Whole-genome sequencing of presumptive MDR-TB isolates from a tertiary healthcare setting in Mumbai

•The study was conducted as a blinded SNP-based genotypic DST to support the reliability and applicability of WGS in public health settings.•The predominant mutation in the katG gene resulting in INH resistance is Ser315Thr.•Mutation at the 1401 position in the rrs gene, imparting resistance to at least one SLID, is the predominant mutation.•A high prevalence of FQ resistance was observed, with most mutations occurring in the gyrA gene.•Four genomic clusters (GCs) were identified among samples belonging to the Beijing lineage.•Implementing WGS for TB instead of LC-DST can reduce the turn-around time from up to three weeks to one week and increase drug testing capacity to 18 drugs.