Relevance. The study of natural foci of infections transmitted by ticks is an integral part of the study of the clinical and epidemiological characteristics of this group of diseases and their manifestations in various endemic areas.The aim of this work was to obtain up-to-date information regarding the spread of the most epidemically significant pathogens of bacterial infections carried by ticks in natural foci of the Baikal region using molecular analysis methods.Materials & Methods. Analyzed infections of I. persulcatus with pathogens transmitted by ticks (Borrelia spp., Ehrlichia spp., Anaplasma spp.) in natural foci in the Baikal region of Russia with determination of the species diversity of Borrelia (B. afzelii, B. garinii, B. miyamotoi) in the studied material. The study used RT-PCR for detection.Results. The total infection of ticks with Borrelia - 45.3%, Ehrlichia - 16.0% and Anaplasma - 15.9%. The study shown the unevenness of infection of ticks by pathogens in the study area. The dominant species of Borrelia was B. garinii - 44.0% of cases, in second place was B. miyamotoi - 15.9%, B. afzelii - 13.6%, Borrelia of unidentified species - 34.0%. The analysis recorded the differences in the infection ticks with B. afzelii, B. garinii and B. miyamotoi between different parts of the Baikal region.Conclusions. The obtained data complement and expand the understanding of the species diversity of natural focal infections carried by ticks in the Baikal region and can be used in further scientific research and in organizing preventive and therapeutic measures in case of infection with the pathogens considered in the study.

Background. The study of recombination processes in the CRISPR-Cas loci of Salmonella enterica can help investigate the fundamental evolutionary mechanisms of the CRISPR-Cas system to better understand the acquisition of phage resistance.The aim of the study. To investigate the recombination processes in the proteincoding regions of CRISPR-Cas loci in the genomes of Salmonella enterica serovars Enteritidis, Infantis, and Typhimurium using in silico methods.Materials and methods. The genomic sequences of the Salmonella serovars Enteritidis, Infantis, and Typhimurium were downloaded from the NCBI GenBank database. The coding sequences of cas genes were extracted from the genomes and aligned according to codon position. Recombination events were identified in the resulting alignment using multiple algorithms. Verification of recombination events was performed.Results. A total of 7683 potential recombination events were identified. Among these, 810 (10.54 %) were verified, and 45 (0.59 %) were recognized as results of convergent evolution. Recombination events are detected more frequently between strains belonging to different serovariants than between those of the same serovariant. All serovariants can recombine with each other; however, recombination primarily occurs between Enteritidis and Infantis strains, as well as between Typhimurium and Infantis strains. Infantis and Typhimurium serovariants also exhibit recombination within themselves. No recombination events were found between strains of the Enteritidis serovariant. The events of convergent adaptive evolution were mainly found in the effector module genes: cas5, cas6, cas7.Conclusion. It has been shown that homologous recombination often occurs in the S. enterica genome in the region of the cas genes. Bioinformatic algorithms detect more recombination events between evolutionarily more distant strains, which are inconsistent with known in vitro studies.

Salmonella enterica is a Gram-negative, facultatively anaerobic bacterium that causes intestinal infections in humans and animals. The species S. enterica includes over 2,600 serovars, among which Typhimurium, Enteritidis, and Infantis are widely distributed in the Russian Federation and often exhibit multidrug resistance to antibiotics. One promising approach to combatting such pathogens is targeted therapy using lytic phages. However, the genomic mechanisms underlying phage-bacterium interactions remain insufficiently understood. Like most bacteria, Salmonella genomes harbor prophages. Investigating prophage abundance in S. enterica genomes may be crucial for developing targeted phage therapy against this pathogen. This study conducted a bioinformatic analysis of prophage content in the genomes of three S. enterica subsp. enterica serovars: Enteritidis (n=50), Infantis (n=50), and Typhimurium (n=50) using the DBSCAN-SWA algorithm. A total of 805 prophage sequences were identified, including 274 in Enteritidis, 212 in Infantis, and 319 in Typhimurium. These sequences were classified into genera including Salmonella, Escherichia, Enterobacter, Cronobacter, Shigella, Klebsiella, and Moraxella. Additionally, cas genes associated with class 1, subtype I-E CRISPR-Cas systems were detected in all analyzed genomes. The strains were divided into two groups: 23 strains with mutations in cas genes and 127 strains without mutations. It was found that Typhimurium genomes contain more prophages compared to the other serovars. Furthermore, strains with mutations in cas genes exhibited higher prophage abundance, highlighting the role of CRISPR-Cas systems in regulating prophage dynamics and bacterial population adaptation. These findings may contribute to the development of more effective phage therapy strategies.

