Identification of pandemic clade-specific genetic marker with genomic insight into Vibrio parahaemolyticus
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Abstract
Vibrio parahaemolyticus is a foodborne pathogen commonly present in seafood. Of the various V. parahaemolyticus 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 V. parahaemolyticus strains by comparing non-pandemic and pandemic strains using whole-genome sequencing. Phylogenetic analysis of 167 V. parahaemolyticus 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 detection of existing markers. The capacity of VPaI5-PCR 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 V. parahaemolyticus and establishes a reliable method for monitoring pandemic strains.
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Abstract
Vibrio parahaemolyticus is a foodborne pathogen commonly present in seafood. Of the various V. parahaemolyticus 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 V. parahaemolyticus strains by comparing non-pandemic and pandemic strains using whole-genome sequencing. Phylogenetic analysis of 167 V. parahaemolyticus 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 detection of existing markers. The capacity of VPaI5-PCR 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 V. parahaemolyticus and establishes a reliable method for monitoring pandemic strains.
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Funding
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Research Institute for Microbial Diseases, Osaka University
(Award JRPRIMD24B8)
- Principal Award Recipient: Masatomo Morita
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National BioResource Project (JP)
- Principal Award Recipient: Tetsuya Iida
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Japan Agency for Medical Research and Development
(Award JP20wm0125006)
- Principal Award Recipient: TOSHIO KODAMA
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Japan Agency for Medical Research and Development
(Award JP22wm0125010)
- Principal Award Recipient: Kazuhisa Okada
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Japan Agency for Medical Research and Development
(Award JP22wm0225023)
- Principal Award Recipient: TOSHIO KODAMA
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Japan Agency for Medical Research and Development
(Award JP23fk0108663)
- Principal Award Recipient: Hidemasa Izumiya
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Japan Agency for Medical Research and Development
(Award JP233fa627004)
- Principal Award Recipient: TOSHIO KODAMA
-
Japan Agency for Medical Research and Development
(Award JP24fk0108683)
- Principal Award Recipient: Yukihiro Akeda
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