Genomic and Pangenomic Insights into Aeromonas salmonicida subsp. oncorhynchi subsp. nov.

The strain A-9^T, isolated from <i>Oncorhynchus mykiss</i> (rainbow trout) in a Turkish aquaculture facility, was characterized through integrated phenotypic, phylogenetic, and genomic analyses. Whole-genome sequencing revealed a 5.21 Mb circular chromosome (GC content: 58.16%) and three plasmids encoding proteins for mobilization and toxin-antitoxin systems. Multilocus phylogenetic analysis (MLPA) using seven housekeeping genes supported the distinct lineage of A-9^T. Digital DNA-DNA hybridization (77.6-78.6%) and average nucleotide identity values (96.59-97.58%) confirmed taxonomic divergence from all currently recognized <i>A. salmonicida</i> subspecies. Comparative proteomic and pangenomic analyses identified 328 strain-specific genes, including virulence factors, secretion system components (Type II and Type VI), and efflux-related proteins. Although genes encoding Type III secretion systems and biofilm formation were absent, A-9^T harbored a broad virulence gene repertoire and resistance determinants, including <i>OXA-956</i>, <i>cphA5</i>, and <i>FOX-20</i>, supporting a multidrug-resistant phenotype. Based on its genomic, phenotypic, and functional distinctiveness, we propose the novel taxon <i>Aeromonas salmonicida</i> subsp. <i>oncorhynchi</i> subsp. nov. (type strain A-9^T = LMG 33538^T = DSM 117494^T), expanding the taxonomic landscape of the <i>A. salmonicida</i> complex and offering insights into fish-associated bacterial evolution.