Salmonella is a genus of gram-negative, facultative and non-spore-forming anaerobic bacteria. The genus includes two species: S. bongori and S. enterica. All Salmonella, which are pathogenic to humans and animals, belong to the species S. enterica. It includes seven subspecies, which includes more than 2500 serotypes. According to global statistics, they cause about 2.8 billion cases of diarrheal diseases annually, and the mortality rate reaches more than 300000 cases. S. enterica spp strains that have acquired multidrug resistance to antibiotics have become especially dangerous. Against the backdrop of this global problem, a detailed study of the complete genomes of various representatives of the genus Salmonella becomes relevant. Repeats play an important role in the regulation of basic genetic processes during the life cycle and evolution. The work examines various manifestations of repetition in the genomes of S. enterica. Taking into account common fragments of different genomes serves as the basis for the formation of a matrix of pairwise relative complexity, which is used in constructing a phylogenetic tree. Long repeats within individual genomes typically correspond to large individual duplications. The main attention is paid to local structural regularities, most of which are represented by tandem repeats. Of significant interest are multivalued repeats, such as tandem repeats forming a palindrome, repeats with regular substitutions or complex monomer structure.

Due to the rich chemical composition of Siberian larch (Larix sibirica Ledeb), its products are widely used in medicine, pharmacology, agriculture, perfumery and cosmetics industry. Larch wood and bark contain a large amount of low molecular weight substances with high biological activity, namely: essential oils, ascorbic acid, tannins, anthocyanins, flavonoids, organic acids. The most important and useful of them are flavonoids due to their significant content in raw materials such compounds as: dihydroquercetin (DHA), arabinogalactan (AG), quercetin (QU), ardixin (ARD). On the basis of dihydroquercetin, preparations for the treatment and prevention of atherosclerosis, capillary-strengthening agents, anti-allergic drugs are created, and due to the high ability to complex formation, it actively removes heavy metals, including radionuclides, from the body. The main experimentally established properties of AG are immunomodulatory and antioxidant effects. In the diet, there is often a deficiency of dietary fiber needed by the human body. Quercetin is a powerful antioxidant that increases the body's resistance to radiation and a food antioxidant. It can also enhance antiinflammatory, antiviral, and immunoprotective effects. Ardiksin is a nanobiocomposite containing no. more than 95.0% of the natural polysaccharide arabinogalactan and no. less than 5% of the bioflavonoid dihydroquercetin. The biological activity of ardixin has shown its effectiveness in the treatment of oncological diseases as a concomitant agent during radiation and chemotherapy. Based on the significant importance of these polysaccharide compounds in the creation of new functional food products and therapeutic agents for medicine, in this study, the goal was to identify the effect of stimulating the growth of the commercial probiotic preparation Bifidobacterium bifidum when cultivated on media with polysaccharide compounds: purified arabinogalactan, dihydroquercetin, quercetin, ardixin. These polysaccharide compounds are processed products of Siberian larch (Larix sibirica Ledeb). In the course of a study on the evaluation of growth stimulation of B. bifidum by polysaccharides: AG-purified, DHA, QU, ADC, it was found that: 1) growth of B. bifidum is most effective in a medium with DHA; 2) when growing on a medium with AG-clean. there is almost five times less growth stimulation compared to DHA; 3) the smallest growth of B. bifidum is observed in the medium with QU, which is more than 208 times less than its growth on the medium with DHA.

