Prophage Abundance Differentiates Clinical and Environmental Isolates of Pseudomonas aeruginosa

Abstract The bacterium Pseudomonas aeruginosa can grow in soil and water environments as well as the human body, where it is an opportunistic pathogen. Here, we have investigated how the number and integrity of prophages present in the P. aeruginosa reflects these adaptations. We analyzed genomic sequences from 139 environmental and 145 clinical P. aeruginosa isolates. We found that genomes of P. Aeruginosa from the respiratory tracts of people with cystic fibrosis (“clinical” genomes) were significantly smaller than environmental genomes and exhibited higher GC content. Genome size was inversely correlated with GC content. Clinical isolates had both smaller genome size and increased GC content. Much of this genome size difference is attributable to mobile genetic elements. Environmental isolates had more and longer intact prophages (average of 8.82 full, high-confidence prophage sequences in comparison to a clinical average of 5.19) and accumulated many fragmented prophage remnants. The differences between these groups do not appear to be lineage-associated--Phylogenetic analyses supported that both transitions from clinical to environmental and environmental to clinical occur. Our findings suggest that reduced genome size and loss of prophage presence are hallmarks of the adaptation of P. aeruginosa to CF body spaces. Overall, these results emphasize the role of prophages both as markers and mediators of ecological development in P. aeruginosa. Competing Interest Statement The authors have declared no competing interest. Footnotes Clearer figures, more in-depth discussion of results, analysis of distribution of phage type in clinical vs environmental bacteria, clearer definition of "fragment" and "clinical".