Molecular Characterization of Drug Resistance-Associated Mutations in Mycobacterium tuberculosis Isolates from the Republic of Congo Using Targeted Nanopore Sequencing

Tuberculosis (TB) remains a major public health challenge, particularly in sub-Saharan Africa, where the emergence of drug-resistant MTB undermines current control efforts. This study aimed to characterize genetic mutations associated with resistance to first- and second-line injectable drugs in MTB isolates from pulmonary TB patients in the Republic of Congo. A total of 45 culture-positive MTB isolates collected between 2018 and 2019 were analyzed using targeted next-generation sequencing on the MinION device. Resistance-associated genes, including rpoB, katG, embB, gyrA, and rrs, were examined. Overall, 22/45 isolates (48%) harbored at least one mutation associated with drug resistance. Among resistant isolates, rifampicin resistance was detected in 15 of 22 (68.2%), predominantly associated with mutations in the rpoB rifampicin resistance–determining region, including p.Ser531Leu, p.Asp516Val, and p.His526Tyr.Ethambutol resistance was observed in 11 of 22 isolates (50.0%) and was mainly associated with the embB p.Met306Val mutation. Isoniazid resistance was detected in 9 of 22 isolates (40.9%), primarily associated with the KatG p.Ser315Thr mutation. Fluoroquinolone resistance was identified in 2 of 22 isolates (9.1%), mainly associated with gyrA p.Ala90Val and p.Asp94Gly mutations. Resistance to second-line injectable drugs was detected in 1 of 22 isolates (4.5%) and was associated with the rrs p.Ala1401Gly mutation. These findings underscore the need to enhance molecular surveillance and strengthen treatment protocols for drug-resistant TB in the Republic of Congo to effectively combat this evolving health crisis.