Comparative genomics of Photobacterium damselae from Penaeus (Marsupenaeus) japonicus: insights into pathogenicity and adaptation.

Abstract

Photobacterium damselae subsp. damselae (PDD), a halophilic, Gram-negative bacterium of the family Vibrionaceae, infects a wide range of aquatic organisms. PDD isolates originating from fish have been characterized in detail, but much less is known about those infecting invertebrates. Currently, only 3 complete PDD genomes isolated from Kuruma shrimp Penaeus (Marsupenaeus) japonicus from Japan are publicly available, severely limiting comparative studies of host adaptation. To address this, we present complete, plasmid-resolved genome assemblies of 4 novel PDD strains (TUMSAT-PD1, -PD2, -PD3, and -PD4) isolated from diseased Kuruma shrimp across multiple prefectures in Japan. Phylogenomic analysis reveals that shrimp PDD strains are genetically heterogeneous and closely related to those infecting other aquatic organisms, suggesting that pathogenicity against shrimp arose independently in multiple PDD strains. While core virulence determinants are chromosomally encoded, we identified key plasmid-borne virulence factors that are likely to enhance the pathogenicity of PDD strains. Comparative analysis with 3 publicly available PDD genomes demonstrated both conserved core virulence determinants and strain-specific accessory genes, reflecting local adaptation and evolutionary diversification. Our findings provide the first geographically expanded genomic framework for Kuruma shrimp-associated PDD, integrating 4 novel Japanese isolates with the existing public genomes. This integrated data set demonstrates that PDD exhibits a generalist evolutionary strategy, capable of rapid adaptation to diverse hosts through conserved virulence machinery and mobile genetic elements. This work significantly expands the genomic basis for understanding PDD epidemiology and pathogenesis within aquaculture systems.