Clinical P. Aerginosa Prophages: Insights Into Their Role Via Their Activity, Abundance, Persiste nce

It remains unclear how much the accessory genome contributes in the complex processes of establishment and virulence of bacterial infections. P. aeruginosa is one of the most common opportunistic human pathogens and can establish difficult-to-eradicate infections. Genome-integrated viruses, known as prophages, are frequent components of this bacterium’s large accessory genome and can contribute to the virulence of P. aeruginosa. However, systematic interpretations of the contributing role of prophages in the evolution and fitness of the ubiquitous P. aeruginosa in its diverse niches are still in their infancy. This study provides insights into these roles by exploring the activity, abundance and persistence of prophages belonging to P. aeruginosa from the cystic fibrosis (CF) lung. We selected a cohort of 12 CF patients with a high-resolution history of difficult-to-eradicate P. aeruginosa infections. Nanopore technology was used to sequence high-contiguity genomes of one early isolate per patient. Subsequently, we applied a strategy that combined bioinformatics, antibiotic-assisted inductions, lysate sequencing and genomics to identify intact prophages in the host genomes and assess their long-term survival in follow-up isolates. From these data, we observed that CF P. aeruginosa genomes harbour a high abundance of intact prophages which can sometimes self-induce. We identified 29 intact prophages with a wide genomic diversity and some unique prophage genomes with minimum similarity to available genomes. All induced prophages were retraced in follow-up isolates for a tested period of 4 to 9 years with minimal genomic changes. In addition to elucidating the role of prophages in P. aeruginosa, we expect our findings to assist in developing novel diagnostics and phage-based therapies for P. aeruginosa infections.