COMPARATIVE ANALYSIS OF CRISPR-CAS SYSTEM STRUCTURES OF YERSINIA PSEUDOTUBERCULOSIS IP32953 AND IP31758

Background. Pseudotuberculosis is still relevant problem in medical science and public health of Russia and other countries. Typing of Y. рseudotuberculosis strains by their CRISPR systems is a perspective tool for monitoring of Yersinia populations as was shown in Y. pestis.Aims. Here we describe and compare CRISPR-Cas systems of Yersinia pseudotuberculosis strains IP32953 and IP31758 causing classic pseudotuberculosis and Far-East scarlet-like fever (FESLF) respectively.Materials and methods. Complete genomes of Y. pseudotuberculosis IP329353 and IP31758 (NC_006155 and NC_009708 respectively) were obtained from NCBI Nucleotide Database. Search; identification; and analysis of CRISPR systems were carried out by online-tools CRISPROne; CRISPRDetect; and CRISPRTarget.Results and discussion. 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 by the combination of program methods. CRISPR-Cas system of this strain consist of 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. CRISPR systems of the analyzed strains differ in CRISPR loci and cas-protein structures that can be used as specific marks of analyzed strains.Conclusions. We suggest that acquisition of certain spacers may play a role in evolution and divergence of Y. pseudotuberculosis strains

PATHOGENIC POTENTIAL AND MUTUAL INTERACTION OF MICROFLORA OF MUCOUS MEMBRANES OF OPEN CAVITIES OF DIFFERENT BIOTOPES IN WOMEN AS IMPORTANT FACTORS OF THEIR REPRODUCTIVE HEALTH

Micro-ecological interrelation between intestinal, vaginal and nasopharyngeal biocoenoses as parts of microbiome of a macroorganism was determined by the latest researches. The research included 44 women with inflammatory diseases of genital tract and reproductive disorders and 28 healthy women. Genospecies structure of enterococcus for each biotope (intestinal, vaginal and nasopharyngeal) had original differences with the most full spectrum of species in intestinal biotope. The contract between the groups is evident at the conclusion of the pathogenicity genes tests

Detection of genes of pathogenicity of symbiotic microflora in adjacent biotopes in women with chronic endometritis and reproductive disorders

Recent researches established microecological relationships between intestinal, vaginal and nasopharyngeal biocenoses in the composition of a macroorganism microbiome. This study included 57 women with chronic endometritis and 21 woman without it (control group). In women with chronic endometritis all studied pathogenicity genes (asal, cylA, stxl and stx2) were identified in representatives of symbiotic microflora in all three studied habitats - vaginal, intestinal and nasopharyngeal, which confirms the presence of a reservoir of potential pathogenicity. Studied genes of pathogenicity were diagnosed in women with CE in 8 cases of the bacteria of the species E. faecalis and E. faecium, which are "harbingers" of impending serious problem. This indicates the importance of these species in etiopathogenetic structure of microbiocenoses of studied habitats, and, possibly, their impact on the course of this disease

SPECIES DIVERSITY OF BIFIDOBACTERIA IN CHILDREN WITH FUNCTIONAL DISORDERS OF GASTROINTESTINAL TRACT

The main aim of this research was to identify species ratio and compatibility in children with functional disorders of gastrointestinal tract (GIT) using PCR method, with, species-specific primers for bifidobacteria. The assessment of intestinal microbiota symbionts composition, was made simultaneously. Dysbiosis changes of I—II degree in large intestine microbiocenosis in 86 children examined, were detected. The definition, of bifidobacteria species profile with, the dominance of B. longum, B. catenulatum. and B. bifidum. will allow to optimize the treatment of this pathology

MICROBIOLOGICAL CHARACTERISTIC OF INTESTINAL MICROFLORA IN CHILDREN WITH ALLERGIC DISEASES

The results of bacteriological research of scatological material from children with allergic diseases (atopic dermatitis, bronchia! asthma combined, with allergic rhinitis, dermal and respiratory syndrome, allergic rhinitis) in Irkutsk are presented, in the article. 62 patients from 1 year to 17 years were examined, and. significant deviations from the scatological norm, were revealed: in lactic acid, bacteria — 75,8 % while the number of bifidobacteria was reduced, in 58 % of patients. The most frequently identified, bacteria were S. aureus (24,2 %) and. K. pneumoniae (14,5 %)

MICROECOLOGICAL AND GENESPECIFIC CHARACTERISTICS OF VAGINAL BIOTOPE LACTOBACILLI IN WOMEN WITH NONSPECIFIC LOWER FEMALE REPRODUCTIVE TRACT INFLAMMATORY DISEASES

