Costs of antibiotic resistance genes depend on host strain and environment and can influence community composition

The prevalence of antibiotic resistance genes (ARGs) is a major contributor to bacterial antibiotic resistance. ARGs are strongly selected in environments containing corresponding antibiotics, but it is less clear how ARGs are maintained in environments where antibiotic selection might be weak or sporadic. In particular, few studies have directly estimated the effect of ARGs on host fitness in the absence of direct selection. To the extent that ARGs impose costs, it is not clear if these are fixed or might depend on the host strain, perhaps marking some ARG-host combinations as low-cost reservoirs that can act to maintain ARGs in the absence of antibiotic selection. We quantified the fitness effects of six ARGs in each of 12 diverse Escherichia spp. strains in two environments. Only one ARG (blaTEM-116, encoding resistance to some β-lactam antibiotics) imposed an overall cost. However, all but one ARG imposed a cost in at least one host strain, reflecting a significant ARG cost-by-strain interaction effect. A simulation model predicts that these interactions cause the ecological success of ARGs to depend on available host strains, and, to a lesser extent, for successful host strains to depend on the ARGs present in a community. Together, these results indicate the need to consider the potential of reservoir strains for maintenance of ARGs. ### Competing Interest Statement The authors have declared no competing interest.