Genomic characterization and comparative genomic analysis of pathogenic Vibrio isolated from aquaculture-grown white-leg shrimp (Penaeus vannamei) in Guangdong and Jiangsu, China

The proliferation of opportunistic pathogens Vibrio parahaemolyticus, Vibrio alginolyticus, and Vibrio owensii have impeded the rapid development of aquaculture farming. The study aimed to analyze the whole genome of pathogenic Vibrio strains associated with hepatopancreatic necrosis in Penaeus vannamei. The analysis included genomic characterization, virulence genes profiling, antibiotic resistance genes (ARGs) identification, antimicrobial resistance phenotypes, clustered regularly interspaced short palindromic repeats (CRISPR) and prophage prediction, multi-locus sequence typing, and pan-genome analysis of Vibrio isolates from Guangdong and Jiangsu provinces, China. Sequence analysis of the specimens revealed 29 V. parahaemolyticus isolates, three V. alginolyticus isolates, and one V. owensii isolate. Their genomes are 4.9–5.9 Mbp in size, with a GC content of 44.4–45.4%. Each Vibrio isolate harbored >120 virulence genes. Out of the 33 isolates, 13 (39%) demonstrated multidrug-resistant (MDR). Notably, at least 14 isolates exhibited heightened resistance to sulfamethoxazole, erythromycin, and amoxicillin, with a cumulative detection of 20 ARGs. Nevertheless, no significant correlation was found between the composition of ARGs and the observed antimicrobial resistance phenotypes. All Vibrio isolates differed in the presence of prophage and CRISPR sequences; and two of these prophages harbored virulence genes but not ARGs. The study identified 17 distinct sequence types (STs) in V. parahaemolyticus isolates, primarily ST415 (n = 5), while two Vibrio isolates were classified as ST3. Using the 117 V. parahaemolyticus strains available in the National Center for Biotechnology Information database as a reference, pan-genomic analysis and phylogenetic analysis of the core genome revealed that clinical isolates of the same STs clustered into the same clade, irrespective of isolation date and geographic origins. In summary, these data enhance our understanding of the molecular characteristics and epidemiological risk of Vibrio strains in southern China, especially regarding shrimp aquaculture.