Modern Molecular Genetic Methods and Prospects for Their Use for Indication and Identification of Yersinia pestis Strains

Abstract

The review provides an analysis of the literature data on the use of various modern molecular genetic methods for the indication and identification of Yersinia pestis strains with different properties and degrees of virulence, which is due to the diverse natural conditions in which they circulate. The methods are also considered from the perspective of their application at three levels of organizations forming the system of laboratory diagnostics of infectious diseases of the Russian Federation (territorial, regional, and federal) to solve the problem of maintaining the sanitary and epidemiological well-being of the country’s population. The main conditional groups of methods are considered: based on the analysis of the lengths of restriction fragments (ribo- and IS-typing, pulse gel electrophoresis); based on the analysis of specific fragments (DFR typing, VNTR typing); based on sequencing (MLST, CRISPR analysis, SNP analysis); PCR methods (including IPCR, SPA); isothermal amplification methods (LAMP, HDA, RPA, SEA, PCA, SHERLOCK); DNA microarray; methods using aptamer technology; bio- and nanosensors; DNA origami; and methods based on neural networks. As a result of the analysis, it can be concluded that there is rapid development of molecular diagnostics and genetics, which is aimed at increasing efficiency, multifactority, and simplification of application with no need for expensive equipment and highly qualified personnel for analysis. At all levels of the organizations forming the system of laboratory diagnostics of infectious diseases of the Russian Federation, it is possible to use methods based on PCR, isothermal amplification, SHERLOCK, biosensors, and small-sized sequencing devices. At the territorial level, at antiplague stations, the use of immuno-PCR and SPA for the indication of Y. pestis is promising. At the regional level, the introduction of technologies based on the use of aptamers and DNA microarray looks promising. At the federal level, the use of DNA origami methods and new technologies of whole genome sequencing is promising in the framework of advanced identification, molecular typing, and sequencing of the genomes of plague pathogen strains.