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Aeromonas salmonicida subsp. salmonicida is a Gram-negative bacterium that causes an infectious septicaemia in salmonid fish called furunculosis. Its genome1 consists of a 4.7 Mb chromosome and five plasmids that together contain 4,758 coding sequences (CDSs). Of these CDSs, 170 are pseudogenes, and there are also 88 insertion sequence (IS) elements — both of these features are hallmarks of a genome that is undergoing reduction. For example, mutations or IS elements in flagellar genes explain why A. salmonicida is non-motile even though it contains an entire suite of flagellar genes. The genome encodes multiple virulence factors, including siderophores, toxins, secreted proteases, adhesins, type III secretion systems, a type VI secretion system and an array of antibiotic resistance proteins.

The Gram-positive bacterium Renibacterium salmoninarum causes a kidney disease in salmonid fish. Its 3.1 Mb genome2 contains 3,507 CDSs and, in common with A. salmonicida, contains many pseudogenes (730) and IS elements (80). It encodes virulence factors, such as iron-sequestering proteins, polyketide and capsular polysaccharide synthesis enzymes, haemolysins and the major surface antigen (MSA), the most important virulence factor, which is encoded by two identical genes. MSA is unique to R. salmoninarum and constitutes ∼70% of all proteins on the cell surface. It is processed by a serine proteinase of >100 kDa, but no candidate gene was identified in the genome.

Comparative analyses show that R. salmoninarum and Arthrobacter spp. share 1,562 CDSs and support the previously held view that R. salmoninarum evolved from an Arthrobacter-like ancestor through genome reduction. However, most of the R. salmoninarum virulence genes do not have orthologues in Arthrobacter spp., and therefore might be responsible for the differences in the diseases caused by these bacteria. Renogen, a vaccine used in Atlantic salmonid, consists of live, lyophilized Arthrobacter spp. but does not provide significant protection to Pacific salmonids. The R. salmoninarum genome might therefore help identify novel vaccine candidates.

Mycobacterium marinum , a close relative of Mycobacterium tuberculosis , causes a tuberculosis-like disease in fish and amphibians, and can cause fish-tank or aquarium-tank granuloma in humans following direct contact, through skin cuts and scratches, with infected fish or contaminated aquatic environments. The genome of M. marinum3 comprises a circular chromosome (6.6 Mb) that encodes 5,424 CDSs and a 23 kb plasmid (pMM23). Multilocus sequence typing identified nine distinct sequence types, which have <3% nucleotide variation. Genome comparisons confirmed the close relationship between M. marinum and M. tuberculosis, and suggested divergence of these two organisms from a common generalist, environmental Mycobacterium ancestor. But in contrast to M. tuberculosis, M. marinum has maintained a stable genome, which is necessary for its dual lifestyle: persistence within a broad host range and environmental survival.

M. marinum shares several important virulence factors with M. tuberculosis and other mycobacteria. It has 29 esx genes, which encode specialized secretion systems required for the export of specific members of the 6-kDa ESAT-6 (early secreted antigenic target) protein family, compared with 23 esx genes in M. tuberculosis. Genes that encode polyketide synthases and non-ribosomal peptide synthases that are responsible for the production of a diverse range of polyketide secondary metabolites, some of which are important virulence factors, are also present in higher numbers in M. marinum than in M. tuberculosis. Furthermore, M. marinum has a large repertoire of gene families that encode acidic or asparagine- or glycine-rich proteins, called PE and PPE proteins, which are involved in several aspects of host–pathogen interactions.