| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Aeromonas salmonicida </it>subsp. <it>salmonicida </it>is a Gram-negative bacterium that is the causative agent of furunculosis, a bacterial septicaemia of salmonid fish. While other species of <it>Aeromonas </it>are opportunistic pathogens or are found in commensal or symbiotic relationships with animal hosts, <it>A. salmonicida </it>subsp. <it>salmonicida </it>causes disease in healthy fish. The genome sequence of <it>A. salmonicida </it>was determined to provide a better understanding of the virulence factors used by this pathogen to infect fish.</p> <p>Results</p> <p>The nucleotide sequences of the <it>A. salmonicida </it>subsp. <it>salmonicida </it>A449 chromosome and two large plasmids are characterized. The chromosome is 4,702,402 bp and encodes 4388 genes, while the two large plasmids are 166,749 and 155,098 bp with 178 and 164 genes, respectively. Notable features are a large inversion in the chromosome and, in one of the large plasmids, the presence of a Tn<it>21 </it>composite transposon containing mercury resistance genes and an In2 integron encoding genes for resistance to streptomycin/spectinomycin, quaternary ammonia compounds, sulphonamides and chloramphenicol. A large number of genes encoding potential virulence factors were identified; however, many appear to be pseudogenes since they contain insertion sequences, frameshifts or in-frame stop codons. A total of 170 pseudogenes and 88 insertion sequences (of ten different types) are found in the <it>A. salmonicida </it>genome. Comparison with the <it>A. hydrophila </it>ATCC 7966<sup>T </sup>genome reveals multiple large inversions in the chromosome as well as an approximately 9% difference in gene content indicating instances of single gene or operon loss or gain.</p> <p>A limited number of the pseudogenes found in <it>A. salmonicida </it>A449 were investigated in other <it>Aeromonas </it>strains and species. While nearly all the pseudogenes tested are present in <it>A. salmonicida </it>subsp. <it>salmonicida </it>strains, only about 25% were found in other <it>A. salmonicida </it>subspecies and none were detected in other <it>Aeromonas </it>species.</p> <p>Conclusion</p> <p>Relative to the <it>A. hydrophila </it>ATCC 7966<sup>T </sup>genome, the <it>A. salmonicida </it>subsp. <it>salmonicida </it>genome has acquired multiple mobile genetic elements, undergone substantial rearrangement and developed a significant number of pseudogenes. These changes appear to be a consequence of adaptation to a specific host, salmonid fish, and provide insights into the mechanisms used by the bacterium for infection and avoidance of host defence systems.</p>
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