Abstract
Vibrio parahaemolyticus is a major foodborne pathogen associated with the consumption of aquatic products. The presence of this bacterium in ready-to-eat (RTE) foods has recently been reported. However, the genomic features and potential risks of V. parahaemolyticus isolated from RTE foods are poorly understood. To help understand the genome-wide characteristics of RTE food isolates, the complete genomes of 27 RTE food isolates were sequenced and compared to those of 20 clinical and 19 other environmental (e.g., water and aquatic product source) isolates using a comparative genomics approach. Analysis revealed that V. parahaemolyticus RTE food isolates had higher numbers of genes on average and possessed more accessory genes than isolates from other sources. Most RTE food isolates were positive for some known virulence-associated genes and pathogenicity islands (PAIs), and some of these isolates were genetically homologous to clinical isolates. Genome-wide association analysis revealed 79 accessory genes and 78 missense single-nucleotide polymorphisms that affected 11 protein-coding genes were significantly associated with RTE food sources. These genes were mostly involved in defense mechanisms and energy production and conversion according to functional annotation in the COG database. KEGG Pathway analysis showed that these genes mainly affected the biofilm formation of V. parahaemolyticus, and subsequent experiments confirmed that nearly all RTE food isolates possessed the ability to form biofilm. The biofilm formation can facilitate the persistence of V. parahaemolyticus in RTE foods, and the presence of virulence-associated genes poses a pathogenic potential to humans. Our findings highlight the potential risk of V. parahaemolyticus in Chinese RTE foods and illustrate the genomic basis for the persistence of these isolates. This study will aid in re-evaluating the food safety threats conferred by this bacterium.
Highlights
Vibrio parahaemolyticus is a gram-negative, halophilic bacterium that is commonly found in estuarine and marine environments worldwide
We identified multiple genes and single-nucleotide polymorphisms (SNPs) that were closely correlated to RTE food sources, and these factors may contribute to defense processes and biofilm formation in V. parahaemolyticus
The size of the draft genomes of the 27 RTE food isolates (Table S1) ranged from 4.95 Mb (Vp34) to 5.99 Mb (Vp26). These isolates contained an average of 4,952 genes, which was significantly more genes than among other environmental (4,718 on average) or clinical isolates (4,580 on average) (Figure 1). This observation suggested that the persistence of V. parahaemolyticus in RTE foods depended on an increased abundance of accessory genes
Summary
Vibrio parahaemolyticus is a gram-negative, halophilic bacterium that is commonly found in estuarine and marine environments worldwide. This microorganism is recognized as one of the most prevalent foodborne pathogens and typically causes acute gastroenteritis in humans (Letchumanan et al, 2014). Our recent report demonstrated the presence of this bacterium in Chinese ready-to-eat (RTE) foods (Xie et al, 2016), a specific type of source that was rarely associated with V. parahaemolyticus infections previously. By adhering to food surfaces and forming biofilms, bacteria may become a persistent source of contamination, threatening the microbiological quality and safety of food products and perhaps even resulting in foodborne disease and economic losses (Van Houdt and Michiels, 2010). In consideration of the mass sale of these foods in China, evaluating the potential pathogenicity of microbes in RTE foods is of critical importance for food security
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