Selective pressure by rifampicin modulates mutation rates and evolutionary trajectories of mycobacterial genomes

Abstract

AbstractResistance to the frontline antibiotic rifampicin constitutes a challenge to the treatment and control of tuberculosis. Here, we analyzed the mutational landscape ofMycobacterium smegmatisduring long-term evolution with increasing concentrations of rifampicin, using a mutation accumulation assay combined with whole genome sequencing. Antibiotic treatment enhanced the acquisition of mutations, doubling the genome-wide mutation rate of the wild type cells. While antibiotic exposure led to extinction of almost all wild type lines, the hypermutable phenotype of the ΔnucSstrain (noncanonical mismatch repair deficient) provided an efficient response to the antibiotic, leading to high rates of survival. This adaptative advantage resulted in the emergence of higher levels of rifampicin resistance, an accelerated acquisition of drug resistance mutations inrpoB(β RNA polymerase) and a wider diversity of evolutionary pathways that led to drug resistance. Lastly, this approach revealed a subset of adaptive genes under positive selection with rifampicin that were able to drive novel rifampicin resistance mechanisms.