Pseudomonas aeruginosa maintains an inducible array of novel and diverse prophages over lengthy persistence in CF lungs

Abstract

Abstract Pseudomonas aeruginosa is a bacterium with increasing relevance in clinical settings and among the most common bacteria occupying the cystic fibrosis (CF) lung niche. Its ability to colonize and persist in diverse niches is attributed to this bacterium’s large accessory genome. In P. aeruginosa, prophages represent a common feature of a strain’s accessory genome. Hence, we hypothesized that prophages play a role in the bacterium’s fitness and persistence in CF. We focused on the CF niche and used longitudinal isolates of patients persistently infected by P. aeruginosa. Via in silico analysis we predicted intact prophages in the genomes of each longitudinal isolate group and scored their long-term persistence. We then confirmed whether they are inducible and where they reside by induction experiments and lysate sequencing. Lastly, we performed comparative genomics to evaluate prophage diversity and confirm their predicted long-term persistence and level of genomic maintenance. In concurrence with other studies, our findings support that most P. aeruginosa harbour prophages, some of which can self-induce. We also found ciprofloxacin, an antibiotic commonly used for P. aeruginosa treatment in CF, to induce prophages. The induced prophage genomes displayed a high degree of diversity and instances of genomic novelty. Finally, we discovered that all induced prophages persisted long-term with their genomes virtually unchanged, suggesting that they likely assist host persistence. In addition to elucidating the role of prophages in P. aeruginosa, we expect our findings to aid in developing novel diagnostics and phage-based therapies for P. aeruginosa infections.