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Background. The ongoing pandemic of the novel coronavirus infection (COVID-19) draws attention to the significance of molecular and genetic monitoring of the SARS-CoV-2 spread among the population of the Russian Federation. The aim of the study was to analyze the dynamics of circulation of SARS-CoV-2 genetic variants in Russia.Materials and methods. The analysis of the circulation dynamics for SARS-CoV-2 genetic variants in Russia was carried out, covering the period from 28/12/2020 to 26/6/2022. The analysis included the data from Rospotrebnadzor Report No. 970 "Information about Infectious Diseases in Individuals with Suspected Novel Coronavirus Infection" and the Virus Genome Aggregator of Russia (VGARus). The presence of SARS-CoV-2 RNA was confirmed by the real-time reverse transcription polymerase chain reaction. The primer panels developed at the Central Research Institute of Epidemiology were used for amplification of genomic fragments and the subsequent sequencing.Results and discussion. Using the Russian VGARus platform developed by the Central Research Institute of Epidemiology, we received the data on mutational variability of SARS-CoV-2. By monitoring the circulation of SARS-CoV-2 genetic variants in Russia from 28/12/2020 to 26/6/2022, we found that Delta and Omicron genetic variants prevailed at different stages of the epidemic.Conclusion. The data of molecular and genetic studies are an essential component of epidemiological surveillance, being critically important for making executive decisions aimed at prevention of further spread of SARS-CoV-2 and laying the groundwork for creating new vaccines.

The constant increase of antibiotic-resistant strains of bacteria is caused by extensive uses of antibiotics in medicine and animal breeding. It was suggested that the gut microbiota serves as a reservoir for antibiotics resistance genes that can be carried from symbiotic bacteria to pathogenic ones, in particular, as a result of transduction. In the current study, we have searched for antibiotics resistance genes that are located inside prophages in human gut microbiota using PHASTER prophage predicting tool and CARD antibiotics resistance database. After analysing metagenomic assemblies of eight samples of antibiotic treated patients, lsaE, mdfA and cpxR/cpxA genes were identified inside prophages. The abovementioned genes confer resistance to antimicrobial peptides, pleuromutilin, lincomycins, streptogramins and multidrug resistance. Three (0.46%) of 659 putative prophages predicted in metagenomic assemblies contained antibiotics resistance genes in their sequences.Uvelichenie doli lekarstvenno-ustoĭchivykh shtammov bakteriĭ neposredstvenno sviazano s shirokim primeneniem antibiotikov v meditsine i zhivotnovodstve. Predpolagaetsia, chto mikroflora kishechnika sluzhit rezervuarom genov antibiotikorezistentnosti, kotorye mogut peredavat'sia ot simbioticheskikh bakteriĭ k patogennym mikroorganizmam, v tom chisle v rezul'tate fagovoĭ transduktsii. S ispol'zovaniem programmy predskazaniia profagov PHASTER i bazy dannykh genov antibiotikorezistentnosti CARD proveden poisk genov antibiotikorezistentnosti, nakhodiashchikhsia v sostave profagov, v mikrobnom soobshchestve kishechnika cheloveka. V rezul'tate analiza metagenomnykh sborok vos'mi obraztsov v sostave posledovatel'nosteĭ profagov byli obnaruzheny geny lsaE, mdfA i cpxR/cpxA, prisutstvie kotorykh obespechivaet ustoĭchivost' bakteriĭ k antimikrobnym peptidam, plevromutilinu, linkomitsinam, streptograminam gruppy A, a takzhe mnozhestvennuiu lekarstvennuiu ustoĭchivost'. Iz 659 predpolozhitel'nykh profagov, predskazannykh v metagenomnykh sborkakh, tri (0,46%) imeli v svoem sostave geny antibiotikorezistentnosti.