The problem of resistance of pathogenic bacteria to antibiotics has become global and, therefore, there is renewed interest in the use of bacteriophages. However, bacteria also have phage defense structures, the CRISPR/Cas system. Therefore, the analysis of the structural diversity of CRISPR-Cas systems in the genomes of pathogenic bacteria and phages is an important fundamental and applied direction. The aim. Investigation of the diversity of structures of CRISPR/Cas systems in the genomes of S. enterica strains from the NCBI database using bioinformatics programs and assessment of the possibilities to identify phage protection of strains through spacers in CRISPR cassettes. The studies were carried out with the genomes of 449 S. enterica strains from the NCBI database. A number of bioinformation software methods were used: 1) MacSyFinder, 2) CRISPR Interactive database, 3) CRISPR R Tool, 4) CRISPI: a CRISPR Interactive database, 5) CRISPRFinder. Screening of phages through spacers CRISPR cassettes was used: 1) CRISPRTarget, 2) Mycobacteriophage Database, 3) Phages database. In the genomes of the studied strains of S. enterica, one type of CRISPR/Cas system, I-E, was identified. Protein genes were present in each locus of the CRISPR/Cas systems: Cas1_0_I-E_7, Cas2_0_I-E_8, Cas3_0_I_1, Cas5_0_I-E_5, Cas6_0_I-E_6, Cas7_0_I-E_4, Cse1_0_I-E_2, Cse2_0_I-E_3. The number of cassettes was from 1 to 3, and the spacers in them varied from 8 to 30. Repeats in CRISPR cassettes varied from 27 to 29 base pairs. The identified phages belonged to bacteria of the genera: Salmonella – 60%, Escherichia – 18%, Enterobacter – 9%, Salmonella – 8%, and Staphylococcus and Enterococcus were up to 5%. The obtained data on the diversity of CRISPR/Cas systems in the genomes of the studied S. enterica strains demonstrate their unique structures. The homogeneity of CRISPR/Cas systems and the rooting of CAS types I-E in genomes can be explained by their participation in the interspecific transmission of these CRISPR systems.

In the genomes of different organisms, there are periodicities, i.e. fragments of DNA (RNA)-sequences formed by tandem repetition of the basic monomer (period). The spectra of periodicities with lengths exceeding the ‘noise’ threshold are quite compact and visible even for complete genomes. This makes them an acceptable tool for differentiating closely related objects. The objects of analysis in this work are the periodicities at genomes of three species of coronavirus: MERS, SARS, and SARS-CoV-2. It has been shown that there are markers in the form of periodicities that make it possible to distinguish between these species of coronaviruses. None of the periodicities identified in the genomes of the MERS species (except for the poly-a tract in the 3‘UTR) is found in the genomes of SARS and SARS-CoV-2 and vice versa. Revealed periodicities common to SARS and SARS-CoV-2, as well as inherent only to genomes of one species. The number of periodicities in SARS and SARS-CoV-2 significantly exceeds the number of periodicities in random sequences. The periodicities found in almost all genomes of only ‘their’ species are of the greatest interest in terms of revealing the pathogenic potential of the virus.

