Encoded metabolic remodeling amplifies drug resistance in Mycobacterium tuberculosis

Antibiotic pressure causes pathogens to evolve many forms of altered drug susceptibility. In addition to target or activator mutations conferring canonical drug resistance, mutations can serve as steppingstones to or enhancers of resistance. In clinical strains of Mycobacterium tuberculosis (Mtb), we find that idsA2, which encodes an isoprenyl pyrophosphate synthase involved in the synthesis of precursors for essential components of the cell wall and electron transport chain, is undergoing diversifying selection in Lineage 4, and that these mutations are associated with the acquisition of first-line antibiotic resistance. By engineering isogenic Mtb strains to express clinically prevalent variants of idsA2, we show that idsA2 variants alter the inhibitory concentrations of first-line drugs, most significantly increasing the inhibitory concentration of ethambutol by two-fold. Targeted lipid analyses reveal that disrupting IdsA2 function redirects limited resources in the isoprenoid synthesis pathway, leading to increased production of decaprenyl phosphate species. This suggests that idsA2 and ubiA mutations share an ethambutol resistance mechanism. Where idsA2 mutations arise after embB mutations, they maintain their multiplicative effect on the inhibitory concentration of ethambutol such that the variants together result in high-level resistance. As a result, identification of idsA2 mutations can be utilized to improve the specificity of genotypic ethambutol susceptibility testing. Together, this work shows how idsA2 mutations remodel bacterial metabolism and augment ethambutol resistance.