Identification of pandemic clade-specific genetic marker with genomic insight into Vibrio parahaemolyticus

<i>Vibrio parahaemolyticus</i> is a foodborne pathogen commonly present in seafood. Of the various <i>V. parahaemolyticus</i> serotypes reported, O3:K6, O1:K25, O1:KUT and O4:K68 represent the major serotypes among pandemic clones that emerged from 1995 onward. However, new molecular markers of pandemic clones remain unidentified, and limited genomic sequence data are available for non-pandemic strains. Therefore, we aimed to identify novel genetic markers specific to pandemic <i>V. parahaemolyticus</i> strains by comparing non-pandemic and pandemic strains using whole-genome sequencing. Phylogenetic analysis of 163 <i>V</i>. <i>parahaemolyticus</i> strains revealed high genomic diversity within the species. The analysis also revealed a pandemic clade consisting of serotypes O3:K6, O1:K25, O1:KUT and O4:K68 strains isolated after 1995. We identified the genomic island GI-110 (VPaI-5) as a potential marker exclusive to the pandemic clade. Multiplex PCR detection of VPaI-5 demonstrated high specificity for pandemic strains, outperforming the detection of existing markers. The capacity of multiplex PCR for VPaI5 in distinguishing between pandemic and non-pandemic strains was confirmed using clinical isolates from Thailand. Our findings provide valuable insights into the genetic diversity of <i>V. parahaemolyticus</i> and establish a reliable method for monitoring pandemic strains.