Aeromonas salmonicida is a globally distributed Gram-negative teleost pathogen, with a wide host range, that live in freshwater and marine environments. A. salmonicida is classified as typical or atypical based on host origin of isolation and phenotype. Five-known subspecies of A. salmonicida have been described, where salmonicida is the only typical subspecies, while the subsp. achromogenes, masoucida, smithia, and pectinolytica are considered as atypical. Genomic differences between A. salmonicida subsp. salmonicida isolates and their relationship with the current classification have not been explored.
Here, we sequenced and compared the genome of four virulent strains to elucidate their molecular diversity and pathogenic evolution. Phenotypes, biochemical and enzymatic profiles were determined. PacBio and MiSeq sequencing platforms were utilized for genome sequencing. Comparative genomics showed that atypical strains belong to the subsp. salmonicida with 99.55 ± 0.25% identity with each other and closely related to typical strains. Typical A. salmonicida J223 is closely related to typical strains, with 99.17% identity to the European strain A449. Genomic differences between atypical and typical strains are strictly related to very distinctive ISs family distribution and plasmid content. Major differences were driven by virulence factors, transcriptional regulators, and non-coding RNAs. Although, plasmidome plays an important role in A. salmonicida virulence and genome plasticity.
In summary, typical strains harbor a larger number of plasmids and virulence related genes, that contribute to their acute virulence. In contrast, atypical strains harbor a single large plasmid and a smaller number of virulence genes, reflected on their less acute and chronic infection. The relationship between the phenotypes and A. salmonicida subspecies taxonomy is not evident. Comparative genomic analysis based on completed genomes revealed that the subspecies classification is a description of different A. salmonicida strains that are adapted to different environmental niches rather than different subspecies.