Mutators drive evolution of multi-resistance to antibiotics

Abstract

Antibiotic combination therapies are an approach used to counter the evolution of resistance; their purported benefit is they can stop the successive emergence of independent resistance mutations in the same genome. Here, we show that bacterial populations with mutators, organisms with defects in DNA repair, readily evolve resistance to combination antibiotic treatment when there is a delay in reaching inhibitory concentrations of antibiotic--under conditions where purely wild-type populations cannot. In populations subjected to combination treatment, we detected a remarkable amount of genomic diversity in resistance-determining mutations, multi-drug efflux pumps, and mutation-rate altering genes. However, using eco-evolutionary simulations, we demonstrate that only the initial mutator allele is required to explain multi-resistance evolution. Unexpectedly, mutators not only allowed multi-resistance to evolve under combination treatment where it was favoured, but also under single-drug treatments. Under both conditions, the mutator allele swept to fixation through hitch-hiking with single-drug resistance, enabling subsequent resistance mutations to emerge. Ultimately, our results suggest that mutators may hinder the utility of combination therapy when mutators are present. Additionally, by raising the rates of population mutation, selection for multi-resistance may have the unwanted side-effect of increasing the potential to evolve resistance to future antibiotic treatments. Significance statementThe global rise in antimicrobial resistance means that we urgently need new approaches to halt its spread. Antibiotic combination therapy, treatment involving more than one antibiotic, is a strategy proposed to do just that. Evolving resistance to combinations is thought to be exceedingly rare, as it would require two independent mutations to occur in the same genetic background before microbial growth is inhibited. We find that wild-type populations cannot achieve this, even when antibiotic concentrations increase gradually. However, populations with mutators, organisms with elevated mutation rates through DNA repair defects, can readily evolve multi-drug resistance under both single-drug and combination treatments. Further, hitch-hiking of mutator alleles alongside resistance increases the evolutionary potential for acquiring further resistance mutations. As mutators are commonly found in natural populations, including infection, our results suggest that combination therapy may not be as resilient a strategy against resistance evolution as was once thought.