Multi-drug resistance and compensatory mutations in Mycobacterium tuberculosis in Vietnam

Vietnam is a hotspot for the emergence and spread of multidrug-resistant Mycobacterium tuberculosis. This study aimed to perform a retrospective study on the compensatory evolution in multidrug-resistant M. tuberculosis strains and the association with drug-resistant mutations and M. tuberculosis genotypes.

Hundred and seventy-three strains resistant to rifampicin (n = 126) and/or isoniazid (n = 170) (multidrug-resistant = 123) were selected according to different drug-resistant patterns and genotypes. The genes/promoter regions including rpoA, rpoB, rpoC, katG, inhA, inhA promoter, ahpC, ahpC promoter, gyrA, gyrB, and rrs were sequenced for each strain.

Frequency of rifampicin- and isoniazid-resistant mutations in multidrug-resistant strains was 99.2% and 97.0%, respectively. Mutations associated with low -high levels of drug resistance with low- or no-fitness costs compared to the wild type, including rpoB_Ser450Leu, katG_Ser315Thr, inhA-15(A-T), gyrA_Asp94Gly, and rrs_A1401GA, accounted for 46.3%, 76.4%, 16.2%, 8.9%, and 11.4%, respectively, in the multidrug-resistant strains. Beijing and Euro-American genotype strains were associated with high-level drug-resistant mutations, rpoB_Ser450Leu, katG_Ser315Thr, and gyrA_Asp94Gly, while East African-Indian genotype strains were associated with low to high-level drug-resistant mutations, rpoB_His445Asp, rpoB_His445Tyr, inhA-15(C-T) and rrs_A1401G. Multidrug-resistant strains (19.5%) harboured compensatory mutations linked to rifampicin resistance in rpoA, rpoB, or rpoC. Notably, the frequency of compensatory mutations in Beijing genotypes was significantly higher than in East African-Indian genotypes (21.1% vs. 3.3%, OR = 7.7; 95% CI = 1.0 to 61.2, p = 0.03). The proportion of multidrug-resistant strains with rpoB_Ser450Leu mutations carrying rpoA-rpoC mutations was higher than that of strains with other rpoB mutations (OR = 5.4; 95% CI = 1.4 to 21.1, p = 0.02) and was associated with Beijing strains. Only 1.2% (2/170) isoniazid-resistant strains carried aphC-52(C-T) mutation in the promoter region of the ahpC gene, which was hypothesised to be the compensatory mutation in isoniazid-resistant strains. Meanwhile, 11 isoniazid-resistant strains carried a katG mutation combined with either inhA-8(T-C) or inhA-15(A-T) mutations and were associated with East African-Indian strains.

Mutations associated with high levels of drug resistance without/with low fitness costs (rpoB_Ser450Leu and katG_Ser315Thr) along with compensatory mutations linked to rifampicin resistance were strongly associated with multidrug-resistant M. tuberculosis Beijing strains in Vietnam.