Phylogeny-aware comparative genomics of Vibrio vulnificus links genetic traits to pathogenicity

Vibrio vulnificus is a natural inhabitant of coastal brackish waters worldwide and an opportunistic pathogen that can cause severe infections and septicemia through seafood consumption or wound exposure. Due to global warming, its abundance is increasing at high latitudes. While the species harbors diverse virulence factors, its precise disease mechanisms remain unclear. Comparative genomics between clinical and environmental isolates can help identify key virulence genes, but the limited availability of genomes from environmental isolates has hindered progress. In this study, we sequenced the genomes of 82 V. vulnificus isolates from water, sediment, and seagrass along the Baltic Sea coast and complemented with published genomes from 208 clinical and 117 globally distributed isolates for comparative analysis. Phylogenetic reconstruction confirmed four major lineages, with Baltic Sea strains confined to lineage L2 and L4, while clinical and environmental strains were distributed across all lineages. This suggests that the phylogenetic structure of V. vulnificus reflects adaptation to environmental conditions rather than pathogenicity. Using the PhyloBOTL pipeline developed here, we identified 128 orthologs significantly enriched in clinical isolates, grouped into 36 co-localization clusters based on proximity in the genomes. These included genes linked to virulence, such as those for capsular polysaccharide synthesis and biofilm formation, as well as previously unrecognized candidates, including chaperone-usher pilus biosynthesis, spermidine synthesis, Type VI secretion effectors, and an RTX toxin-like protein. Several of the clinically enriched gene clusters have been independently lost in three V. vulnificus clades, suggesting convergent evolution and a distinct ecological niche shared by these claded. Finally, we used the clinically enriched genes to design PCR primers for detecting and monitoring pathogenic V. vulnificus strains, providing a valuable tool for surveillance and public health efforts.