Genomic and Pangenomic Insights into subsp. subsp. nov.

The strain A-9, isolated from (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. Digital DNA-DNA hybridization (77.6-78.6%) and average nucleotide identity values (96.59-97.58%) confirmed taxonomic divergence from all currently recognized 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 harbored a broad virulence gene repertoire and resistance determinants, including , , and , supporting a multidrug-resistant phenotype. Based on its genomic, phenotypic, and functional distinctiveness, we propose the novel taxon subsp. subsp. nov. (type strain A-9 = LMG 33538 = DSM 117494), expanding the taxonomic landscape of the complex and offering insights into fish-associated bacterial evolution.