Unmasking Vibrio paracholerae: Genomic Reclassification and Epidemiology

Abstract

The genus Vibrio encompasses globally relevant pathogens, of which Vibrio cholerae is the best known due to its role in cholera. Closely related species within the Cholerae clade--Vibrio paracholerae, Vibrio metoecus, and Vibrio tarriae--were long misclassified as non-O1/O139 V. cholerae. The objective of this study was to analyze all 13,000+ available V. cholerae genomes in GenBank to determine the presence of species from the Cholerae clade. Genome-wide analyses using Mash, Whole-genome based Average Nucleotide Identity (gANI), and digital DNA-DNA hybridization (dDDH) reclassified 193 unique genomes as V. paracholerae, while V. metoecus and V. tarriae were not identified. Phylogenomic analyses revealed that V. paracholerae forms distinct but relatively homogeneous lineages, spanning clinical, environmental, and animal sources over a period of more than a century. Virulence profiling revealed the absence of CTX and TCP; however, most genomes exhibited other virulence factors, including hemolysins, RTX toxins, colix toxin, and a conserved type VI secretion system. Resistome analysis revealed several antibiotic resistance genes, many of which were incorporated into superintegrons, highlighting the role of V. paracholerae as a reservoir of resistance determinants. Importantly, two genomic markers exhibited high discriminatory power for species identification, providing robust tools for epidemiological surveillance. These findings underscore the relevance of V. paracholerae for clinical and epidemiological monitoring.