Intra-seafood strain diversity and temporal dynamics of Vibrio parahaemolyticus in a retail stall

Understanding the reservoirs and transmission dynamics of foodborne pathogens is critical for developing effective surveillance and control strategies. Here, we investigate the strain-level diversity and temporal dynamics of Vibrio parahaemolyticus, the leading cause of seafood-associated infections worldwide, through a three-month longitudinal sampling of a single retail seafood stall. Whole-genome sequencing of 238 isolates (2-38 per item) from individual oysters and clams revealed exceptionally high intra-seafood strain diversity, with a median of eight (range: 2-32) distinct sequence types per item. Clonal groups (CGs), defined as clusters of closely related strains sharing recent ancestry, were rarely observed across sampling time points, indicating a highly dynamic and transient population structure in the retail environment. Only a small subset of CGs was shared between seafood items or aquaculture water, suggesting that cross-contamination within the stall occurs less frequently than anticipated. Together, these findings provide the first direct evidence of pronounced intra-seafood strain diversity, rapid temporal turnover, and possibly limited cross-item transmission of V. parahaemolyticus in retail seafood, highlighting the complexity of the ecological reservoirs and transmission dynamics of foodborne pathogens.