Insights from the genomic epidemiology of Vibrio parahaemolyticus in Nantong, China: A comparative genomics study of the classic ST3 and emerging ST2516 lineages.

Vibrio parahaemolyticus is a major foodborne pathogen transmitted mainly through contaminated seafood. This study analyzed 157 isolates collected from Nantong, China, during 2023-2024 through antimicrobial susceptibility testing and whole-genome sequencing. Compared with 2018-2021 data, ampicillin resistance dropped from 64.2% (68/106) to 28.7% (45/157), and tetracycline resistance declined from 29.2% (31/106) to zero, reflecting effective antimicrobial management. Fifty-six sequence types (STs) were identified, with ST3 (49.0%, 77/157) and ST2516 (10.2%, 16/157) as the predominant local lineages, mostly from human cases. Food-derived isolates showed greater genetic diversity, with novel STs in 35.2% (19/54) compared with 1.0% (1/101) in human isolates. Global comparative genomics revealed clear genetic divergence between ST3 and ST2516. Virulence gene analysis showed that the tdh gene was detected more frequently in ST3 (81.1%, 309/381) than in ST2516 (42.7%, 135/316). Almost all ST2516 isolates (99.7%, 315/316) lacked the VP1388-VP1390 region in the T6SS1 cluster, a deletion rarely seen in ST3 (0.3%, 1/381). The antimicrobial resistance gene CRP was consistently found in ST2516 but absent in ST3. Core-genome SNP analysis showed that the ST2516 isolate NTVP12 differed by only 26 SNPs from a V. parahaemolyticus strain isolated from an aquatic bird in Thailand, suggesting possible cross-border transmission via avian hosts. Bayesian phylogenetic analysis dated the emergence of ST2516 to around 1987, marking it as a recently evolved lineage adapted to the local environment. This study defines the distinct genomic characteristics of the classical pandemic lineage ST3 and the emerging ST2516, providing key scientific evidence for developing precise prevention and control strategies tailored to different lineages.