Diversity and Role of Prophages in Pseudomonas aeruginosa: Resistance Genes and Bacterial Interactions

Pseudomonas aeruginosa is a major pathogen associated with hospital-acquired infections, and the spread of carbapenem-resistant isolates highlights the urgency of developing non-conventional therapies, such as phage therapy. For this alternative to be effective, un-derstanding phage-host interactions is crucial for the selection of candidate phages and offers new insights into these dynamics. Background/Objectives: This study aimed to characterize prophage diversity in clinical P. aeruginosa genomes, assess the relationship between phages and the CRISPR/Cas system, and investigate the potential role of phages in disseminating resistance genes. Methods: A total of 141 genomes from Brazilian hos-pitals were analyzed. Prophage detection was performed using VIBRANT, and in silico analyses were conducted to evaluate taxonomic diversity, presence of resistance genes, phage life cycle, genomic distribution, and the presence of the CRISPR/Cas system. Re-sults: In total, 841 viral sequences were identified, with a predominance of the class Cau-doviricetes and high overall phage diversity. No statistically significant difference was ob-served in the number of prophages between isolates with and without CRISPR/Cas sys-tems. Phages carrying resistance genes were detected in isolates harboring the type I-C CRISPR/Cas system. Additionally, prophages showed no preference for specific insertion sites along the bacterial genome. Conclusions: These findings provide evidence of a well-established phage-host relationship. The dual role of phages—as vectors of antimi-crobial resistance and as potential therapeutic agents—reflects their dynamic impact on bacterial communities and reinforces their importance in developing new strategies to combat antimicrobial resistance.