Interspecies interaction alters the trajectory of antibiotic resistance evolution by amplifying negative fitness epistasis

Interspecies interactions can influence the physiology of competing species, shaping their long-term evolutionary trajectories. While the role of interspecific competition in community dynamics is well-documented, its impact on evolutionary outcomes and their underlying mechanisms is less explored. Here, we investigate how interspecies competition affects antibiotic resistance evolution in the gut pathogen Salmonella enterica within synthetic microbial communities. Specifically, we examine how the presence of an interspecific competitor, Escherichia coli—a key member of the human gut microbiota—modulates resistance evolution at low streptomycin concentrations. Our findings reveal that interspecies competition results in the selection of S. enterica mutants with higher resistance levels and fitness costs. By analyzing resistant mutants (ten each isolated from conditions with and without interspecies competition), we demonstrate that interspecific competition increases the likelihood of accumulating resistance mutations that follow a trajectory of negative fitness epistasis, requiring larger changes in resistance for smaller gains in fitness. We show that this effect is driven by the activation of starvation response pathways in S. enterica, leading to enhanced expression of the cryptic aminoglycoside transferase gene (aadA). Our study links antibiotic resistance evolution to competition-induced physiological changes, emphasizing the interplay between interspecies interaction and genetic adaptation to environmental conditions.