOSIS","issue":"1","license":[{"start":{"date-parts":[[2023,2,6]],"date-time":"2023-02-06T00:00:00Z","timestamp":1675641600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Afr. J. Lab. Med."],"abstract":"<jats:p>Background:\u00a0Rifampicin resistance missed by commercial rapid molecular assays but detected by phenotypic assays may lead to discordant susceptibility results and affect patient management.Objective:\u00a0This study was conducted to evaluate the causes of rifampicin resistance missed by the GenoType MTBDRplus\u00a0and its impact on the programmatic management of tuberculosis in KwaZulu-Natal, South Africa.Methods:\u00a0We analysed routine tuberculosis programme data from January 2014 to December 2014 on isolates showing rifampicin susceptibility on the GenoType MTBDRplus\u00a0assay but resistance on the phenotypic agar proportion method. Whole-genome sequencing was performed on a subset of these isolates.Results:\u00a0Out of 505 patients with isoniazid mono-resistant tuberculosis on the MTBDRplus, 145 (28.7%) isolates showed both isoniazid and rifampicin resistance on the phenotypic assay. The mean time from MTBDRplus\u00a0results to initiation of drug-resistant tuberculosis therapy was 93.7 days. 65.7% of the patients had received previous tuberculosis treatment. The most common mutations detected in the 36 sequenced isolates were I491F (16; 44.4%) and L452P (12; 33.3%). Among the 36 isolates, resistance to other anti-tuberculosis drugs was 69.4% for pyrazinamide, 83.3% for ethambutol, 69.4% for streptomycin, and 50% for ethionamide.Conclusion:\u00a0Missed rifampicin resistance was mostly due to the I491F mutation located outside the MTBDRplus\u00a0detection area and the L452P mutation, which was not included in the initial version 2 of the MTBDRplus. This led to substantial delays in the initiation of appropriate therapy. The previous tuberculosis treatment history and the high level of resistance to other anti-tuberculosis drugs suggest an accumulation of resistance.\u00a0<\/jats:p>","DOI":"10.4102\/ajlm.v12i1.1975","type":"journal-article","created":{"date-parts":[[2023,2,3]],"date-time":"2023-02-03T11:07:07Z","timestamp":1675422427000},"source":"Crossref","is-referenced-by-count":13,"title":["Consequences of rpoB mutations missed by the GenoType MTBDRplus assay in a programmatic setting in South Africa"],"prefix":"10.4102","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6037-9679","authenticated-orcid":false,"given":"Nomonde R.","family":"Mvelase","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2148-7439","authenticated-orcid":false,"given":"Lindiwe P.","family":"Cele","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0407-4635","authenticated-orcid":false,"given":"Ravesh","family":"Singh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9040-963X","authenticated-orcid":false,"given":"Yeshnee","family":"Naidoo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2944-4583","authenticated-orcid":false,"given":"Jennifer","family":"Giandhari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2503-9441","authenticated-orcid":false,"given":"Eduan","family":"Wilkinson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3027-5254","authenticated-orcid":false,"given":"Tulio","family":"De Oliveira","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4574-6258","authenticated-orcid":false,"given":"Khine","family":"Swe Swe-Han","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8436-3268","authenticated-orcid":false,"given":"Koleka P.","family":"Mlisana","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2580","published-online":{"date-parts":[[2023,2,6]]},"reference":[{"key":"ref0","unstructured":"WHO. WHO operational handbook on tuberculosis. Module 3: Diagnosis - Rapid diagnostics for tuberculosis detention, 2021 update. Geneva: World Health Organization; 2021."},{"key":"ref1","unstructured":"WHO. Molecular line probe assays for rapid screening of patients at risk of multidrug-resistant tuberculosis (MDR-TB). Geneva: World Health Organization; 2008."},{"key":"ref2","unstructured":"WHO. Automated real-time nucleic acid amplification technology for rapid and simultaneous detection of tuberculosis and rifampicin resistance: Xpert MTB\/RIF system. Policy statement. Geneva: World Health Organization; 2011."