Sea Cucumber Disease Linked to Multidrug-Resistant Bacterial Strain

Skin ulceration disease (SUD) increasingly threatens sea cucumber (Apostichopus japonicus) aquaculture. In this study, we isolated and characterized the associated pathogen from diseased sea cucumbers using phenotypic and whole-genome analyses. Naturally infected individuals exhibited white ulcer spots, evisceration, and tissue disintegration. Multiple strains were isolated and identified as Pseudomonas putida using ANI and dDDH, supported by 16S rRNA NJ phylogenetic analysis. One representative strain, designated WL2, was selected for further analysis, with its species classification confirmed by Non-Redundant Protein database (NR) annotation, bacterial morphology observation, and biochemical identification. The pathogenicity of WL2 was demonstrated by a challenge assay, which determined a median lethal dose (LD50) of 2.54 × 107 CFU/mL using probit analysis, indicating high virulence. Furthermore, whole-genome sequencing was used to elucidate the mechanistic basis of pathogenicity and identify a suite of virulence-associated genes mainly involved in motility (flagella and type IV pili), immune evasion (LPS, LOS, and alginate), and iron acquisition (pyoverdine), providing a genetic framework for understanding SUD pathogenesis. Antibiotic susceptibility testing showed multidrug resistance to 19 antibiotics and susceptibility to cefotaxime, ceftriaxone, imipenem, and aztreonam; the resistance phenotype was supported by a corresponding resistome, including mexw, mexb, mexf, baca, and adeF. The observed optimal growth at 30.22 °C and low salinity (10.78‰) raises the testable hypothesis that outbreak risk may be elevated when environmental conditions favor bacterial proliferation. For therapeutic management, we propose a framework incorporating environmental monitoring (temperature, salinity, pH), targeted antibiotic selection (prioritizing cephalosporins), and long-term alternatives such as phage therapy. To our knowledge, this study provides the first complete whole-genome and genetic blueprint of P. putida associated with SUD in sea cucumbers, providing actionable insights for SUD control.