Abstract
Vibrio parahaemolyticus is a major foodborne pathogen worldwide. The increasing number of cases of V. parahaemolyticus infections in China indicates an urgent need to evaluate the prevalence and genetic diversity of this pathogenic bacterium. In this paper, we introduce the Foodborne Vibrio parahaemolyticus genome database (FVPGD), the first scientific database of foodborne V. parahaemolyticus distribution and genomic data in China, based on our previous investigations of V. parahaemolyticus contamination in different kinds of food samples across China from 2011 to 2016. The dataset includes records of 2,499 food samples and 643 V. parahaemolyticus strains from supermarkets and marketplaces distributed over 39 cities in China; 268 whole-genome sequences have been deposited in this database. A spatial view on the risk situations of V. parahaemolyticus contamination in different food types is provided. Additionally, the database provides a functional interface of sequence BLAST, core genome multilocus sequence typing, and phylogenetic analysis. The database will become a powerful tool for risk assessment and outbreak investigations of foodborne pathogens in China.
Highlights
Background & SummaryVibrio parahaemolyticus is a halophilic, gram-negative bacterium that is commonly found in estuarine and marine environments worldwide
A core genome multilocus sequence typing scheme was provided to analyze the epidemiology of V. parahaemolyticus in China according to the genomic information
This database demonstrates the risk level of V. parahaemolyticus contamination in different kinds of food samples collected from all over China and provides a series of high-quality genomes for investigating the genetic relationships of foodborne V. parahaemolyticus strains from multiple temporal-spatial niches
Summary
Vibrio parahaemolyticus is a halophilic, gram-negative bacterium that is commonly found in estuarine and marine environments worldwide. A core genome multilocus sequence typing (cgMLST) scheme was provided to analyze the epidemiology of V. parahaemolyticus in China according to the genomic information This database demonstrates the risk level of V. parahaemolyticus contamination in different kinds of food samples collected from all over China and provides a series of high-quality genomes for investigating the genetic relationships of foodborne V. parahaemolyticus strains from multiple temporal-spatial niches. This database will facilitate the risk assessment of foodborne V. parahaemolyticus in China and contamination tracing of V. parahaemolyticus infections in the future
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