The tick-borne encephalitis virus (TBEV), a member of the Flaviviridae family, is currently subdivided into three main subtypes-the European (TBEV-Eu), the Far-Eastern (TBEV-FE), and the Siberian (TBEV-Sib). The TBEV-Sib is the most common subtype and found in all regions where TBEV was detected, except for Central and Western Europe. Currently, four genetic lineages have been described within TBEV-Sib. In this study, detailed analysis of TBEV-Sib genetic diversity, geographic distribution, phylogeography and divergence time of different TBEV-Sib genetic lineages based on E gene fragments, complete genome sequences, and all currently available data in the GenBank database was performed. As a result, a novel Bosnia lineage within the TBEV-Sib was identified. It was demonstrated that the Zausaev lineage is the most widely distributed among the TBEV-Sib lineages, and was detected in all studied regions except the Far East. The Vasilchenko lineage was found from Western Siberia to the Far East. The Baltic lineage is presented from Europe to Western Siberia. The Obskaya lineage was found only in Western Siberia. TBEV strains from a newly described Bosnia lineage were detected in Bosnia, the Crimean peninsula, Kyrgyzstan and Kazakhstan. The greatest divergence of the TBEV-Sib genetic variants was observed in Western Siberia. Within the TBEV-Sib, the Obskaya lineage diverged from the common ancestor the earliest, after that the Bosnia lineage was separated, then the Baltic lineage, and the Zausaev and Vasilchenko lineages diverged most recently.

We have studied 13 enzyme systems encoded by 15 loci of the I. persulcatus tick populations from two suburban areas of the city of Irkutsk. We have identified a high intrapopulation heterogeneity and insignificant differences between the two populations. This indicates a high rate of gene migration.

In the modern world, infections caused by multidrug-resistant (MDR) bacteria have become carriers of global threats to human health. Today these pathogenic bacteria have come to be referred to as "superbugs" and their number and aggressiveness is growing. This group of "superbugs" also includes Staphylococcus aureus. It is capable of infecting almost any tissue in the human body. Therefore, it became necessary to find alternative antibiotic methods of treating bacterial infections. The use of bacteriophages is again among them. We propose a new approach in the search for strain-specific (target) phages through the structures of the CRISPR/Cas-systems of bacteria. As is known, CRISPR/Cas systems are the most ancient system of "adaptive immunity" in bacteria. This system makes bacteria resistant to phages and plasmids. This approach is based on the use of methods of structural genomics and software bioinformatics modeling. Using them, an algorithm was developed to search for the structures of CRISPR/Cas systems in bacterial genomes presented in the NCBI databases and screening through their CRISPR cassettes of phages with which a particular strain could meet. The design of the developed algorithm was tested on the genome of methicillin-resistant S. aureus strain (ST228-MRSA-I) from the GenBank database. The results of the search for loci and structures of the CRISPR/Cas system in the genome of this strain showed that the identified system belongs to type III-A. It was found that the cas genes and the CRISPR cassette are located at a distance from each other and between them are located several genes that perform other functions in the genome of the S. aureus strain. It was shown that the structures of spacers in the detected CRISPR cassette are identical to protospacers of phages, the hosts of which are bacteria of the following genera – Staphylococcus, Mycobacterium, Streptococcus, Bacillus, Gordonia, Arthrobacter, Streptomyces. Thus, it can be stated that the developed algorithm of software methods for searching for loci of CRISPR/Cas systems and screening for phages makes it possible to type both the system itself and through its spacers to detect and identify phage races with which a particular bacterial strain could meet. The degree of resistance of a particular bacterial strain to specific phages is also determined, which in the long term should ensure the effectiveness of targeted phage therapy for infections caused by pathogenic bacteria, including "superbugs".

