General assessment of approaches to the identification of aquatic bacterial pathogens: A methodological review

Abstract

In the evolving biosphere, pathogenic microorganisms that cause disease may undergo phenotypic changes. While some of these changes result in new variants or mutants, others lead to the emergence of novel pathogens. Such phenotypic changes as well as advances in technology and analytical methods and the identification of genomic sequences of microbial DNA have brought about new methodological approaches in the diagnosis of bacterial diseases. Although bacterial identification was originally based on phenotypic characteristics, later researchers claimed that bacteria could be accurately identified by only gene sequencing and generally by the sequencing of the 16S ribosomal RNA gene region. Currently, there is still disagreement between classical microbiologists and those using new genomic sequence technology over the best method for identification. Fish are cold-blooded animals, and fish pathogens generally exhibit psychrophilic characteristics. Many bacterial identification systems that are used to identify mesophilic bacteria remain useless for identifying fish pathogens because the optimum incubation temperatures for mesophilic bacteria are 35-37 degrees C. Bacteria that are pathogenic to piscine species require specific media for their cultivation at lower incubation temperatures (15-28 degrees C), and this limits both their growth in culture and subsequent identification by phenotype-based methods. This review presents a comprehensive overview of the isolation and identification of bacterial fish pathogens by optimal culture conditions, biochemical tests, colorimetric methods for rapid identification systems, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and immunological and molecular methods, as well as an overview of the detection of uncultivable bacteria and the use of anamnesis. We conclude that the accurate identification of fish pathogens requires the use of different methods, including phenotype- and genotype-based tests, and the evaluation of anamnesis.