Genomic mutations in rpoB, KatG and inhA genes among multi-drug resistant Mycobacterium tuberculosis complex strains isolated from Çukurova region

Multidrug-resistant Mycobacterium tuberculosis (MDR-TB), which is resistant to at least rifampicin (RIF) and isoniazid (INH), is a major threat to public health due to the greater complexity, cost, and side effects of treatment. Resistance to RIF and INH generally occurs by mutations in the rpoB and KatG genes, the inhA promoter, and the oxyR-ahpC intergenic regions. The development of modern genomics provides an effective method to understand the molecular mechanism of drug resistance and diagnose drug-resistant M. tuberculosis. We used whole-genome sequencing (WGS) to find changes in 4 genes or intergenic regions in 70 clinical M. tuberculosis strains from the Cukurova Region of Turkey. The strains included 40 MDR-TB and 30 pan-susceptible isolates. We then looked at how these changes were related to resistance to RIF and INH. The results show that, compared to the phenotypic proportional method, the sensitivity and specificity of WGS for resistance detection were 77.5 and 100.0% for RIF (based on mutations in rpoB), 80% and 100%, 30% and 100%, and 12.5% and 93.3% for INH (based on mutations in katG, inhA, and oxyR-ahpC, respectively). WGS data also showed that mutations in the inhA promoter increased only 5% sensitivity for INH based on mutations in katG. Also, mutations in the oxyR-ahpC intergenic regions decreased by 6.3% specificity for INH based on mutations in the katG gene and inhA promotor. The codons S450L (52.5%), H445T (7.5%), A435V (7.5%), L430P (5%), L430L (2.5%), and 494 (2.5%) of RIF-resistant isolates exhibited the highest rate of mutation within the rpoB gene. The parts of the katG gene that changed the most were codons S315T (52.5%), S315A (2.5%), G316S (7.5%), L336P (5%), S309T (5%), T328C (2.5%), A311P (2.5%), and in one strain, both T328C, and S315A (2.5%); the positions C-15T (25%), G-47C (2.5%), and G-64C (2.5%) of the inhA promoter; and the positions G-88A (5%), G-48A (2.5%), and T17C (5%) of oxyR-ahpC among INH-resistant isolates.