Genome-Resolved Co-Infection by <i>Aeromonas veronii</i> and <i>Shewanella</i> sp. in Koi Carp: A Zoonotic Risk for Aquarists

Co-infections are increasingly recognized as drivers of disease in ornamental fish, yet their genomic underpinnings and zoonotic implications remain underexplored compared to farmed species. Leveraging a One Health perspective, we investigated an acute mortality event in koi carp and characterized a co-infection by opportunistic aquatic bacteria that are also implicated in human disease. We isolated <i>Aeromonas veronii</i> and <i>Shewanella</i> sp. from a moribund koi using culture, biochemical assays, and MALDI-TOF MS, then generated draft genomes and performed orthology (OrthoVenn3), pathway annotation (KEGG BlastKOALA/Mapper), secondary-metabolite mining (antiSMASH), and virulence/resistome screening (VFDB/CARD), complemented by antimicrobial susceptibility testing. Clinically, affected fish showed dropsy/ascites, scale loss, abnormal buoyancy, and reduced activity. Phylogenomics positioned <i>A. veronii</i> Koi-2 within the <i>A. veronii</i> complex near species thresholds (ANI ~96.1%; dDDH ~70.2%), while <i>Shewanella</i> sp. Koi-1 formed a distinct lineage below accepted cut-offs relative to <i>S. seohaensis</i> (ANI ~95.9%; dDDH ~67.6%). The virulome comprised 194 loci in <i>A. veronii</i> Koi-2 and 152 in <i>Shewanella</i> sp. Koi-1 is enriched for adhesion, secretion, iron uptake, and immune-evasion functions. Genotype-phenotype agreement was high for multidrug resistance: <i>Shewanella</i> sp. encoded OXA-436 and <i>rsm</i>A, matching β-lactam resistance and reduced fluoroquinolone/phenicol susceptibility, whereas <i>A. veronii</i> carried <i>tet</i>(A), OXA-1157, <i>cph</i>A3, <i>sul</i>1, and <i>aad</i>A3 consistent with tetracycline, β-lactam, sulfonamide, and aminoglycoside resistance profiles. In conclusion, genome-resolved diagnostics confirmed a mixed <i>Aeromonas-Shewanella</i> co-infection with broad virulence potential and convergent resistance mechanisms, supporting the routine use of genomics to distinguish single- versus mixed-agent disease and to guide dual-coverage, mechanism-aware therapy in ornamental fish medicine while informing zoonotic risk mitigation.