Genomic and Pangenomic Insights into Aeromonas salmonicida subsp. oncorhynchi subsp. nov.
2025
Nihed Ajmi | Muhammed Duman | Hilal Ay | Izzet Burcin Saticioglu
The strain A-9T, isolated from Oncorhynchus mykiss (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&ndash:antitoxin systems. Multilocus phylogenetic analysis (MLPA) using seven housekeeping genes supported the distinct lineage of A-9T. Digital DNA&ndash:DNA hybridization (77.6&ndash:78.6%) and average nucleotide identity values (96.59&ndash:97.58%) confirmed taxonomic divergence from all currently recognized A. salmonicida 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-9T harbored a broad virulence gene repertoire and resistance determinants, including OXA-956, cphA5, and FOX-20, supporting a multidrug-resistant phenotype. Based on its genomic, phenotypic, and functional distinctiveness, we propose the novel taxon Aeromonas salmonicida subsp. oncorhynchi subsp. nov. (type strain A-9T = LMG 33538T = DSM 117494T), expanding the taxonomic landscape of the A. salmonicida complex and offering insights into fish-associated bacterial evolution.
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