Objective This study aims to investigate the genomic characteristics, virulence, and drug resistance of a pathogenic Aeromonas hydrophila strain isolated from the liver of a diseased Pelteobagrus fulvidraco from a large aquaculture farm in Shanghai. This analysis seeks to provide theoretical insights into the etiology, prevention, and control of the disease.

Method Bacterial strains were isolated and purified bacterial strains from the affected fish, and their identification was based on morphological, physiological, and biochemical traits. PCR detection for virulence genes and drug sensitivity tests were conducted. Strain A01 underwent whole-genome sequencing using the Illumina platform, followed by genome assembly with SPAdes, gene prediction via Prokka, and functional annotation through KEGG, GO, and COG databases. The VFDB and CARD/AMRFinderPlus databases facilitated the identification of virulence and resistance genes, respectively. Strain affinities were evaluated through ANI analysis and phylogenetic tree construction based on homologous single-copy genes, complemented by multilocus sequence typing (MLST) to discern genetic backgrounds.

Result The pathogenic bacterium A01 of P. fulvidraco is A. hydrophila, with a circular genome of approximately 4.93 Mb in length and a GC content of 61.09%. It encodes 4 500 protein genes, 121 tRNAs, and 3 rRNAs. Functional annotation highlighted its genes were involved in carbohydrate metabolism, amino acid metabolism, and membrane transport, suggesting strong environmental adaptability. Analysis uncovered 527 virulencerelated genes, encompassing flagellar assembly, chemotaxis, and secretion system genes, pointing to A01's high invasiveness and pathogenicity. Additionally, 279 resistance genes were identified, including antibiotics such as β-lactams, tetracyclines, aminoglycosides, and polymyxins, indicating a significantly higher MDR risk compared to the reference strain ATCC7966. ANI analysis (>96%) and phylogenetic trees confirmed A01 was closely related to ATCC7966, while MLST typing hinted at a possible correlation between genetic differentiation and variations in pathogenicity and drug resistance. A01 carries nine important virulence genes (aer, act, fla, lip, gcaT, exu, ast, alt and ahyB), indicating strong pathogenicity. Drug sensitivity tests showed that A01 exhibits multidrug resistance (MDR) to 16 of the 24 antibiotics tested.

Conclusion This whole-genome analysis of A. hydrophila strain A01 from P. fulvidraco revealed fundamental genomic characteristics, virulence levels, and resistance gene levels, laying a theoretical groundwork for future studies on the infection mechanism of this pathogen in P. fulvidraco.