title: Genome-wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus biotype 3.
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.
authors.affiliation: Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Nili
authors.initials: N
authors.lastname: Raz
authors.affiliation: Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Yael
authors.initials: Y
authors.lastname: Danin-Poleg
authors.affiliation: Department of Chemistry, Tufts University, Medford, Massachusetts, United States of America.
authors.forename: Ryan B
authors.initials: RB
authors.lastname: Hayman
authors.affiliation: Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Yudi
authors.initials: Y
authors.lastname: Bar-On
authors.affiliation: Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Alex
authors.initials: A
authors.lastname: Linetsky
authors.affiliation: Bioinformatics Knowledge Unit, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Michael
authors.initials: M
authors.lastname: Shmoish
authors.affiliation: Department of Microbiology, Faculty of Biology, University of Valencia, Valencia, Spain.
authors.forename: Eva
authors.initials: E
authors.lastname: Sanjuán
authors.affiliation: Department of Microbiology, Faculty of Biology, University of Valencia, Valencia, Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Amaro
authors.affiliation: Department of Chemistry, Tufts University, Medford, Massachusetts, United States of America.
authors.forename: David R
authors.initials: DR
authors.lastname: Walt
authors.affiliation: Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Yechezkel
authors.initials: Y
authors.lastname: Kashi
mesh_terms: D019143:Evolution, Molecular; D016679:Genome, Viral; D020641:Polymorphism, Single Nucleotide; D041261:Vibrio vulnificus / Q000235:genetics*