A Robust Genome-Wide Association Study Uncovers Signature Genetic Alterations among Pseudomonas aeruginosa Cystic Fibrosis Isolates

Pseudomonas aeruginosa (PA) is an opportunistic pathogen that causes diverse human infections such as chronic airway infection in cystic fibrosis (CF) patients. Although many sequenced genomes are available, a comprehensive comparison between genomes of CF versus non-CF PA isolates remains yet to be conducted. In order to gain a deeper understanding into the PA adaptation in the CF airway, we performed a Genome-Wide Association Study (GWAS) using a total of 1,001 PA genomes. Genetic variations uniquely identified among CF isolates were categorized into (i) alterations in protein-coding regions either large- or small-scale and (ii) polymorphic variations in intergenic regions. We introduced each CF-specific genetic alteration into the genome of PAO1, a prototype PA strain and experimentally validated their outcomes. Loci readily mutated among CF isolates include genes encoding a probable sulphatase and a probable TonB-dependent receptor (PA2332~PA2336), L-cysteine transporter (YecS, PA0313) and a probable transcriptional regulator (PA5438). A promoter region of heme/hemoglobin uptake outer membrane receptor (PhuR, PA4710) was similarly identified as meaningfully different between the CF and non-CF isolate groups. Our analysis, the first of its kind, highlights how PA evolves its genome to persist and survive within the context of chronic CF infection.