During the past 3 decades, molecular methods have been progressively introduced for studying bacterial pathogens. These methods have allowed comparisons of bacterial strains and species at the genomic level, and their use has yielded many interesting data. Each of these methods has a certain taxonomic validity range; thus, the molecular method(s) performed in the course of a given study must be adapted to the level of taxonomic data required. For instance, as the 16S rRNA fraction is an excellent "molecular clock", the methods used for investigating the sequence of this molecule (first by oligonucleotide cataloging, then by DNA/rRNA hybridization and actual sequencing) were mostly effective for determining basic relationships among bacteria. Thus, they have yielded interesting information on bacterial phylogeny in the form of dendrograms. Another widely useful molecular method is DNA/DNA hybridization. Utilizing several different techniques, it has proved to be the best way to compare bacterial strains for the purpose of determining whether or not they belong to the same bacterial species. Thus, new bacterial species can be described based on firm genomic grounds. Data obtained by both 16S rRNA investigations and DNA/DNA hybridizations have produced many taxonomic and nomenclatural consequences. Gene detection and production of DNA fingerprints (by restriction endonuclease digestion, hybridization with specific probes, polymerase chain reaction, or any combination of these techniques) potentially allow the detection and identification of bacterial species as well as comparisons of strains within a bacterial species. Thus, these methods became increasingly applicable in diagnosis of infectious diseases and in epidemiological studies. There has been a delay between the application of genomic methods for characterizing human bacterial pathogens and their use for investigating fish-pathogenic bacteria. It is only recently that these techniques have been used for study of such important fish pathogens as Aeromonas salmonicida, Vibrio anguillarum, Renibacterium salmoninarum, and the Flavobacterium-Cytophaga group; but the first results are highly encouraging and the future of DNA-based methods in fish bacteriology seems promising.
DNA/DNA hybridization, 16S rRNA, DNA fingerprints, Molecular probes
