Variation in multiple classes of simple sequence repeats can alter drug susceptibility in Mycobacterium tuberculosis

Insertions and deletions (INDELs) within simple sequence repeats (SSRs) have been found to significantly impact drug susceptibility in Mycobacterium tuberculosis (Mtb), a pathogen responsible for tuberculosis. Studies of global Mtb isolates suggest that a majority of SSRs are undergoing diversifying selection, leading to various INDELs in homopolymer tracts (HTs) that enhance the pathogen's fitness under host and antibiotic stresses.

However, the functional implications of most variable SSRs, especially those within more complex repeat sequences other than HTs, are not yet well-understood. To address this gap, researchers have conducted a phylogenomic analysis of clinical Mtb strains from Vietnam and Peru, followed by in vitro experimental validation of engineered strains to identify SSR INDELs that change antibiotic susceptibility.

Their results reveal that INDELs across multiple SSRs, regardless of their repeat composition, exhibit high variability and are correlated with clinical antibiotic resistance. These findings include frameshifting HT INDELs in genes such as ppe13, glpK, Rv2081c, and ppsA, as well as in-frame trinucleotide (triplet) SSR INDELS in genes like ponA1, ppe53, and ppe59, which cause more subtle alterations in protein structure.

By reconstructing these INDELs in an isogenic background, the researchers identified four variants that directly decrease drug potency. Notably, a triplet SSR deletion in ppe53 resulted in intermediate resistance to isoniazid, rifampicin, and streptomycin. The prevalent ppe53 CGCdel mutation shortens a polyalanine stretch close to the conserved WxG domain, impairing the protein's processing and secretion.

Overall, this research underscores the selective pressure exerted by Mtb SSRs and highlights the importance of in-frame INDELs within triplet SSRs in the evolution of antibiotic resistance.