Environment-mediated metabolic constraints shape antimicrobial resistance evolution in Pseudomonas aeruginosa
Year: 2026
Type: preprint
Abstract: Pseudomonas aeruginosa rapidly evolves resistance to multiple antibiotics, complicating treatment of chronic infections. While resistance mechanisms are well described, the influence of host-relevant environmental conditions on resistance evolution remains unclear. Here, we investigated how nutrient composition, pH, and oxygen availability influence resistance evolution to piperacillin, tobramycin, and ciprofloxacin. We evolved P. aeruginosa in different synthetic media mimicking different infection niches as well as variations in pH and oxygen availability. We also performed whole-genome sequencing to identify mutational adaptive strategies. Our findings reveal that environmental context profoundly affects both the rate and mechanisms of resistance evolution. Nutrient-rich conditions and aerobic metabolism favored canonical resistance mutations, while nutrient-limited or anaerobic environments promoted adaptations involving efflux regulation, metabolic remodeling, and biofilm-associated traits. pH and oxygen availability acted as selective pressures, modulating which pathways were accessible as well as the stability of resistance phenotypes. Additionally, the mutations that arose in the lab-evolved isolates were also actively maintained across a large population of clinical P. aeruginosa genomes, confirming that spatial oxygen gradients in host tissues drive parallel evolutionary pathways in vivo . These results underscore that resistance evolution is not uniform but highly contingent on the metabolic and redox environment. Understanding how infection-specific conditions shape evolutionary trajectories provides insight into the emergence of multidrug resistance and highlights potential avenues for therapeutic intervention. Importance Antibiotic resistance in Pseudomonas aeruginosa is a leading cause of treatment failure in chronic infections, yet the relationship between the infection-site environment, bacterial metabolism, and the development of resistance remains poorly understood. Here, we use synthetic media that mimic chronic wounds, urinary tract infections, and the cystic fibrosis lung to demonstrate that the development of resistance is both drug- and niche-specific, with pH and oxygen availability of further shaping evolutionary outcomes in drug-dependent manner. Whole-genome sequencing reveals that oxygen availability during evolution selects for distinct resistance mutations. These findings are recapitulated in a clinical cohort of P. aeruginosa genomes, confirming their translational relevance. Together, these results establish resistance evolution as a highly environment-contingent process and suggest that a deeper understanding of how infection-site conditions constrain evolutionary trajectories could inform the development of more precise, niche-targeted therapeutic strategies.
Institution: University of Virginia
Language: English
Subfield: Microbiology (medical)
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W7223129665