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.

Download full-text


Available from: Yael Danin-Poleg
  • Source
    • "However, the use of 'biotyping' in the taxonomy of VV is somewhat controversial. Recently, Broza[100]challenged the classification of VV strains by the biotype scheme because of the ambiguity of this scheme as observed by Biosca et al.[101]for indole-positive, eel-infecting VV strains. Although indole, ODC, and ONPG findings are certainly useful to some extent and are still widely used for taxonomic tests to differentiate sub-species groups of VV, we agree that classification systems of VV based on only three enzymatic reactions might not properly reflect the exquisite taxonomic patterns of VV. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The genetic diversity and population structure of Vibrio vulnificus isolates from Korea and Taiwan were investigated using PCR-based assays targeting putative virulence-related genes and multilocus sequence typing (MLST). BOX-PCR genomic fingerprinting identified 52 unique genotypes in 84 environmental and clinical V. vulnificus isolates. The majority (> 50%) of strains had pathogenic genotypes for all loci tested; moreover, many environmental strains had pathogenic genotypes. Although significant (p < 0.05) inter-relationships among the genotypes were observed, the association between genotype and strain source (environmental or clinical) was not significant, indicating that genotypic characteristics alone are not sufficient to predict the isolation source or the virulence of a given V. vulnificus strain and vice versa. MLST revealed 23–35 allelic types per locus analyzed, resulting in a total of 44 unique sequence types (STs). Two major monophyletic groups (lineages A and B) corresponding to the two known lineages of V. vulnificus were observed; lineage A had six STs that were exclusively environmental, whereas lineage B had STs from both environmental and clinical sources. Pathogenic and nonpathogenic genotypes predominated in MLST lineages B and A, respectively. In addition, V. vulnificus was shown to be in linkage disequilibrium (p < 0.05), although two different recombination tests (PHI and Sawyer’s tests) detected significant evidence of recombination. Tajima’s D test also indicated that V. vulnificus might be comprised of recently sub-divided lineages. These results suggested that the two lineages revealed by MLST correspond to two distinct ecotypes of V. vulnificus.
    Full-text · Article · Nov 2015 · PLoS ONE
  • Source
    • "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). "
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Dec 2013 · Frontiers in Microbiology
    • "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. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Enterococcus faecalis is a common inhabitant of the gastrointestinal tracts of different animals and is also found in other environments, such as plants, soil, food and water. The diverse nature of E. faecalis, which includes pathogenic, commensal and probiotic strains, calls for the development of tools for accurate discrimination and characterization at the strain level. Here we studied the genetic relationships among 106 E. faecalis strains isolated from diverse origins and possessing different degrees of virulence. Strain typing was conducted using a set of selected simple-sequence repeat (SSR) loci combined with multilocus sequence typing (MLST) analysis, which discriminated among the strains and separated them into three main clusters. While pathogenic and commensal isolates were dispersed along the dendrogram, probiotic and cheese-originated strains were highly associated with one specific cluster (cluster 1). The strain panel was further characterized by testing the occurrence of two virulence determinants (esp gene and β-hemolysis). The two determinants showed low abundance among probiotic and cheese-originated strains within cluster 1 when compared to non-cluster 1 cheese-originated strains, indicating a possible association of cluster 1 with non-virulent strains. Our results further emphasize the importance and challenge of precise characterization of E. faecalis strains from various sources.
    No preview · Article · Apr 2013 · International journal of food microbiology
Show more