Pseudomonas aeruginosa intrastrain population genetic heterogeneity increases antibiotic resistance and pathogenesis in cystic fibrosis

Chronic pulmonary infections with Pseudomonas aeruginosa is a major cause of loss of lung function in people with cystic fibrosis (pwCF). Intrastrain P. aeruginosa population genetic heterogeneity in CF airways is well known, but the effects of this intrastrain genetic and phenotypic heterogeneity on antimicrobial resistance and pathogenesis are not known. Here we aimed to determine how prolonged antibiotic treatments affect the P. aeruginosa population structure and dynamics over time. To examine this, we collected whole Pseudomonas populations from expectorated sputum samples of three adult pwCF over two years as part of routine clinic visits. We then isolated 81 colonies from each sputum sample. We found fourteen distinct colony morphotypes across all three samples over time, with a single morphotype dominating in each sputum sample. To determine the intrastrain population structure and dynamics, we deep sequenced (300x coverage) whole P. aeruginosa populations and examined the changes in allele frequency and genetic heterogeneity in each sputum sample and its impact on antimicrobial resistance and lung function. We found an increase in allele frequency of genes involved in genetic regulation and transcription. This research provides novel insights into intrastrain P. aeruginosa population dynamics and underscores the role that each member of the population plays in resisting prolong antimicrobial treatments and damage to the airways.