The processes of virulence evolution and host adaptation have frequently led to the emergence of dangerous bacterial pathogens both in human and veterinary fields. Photobacterium damselae is a multi-chromosome member of the family Vibrionaceae that comprises two remarkably different subspecies and can be considered a model for investigation of the evolution of pathogenicity. While Ph. damselae subspecies damselae (Pdd) is a generalist, free-living opportunist, the sister subspecies Ph. damselae ssp. piscicida (Pdp) is a highly adapted, fish-restricted pathogen that can also thrive intracellularly. Despite their taxonomical classification, Pdd and Pdp are very different, but it is still unclear what underlies their different pathogenicity.
Using highly curated genome assemblies for phylogenetic analyses and genome comparisons, we provide deeper insight into the gradual transition from a generalist opportunist to a highly specialised fish pathogen. Three major phylogenetic clades have been identified: two clusters of Pdd strains and a single cluster of Pdp that is nested into one of the Pdd clusters. Furthermore, preliminary investigations show that sets of functionally related genes, such as a capsular operon, motility-associated genes and several transport proteins, are unique to Pdp. Conversely, conjugal transfer and toxin-antitoxin systems are found only in the sister subspecies. These results suggest that both acquisition and loss of metabolic pathways may have shaped an ancestral Pdd strain into the specialised fish pathogen Pdp. Elucidating these key changes may greatly improve our understanding of the evolution of pathogenicity and host adaptation in Eubacteria.