Fitness costs of antibiotic resistance mutations in rich media do not reliably predict those in infection-like environments

The acquisition of antibiotic resistance is typically associated with a fitness cost, reducing the competitive ability of cells in the absence of antibiotics. Our ability to predict these costs informs our ability to predict how likely it is that resistance will subside in the absence of treatment. Fitness costs are typically measured in laboratory cultures using a nutritionally rich medium for growth. Here, we tested the impact of infection-like environments on the prevalence and magnitude of fitness costs associated with antibiotic resistance mutations in the opportunistic pathogen Pseudomonas aeruginosa. We assessed two different clinically relevant infection niches, the lung and urinary tract, through the use of infection-niche mimicking media that models the chemical compositions of these niches. The fitness costs of resistance mutations in rich media did not reliably predict those in infection-like environments, on average costs were increased in the lung-mimicking environment and costly mutations were less prevalent in the urinary tract-mimicking environment. Synthetic human urine significantly enhanced the fitness of P. aeruginosa with resistance mutations in nfxB, encoding a multidrug efflux pump transcriptional repressor, and we identified oxalate as the likely component driving this effect. Our findings highlight the importance of environmental chemical composition for shaping the fitness costs of resistance in P. aeruginosa and suggest that nfxB mutants may have a selective advantage in the urinary tract, mediated by the presence of oxalate.