Abstract
Mycobacterium tuberculosis
adapts to the environment by selecting for advantageous single-nucleotide polymorphisms (SNPs). We studied whether advantageous SNPs could be distinguished from neutral mutations within genes associated with drug resistance. A total of 1,003 clinical isolates of
M. tuberculosis
were related phylogenetically and tested for the distribution of SNPs in putative drug resistance genes. Drug resistance-associated versus non-drug-resistance-associated SNPs in putative drug resistance genes were compared for associations with single versus multiple-branch outcomes using the chi-square and Fisher exact tests. All 286 (100%) isolates containing isoniazid (INH) resistance-associated SNPs had multibranch distributions, suggestive of multiple ancestry and convergent evolution. In contrast, all 327 (100%) isolates containing non-drug-resistance-associated SNPs were monophyletic and thus showed no evidence of convergent evolution (
P
< 0.001). Convergence testing was then applied to SNPs at position 481 of the
iniA
(Rv0342) gene and position 306 of the
embB
gene, both potential drug resistance targets for INH and/or ethambutol. Mutant
embB306
alleles showed multibranch distributions, suggestive of convergent evolution; however, all 44
iniA
(
H481Q
) mutations were monophyletic. In conclusion, this study validates convergence analysis as a tool for identifying mutations that cause INH resistance and explores mutations in other genes. Our results suggest that
embB306
mutations are likely to confer drug resistance, while
iniA
(
H481Q
) mutations are not. This approach may be applied on a genome-wide scale to identify SNPs that impact antibiotic resistance and other types of biological fitness.