Antibiotic resistance markers were analyzed in C. trachomatis clinical isolates obtained after ineffective therapy of urogenital chlamydiasis with fluoroquinolones and macrolides. Heterotypical resistance to fluoroquinolones and macrolides was detected in all clinical isolates. No significant mutations in the target genes were detected. ispartof: Bulletin of Experimental Biology and Medicine vol:143 issue:6 pages:713-717 ispartof: location:United States status: published

Optochin-resistant pneumococci can be rarely caught in clinical microbiology laboratories because of the routine identification of all such strains as viridans group non-pneumococci. We were lucky to find four non-typeable Streptococcus pneumoniae clones demonstrating the different susceptibilities to optochin: one of them (Spn_13856) was resistant to optochin, while the other three (Spn_1719, Spn_27, and Spn_2298) were susceptible. Whole genome nucleotide sequences of these strains were compared to reveal the differences between the optochin-resistant and optochin-susceptible strains. Two adjacent genes coding maltose O-acetyltransferase and uridine phosphorylase which were presented in the genomes of all optochin-susceptible strains and missed in the optochin-resistant strain were revealed. Non-synonymous substitutions in 14 protein-coding genes were discovered, including the Ala49Ser mutation in the C-subunit of the F0 part of the ATP synthase rotor usually associated with pneumococcal optochin resistance. Modeling of a process of optochin interaction with the F0 part of the ATP synthase rotor indicates that the complex of optochin with "domain C" composed by wild-type C-subunits is more stable than the same complex composed of Ala49Ser mutant C-subunits.

A complex method for detection of genetic markers of N. gonorrhoeae resistance to penicillin was developed. Mutations in penA and ponA genes were detected by minisequencing reaction with subsequent detection of reaction products by MALDI-TOF mass spectrometry. This approach was tested on 31 clinical strains of N. gonorrhoeae with minimum inhibitory concentration of penicillin from 0.03 to 8 microg/ml and higher. Mutations in penA and ponA genes in moderately resistant strains were shown (minimum inhibitory concentration up to 0.5 microg/ml) and mutations in penA, ponA, and penB genes in resistant strains (minimum inhibitory concentration more than 1.0 microg/ml). beta-Lactamase genes were detected in 4 strains with high resistance (minimum inhibitory concentration 4-8 and more microg/ml). Correlation between microbiological resistance and presence of respective mutations in the studied locuses was detected.

Complete sequences of omp1 gene encoding chlamydial main outer membrane protein were analyzed in 76 clinical strains of C. trachomatis. Thirty-four serovar-specific single-nucleo-tide polymorphisms were identified, 20 of them meet two criteria: unique position of the nucleotide and unique nucleotide substitution. Evaluation of serovar-specific single-nucleotide polymorphisms of omp1 gene can appreciably simplify and accelerate genetic diagnosis of C. trachomatis serovars.

Genetic polymorphism of Russian population of N. gonorrhoeae was detected and a system for genotyping of its clinical strains was introduced into practice. Comparative analysis of the prevalence of N. gonorrhoeae genotypes in Russia and abroad was carried out. For adaptation of the methods of molecular typing of N. gonorrhoeae strains and its approbation on clinical strains isolated in Russia 41 clinical strains of N. gonorrhoeae were typed. The predominance of PIB serovar (83%) was demonstrated.

We studied the correlation between genetic transfer of tetM determinant in Tn916 conjugative transposon by urogenital mycoplasmas (Mycoplasma hominis and Ureaplasma urealyticum) and changes in the bacterial repertoire during treatment with a tetracycline antibiotic. Basic conditions favoring the nonspecific transfer of tetM determinant into mollicute cells are determined and the allele polymorphism of tetM determinant in clinical strains of M. hominis and U. urealyticum is evaluated. The structure of tetM gene in clinical mycoplasma and ureaplasma strains is characterized by a peculiar mosaic pattern and differs from all previously described alleles of this gene. The results suggest that tetracycline resistance in mollicutes is determined by mechanisms alternative to genetic transfer of tetM determinant.