},{"key":"ref3","doi-asserted-by":"publisher","unstructured":"Andre E, Goeminne L, Cabibbe A, et al. Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria. Clin Microbiol Infect. 2017;23(3):167-172. https:\/\/doi.org\/10.1016\/j.cmi.2016.09.006","DOI":"10.1016\/j.cmi.2016.09.006"},{"key":"ref4","doi-asserted-by":"publisher","unstructured":"Telenti A, Imboden P. Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis. Lancet. 1993;341(8846):647-650. https:\/\/doi.org\/10.1016\/0140-6736(93)90417-F","DOI":"10.1016\/0140-6736(93)90417-F"},{"key":"ref5","doi-asserted-by":"publisher","unstructured":"Ng KCS, Supply P, Cobelens FGJ, et al. How well do routine molecular diagnostics detect rifampin heteroresistance in Mycobacterium tuberculosis? J Clin Microbiol. 2019;57(11):e00717-e00719. https:\/\/doi.org\/10.1128\/JCM.00717-19","DOI":"10.1128\/JCM.00717-19"},{"key":"ref6","doi-asserted-by":"publisher","unstructured":"Siu GKH, Zhang Y, Lau TCK, et al. Mutations outside the rifampicin resistance-determining region associated with rifampicin resistance in Mycobacterium tuberculosis. J Antimicrob Chemother. 2011;66(4):730-733. https:\/\/doi.org\/10.1093\/jac\/dkq519","DOI":"10.1093\/jac\/dkq519"},{"key":"ref7","doi-asserted-by":"publisher","unstructured":"Heep M, Brandst\u00e4tter B, Rieger U, et al. Frequency of rpoB mutations inside and outside the cluster I region in rifampin-resistant clinical Mycobacterium tuberculosis isolates. J Clin Microbiol. 2001;39(1):107-110. https:\/\/doi.org\/10.1128\/JCM.39.1.107-110.2001","DOI":"10.1128\/JCM.39.1.107-110.2001"},{"key":"ref8","doi-asserted-by":"publisher","unstructured":"Sanchez-Padilla E, Merker M, Beckert P, et al. Detection of drug-resistant tuberculosis by Xpert MTB\/RIF in Swaziland. N Engl J Med. 2015;372:1181-1182. https:\/\/doi.org\/10.1056\/NEJMc1413930","DOI":"10.1056\/NEJMc1413930"},{"key":"ref9","doi-asserted-by":"publisher","unstructured":"Makhado NA, Matabane E, Faccin M, et al. Outbreak of multidrug-resistant tuberculosis in South Africa undetected by WHO-endorsed commercial tests: An observational study. Lancet Infect Dis. 2018;18(12):1350-1359. https:\/\/doi.org\/10.1016\/S1473-3099(18)30496-1","DOI":"10.1016\/S1473-3099(18)30496-1"},{"key":"ref10","doi-asserted-by":"publisher","unstructured":"Van Deun A, Barrera L, Bastian I, et al. Mycobacterium tuberculosis strains with highly discordant rifampin susceptibility test results. J Clin Microbiol. 2009;47(11):3501-3506. https:\/\/doi.org\/10.1128\/JCM.01209-09","DOI":"10.1128\/JCM.01209-09"},{"key":"ref11","doi-asserted-by":"publisher","unstructured":"Torrea G, Ng KCS, Van Deun A, et al. Variable ability of rapid tests to detect Mycobacterium tuberculosis rpoB mutations conferring phenotypically occult rifampicin resistance. Sci Rep. 2019;9:11826. https:\/\/doi.org\/10.1038\/s41598-019-48401-z","DOI":"10.1038\/s41598-019-48401-z"},{"key":"ref12","unstructured":"NICD. Microbiologically confirmed tuberculosis 2004-15 South Africa. Johannesburg: National Institute for Communicable Diseases; 2017."},{"key":"ref13","unstructured":"Lifescience H. GenoType MTBDRplus VER 2.0: Molecular genetic assay for identification of the M. tuberculosis complex and its resistance to rifampicin and isoniazid from clinical specimens and cultivated samples. 2015; Nehren, Germany: Hain Lifescience."},{"key":"ref14","unstructured":"Woods GL, Brown-Elliott BA, Conville PS, et al. CLSI standards: Guidelines for health care excellence. Susceptibility testing of mycobacteria, nocardiae, and other aerobic actinomycetes. Wayne, PA: Clinical and Laboratory Standards Institute; 2011."},{"key":"ref15","doi-asserted-by":"publisher","unstructured":"Schleusener V, K\u00f6ser CU, Beckert P, Niemann S, Feuerriegel S. Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: Comparison of automated analysis tools. Sci Rep. 2017;7:46327. https:\/\/doi.org\/10.1038\/srep46327","DOI":"10.1038\/srep46327"},{"key":"ref16","unstructured":"WHO. Meeting report of the WHO expert consultation on drug-resistant tuberculosis treatment outcome definitions, 17-19 November 2020. Geneva: World Health Organization; 2021."