Journal
NATURE MICROBIOLOGY
Volume 7, Issue 8, Pages 1221-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41564-022-01182-0
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Funding
- National Key Research and Development Program of China [2018YFC1603902, 2017YFC1601500]
- Sanming Project of Medicine in Shenzhen [SZSM201811071]
- China National Science and Technology Major Projects Foundation [2017ZX10303406]
- National Natural Science Foundation of China [32000008, 31770001]
- China Postdoctoral Science Foundation [2020M672836]
- Natural Science Foundation of Guangdong Province [2019A1515011523]
- Youth Innovation Promotion Association, CAS [2022278]
- Shenzhen Key Medical Discipline Construction Fund [SZXK064]
- Key scientific and technological project of Shenzhen Science and Technology Innovation Committee [KCXFZ202002011006190]
- Non-profit Central Research Institute Fund of the Chinese Academy of Medical Sciences [2020-PT330-006]
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This study uses large-scale phylogenomic analysis and epidemiological data to investigate the long-term outbreak dynamics of Vibrio parahaemolyticus, a leading seafood-associated pathogen, in Shenzhen, China. The findings challenge the notion that foodborne infections are predominately caused by sporadic cases and independent point-source outbreaks, instead suggesting that hidden persistent reservoirs are the major source of outbreaks.
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. Long-term spatiotemporal dynamics of foodborne pathogen Vibrio parahaemolyticus outbreaks suggests hidden reservoirs as source of infections.
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