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 Vibrio cholerae . The objective of this study was to analyse 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 and digital DNA–DNA hybridization reclassified 190 unique genomes as V. paracholerae , while V. metoecus and V. tarriae were not detected. Phylogenomic analyses revealed that V. paracholerae forms distinct lineages, spanning clinical, environmental and animal sources over a period of more than a century. Virulence profiling revealed the absence of cholera toxin and toxin-coregulated pilus; however, most genomes exhibited other virulence factors, including haemolysins, RTX toxins, cholix toxin and a conserved type VI secretion system. Resistome analysis revealed multiple antibiotic resistance genes, several of which were embedded within superintegron regions, reinforcing the role of V. paracholerae as a reservoir of resistance determinants. Importantly, we identified five putative gene markers with high sensitivity and specificity for discriminating the two species, providing a tool for diagnostic applications and epidemiological surveillance. These findings reveal an unsuspected epidemiological scenario for V. paracholerae , which should be considered in clinical monitoring and public health strategies involving the Cholerae clade.
Morgado et al. (Mon,) studied this question.