Genomic population dynamics of Vibrio parahaemolyticus from shrimp farms and retail markets.

Vibrio parahaemolyticus is a major seafood-associated bacterial pathogen that occurs in marine and aquaculture environments. This study examined genome-wide diversity among 109 V. parahaemolyticus isolates recovered from shrimp farms and retail markets in Zhejiang Province, China. Whole-genome data were analyzed using an all-core-genome single-nucleotide polymorphism (SNP) phylogeny, multilocus sequence typing (MLST), O- and K-locus genotyping, accessory-gene composition, and virulence- and antimicrobial-resistance gene screening. The callable core genome comprised 4,219,518 bp (77.8% of the 5,423,743-bp reference genome), and 396,244 variable core-genome SNP sites were retained for phylogenetic reconstruction. The isolate collection was highly diverse, with 80 isolates assigned to 47 established sequence types, 12 showing complete allelic profiles without an established ST, and 17 showing unresolved MLST profiles. Eleven O-locus and 30 K-locus categories were represented, producing 70 distinct ST-O-K profiles. Accessory-gene ordination showed extensive overlap between farm and market isolates. Sampling source explained 2.6% of accessory-genome variation, whereas sample matrix was not significantly associated after false-discovery-rate correction. Virulence and antimicrobial-resistance determinants included widely detected genes and less frequent accessory determinants. Among 23 ST-O-K profiles represented by at least two isolates, within-profile pairwise core-SNP differences ranged from 3 to 47,402 SNPs, showing that identical conventional typing profiles did not consistently indicate close genome-wide similarity. These findings define a genetically heterogeneous V. parahaemolyticus population within shrimp production and retail environments and demonstrate the value of genome-wide characterization for distinguishing bacterial isolates associated with seafood production and distribution.