{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T15:35:50Z","timestamp":1789659350115,"version":"4.0.1"},"reference-count":107,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T00:00:00Z","timestamp":1766361600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Universitas Padjadjaran through the University Assignment Research (Riset Penugasan Universitas, RPU) scheme"},{"name":"Unpad through the Indonesian Endowment Fund for Education","award":["4303\/B3\/DT.03.08\/2025"],"award-info":[{"award-number":["4303\/B3\/DT.03.08\/2025"]}]},{"name":"Unpad through the Indonesian Endowment Fund for Education","award":["3927\/UN6.RKT\/HK.07.00\/2025"],"award-info":[{"award-number":["3927\/UN6.RKT\/HK.07.00\/2025"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Rifampicin-resistant tuberculosis (RR-TB) remains a major threat to global TB control, primarily driven by mutations in the rpoB gene of Mycobacterium tuberculosis (Mtb). Most resistance-conferring mutations occur within the 81-base pair RIF resistance determining region (RRDR), particularly at codons S450L, H445Y\/D, and D435V, which are strongly associated with high level resistance. However, increasing evidence of low-frequency and disputed variants both within and beyond the RRDR reveals a broader genetic spectrum that contributes to diagnostic uncertainty and variable phenotypic outcomes. This review summarizes current knowledge of high frequency, low frequency, and disputed rpoB mutations and their implications for molecular detection of RIF resistance. Structural analyses show that specific amino acid substitutions alter key hydrogen bonds or create steric hindrance in the RIF-binding pocket, leading to diverse resistance levels. Despite the success of molecular platforms such as Xpert MTB\/RIF and line probe assays, their hotspot-based detection limits sensitivity to noncanonical variants. Lowering the minimum inhibitory concentration (MIC) breakpoint and integrating sequencing-based approaches, such as targeted and whole-genome sequencing, can enhance detection accuracy. A combined genomic and phenotypic framework will be essential to close existing diagnostic gaps and advance precision guided management of RIF-resistant and multidrug-resistant tuberculosis.<\/jats:p>","DOI":"10.3390\/pathogens15010016","type":"journal-article","created":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T16:19:26Z","timestamp":1766420366000},"page":"16","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Beyond Hotspot Mutations: Diagnostic Relevance of High Frequency, Low Frequency, and Disputed rpoB Variants in Rifampicin-Resistant Mycobacterium tuberculosis"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0650-6905","authenticated-orcid":false,"given":"Siti","family":"Soidah","sequence":"first","affiliation":[{"name":"Doctoral Program in Biotechnology, Graduate School, Universitas Padjadjaran, Bandung 40132, Indonesia"},{"name":"Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40132, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1629-407X","authenticated-orcid":false,"given":"Toto","family":"Subroto","sequence":"additional","affiliation":[{"name":"Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40132, Indonesia"},{"name":"Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7555-0678","authenticated-orcid":false,"given":"Irvan","family":"Faizal","sequence":"additional","affiliation":[{"name":"Research Cente for Vaccine and Drugs, National Research and Innovation Agency Republic of Indonesia, Tangerang Selatan 15314, Indonesia"},{"name":"School of Bioscience, Technology, and Innovation, Atma Jaya Catholic University of Indonesia, Tangerang 15345, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1627-1553","authenticated-orcid":false,"given":"Muhammad","family":"Yusuf","sequence":"additional","affiliation":[{"name":"Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40132, Indonesia"},{"name":"Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"16076","DOI":"10.1038\/nrdp.2016.76","article-title":"Tuberculosis","volume":"2","author":"Pai","year":"2016","journal-title":"Nat. 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