Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that chronically infects cystic fibrosis (CF) lungs by forming antibiotic resistant biofilms. Emergence of phenotypically diverse isolates within P. aeruginosa infections has previously been reported, however, the impact of heterogeneity on social behaviors is poorly understood. Here we test how diversity impacts on traits by evolving the strain PAO1 in biofilms grown in a synthetic sputum medium for 50 days. We measured social trait production and used a metagenomic approach to analyze and assess genomic changes over the duration of the evolution experiment. We found that (i) evolutionary trajectories were reproducible in independently evolving populations; (ii) over 60% of genomic diversity occurred within the first 10 days of selection. We then focused on quorum sensing (QS), a well-studied P. aeruginosa trait that is commonly mutated in strains isolated from CF lungs. We found that at the population level (i) evolution in sputum medium selected for decreased production of QS and QS-dependent traits due to accumulation of a SNP in the lasR gene; (ii) there was a significant correlation between lasR mutant frequency, the loss of protease and the 3O-C12-HSL signal, and an increase in resistance to clinically relevant β-lactam antibiotics, despite no previous antibiotic exposure. Overall, our findings provide insights into the impact of allele polymorphism on the collective phenotypes of diverse P. aeruginosa populations. Further, we demonstrate that P. aeruginosa population and evolutionary dynamics can impact on traits important for virulence and could also provide reasons for antibiotic resistance found in CF infections.
Significance Pseudomonas aeruginosa is a major cause of chronic infection of the lungs in individuals with cystic fibrosis (CF). Epidemic P. aeruginosa strains dominate and displace others in the lung and become phenotypically and genotypically diverse over time. How this diversity impacts on clinically relevant traits such as virulence or antibiotic resistance has received little attention. Here we demonstrate that the accumulation and frequency of genetic variants within heterogenous P. aeruginosa populations, results in population level changes in important traits including quorum sensing and antimicrobial resistance. Our work suggests that in the future, we should consider metagenomic and metaphenotypic assessments of P. aeruginosa populations collected from CF patients, rather than focusing on single random colonies isolated from infection.