Genetic diversity of the fish pathogen Aeromonas Salmonicida in Israeli cyprinid aquaculture

Aeromonas Salmonicida is a gram-negative, rod-shaped, facultative anaerobic bacterium considered a major pathogen of salmonid species, causing severe damage to aquaculture industries worldwide. In Israel, A. Salmonicida is considered a winter pathogen, mainly affecting aquacultured cyprinid species. We are currently analyzing a collection of 24 A. salmonicida strains, isolated from diseased fish received at the central Fish Health Laboratory in Nir David between 2013 and 2018. Despite being isolated from different fish species and different sites over a period of 6 years, these isolates are remarkably similar with >99% similarity based on Multi Locus Sequence Typing (MLST). VapA is the gene encoding for the virulence array protein termed “the A-layer”, surrounding the outer membrane of the bacterium. It plays a significant role in pathogenesis since it allows for cell adhesion, including to the immune-response fish macrophages. Based on this finding we sequenced the genomes of 5 of these strains, representing the 2 clades, to further identify differences between them and elucidate their evolutionary history and possible origins. Our results suggest that the two clades are derived from different ancestral populations, and this separation is relatively well maintained despite their co-habitation of the same ecological niche. We further identified several large plasmids, some of which are known from previously sequenced A. salmonicida strains, encoding important virulence factors, and suggest a possible exchange of at least one plasmid between strains from the two clades which appears to have occurred fairly recently. Combined, our results provide an inside look on the evolution of fish pathogen within aquaculture environments.