The study of phytopathogenic bacteria is a topical issue in most discussion.Since that time, when microorganisms disrupt the carbohydrate and protein exchanges of a plant.The object of the study is full genome sequence of the Agrobacterium fabrum str.C58 chromosome circular, downloaded from the RefSeq database (NC_003062.2.).Pathogenic strains of Agrobacterium spp.carry at least one Ti or Ri -plasmid.To date, to avoid mass death of plants, targeted genetically modified approaches are being developed, for example, CRISPR/Cas.To find CRISPR/Cas-systems MacSyFinder were used.The research for the structural and functional characteristics of the Cas-genes was carried out using the HMMER and makeblastdb software.CRISPI, CRISPRFinder, CRISPRDetect were used to select CRISPR-arrays in the genome of the bacterium.To looking for phages through decoded spacer sequences was taken the BLASTn.The results of the bioinformatics study have showed the following: 1 CRISPR-array was found, having 3 spacer sections separated by repeat.Spacers are 18 b.p., repeat -5 b. p.The total length of the CRISPR-array was 510 b. p. with repeat (C-GGCGGCTGTTCGGCAGG).The obtained spacer sites were analyzed in the CRISPR-array for phage identification in such software: Phages, CRISPRTarget.It was possible to identify the belonging of the spacers to the phages of Mycobacterium Phage Shipwreck (13 repeats), Gordonia phage GMA2 (15 repeats).Also, using the BLASTn, we have found that Agrobacterium fabrum has full identity with Plantactinospora sp.BC1 chromosome, Streptomyces sp.1H-SSA4 genome, Xanthomonas perforans 91-118 etc.These results help us to suggest that, in addition to virulent plasmids, the total repeat plays a role in pathogenicity trough the CRISPR-array.Thus, the bioinformatics analysis of the CRISPR/Cas-system of the phytopathogenic bacterium Agrobacterium fabrum str.C58 chromosome circular made it possible to find out which part of the DNA in the bacterium in order to change its pathogenic properties.

A new biodegradable derivative of the biocompatible, biodegradable beta-polysaccharide arabinogalactan is synthesized: arabinogalactan polyaldehyde. Biodegradable hydrogels with chitosan and para-aminobenzoic acid are obtained from the latter. The spectral characteristics of the new compounds and colorimetric tests of their biodegradability by bifidobacteria are discussed.

The aim of this research was to analyze and compare CRIPSR loci and cas-proteins of Yersinia pseudotuberculosis strains isolated in different territories from patients with various clinical manifestations of pseudotuberculosis.Materials and Methods. Complete genomes of Y. pseudotuberculosis IP329353 (NC_006155) and IP31758 (NC_009708) were obtained from NCBI Nucleotide Database. Strains were isolated from patients with gastroenteritis and systemic infection respectively. Search, identification, and analysis of CRISPR systems were carried out by onlinetools CRISPROne, CRISPRDetect, and CRISPRTarget.Results. Analyzed strains have CRISPR-Cas systems that include one set of cas-genes and arrays situated at the long distances from each other. We defined three CRISPR arrays in Y. pseudotuberculosis IP32953: array YP1 located near cas-genes, arrays YP2 and YP3. CRISPR-Cas system of Y. pseudotuberculosis IP31758 includes two arrays – YP1 and YP3. CRISPR systems do not share similar spacers.Conclusion. CRISPR systems of the analyzed strains differ in CRISPR loci and cas-protein structures that can be used as specific molecular marks of analyzed strains during the study of intra-species variability and evolution of Y. pseudotuberculosis.

Tick-borne encephalitis is one of the most dangerous natural focal infections. The causative agent of the disease is tick-borne encephalitis virus (TBEV ) transmitted by ticks . There are three main subtypes of TBEV with different clinical manifestations of the disease, but existence of other subtypes is also possible. Effectiveness of the disease treatment can largely depend on the correct identification of TBEV genotype. Comprehensive information about the genotype is contained in the full coding sequence of TBEV genome. А limited number of genotyping markers can be extracted from it in the form of relatively short structured RNA fragments. In this paper, a rather general approach to the isolation of structured RNA markers for the genotyping of TBEV is formulated. Three types of structures are considered: periodicity, fractal-like constructs and compactly localized combinations of different types of repetitions. The choice of these structures for the purposes of genotyping and their possible role in the formation of the pathogenic potential of the virus is substantiated. The approach was tested on the full coding sequences of TBEV (161 strains). Examples of the most characteristic markers of each of the three types are given.

