Phenotypic drug susceptibility testing and genotypic characterization of Bedaquiline resistance in drug resistant Mycobacterium tuberculosis

PURPOSE: The new drugs bedaquiline, delamanid, and pretomanid have been approved for treating drug-resistant tuberculosis. The World Health Organization currently recommends the BPaL(M) regimen, which lasts 6-9 months, for managing drug-resistant tuberculosis. This study aimed to perform phenotypic drug susceptibility testing and identify mutations linked to bedaquiline resistance through whole genome sequencing. METHODS: We conducted a prospective cohort study involving 297 drug-resistant Mycobacterium tuberculosis isolates from patients visiting the respiratory medicine outpatient department at Christian Medical College, Vellore, and district TB centers across six districts in Tamil Nadu over the course of five years (2019-2023). These isolates underwent phenotypic drug susceptibility testing for bedaquiline using the BACTEC™ MGIT™ 960 system, following WHO guidelines. WGS was performed on a subset of 150 isolates using the Illumina platform, followed by mutation analysis using BLASTIN. RESULTS: The study found a 7% prevalence of bedaquiline resistance. A total of 39 variants were identified across four candidate genes associated with BDQ resistance: Rv0678, mmpL5 (Rv0676c), pepQ, and Rv1979c. No variants were observed in the Rv0677c, Rv1304, or atpE genes in any of the tested isolates. All isolates (100%) had at least one variant in the Rv0676c gene. CONCLUSION: This study identified the most common genetic variants linked to BDQ resistance from a tertiary care center in India. Larger studies across the country are necessary to explore the phenotypic and genotypic resistance profiles of BDQ and other drugs used in all-oral shorter regimens being introduced in India for the treatment of multidrug-resistant TB.