Involvement of Pf-like phages in resistance to phage infection in clinical isolates of P. aeruginosa from cystic fibrosis patients

Pseudomonas aeruginosa is a bacterial pathogen that is a major cause of lung infections in cystic fibrosis (CF) and other patients. Isolates of P. aeruginosa from CF patients commonly carry filamentous phages (Pf phages), a type of temperate phage known to be related to biofilm production and antibiotic sequestration. In this study, 12 new Pf-like phages were identified in a collection of clinical isolates of P. aeruginosa from CF patients. Analysis of the phage genomes revealed different anti-phage defence systems, described here for first time in these types of phages. Finally, relationships between resistance to phage infection and the presence of Pf-like phages and also between each defence system and resistance were observed. IMPORTANCEBacteria harbour a wide range of defence mechanisms to avoid phage infections. These mechanisms hamper the application of phage therapy because they can lead to the rapid acquisition of phage resistance. Temperate phages, including the filamentous phages, carry genes encoding virulence factors and also anti-phage defence mechanisms, as their survival depends on the host survival. In this study, we identified 12 new Pf-like phages encoding several different anti-phage defence mechanisms, some observed for the first time in this type of phage. A relationship between these phages and resistance to phage infection was also observed. The study findings are important as they provide information about newly discovered filamentous phages and their proteomes and also about the role of these phages in resistance to phage infections. Studying the genome of clinical isolates carrying these phages could help to improve phage therapy by targeting these phages or its genes.