The effect of environmental heterogeneity on the fitness of antibiotic resistance mutations in Escherichia coli

Antimicrobial resistance (AMR) is widespread, with resistant pathogens found not only in the clinic but throughout the natural and built environments. It is unclear, however, to what extent AMR should be expected to persist in the environment: Laboratory experiments have suggested that resistance is typically costly, and hence should be selected against. However, such studies may not generalize to broader environmental settings. As such, we estimated the fitness of six AMR mutants of Escherichia coli in ten media reflecting ecological niches, human hosts, and standard lab conditions. We found extensive evidence for genotype × environment interactions, with different genotypes favored in different environments. Resistance alleles did not suffer a cost in some environments, raising the possibility of environmental reservoirs of resistance. Interestingly, fitness tended to be higher in lower quality environments. Our findings emphasize the need to consider the ecology and evolution of resistance in the broader environment in the management of AMR.