Comparative genomics reveals specialization and divergent virulence potential in Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii.

Vibrionaceae are a diverse family of bacteria that contain pathogenic species, including those within the Vulnificus clade: Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii. While V. vulnificus is a generally well-characterized environmental pathogen, V. cidicii and V. navarrensis are relatively rare, recently identified species that our current understanding of virulence and environmental adaptation is limited. Here, we investigate genetic relatedness across these three species to identify shared and species-specific genes, including markers of virulence. Using publicly available genome assemblies (n = 76), we evaluated phylogenetic and genomic diversity across this clade. We sampled all available V. navarrensis and V. cidicii genomes and a biodiverse curated set of four V. vulnificus ecotypes to ensure representative coverage. Our results indicate that all three species share 2,313 core genes, many of which are core bacterial functions in addition to pathways important to environmental response, host immune evasion, and iron acquisition. Moreover, V. cidicii and V. navarrensis have extensive genetic similarity between them, including average nucleotide identities >95% and 370 shared genes. Despite this similarity, they both remain more phylogenetically distant from V. vulnificus and lack key virulence genes, such as rtxA, indicating alternative pathogenic potential. Overall, these findings reveal distinct evolutionary strategies within the Vulnificus clade, with V. vulnificus specializing in enhanced pathogenesis, while V. navarrensis and V. cidicii have evolved enhanced environmental persistence capabilities. IMPORTANCE: Vibrio species are important environmental aquatic bacteria that pose a threat to human and animal health across the globe. This study applied comparative genomics to investigate the genetic relatedness of Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii, with special focus on genes associated with environmental adaptation and virulence between and within each species. Results indicate V. navarrensis and V. cidicii share many genes, are phylogenetically close, and exhibit genomic signatures of enhanced environmental persistence and stress tolerance in addition to survival in anthropogenically impacted marine systems. Furthermore, V. vulnificus possesses an overall different virulence potential with the presence of RTX systems. This adds to our understanding of genetic diversity and pathogenic mechanisms within an important group of marine pathogens.