Evolutionary Drivers of Antimicrobial Resistance Diversity ofPseudomonas aeruginosain Cystic Fibrosis Lung Infection

Pseudomonas aeruginosa is an opportunistic pathogen, responsible for chronic, drug-resistant lung infections in individuals with cystic fibrosis (CF). Although extensive heterogeneity in antimicrobial resistance (AMR) phenotypes of P. aeruginosa CF lung populations has been previously described, the roles of genomic diversification and evolutionary trade-offs in driving AMR diversity within a population are not fully understood. In this study, we harnessed sequencing from a collection of 300 clinical isolates of P. aeruginosa to unravel the evolution of resistance diversity in four individuals with CF. We found that genomic diversity was not always a reliable predictor of phenotypic AMR diversity within a population, and notably, the least genetically diverse population in this cohort displayed AMR diversity comparable to that of populations with up to two orders of magnitude more SNPs. Hypermutator strains often displayed increased sensitivity to antimicrobials, even when there was a history of use of a given antimicrobial in the treatment of the patient. Lastly, we sought to determine whether diversity in AMR could be explained by evolutionary trade-offs with other traits. Our results showed no strong evidence of collateral sensitivity between aminoglycoside, beta-lactam, or fluoroquinolone antibiotics within these populations. Additionally, there was no evidence of trade-offs between AMR and growth in a sputum-mimicking environment. Overall, our findings highlight that (i) genomic diversity within a population is not a necessary precursor to phenotypic diversity in AMR; (ii) hypermutator populations can evolve increased sensitivity to antimicrobials even under apparent antibiotic selection; (iii) collateral sensitivity is not robust in naturally occurring infectious strains; and (iv) resistance to a single antibiotic may not impose enough of a fitness cost to elicit trade-offs with fitness.