Microbiological diagnostics: From traditional to molecular genetic methods: A literature review

Abstract

The development of new and optimisation of known cultural and molecular genetic methods for accurate species identification of microorganisms is an urgent and practically necessary task that is receiving great attention from researchers. The purpose of this study was to analyse and systematise theoretical scientific data on methods of microbial identification and assess their main advantages and disadvantages. For this purpose, a systematic review of 53 randomised research papers published between 2018 and 2023 was conducted. The search for publications using the keywords “microbiome”, “microbiological diagnostics”, “identification of microorganisms”, “sequencing”, and “omics technologies” in the title or text of the research paper was carried out in Web of Science, Scopus, PubMed, and Google Scholar. The study provides generalised information on traditional and modern methods of microbial identification. It is established that the advantages of traditional diagnostic methods include the possibility of preserving the obtained microorganisms for further research, in particular, for determining their antibiotic sensitivity. Modern molecular genetic methods open up new possibilities for the accurate identification of microorganisms, including those that are difficult to incubate using traditional cultural methods. The use of these methods allows obtaining detailed data on the genetic structure and diversity of microorganisms, which is important in many fields, including microbiology, medicine, and ecology. However, molecular methods are more sensitive to contamination or errors in the sample collection and processing. Moreover, omics technologies (genomics, transcriptomics, proteomics, and metabolomics) open up new opportunities for studying cells at more complex levels of life organisation. In everyday clinical practice, the microbiological method of isolating microbial cultures remains the main one, as it is the only one that allows determining not only the cause of the infection but also the antibiotic sensitivity. However, cultural methods for studying fastidious microorganisms are quite limited. Thus, the results obtained contribute to the development of fast and accurate methods for identifying, classifying, and systematising microorganisms, which facilitates the processes of diagnosis and development of strategies for the control and treatment of infectious diseases in laboratories and clinical institutions