The study included 30 reproductive age women with lower female reproductive tract nonspecific inflammatory diseases. The analysis of the qualitative and quantitative pathogenic microorganisms as well as lactobacilli composition was conducted. It was shown that in women observed the opportunistic microflora detected often (73,3 %) in the rest part of patients (26,7 %) in case if opportunistic microflora was absent the disbiotic changes occurred in lower concentration of normal microflora of vagina represented mostly by lactoflora. Deficiency of lactobacilli was observed almost in all women of this group (96,6 %) and only in one case (3,4 %) the concentration of lactobacilli was consistent with normal physiological range. Molecular genetic methods (PCR amplification) with visualization by means of electrophoresis in agarose gel was made for identification of Lactobacilli species. Consistency index (c) and species saturation index (sri) for opportunistic microorganisms in women vaginal biotope examined were calculated. Prevalence of Lactobacillus plantarum and Lactobacillus jensoni isolating in 83 and 50 % respectively was shown. Also it was shown that in the structure of quantitative compatibility of studied species of lactobacilli the highest rate is characterized to the association of two types that makes 53 %

APPLICATION OF MATHEMATICAL METHOD PREDICTIONS FOR IDENTIFICATION OF PATTERNS RELATIONS MUTATIONS IN PROTEINS ENCEPHALITIS VIRUS AND A MANIFESTATION OF ITS PHENOTYPIC TRAITS

We studied the natural connections between the amino acid sequences of proteins C, prM, E and NS1 virus strains of tick-borne encephalitis (TBE) and their three phenotypic traits -neuroinvasiveness, thermal stability and thermoresistance. Coupling strength is assessed using measures of competitive sequence similarity of each strain with reference strains. For such purposes subsets of strain sections are chosen amino acid composition specifics of which can predict the value of a phenotypic trait of interest. The possibility to predict missing elements in data both in amino acid composition, and in target properties is demonstrated. The relationships between pairs of phenotypic traits of strains were evaluated

BIOINFORMATION SEARCH AND ANALYSIS OF STRUCTURES OF CRISPR/CAS SYSTEMS IN PHAGE STAPHYLOCOCUS AUREUS GENOME AND ESTIMATION OF PROFILES OF PHAGE DETECTED THROUGH CRISPR-CASSETTE BACTERIA

The emergence of resistance among the most important bacterial pathogens is generally recognized as one of the major public health problems. The most important of these organisms are penicillin-resistant Streptococcus pneumoniae, vancomycin-resistant enterococci and methicillin- and vancomycin-resistant Staphylococcus aureus. These antibiotic resistance in common pathogens have made antimicrobial therapy of many infections. Scientists need to look for new ways of treating bacterial infections in the work, using the developed algorithm from the methods of search software in the genomic structure of Staphylococcus aureus subsp. aureus ST228, the CRISPR/Cas locus and the division structures of its CRISPR cassette. The results of the bacteriophage search through the decoded spacer sequences of CRISPR-cassettes of this strain were also obtained using the developed algorithm of the software methods of bioinformatics. It was determined that the CRISPR/Cas system of strain of ST228 of S. aureus was of type IIIA. It is shown that cas-genes are in the immediate vicinity of CRISPR cassettes. The spacer structures in the detected CRISPR cassette are the Staphylococcus, Mycobacterium, Streptococcus, Bacillus, Gordonia, Arthrobacter, Streptomyces. The implementation of the algorithm of program methods for locating CRISPR/Cas-loci can be applied to many other decoded bacterial genomes to return bacteriophage therapy

MICROECOLOGICAL CHARACTERISTICS OF KLEBSIELLA SPP. REGIONAL POPULATIONS IN THE INTESTINAL MICROBIOTA OF IRKUTSK CHILDREN

In this paper the microecological characteristics of Klebsiella spp. regional populations in the intestinal microbiota of infants were represented. 373 children (55,9 % of general quantity of researched) had disbiotic changes of intestinal microbiota related to increasing number of Klebsiella. The autostrains sensitivity to antibiotic drugs (в-lactams, aminoglycosides, quinolones) and to purified Klebsiella pneumoniae phage and purified polyvalent Klebsiella phage were researched. Samples of isolates (n = 142) characterized by a high proportion of antibiotic susceptible strains. Phage sensitivity of bacteriophage to the commercial preparations was determined in 268 strains of Klebsiella spp. of two types (146 strains of K. Oxytoca and 122 strains of K. pneumonia). Probably high frequency of pathogens resistant to studied bacteriophages (K. oxytocain 66 % and K. pneumoniae in 77.8 % of cases) was the reason of low efficiency of phage therapy by specific phage and can explain high frequency of occurrence of Klebsiella at dysbiosis in children of early age

RESULTS OF GENOTYPING OF STRAINS AND RNA ISOLATES OF TICK-BORNE ENCEPHALITIS VIRUS ISOLATED FROM SICK PEOPLE IN IRKUTSK REGION AND BURYAT REPUBLIC

Genotyping of nine strains and nine isolates of tick-borne encephalitis virus RNA (TBE) isolated from patients in the Irkutsk Region and. the Buryat Republic in 1963-2009 years conducted. The investigations revealed that three TBE virus genotypes are involved in the etiology of the TBE: Ural-Siberian (genotype 3), Far Eastern (genotype 1) and. European (genotype 2). It is found that the TBE virus of Far East and. Ural-Siberian genotypes can cause disease with a wide spectrum of clinical manifestations: acute TBE (focal and. nonlocal forms), chronic TBE (encephalitic form, progressive course.) Prospects of application of molecular genetic techniques for the rapid indication and. identification of the TBE virus in the blood of sick people are shown