Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs

Chao Yang, Yinghui Li, Min Jiang, Lei Wang, Yixiang Jiang, Lulu Hu, Xiaolu Shi, Lianhua He, Rui Cai, Shuang Wu, Yaqun Qiu, Linying Lu, Le Zuo, Qiongcheng Chen, Yarong Wu, Jaime Martinez-Urtaza, Chengsong Wan, Ruifu Yang, Yujun Cui, Qinghua Hu*

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)


Controlling foodborne diseases requires robust outbreak detection and a comprehensive understanding of outbreak dynamics. Here, by integrating large-scale phylogenomic analysis of 3,642 isolates and epidemiological data, we performed ‘data-driven’ outbreak detection and described the long-term outbreak dynamics of the leading seafood-associated pathogen, Vibrio parahaemolyticus, in Shenzhen, China, over a 17-year period. Contradictory to the widely accepted notion that sporadic patients and independent point-source outbreaks dominated foodborne infections, we found that 71% of isolates from patients grouped into within-1-month clusters that differed by ≤6 single nucleotide polymorphisms, indicating putative outbreaks. Furthermore, we showed that despite the long time spans between clusters, 70% of them were genomically closely related and were inferred to arise from a small number of common sources, which provides evidence that hidden persistent reservoirs generated most of the outbreaks rather than independent point-sources. Phylogeographical analysis further revealed the geographical heterogeneity of outbreaks and identified a coastal district as the potential hotspot of outbreaks and as the hub and major source of cross-district spread events. Our findings provide a comprehensive picture of the long-term spatiotemporal dynamics of foodborne outbreaks and present a different perspective on the major source of foodborne infections, which will inform the design of future disease control strategies.

Original languageEnglish
Pages (from-to)1221-1229
Number of pages9
JournalNature Microbiology
Issue number8
Publication statusPublished - Aug 2022


  • Disease Outbreaks
  • Foodborne Diseases/epidemiology
  • Humans
  • Phylogeny
  • Vibrio Infections/epidemiology
  • Vibrio parahaemolyticus/genetics


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