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 Vibrio species due to the emergence of epidemic lineages. In Colombia, active surveillance by the National Institute of Health (INS) has confirmed the presence of Vibrio; however, in routine surveillance, these isolates are not genomically characterized. This study focused on the pangenome analysis of six Vibrio species: V. parahaemolyticus, V. vulnificus, V. alginolyticus, V. fluvialis, V. diabolicus and V. furnissii 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 V. parahaemolyticus, we found the virulent ST3 and ST120 genotypes. For V. vulnificus, we identified isolates belonging to lineages 1 and 2. Virulence gene homologues between species were found even in non-pathogenic species such as V. diabolicus. 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.

Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil

“…Analyzing the virulence profiles of our strain, we found genes that encode conserved virulence factors, which have been previously identified in C. indologenes ( 127 ) and other pathogens ( 128 ). The virulence factors found were associated with oxidative stress such as catalase ( kat A, kat G) ( 129 , 130 ); adhesion to host cells and extracellular matrix components (elongation factor Tu ) ( 131 ); colonization of a host organism and in maintenance of bacterial cells in tissues ( ure B) ( 132 ); bacterial growth, stress tolerance, and biofilm formation ( clp P) ( 133 ); modulating the expression of virulence determinants and metabolism-related factor ( clp E) ( 134 ); cell envelope structure, swarmer cell elongation, and subsequent swarm motility ( rff G) ( 135 , 136 ); serum resistance and biofilm formation ( gal E) ( 137 – 139 ); O-antigen nucleotide sugar biosynthesis ( wlb B) ( 140 ); O-antigen-synthesis ( rfb A) ( 141 ); polysaccharide biosynthesis (tviB) ( 142 ); capsular polysaccharide synthesis and antiphagocytosis ( cap 8E, cap 8G) ( 143 , 144 ); survival and virulence ( mgt B) ( 145 , 146 ), stress response ( gro L) ( 147 ); induction of cytokine production, adhesion, and cytotoxicity ( ilp A) ( 148 , 149 ); and infection and immune evasion capacity ( icl , acp ) ( 150 ). Our data indicate that C. indologenes may be a highly virulent strain, presenting putative virulence factors related to structural functions, physiological activity, defense, or invasion that favor the course of pathogenesis.…”

Aeromonas species isolated from aquatic organisms, insects, chicken, and humans in India show similar antimicrobial resistance profiles

“…isolated from infant food ( Carvalho et al, 2020 ), C. sakazakii from powdered milk ( Holý et al, 2020 ), Enterobacter hormaechi from yoghurt ( Tóth et al, 2020 ), Salmonella enterica from ducks, ( Yu et al, 2022 ), and Vibrio spp. from human and environmental samples ( Pérez-Duque et al, 2021 ; Nguyen et al, 2022 ).…”

Distribution and Molecular Characteristics of Vibrio Species Isolated from Aquatic Environments in China, 2020

“…cholerae strains, the absence of antibiotic-resistant genes may because of the absence of the SXT element, which contributes to the trend of drug resistance [ 69 ]. Several aminoglycosides resistance genes strA , strB , aadA , aph(3’)-Ia ( aphA1 ), two chloramphenicol resistance genes cmlA1 , floR and one tetracycline resistance gene tetA were identified in strain B19, indicating that environmental isolates could be reservoirs of resistance genes [ 70 ]. The proportion of antibiotic-resistant gene containing isolates (2.1%, 3/143) in our study was lower than in previous studies focused on environmental Vibrio isolates.…”