Genetic diversity of the human pathogen Vibrio vulnificus: A new phylogroup

Department of Biotechnology and Food Engineering, Technion, Israel Institute of Technology, Haifa 32000, Israel.
International journal of food microbiology (Impact Factor: 3.08). 02/2012; 153(3):436-43. DOI: 10.1016/j.ijfoodmicro.2011.12.011
Source: PubMed


The biotype 3 group of the human pathogen Vibrio vulnificus emerged in Israel probably as a result of genome hybridization of two bacterial populations. We performed a genomic and phylogenetic study of V. vulnificus strains isolated from the environmental niche from which this group emerged - fish aquaculture in Israel. The genetic relationships and evolutionary aspects of 188 environmental and clinical isolates of the bacterium were studied by genomic typing. Genetic relations were determined based on variation at 12 variable number tandem repeat (VNTR, also termed SSR) loci. Analysis revealed a new cluster, in addition to the main groups of biotype 1& 2 and biotype 3. Similar grouping results were obtained with three different statistical approaches. Isolates forming this new cluster presented unclear biochemical profile nevertheless were not identified as biotype 1 or biotype 3. Further examination of representative strains by multilocus sequence typing (MLST) of 10 housekeeping genes and 5 conserved hypothetical genes supported the identification of this as yet undiscovered phylogroup (phenotypically diverse), termed clade A herein. This new clonal subgroup includes environmental as well as clinical isolates. The results highlight the fish aquaculture environment, and possibly man-made ecological niches as a whole, as a source for the emergence of new pathogenic strains.

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    • "V. vulnificus colonies were PCR-amplified for detection of the vvh gene (Broza et al., 2007). V. vulnificus isolates were identified by biochemical tests as previously described (Broza et al., 2012). "
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    ABSTRACT: Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains of V.vulnificus are biochemically classified into three biotypes. The newly emerged biotype 3 appears to be rather clonal and geographically restricted to Israel, where it caused an outbreak of wound infections and bacteremia. To understand the evolution of the bacterium's genome, we sequenced and analyzed the genome of biotype 3 strain VVyb1(BT3), and then conducted a microbial environmental survey of the hypothesized niche from which it probably evolved. The genome of this environmental isolate revealed higher similarity to the published biotype 1 genomes of clinical strains (90%) than to the environmental strains (87%), supporting the virulence of the biotype 3 group. Moreover, 214 of the total 5361 genes were found to be unique to strain VVyb1(BT3), having no sequence similarity to any of the known genomes of V.vulnificus; 35 of them function in DNA mobility and rearrangement, supporting the role of horizontal gene transfer in genome evolution. Interestingly, 29 of the ‘unique’ genes had homologies among Shewanella species. In a survey conducted in aquaculture ponds in Israel, we successfully co-isolated Shewanella and V.vulnificus from the same niche, further supporting the probable contribution of Shewanella to the genome evolution of biotype 3. Indeed, one gene was found in a S.algae isolate. Surprisingly, molecular analysis revealed that some of the considered unique genes are harbored by nonsequenced biotype 1 strains isolated from the same environment. Finally, analyses of the biotype 3 genome together with the environmental survey suggested that its genome originated from a biotype 1 Israeli strain that acquired a rather small number of genes from other bacterial species in the niche, such as Shewanella. Therefore, aquaculture is likely to play a major role as a man-made ecological niche in bacterial evolution, leading the emergence of new pathogenic groups in V.vulnificus.
    Frontiers in Microbiology 12/2013; 4:393. DOI:10.3389/fmicb.2013.00393 · 3.99 Impact Factor
    • "MLST of housekeeping genes together with antigenencoding genes successfully differentiated E. faecalis at the strain level, and showed a genetic relatedness among BVE (beta-lactamase + , vancomycin R , endocarditis) clinical isolates (Nallapareddy et al., 2002, 2005). MLST may be relied on additional sources of sequence variation, such as 'conserved hypothetical' genes, which were successfully used for strain typing of other bacterial species (Broza et al., 2012; Buhnik-Rosenblau et al., 2012). This cluster of genes with unknown function is predicted to be present in the genomes of all members of the same species, and different 'conserved hypothetical' genes may present various degrees of polymorphism among strains. "
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    International journal of food microbiology 04/2013; 165(1):27-34. DOI:10.1016/j.ijfoodmicro.2013.04.009 · 3.08 Impact Factor
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    ABSTRACT: We report the first genome sequence of the pathogenic Vibrio vulnificus biotype 3. This draft genome sequence of the environmental strain VVyb1(BT3), isolated in Israel, provides a representation of this newly emerged clonal group, which reveals higher similarity to the clinical strains of biotype 1 than to the environmental ones.
    Genome Announcements 02/2013; 1(2). DOI:10.1128/genomeA.00136-13
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