MOLECULAR EPIDEMIOLOGY OF DRUG RESISTANCE ASSOCIATED MUTATIONS (RPOB, KATG, INHA, GYRA, RRS, AND EIS) IN MYCOBACTERIUM TUBERCULOSIS ISOLATES

Abstract

Background: Drug-resistant tuberculosis (DR-TB) constitutes a critical public health emergency in Pakistan, with Sindh province bearing a disproportionately high burden. However, comprehensive province-level molecular data on resistance-conferring mutations remain scarce. This study aimed to determine the frequency, spectrum, and distribution of drug resistance-associated mutations (rpoB, katG, inhA, gyrA, rrs, and eis) in Mycobacterium tuberculosis (MTB) isolates from Sindh, Pakistan. Methods: A hospital-based, multicentre, cross-sectional study was conducted across four tertiary-care hospitals (JPMC and Civil Hospital/DUHS, Karachi; LUH, Hyderabad; PMUH, Nawabshah). A total of 195 MTB isolates from clinically suspected pulmonary TB patients were processed using the NALC–NaOH method and confirmed by GeneXpert MTB/RIF Ultra. Resistance-associated mutations were detected by line probe assay targeting the six resistance genes. Data were analysed using IBM SPSS version 26.0; p < 0.05 was considered statistically significant. Results: The overall mutational frequencies were: rpoB 37.9% (74/195), inhA 22.1% (43/195), katG 16.4% (32/195), gyrA 11.8% (23/195), rrs 9.2% (18/195), and eis 5.6% (11/195). The predominant mutations were rpoB S531L, katG S315T, inhA −15 C→T, gyrA D94G, rrs A1401G, and eis −14 C→T. Genotypic MDR-TB was identified in 31.8% (62/195) of isolates, while pre-XDR and XDR profiles accounted for 5.6% (11/195) and 6.2% (12/195), respectively. Mutation frequencies did not differ significantly across the four hospitals (p > 0.05), indicating homogeneous province-wide dissemination of resistant strains. Previously treated patients exhibited a significantly higher resistance burden than new cases (p < 0.001). Conclusion: The high prevalence of first- and second-line resistance mutations confirms the extensive circulation of MDR, pre-XDR, and XDR-TB strains across Sindh. These findings support the expanded deployment of second-line molecular diagnostics, continuous genomic surveillance, and strengthened programmatic interventions, and provide a province-specific baseline for diagnostic validation and evidence-based treatment policy.