Comparative Genomics of Clinical and Environmental Isolates of Vibrio spp. of Colombia: Implications of Traits Associated with Virulence and Resistance

Abstract

There is widespread concern about the increase in cases of human and animal infections caused by pathogenic <i>Vibrio</i> species due to the emergence of epidemic lineages. In Colombia, active surveillance by the National Institute of Health (INS) has confirmed the presence of <i>Vibrio</i>; however, in routine surveillance, these isolates are not genomically characterized. This study focused on the pangenome analysis of six <i>Vibrio</i> species: <i>V. parahaemolyticus</i>, <i>V. vulnificus</i>, <i>V. alginolyticus</i>, <i>V. fluvialis</i>, <i>V. diabolicus</i> and <i>V. furnissii</i> to determine the genetic architectures of potentially virulent and antimicrobial resistance traits. Isolates from environmental and clinical samples were genome sequenced, assembled and annotated. The most important species in public health were further characterized by multilocus sequence typing and phylogenomics. For <i>V. parahaemolyticus</i>, we found the virulent ST3 and ST120 genotypes. For <i>V. vulnificus</i>, we identified isolates belonging to lineages 1 and 2. Virulence gene homologues between species were found even in non-pathogenic species such as <i>V. diabolicus</i>. Annotations related to the mobilome, integrative mobile and conjugative elements and resistance genes were obtained from environmental and clinical isolates. This study contributes genomic information to the intensified surveillance program implemented by the INS to establish potential sources of vibriosis in Colombia.