Mutators can drive the evolution of multi-resistance to antibiotics

Author summaryThe global rise in antimicrobial resistance means we urgently need new approaches that halt its spread. Combination therapy, using multiple antibiotics as one treatment, proposes to do just that. Evolving resistance to combinations should be exceedingly rare, as it requires multiple mutations to occur in the same genetic background before microbial growth is inhibited. We find that wild-type bacteria cannot achieve this, even when inhibition does not occur rapidly. However, we show that introducing a small number of 'mutators' defective in DNA repair allows multi-drug resistance to readily evolve during both single-drug and combination treatments. As mutators are common in natural populations and infections, our results suggest that combination therapy may not be as resilient against resistance evolution as once thought. 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 of Escherichia coli subjected to combination treatment, we detected a diverse array of acquired mutations, including multiple alleles in the canonical targets of resistance for the two drugs, as well as mutations in multi-drug efflux pumps and genes involved in DNA replication and repair. Unexpectedly, mutators not only allowed multi-resistance to evolve under combination treatment where it was favoured, but also under single-drug treatments. Using simulations, we show that the increase in mutation rate of the two canonical resistance targets is sufficient to permit multi-resistance evolution in both single-drug and combination 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 genetic mutation, selection for multi-resistance may have the unwanted side-effect of increasing the potential to evolve resistance to future antibiotic treatments.

Automated summary

Combination therapy of antibiotics aims to prevent the evolution of resistance, but researchers have found that mutators with defects in DNA repair can readily evolve resistance in both single-drug and combination treatments. This suggests that combination therapy may not be as effective against resistance evolution as once thought.