Seasonal Occurrence, Population Diversity, and Mobilome Features of Environmental Vibrio parahaemolyticus in Coastal and Estuarine Waters of Haiyan, Zhejiang, China

Vibrio parahaemolyticus is a leading cause of seafood-associated gastroenteritis, yet the ecological and genomic significance of environmental populations as potential reservoirs remains incompletely characterized. From May to October 2024, 108 water samples were collected monthly at one coastal and two estuarine sites in Haiyan, Zhejiang. Confirmed isolates (n = 39) underwent whole-genome sequencing, MLST/cgMLST, virulence and AMR gene screening, integron characterization with BLASTp (+2.17.0) integrase family typing, and viral-region prediction. Culture-based detection was absent in May and rose to 66.7% in October (Cochran–Armitage trend, p = 0.003), with descriptively higher detection at the coastal site. MLST identified 28 STs including four novel types (Simpson’s diversity = 0.953). All isolates lacked tdh, trh, and T3SS2 but retained T3SS1 and MAM7. One estuarine isolate carried CALIN-associated dfrA31 and qnrVC5. All integrases matched VpaIntIA (95.9–100% identity), not mobile class 1–3 integrases. Viral regions were detected in 38/39 isolates; filamentous phage annotations in 52.6%. Haiyan coastal V. parahaemolyticus shows seasonal and spatial patterns, high diversity, and a mobilome dominated by chromosomal super-integrons, underscoring the need for integrase family typing in environmental surveillance.