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Updated: Sep 18, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Genomic and Pangenomic Insights into Aeromonas salmonicida subsp. oncorhynchi subsp. nov
Nihed Ajmi1, Muhammed Duman2, Hilal Ay3
1Department of Aquatic Animal Diseases, Graduate School of Health Science, Bursa Uludag University, Bursa 16059, Türkiye.
Abstract:
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-antitoxin systems. Multilocus phylogenetic analysis (MLPA) using seven housekeeping genes supported the distinct lineage of A-9T. Digital DNA-DNA hybridization (77.6-78.6%) and average nucleotide identity values (96.59-97.58%) 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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