Bacterial diseases remain a critical bottleneck in sustainable Chilean salmon aquaculture. Among them, Salmonid Rickettsial Septicemia (SRS) caused by Piscirickettsia salmonis and tenacibaculosis caused by Tenacibaculum species are the most impactful, accounting for high mortality and persistent antibiotic use. Bacteriophage-based strategies have emerged as promising alternatives; however, a deeper understanding of the genomic phage-host interplay is required to guide their rational development.
In this study, we performed a comparative analysis of prophage content and antiphage defense systems in 79 genomes of P. salmonis and 212 genomes/assemblies of Tenacibaculum spp., using the PHASTEST and DefenseFinder tools. In P. salmonis (Fig.1), 70% of chromosomal and 75% of plasmid sequences harbored prophage regions, predominantly related to Escherichia and Burkholderia phages. These regions were enriched in transposases, structural proteins, and phage-like CDSs. Notably, a strong correlation (ρ = 0.72, p < 0.001) was observed between the number of chromosomal prophage regions and the presence of antiphage defense systems, with dGTPase, AbiD, and SoFIC being the most prevalent in chromosomes, and MazEF in plasmids.
In Tenacibaculum spp., only 11% of the analyzed assemblies contained prophage regions, with T. maritimum and T. mesophilum concentrating most elements. Six intact prophages were identified, containing hallmark structural proteins and a putative endolysin with a CHAP domain structurally related to phage K endolysin from S. aureus. The restriction-modification (RM) and Mokosh systems were predominant across these strains, while CRISPR-Cas systems were detected exclusively in T. maritimum.
These findings reveal distinct prophage-host dynamics between the two pathogens and highlight the co-evolution of defense mechanisms. The identification of stable endolysins and conserved antiphage systems underscores their potential for novel phage-derived therapeutics. This comparative genomic framework supports the development of phage-based tools adapted to the ecological and genomic context of Chilean aquaculture pathogens.