Whole genome sequencing reveals recA gene recombination, virulence factors, antibiotic resistance, and emergence of clonal complexes in Vibrio parahaemolyticus associated with acute hepatopancreatic necrosis disease (AHPND) in shrimp.

The AHPN disease, caused by Vibrio parahaemolyticus, is a critical threat to global shrimp aquaculture. In this study, we sequenced and analyzed 5 AHPND-associated V. parahaemolyticus genomes, referred to as CGVP strains (CGVP3, CGVP8, CGVP10, CGVP11, and CGVP18) that were isolated during the 2016 disease outbreak in Korea. These genomes, averaging ∼ 5.3 Mbp, consist of two circular chromosomes (3.3-3.4 Mbp and 1.8-2.0 Mbp) and a 69 kbp plasmid carrying pirABvp toxin genes. Within the genomes, a unique 20.6 kbp insertion in the recA gene, characterized by a lower GC content and 15 open reading frames (ORF), was identified, suggesting a novel genetic recombination event. The phylogenetic and population analyses assigned these genomes to a clonal complex (CC) named CC 917, which exhibits high intra-complex similarity (1-826 SNPs and 99.62-99.98 % ANI) but diverges significantly from strains outside this complex (>20,000 SNPs, <98.09 % ANI). Comparative plasmid analysis revealed high ANI (≥99.86 %) among CC 917 plasmids despite its differences in phylogenetic clustering. Antibiotic resistance profiling identified conserved resistance genes for tetracyclines, beta-lactams, and fluoroquinolones in the CC 917. Virulence factor analysis highlighted diverse profiles for adherence, antiphagocytosis, and chemotaxis genes, while prophage analysis revealed distinct insertions among 5 V. parahaemolyticus genomes in the CC 917. The findings of this study highlight the emergence of AHPND-causing CCs in Korea and the genetic recombination in recA gene, advancing our understanding of the epidemiology, virulence mechanisms, and resistance patterns of this pathogen. This knowledge contributes to improved strategies for controlling AHPND outbreaks and mitigating impacts on shrimp aquaculture.