Abstract
Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains of V. vulnificus are classified into three different biotypes. The newly emerged biotype 3 has been found to be clonal and restricted to Israel. In the family Vibrionaceae, horizontal gene transfer is the main mechanism responsible for the emergence of new pathogen groups. To better understand the evolution of the bacterium, and in particular to trace the evolution of biotype 3, we performed genome-wide SNP genotyping of 254 clinical and environmental V. vulnificus isolates with worldwide distribution recovered over a 30-year period, representing all phylogeny groups. A custom single-nucleotide polymorphism (SNP) array implemented on the Illumina GoldenGate platform was developed based on 570 SNPs randomly distributed throughout the genome. In general, the genotyping results divided the V. vulnificus species into three main phylogenetic lineages and an additional subgroup, clade B, consisting of environmental and clinical isolates from Israel. Data analysis suggested that 69% of biotype 3 SNPs are similar to SNPs from clade B, indicating that biotype 3 and clade B have a common ancestor. The rest of the biotype 3 SNPs were scattered along the biotype 3 genome, probably representing multiple chromosomal segments that may have been horizontally inserted into the clade B recipient core genome from other phylogroups or bacterial species sharing the same ecological niche. Results emphasize the continuous evolution of V. vulnificus and support the emergence of new pathogenic groups within this species as a recurrent phenomenon. Our findings contribute to a broader understanding of the evolution of this human pathogen.
Highlights
Vibrio vulnificus is a gram-negative halophilic bacterium that is naturally found in marine and estuarine environments the world over [1,2,3]
472 single-nucleotide polymorphism (SNP) were selected by in silico genomewide comparison of genes from two V. vulnificus biotype 1 genomes (YJ016 and CMCP6) [53, 54] and one SNP per gene was picked based on the findings that SNPs are randomly distributed along the two chromosomes (S1 Fig.), ensuring that the genes can be randomly selected for the construction of the variation database
A custom genome-wide SNP microarray was developed to study the evolution of the human pathogen V. vulnificus and to find a common ancestor between biotypes 1 and 3
Summary
Vibrio vulnificus is a gram-negative halophilic bacterium that is naturally found in marine and estuarine environments the world over [1,2,3]. The clinical relevance of V. vulnificus has led to attempts to find indicators of its virulence and pathogenicity [14,15,16,17,18,19], as well as studies into its genetic diversity using various molecular tools, mostly aimed at differentiating clinical from environmental strains [18,19,20,21,22,23,24] Among these tools are molecular typing methods based on a few (,20) genomic loci [12, 21, 25,26,27,28], including multilocus sequence typing (MLST). This latter tool was used with various collections of V. vulnificus isolates (composed of 63 and 115 strains), dividing the species into a few distinct evolutionary lineages with indications of different pathogenic potential [29, 30]: lineages (L) III and I contained isolates of biotype 1 and biotypes 1 and 2, respectively, whereas LII was made up of biotype 3 strains from Israel [30]
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