Genome-wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus biotype 3

• Published in: PloS one Vol. 9; no. 12; p. e114576
• Main Authors: Raz, Nili, Danin-Poleg, Yael, Hayman, Ryan B, Bar-On, Yudi, Linetsky, Alex, Shmoish, Michael, Sanjuán, Eva, Amaro, Carmen, Walt, David R, Kashi, Yechezkel
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 19-12-2014; Public Library of Science (PLoS)
• Subjects: Bacteria; Bioinformatics; Biological evolution; Biology; Biology and Life Sciences; Biotechnology; Biotypes; Clinical isolates; Data analysis; Data processing; Deoxyribonucleic acid; DNA; Earth Sciences; Ecological effects; Ecological niches; Ecology and Environmental Sciences; Emergence; Engineering; Evolution; Evolution (Biology); Evolution, Molecular; Evolutionary biology; Fish; Food; Gene transfer; Genome, Viral; Genomes; Genomics; Genotyping; Gram-positive bacteria; Haplotypes; Infections; Luminance distribution; Pathogens; Phylogeny; Polymorphism; Polymorphism, Single Nucleotide; Salmonella; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Species; Studies; Typhoid; Vibrio vulnificus; Vibrio vulnificus - genetics; Water-borne diseases; Waterborne diseases; Israel; United States > US; Massachusetts; Spain
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0114576

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.