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The ubiquitous water-borne Gram-negative bacterium Aeromonas salmonicida subsp. salmonicida is the causative agent of furunculosis, a worldwide disease in fish farms. Plasmids carrying antibiotic resistance genes have already been described for this bacterium. The aim of the present study was to identify and characterize additional multidrug resistance plasmids in A. salmonicida subsp. salmonicida. We sequenced the plasmids present in two multiple antibiotic-resistant isolates using highthroughput technologies. We also investigated 19 other isolates with various multidrug resistance profiles by genotyping PCR and assessed their resistance to tetracycline. We identified variants of the pAB5S9 and pSN254 plasmids that carry several antibiotic resistance genes and that have been previously reported in bacteria other than A. salmonicida subsp. salmonicida, which suggests a high level of interspecies exchange. Genotyping analyses and the antibiotic resistance profiles of the 19 other isolates support the idea that multiple versions of pAB5S9 and pSN254 exist in A. salmonicida subsp. salmonicida. We also identified variants of the pRAS3 plasmid. The present study revealed that A. salmonicida subsp. salmonicida harbors a wide variety of plasmids, which suggests that this ubiquitous bacterium may contribute to the spread of antibiotic resistance genes in the environment. The Gram-negative bacterium Aeromonas salmonicida subsp. salmonicida is an opportunistic fish pathogen (1). It is the etiological agent of furunculosis, a disease that especially affects salmonids in fish farms (2). While antibiotics are commonly used to treat A. salmonicida subsp. salmonicida infections, multidrug-resistant isolates have been frequently detected (3-5), preventing the effective treatment of furunculosis.Many fully characterized plasmids from A. salmonicida subsp. salmonicida have provided antibiotic resistance to this species (2). All the known plasmids in A. salmonicida subsp. salmonicida harboring antibiotic resistance genes include at least a tetracycline resistance gene. The vast majority of the plasmids bearing antibiotic resistance genes confer multiple types of resistance to A. salmonicida subsp. salmonicida, including the large (167-kb) plasmid pAsa4, which provides resistance against chloramphenicol, spectinomycin, streptomycin, sulfonamides, tetracycline, mercury, and quaternary ammonium compounds (6). A plasmid bearing multiple resistance genes that is similar to the large pSN254 plasmid in Salmonella enterica (7) has been partially described in A. salmonicida subsp. salmonicida (3). This pSN254-like plasmid can be transferred via conjugation from A. salmonicida subsp. salmonicida to multiple receivers, including Escherichia coli, Edwardsiella tarda, and Aeromonas hydrophila (3).Plasmid variants appear to be relatively frequent in A. salmonicida subsp. salmonicida. The best example is the pRAS3 plasmid. To date, two variants of this plasmid (pRAS3.1 and pRAS3.2) have been described (8). The differences between them are very s...

BackgroundAeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes of A. salmonicida subspecies have been reported to date.ResultsWe sequenced the genomes of additional A. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between A. salmonicida subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with A. salmonicida subsp. pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike the A. salmonicida psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy.ConclusionInsertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in A. salmonicida subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2381-3) contains supplementary material, which is available to authorized users.