Genetic Structure, Function, and Evolution of Capsule Biosynthesis Loci in Vibrio parahaemolyticus

Abstract

Capsule-forming extracellular polysaccharides are crucial for bacterial host colonization, invasion, immune evasion, and ultimately pathogenicity. Due to warming ocean waters and human encroachment of coastal ecosystems, Vibrio parahaemolyticus has emerged as a globally important foodborne enteropathogen implicated in acute gastroenteritis, wound infections, and septic shock. Conventionally, the antigenic properties of lipopolysaccharide (LPS, O antigen) and capsular polysaccharide (CPS, K antigen) have provided a basis for serotyping V. parahaemolyticus, whereas disclosure of genetic elements encoding 13 O-serogroups have allowed molecular serotyping methods to be developed. However, the genetic structure of CPS loci for 71 K-serogroups has remained unidentified, limiting progress in understanding its roles in V. parahaemolyticus pathophysiology. In this study, we identified and characterized the genetic structure and their evolutionary relationship of CPS loci of 40 K-serogroups through whole genome sequencing of 443 V. parahaemolyticus strains. We found a distinct pattern of CPS gene cluster across different K-serogroups and expanded its new 3′-border by identifying glpX as a key gene conserved across all K-serogroups. A total of 217 genes involved in CPS biosynthesis were annotated. Functional contents and genetic structure of the 40 K-serogroups were analyzed. Based on inferences from species trees and gene trees, we proposed an evolution model of the CPS gene clusters of 40 K-serogroups. Horizontal gene transfer by recombination from other Vibrio species, gene duplication is likely to play instrumental roles in the evolution of CPS in V. parahaemolyticus. This is the first time, to the best of our knowledge, that a large scale of CPS gene clusters of different K-serogroups in V. parahaemolyticus have been identified and characterized in evolutionary contexts. This work should help advance understanding on the variation of CPS in V. parahaemolyticus and provide a framework for developing diagnostically relevant serotyping methods.

VPsero: Rapid Serotyping of Vibrio parahaemolyticus Using Serogroup-Specific Genes Based on Whole-Genome Sequencing Data

“…A total of 260 gene orthogroups could be annotated from these representative gene clusters (Supplementary Table 3). Nomenclature or numbering of these orthogroups is compatible with our previous study (Bian et al, 2020). Numbering of gene orthogroups was first recognized in Bian et al (2020) and was kept as is in this study, while numbering of novel gene orthogroups was assigned using OrthoFinder.…”

“…Nomenclature or numbering of these orthogroups is compatible with our previous study (Bian et al, 2020). Numbering of gene orthogroups was first recognized in Bian et al (2020) and was kept as is in this study, while numbering of novel gene orthogroups was assigned using OrthoFinder. Among these gene orthogroups, only 33 appear in LPSgcs.…”

“…In the meantime, the genetic structure of the CPS biosynthesis loci became gradually elucidated over the past two decades ( Guvener and McCarter, 2003 ; Okura et al, 2008 ; Chen et al, 2010 ; Pang et al, 2019 ). Recently, our group identified and characterized the genetic structure of whole CPS loci by expanding our analytical scope into a new 3′ border gene, glpX , which is conserved among all K serogroups ( Bian et al, 2020 ). Collectively, these efforts on clarifying V. parahaemolyticus PSgcs have made in silico serotyping with WGS data possible.…”

“…Incorporating novel genes from other species through recombination may play instrumental roles in the evolution and divergence of PS loci in V. parahaemolyticus , reflecting emergence of novel serogroup populations ( Guo et al, 2017 ; Bian et al, 2020 ). Indeed, unique serogroup-specific gens can also be found in most serogroups ( Chen et al, 2012 ; Bian et al, 2020 ).…”

“…Incorporating novel genes from other species through recombination may play instrumental roles in the evolution and divergence of PS loci in V. parahaemolyticus , reflecting emergence of novel serogroup populations ( Guo et al, 2017 ; Bian et al, 2020 ). Indeed, unique serogroup-specific gens can also be found in most serogroups ( Chen et al, 2012 ; Bian et al, 2020 ). In order to prove the feasibility and test the robustness of unique genes in in silico typing, in the current study, we made comparisons between LPSgc and CPSgc from 43 K and all 12 O serogroups, identified serogroup-specific genes, and developed an in silico algorithm VPsero using these genes as markers.…”