},{"key":"ref17","doi-asserted-by":"publisher","unstructured":"Huang WL, Chen HY, Kuo YM, Jou R. Performance assessment of the GenoType MTBDRplus test and DNA sequencing in detection of multidrug-resistant Mycobacterium tuberculosis. J Clin Microbiol. 2009;47(8):2520-2524. https:\/\/doi.org\/10.1128\/JCM.02499-08","DOI":"10.1128\/JCM.02499-08"},{"key":"ref18","doi-asserted-by":"publisher","unstructured":"K\u00f6ser CU, Georghiou SB, Sch\u00f6n T, Salfinger M. On the consequences of poorly defined breakpoints for rifampin susceptibility testing of Mycobacterium tuberculosis complex. J Clin Microbiol. 2021;59(4):e02328-20. https:\/\/doi.org\/10.1128\/JCM.02328-20","DOI":"10.1128\/JCM.02328-20"},{"key":"ref19","doi-asserted-by":"publisher","unstructured":"Shea J, Halse TA, Kohlerschmidt D, et al. Low-level rifampin resistance and rpoB mutations in Mycobacterium tuberculosis: An analysis of whole-genome sequencing and drug susceptibility test data in New York. J Clin Microbiol. 2021;59:e01885-20. https:\/\/doi.org\/10.1128\/JCM.01885-20","DOI":"10.1128\/JCM.01885-20"},{"key":"ref20","doi-asserted-by":"publisher","unstructured":"Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE 3rd, et al. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nat Genet. 2017;49:395-402. https:\/\/doi.org\/10.1038\/ng.3767","DOI":"10.1038\/ng.3767"},{"key":"ref21","doi-asserted-by":"publisher","unstructured":"Cohen KA, Abeel T, Manson McGuire A, et al. Evolution of extensively drug-resistant tuberculosis over four decades: Whole genome sequencing and dating analysis of Mycobacterium tuberculosis isolates from KwaZulu-Natal. PLoS Med. 2015;12:e1001880. https:\/\/doi.org\/10.1371\/journal.pmed.1001880","DOI":"10.1371\/journal.pmed.1001880"},{"key":"ref22","doi-asserted-by":"publisher","unstructured":"Gegia M, Winters N, Benedetti A, Van Soolingen D, Menzies D. Treatment of isoniazid-resistant tuberculosis with first-line drugs: A systematic review and meta-analysis. Lancet Infect Dis. 2017;17(2):223-234. https:\/\/doi.org\/10.1016\/S1473-3099(16)30407-8","DOI":"10.1016\/S1473-3099(16)30407-8"},{"key":"ref23","doi-asserted-by":"publisher","unstructured":"Gandhi NR, Moll A, Sturm AW, et al. Extensively drug-resistant tuberculosis as a cause of death in patients co-infected with tuberculosis and HIV in a rural area of South Africa. Lancet. 2006;368(9547):1575-1580. https:\/\/doi.org\/10.1016\/S0140-6736(06)69573-1","DOI":"10.1016\/S0140-6736(06)69573-1"},{"key":"ref24","doi-asserted-by":"publisher","unstructured":"Pillay M, Sturm AW. Evolution of the extensively drug-resistant F15\/LAM4\/KZN strain of Mycobacterium tuberculosis in KwaZulu-Natal, South Africa. Clin Infect Dis. 2007;45:1409-1414. https:\/\/doi.org\/10.1086\/522987","DOI":"10.1086\/522987"},{"key":"ref25","unstructured":"WHO. The use of next-generation sequencing technologies for the detection of mutations associated with drug resistance in Mycobacterium tuberculosis complex: Technical guide. Geneva: World Health Organization; 2018."},{"key":"ref26","doi-asserted-by":"publisher","unstructured":"Sch\u00f6n T, Jur\u00e9en P, Giske CG, et al. Evaluation of wild-type MIC distributions as a tool for determination of clinical breakpoints for Mycobacterium tuberculosis. J Antimicrob Chemother. 2009;64(4):786-793. https:\/\/doi.org\/10.1093\/jac\/dkp262","DOI":"10.1093\/jac\/dkp262"},{"key":"ref27","doi-asserted-by":"publisher","unstructured":"Zhang Y, Permar S, Sun Z. Conditions that may affect the results of susceptibility testing of Mycobacterium tuberculosis to pyrazinamide. J Med Microbiol. 2002;51(1):42-49. https:\/\/doi.org\/10.1099\/0022-1317-51-1-42","DOI":"10.1099\/0022-1317-51-1-42"},{"key":"ref28","doi-asserted-by":"publisher","unstructured":"Werngren J, Stureg\u00e5rd E, Jur\u00e9en P, \u00c4ngeby K, Hoffner S, Sch\u00f6n T. Reevaluation of the critical concentration for drug susceptibility testing of Mycobacterium tuberculosis against pyrazinamide using wild-type MIC distributions and pncA gene sequencing. Antimicrob Agents Chemother. 2012;56(3):1253-1257. https:\/\/doi.org\/10.1128\/AAC.05894-11","DOI":"10.1128\/AAC.05894-11"},{"key":"ref29","doi-asserted-by":"publisher","unstructured":"Gandhi NR, Brust JCM, Moodley P, et al. Minimal diversity of drug-resistant Mycobacterium tuberculosis strains, South Africa. 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