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 x 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.