In the territory of the Russian Federation over the period of 2008–2017 in the course of surface water bodies monitoring, 725 non-toxigenic strains of cholera vibrios with ctxA tcpA and ctxAtcpA genotypes were isolated. The question regarding the origins of non-toxigenic strains and their genomic diversity remains an open one. In this context, objective of the study was to investigate genomic diversity of non-toxigenic V. cholerae El Tor strains, evaluate their epidemic significance, using a designed multiplex PCR. We applied conventional microbiological and molecular-genetic methods, as well as whole-genome sequencing tools. The analysis included isolated natural and experimentally obtained non-toxigenic strains. For non-toxigenic strains the presence of a complete set of mobile genetic elements (MGE), responsible for pathogenic (CTXφ, TLCφ, RS1, VPI-1, VPI-2) and epidemic (VSP-I и VSP-II) potential was characteristic. Non-toxigenic strains turned out to be genetically heterogeneous and were divided into three groups. The first group of ctxAtcpA strains lacked CTXφ, TLCφ, RS1, VPI-1, VSP-I, and VSP-II elements. Pathogenicity island, VPI-2, had the deletions the size of 33–49 kb, depending upon the strain. The second group of ctxAtcpA strains was devoid of CTXφ, RS1, VSP-I, VSP-II, but preserved pathogenicity islands, VPI-1 with tcpA, and VPI-2. The latter one had the deletions the size of approximately 34 kb. The third group consisted of experimentally obtained non-toxigenic strains that lost CTXφ prophage in aqueous medium, but retained pandemicity islands, VSP-I and VSP-II. Among the studied non-toxigenic strains isolated in the territory of Russia, this type of strains was not found. According to the international NCBI GenBank database, such non-toxigenic strains were detected in endemic as regards cholera regions. Genome analysis of the mentioned strains showed that they were deprived of CTXφ prophage only, but contained all other MGEs with genes of virulence and epidemicity. The data gathered suggest that natural non-toxigenic ctxAtcpA strains may be derivatives of toxigenic ones. Thus, in the territory of the Russian Federation two main groups of non-toxigenic strains with ctxAtcpA and ctxAtcpA genotypes circulate. Heterogeneity of nontoxi genic ctxAtcpA strains by the structure of the genome and epidemiological significance pointed to the necessity of PCR construction for their differentiation. We designed multiplex PCR which simultaneously separates toxigenic from non-toxigenic strains by the presence/absence of ctxA and tcpA genes, and differentiates the latter ones into potentially epidemically hazardous and epidemically safe ones by the presence/absence of pandemicity islands’ genes, VSP-I (VC0180) and VSP-II (VC0514). Non-toxigenic V. cholerae El Tor strains with ctxA tcpA genotype are genetically inhomogeneous group with varying epidemiological significance. The strains of ctxA tcpAVSP can pose a potential epidemic threat and circulate only in endemic territory. ctxAtcpAVSP strains circulating in the territory of Russia are epidemically safe due to the loss of considerable genome regions.

Background. During the study of the genetic variability of the tick-borne encephalitis virus (TBEV) in Eastern Siberia, a group of 22 strains with a unique genetic structure significantly different from all known TBEV subtypes was identified. This TBEV variant was tentatively called “group 886”. Therefore, for this original TBEV variant it was necessary to study the genetic, biological properties of the “group 886” strains, clarify its TBEV taxonomic status, its range, evolutionary history, etc.Aim. The generalization of the currently available data on genetic and biological properties of TBEV “886” group.Materials and methods. The genetic structure of “group 886” strains was studied by the complex of molecular-genetic methods (MHNA, sequencing of fragments or the complete genome).Results. It was shown that “group 886” strains form a separate cluster on phylogenetic tree, and the level of genetic differences from other genotypes is more than 12 %. It was defined that this TBEV variant has its own area (Irkutsk region, Republic of Buryatia, Trans-Baikal region, Northern Mongolia). Its ecological connection with all links of the transmissive chain (ixodid ticks, small mammals, human), participation in human pathology, stability and duration of circulation in the Baikal region, individual evolutionary history were proved. Some phenotypic characteristics of the “group 886” strains were considered.Conclusion. The presented data testify to the validity of the “886 group” isolation as an independent genetic type. Taking into account the geographical distribution of this TBEV genotype, we propose to assign it the name “Baikal genotype/subtype”.