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The genome of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of a fish pathogen

Michael E Reith1*, Rama K Singh1, Bruce Curtis13, Jessica M Boyd1, Anne Bouevitch24, Jennifer Kimball1, Janet Munholland1, Colleen Murphy1, Darren Sarty1, Jason Williams1, John HE Nash25, Stewart C Johnson16 and Laura L Brown16

Author Affiliations

1 NRC Institute for Marine Biosciences, 1411 Oxford Street, Halifax, NS, B3H 3Z1, Canada

2 NRC Institute for Biological Sciences, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada

3 Present address: Biochemistry Department, Dalhousie University, Halifax, NS, B3H 1X5, Canada

4 Present address: DNA Genotek Inc., 29 Camelot Drive, Ottawa, ON, K2G 5W6, Canada

5 Present address: Public Health Agency of Canada, 130 Colonnade Road, Ottawa, ON, K1A 0K9, Canada

6 Present address: DFO Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada

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BMC Genomics 2008, 9:427  doi:10.1186/1471-2164-9-427

Published: 18 September 2008



Aeromonas salmonicida subsp. salmonicida is a Gram-negative bacterium that is the causative agent of furunculosis, a bacterial septicaemia of salmonid fish. While other species of Aeromonas are opportunistic pathogens or are found in commensal or symbiotic relationships with animal hosts, A. salmonicida subsp. salmonicida causes disease in healthy fish. The genome sequence of A. salmonicida was determined to provide a better understanding of the virulence factors used by this pathogen to infect fish.


The nucleotide sequences of the A. salmonicida subsp. salmonicida 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 Tn21 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 A. salmonicida genome. Comparison with the A. hydrophila ATCC 7966T 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.

A limited number of the pseudogenes found in A. salmonicida A449 were investigated in other Aeromonas strains and species. While nearly all the pseudogenes tested are present in A. salmonicida subsp. salmonicida strains, only about 25% were found in other A. salmonicida subspecies and none were detected in other Aeromonas species.


Relative to the A. hydrophila ATCC 7966T genome, the A. salmonicida subsp. salmonicida 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.