Isolation, identification, and whole-genome analysis of a highly virulent and multidrug-resistant Vibrio harveyi strain associated with mass mortality of Chu’s croaker (Nibea coibor)

Chu's croaker ( Nibea coibor ) is a marine fish species with high nutritional and economic value, particularly due to its premium dried swim bladder. However, intensive farming practices have led to increased disease incidence. During October-November 2024, a sustained mass mortality event occurred in cultured Chu’s croaker in the southern coastal areas of China. To determine the etiology of this outbreak, diseased fish were subjected to necropsy, histopathological examination, and microbiological analysis. Clinical signs of infected fish included ascites, variable-sized white spots in the liver and spleen, and swollen, empty intestines. Histopathological analysis confirmed the liver, spleen, kidney, and gastrointestinal tract as target organs, characterized by multifocal necrotizing granuloma-like lesions in the liver, spleen, and kidney, as well as severe necrosis and inflammation in the gastrointestinal tract. Isolated bacterial strains were identified as Vibrio harveyi through 16S rRNA phylogenetic analysis. Artificial challenge experiments reproduced similar clinical symptoms, with the cumulative mortality rate of 86.7% following infection with strain ZLBH1. This highly virulent, multidrug-resistant strain (ZLBH1), was sequenced using Nanopore sequencing technology, and the whole genome was assembled to investigate its molecular basis for its high virulence and multidrug resistance. Comparative genomics analysis revealed that the isolated strain ZLBH1 carries seven antimicrobial resistance (AMR) genes on its chromosome, including a unique resistance gene, ugd . These AMR genes confer inherent resistance to β-lactam and cephalosporin antibiotics, aligning well with its observed antibiotic resistance phenotype. The virulence factor analysis indicated that ZLBH1 harbors multiple copies of genes associated with adhesion, motility, and immune modulation. Additionally, the key Vibrio virulence gene tlh has also been identified in multiple copies. To our knowledge, this study provides the first comprehensive characterization of V. harveyi infection in Chu’s croaker through integrated bacteriological, histopathological, and genomic approaches, offering valuable references for the sustainable culture of this economically important species and the prevention and control of related diseases. • We isolated a highly virulent and multidrug-resistant Vibrio harveryi strain ZLBH1 from diseased Chu’s croaker ( Nibea coibor ). • The liver, spleen, kidney, and gastrointestinal tract were identified as the primary target organs during infection. • The ZLBH1 genome carried many multicopy virulence genes, including the key Vibrio virulence gene tlh . • The genome harbors resistance genes to β‑lactams, cephalosporins, and tetracycline, consistent with the phenotypic profiles.