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

Abstract Antibiotic resistance genes (ARGs) is a major contributor to increasing levels of antibiotic resistance in clinical and agricultural settings. 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 11 diverse Escherichia spp. strains in two environments. While three ARGs (bla TEM-116 , cat , and dfrA5 , encoding resistance to β-lactam antibiotics, chloramphenicol, and trimethoprim, respectively) imposed an overall cost, all ARGs had an effect in at least one host strain, reflecting a significant ARG effect-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 importance of considering ARG effects over different host strains, especially the potential of reservoir strains that allow resistance to persist in the absence of direct selection, in efforts to understand resistance dynamics. Importance Antibiotic resistance is a major and increasing public health concern. Resistance occurs through a variety of mechanisms but commonly involves bacterial strains acquiring antibiotic resistance genes (ARGs) encoded by mobile elements. It is obvious and well-documented that ARGs will be selected in bacteria that are exposed to the antibiotics they confer resistance to. ARGs can also confer costs to bacteria—in environments that do not contain antibiotics, these costs can lead to the loss of ARGs. We show that ARG costs can be significant and that they depend on the host bacterial strain and the environment in which strains are grown. This dependence creates host-environment refuges for many ARGs, allowing them to be maintained in the absence of direct selection.