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Volume 8, Issue 2

Identification of pandemic clade-specific genetic marker with genomic insight into Open Access

Abstract

is a foodborne pathogen commonly present in seafood. Of the various 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 strains by comparing non-pandemic and pandemic strains using whole-genome sequencing. Phylogenetic analysis of 163 . 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 and establish a reliable method for monitoring pandemic strains.

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  • Accepted:
  • Published Online:
Keyword(s): genetic marker , genomic island , pandemic clade , Vibrio parahaemolyticus and whole-genome sequencing
Funding
This study was supported by the:
  • Research Institute for Microbial Diseases, Osaka University (Award JRPRIMD24B8)
    • Principal Award Recipient: MasatomoMorita
  • National BioResource Project (JP)
    • Principal Award Recipient: TetsuyaIida
  • Japan Agency for Medical Research and Development (Award JP20wm0125006)
    • Principal Award Recipient: TOSHIOKODAMA
  • Japan Agency for Medical Research and Development (Award JP22wm0125010)
    • Principal Award Recipient: KazuhisaOkada
  • Japan Agency for Medical Research and Development (Award JP22wm0225023)
    • Principal Award Recipient: TOSHIOKODAMA
  • Japan Agency for Medical Research and Development (Award JP23fk0108663)
    • Principal Award Recipient: HidemasaIzumiya
  • Japan Agency for Medical Research and Development (Award JP233fa627004)
    • Principal Award Recipient: TOSHIOKODAMA
  • Japan Agency for Medical Research and Development (Award JP24fk0108683)
    • Principal Award Recipient: YukihiroAkeda
© 2026 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2026-02-26
2026-03-12

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/content/journal/acmi/10.1099/acmi.0.001067.v4
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Identification of pandemic clade-specific genetic marker with genomic insight into Vibrio parahaemolyticus
Access Microbiology 8, 001067.v4 (2026); https://doi.org/10.1099/acmi.0.001067.v4
/content/journal/acmi/10.1099/acmi.0.001067.v4
/content/journal/acmi/10.1099/acmi.0.001067.v4
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