Know Your Enemy: Piscirickettsia salmonis and Phage Interactions Using an In Silico Perspective

<b>Background:</b> Aquaculture faces significant challenges due to bacterial infections, particularly <i>Piscirickettsia salmonis</i>, leading to extensive antibiotic use and raising concerns about antimicrobial resistance. In this context, bacteriophages and bacterial defense systems play a critical role in the evolutionary dynamics of <i>P. salmonis</i>. <b>Objective.</b> This study aimed to investigate the genomic landscape of prophage regions and antiphage defense systems in Piscirickettsia salmonis to better understand their co-evolutionary dynamics and explore their potential role in alternative disease control strategies for aquaculture. <b>Methods:</b> We analyzed 79 genomes of <i>Piscirickettsia salmonis</i> using bioinformatic tools to identify and characterize prophage regions and antiphage defense systems. <b>Results:</b> At the chromosomal level, 70% of the strains contained prophage regions, with a total of 92 identified regions, most of which were classified as intact. At the plasmid level, 75% of plasmids carried prophage regions, with a total of 426 identified regions, predominantly associated with <i>Escherichia phage RCS47</i>, <i>Burkholderia phage Bcep176</i>, and <i>Enterobacteria phage mEp235</i>. Prophage regions were enriched in transposases, head proteins, tail proteins, and phage-like proteins. The analysis of antiphage defense systems revealed that <i>P. salmonis</i> predominantly harbors dGTPase, AbidD, and SoFIC at the chromosomal level, whereas MazEF was the most frequent system in plasmids. A strong positive correlation was found between the number of prophage regions and defense systems in chromosomes (ρ = 0.72, <i>p</i> = 6.3 × 10^-14), while a weaker correlation was observed in plasmids. These findings highlight the complex interplay between <i>P. salmonis</i> and its bacteriophages, with implications for disease control in aquaculture. <b>Conclusions:</b> Overall, these insights into the prophage and defense system dynamics provide potential avenues for developing alternative strategies to combat <i>P. salmonis</i> infections and reduce reliance on antibiotics in aquaculture systems.