Pathogenic bacterium Citrobacter braakii isolated from Procambarus clarkii triggers oxidative stress, apoptosis, and changes in the intestinal microbiome and metabolome

• Pathogenic mechanisms of Citrobacter braakii in Procambarus clarkii • Oxidative Stress and Apoptosis Induced by C. braakii Infection • Disruption of Gut Microbiota and Metabolic Pathways by C. braakii • High Antibiotic Resistance of C. braakii YDB-2 in Aquaculture Foodborne pathogens pose significant threats to the safety of aquatic products. This study investigated the pathogenic effects and mechanisms of Citrobacter braakii YDB-2, a bacterium isolated from diseased crayfish ( Procambarus clarkii ). Through 16S rRNA sequencing, untargeted metabolomics, and comprehensive biochemical and histopathological analyses, we found that YDB-2 infection markedly disrupted the intestinal microbiota of P. clarkii , reducing alpha-diversity and altering microbial composition. Metabolomic analysis revealed significant perturbations in pathways such as arachidonic acid metabolism, ABC transporters, and serotonergic synapses, closely associated with oxidative stress and apoptosis. Infected P. clarkii exhibited elevated malondialdehyde and cortisol levels, enhanced antioxidant enzyme activities (SOD, CAT), and upregulated expression of immune-regulatory ( IL-10, TNF-α ) and apoptotic ( p53, caspase-3 ) genes. Histopathological examination confirmed severe intestinal damage. Additionally, antimicrobial susceptibility tests showed YDB-2’s high resistance to multiple common antibiotics, posing challenges for pathogen control. These findings provide critical insights into the pathogenicity of C. braakii and its impact on aquatic animal health and food safety, with implications for aquaculture management.