Polymerase chain reaction was clinically used to diagnose chlamydial and mycoplasma infection in the cervix and male urethra. Examinations of 2260 patients with disorders of reproductive function detectedC. trachomatis, M. hominis, andU. urealyticum in 32.9, 9.7, and 25.7% of cases, respectively. A high incidence of mixed nongonococcal urogenital infections was observed, particularly in women. Seasonal fluctuations were shown in the detection rates of chlamydial and ureaplasmic infections.

A procedure for identifying chlamydia, mycoplasmas, and ureaplasmas by the polymerase chain reaction is described which uses a system of four primers complementary to fragments of the 16S RNA gene, one of which detects all three microorganisms and the other three are each specific for a particular organism. With this primer system, chlamydia, mycoplasmas, and ureaplasmas are detectable in a single reaction. The procedure may be used for routine diagnoses in diagnostic laboratories.

Two-dimensional electrophoresis and mass spectrometry detection were used to evaluate the range of proteins in rat brain after single treatment with ladasten (50 mg/kg). We identified 13 proteins with various levels of expression.

The present study investigates epidemiological diversity and multidrug resistance spreading among Mycobacterium tuberculosis strains circulating in Moscow, Russian Federation. Among 115 M. tuberculosis strains selected randomly from the sputum of epidemiologically unrelated tuberculosis (TB) patients, multidrug-resistant (MDR) strains predominated. Mutations in the RRDR of the rpoB gene were detected in 64 (83.1%) of 77 rifampicin (RIF)-resistant strains. The Ser531→Leu substitution was prevalent among them (76.5%). Aberrations in the Ser315 codon of katG and/or in the inhA promoter region were found in 79 (84.0%) of 94 isoniazid (INH)-resistant strains. Strains belonging to the Beijing family prevailed. Seventy-one different patterns were identified using the 24-VNTR loci typing scheme. Three main 24-loci VNTR clusters included 34 strains which belonged to the Beijing family. The spoligotyping and 24-loci VNTR typing combination demonstrated maximal discriminatory power. Among the Beijing strains, the MDR phenotype was revealed more frequently than among the others. High genetic heterogeneity of the studied population was shown by the assessment of VNTR loci variability in the analyzed group and in the strains from other parts of Russia. Comparison of the 24-VNTR locus typing and spoligotyping data with revealed resistance-associated mutation allows us to make a suggestion that the active transmission of MDR strains and the independent appearance of drug resistance during chemotherapy occurred in the studied population simultaneously.

Mini-sequencing with subsequent result registration using MALDI-ToF mass-spectrometry was employed for hepatitis B virus genetic typing in Russian population. This approach was employed for hepatitis B virus genetic typing in HBsAg-positive patients with chronic hepatitis B, hepatitis of combined etiology and hepatic cirrhosis and allowed to show the prevalence of D genotype (83.3%) in all groups of patients. Other hepatitis B virus genotypes: genotype A (5.9%), genotype C (3.6%), and mixed infection with D and C (7.2%) were also found in patients with chronic hepatitis B and hepatic cirrhosis. All genotypes were found in patients with chronic hepatitis B and hepatic cirrhosis. Chronic hepatitis of combined etiology was noted only in patients with genotype D. Possibility of detection of mixed infection with hepatitis B viruses of various genotypes is a distinct advantage of mini-sequencing approach over direct nucleotide sequence evaluation for hepatitis B virus genetic typing.

We applied complex genetic analysis for evaluation of tetracycline-resistance markers in 129 clinical strains of Neisseria gonorrhoeae from Central, Privolzhskii, and Siberian regions. For detection of mutations in rpsJ gene and MtrRCDE locus we first used minisequence reaction followed by identification of products by MALDI-TOF mass spectrometry. The incidence of detection of resistance markers among the analyzed strains were: tetM — 3.1%, mutations in genes rpsJ — 82.2 %, penB — 62.8%, and mtrR — 54.3%. The analyzed genetic markers were not detected in 17.5% strains. tetM gene was detected in only 12.5% strains from the Central Region. No differences were revealed in regional distribution of other genotypes. Genotypes tetM pres, rpsJ mut, mtrR mut, and rpsJ mut, penB mut, mtrR mut reliably predict tetracycline resistance. Microbiological and genetic testing of tetracycline resistance yielded similar results.

