Allelic polymorphism shapes collective phenotypes in evolving Pseudomonas aeruginosa populations

Pseudomonas aeruginosa is an opportunistic pathogen that chronically infects cystic fibrosis (CF) lungs and chronic wounds by forming antibiotic resistant multi-cellular biofilms. Emergence of phenotypically diverse isolates within P. aeruginosa infections has previously been reported, however, the impact of this heterogeneity social behaviors is poorly understood. Here we test how this phenotypic and genomic diversity specifically 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 phenotypic and genomic changes over the duration of the evolution experiment. We hypothesized that we would observe parallel phenotypic and genomic diversification in independently evolving lines, and that diversity would have an impact on collective phenotypes in evolved populations. 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 more specifically on quorum sensing (QS), a well-studied P. aeruginosa social 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 the clinically relevant B-lactam antibiotics ceftazidime and piperacillin/tazobactam, 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.