Genetic and Risk Profiling of Antibiotic Resistance in Vibrio parahaemolyticus: Genomic Insights from 1950 to 2023

Background: The misuse of antibiotics in aquaculture and clinical settings promotes drug resistance in food-related microbes. Vibrio parahaemolyticus, a global pathogen linked to diarrheal disease and food safety concerns, warrants a systematic assessment of its resistance. Methods: We analyzed 9757 high-quality V. parahaemolyticus genomes retrieved from NCBI (1950–2023). ARGs, mobile genetic elements (MGEs), plasmid replicons, sequence types, and virulence genes were identified. Associations between ARGs and genomic/macro-level factors were assessed, and strain-level resistance risk was evaluated using arg_ranker. Results: Among all sequenced strains, 99.59% were pathogenic, and 23.57% were food and aquatic animal sources. Furthermore, pan-resistome analysis indicated that ARGs carried by the V. parahaemolyticus population are expanding. Notably, most ARG types were enriched in strains from food and aquatic animals. In terms of temporal trends, shifts in resistance categories highlight tetracyclines, penams, and phosphonic acid antibiotics as priority surveillance targets, given that their associated ARGs have recently increased. Consistent with these findings, a positive correlation was found between ARG abundance and mobile genetic element (MGE) count per strain, specifically with tnpA as the most frequently co-occurring MGE. In addition, dynamic changes in predominant plasmid replicon types were documented, among which IncA/C2 and Col3M show co-occurrence with high-risk ARGs. Finally, risk assessment classified 95.18% of strains as Risk Level IV (lowest). Conclusions: Although the overall global resistance risk remains low, strains from food and aquatic animals contained the highest proportion of higher-risk (Rank I and II) strains among all sources. This study provides updated insights into antimicrobial resistance trends in V. parahaemolyticus and offers a theoretical foundation for guiding future resistance management strategies.