Plasma constructions including genes encoding C. trachomatis inclusion membrane protein as composite proteins with reporter green fluorescent protein were obtained. After transfection of HeLa cell culture with the resultant plasmid constructions the location of inclusion membrane proteins in transfected cell was for the first time detected by confocal microscopy.

Numerous studies have indicated that Helicobacter pylori is one of the most frequent pathogens, affecting up to 50% of the human population worldwide [1, 2, 3]. While the majority of infected people have no clinical manifestation, they nevertheless constitute a risk group for subsequent development of chronic gastritis, gastric ulcer, duodenal ulcer, extranodal B-cell MALT lymphoma or gastric adenocarcinoma. There is evidence that genetic variability of Helicobacter pylori is related to the risk of disease. Several genes of Helicobacter pylori, such as cagA, vacA, iceA and babA are considered to be associated with virulence. Clinical isolates of Helicobacter pylori may vary markedly with geographic location, and studies on the incidence and distribution of pathogenicity markers of the bacterium may shed light on their significance and versatility. Much work has been done on genotyping Helicobacter pylori all over the world [4]. Yet, clinical isolates obtained in Russia (which occupies as much as about 1/6th of the world’s land mass) have not been genotyped so far. In the study presented here, we investigated the prevalence of the cagA, vacA, iceA and babA genes and the subtyping of vacA in Helicobacter pylori isolates recovered from patients with duodenal ulcers and chronic gastritis in Russia. A total of 42 Helicobacter pylori isolates obtained from patients in different locations throughout Russia (central region, 20; Siberia, 5; Volga region, 11; and northwestern region, 6) were used. Helicobacter pylori isolates were obtained from the antrum and the corpus of patients with histologically confirmed duodenal ulcer (n=20) and chronic gastritis (n=22). Patients (23 male, 19 female) were age matched, with a median age of 45 years (range, 19–62 years). Three of the patients were Mongolian and 39 were mixed European. Patients receiving antisecretory therapy or nonsteroidal anti-inflammatory drugs were excluded. All biopsies were collected at the Institute of PhysicoChemical Medicine, Moscow, Russia. Chromosomal DNA was extracted from 72-h plate cultures of each strain using the Helicopol Isolation Kit (Lytech, Russia) in accordance with the manufacturer’s recommendations. For each isolate, cagA, vacA, iceA and babA genotypes were characterized by PCR as described previously [5, 6, 7, 8]. Genotypes were successfully and fully determined for all isolates, and the results are given in Table 1. Of the 42 isolates examined, 39 were positive for the cagA gene. The iceA2 gene was not found independently in clinical isolates. It was found only in combination with iceA1 in 10 of the 42 isolates. The iceA1 gene alone was detected in 26 Helicobacter pylori isolates. The babA2 gene was verified in 31 isolates. The vacA genotypes were identified in all 42 Helicobacter pylori isolates. The vacAs1 genotype was found in 31 of the 42 clinical isolates. Seven Helicobacter pylori strains verified in clinical isolates had the vacAs2 genotype. No samples with the vacAs2/m1 genotype were found. Interestingly, mixed vacA genotypes (s1/s2 or m1/m2), indicative of more than one strain variant of Helicobacter pylori, were found in 15 of the 42 clinical isolates. Certain combinations of the vacAs1, cagA, iceA1 and babA2 were revealed. The type 1 gene combination (vacAs1, cagA and babA2) was found in 57.1% of the clinical isolates and the type 2 combination (vacAs1, cagA, iceA1 and babA2) was found in 45.2%. No association was found between the babA2-positive genotype and vacAs1, cagA or iceA1 genotypes in the clinical isolates of Helicobacter pylori (P>0.2 in all cases). Therefore, we investigated the presence of cagA, vacA, iceA1 and babA2 genes in clinical Helicobacter pylori isolates and correlated these data with the presence of gastritis and duodenal ulcer. K. Momynaliev ()) · V. Govorun Department of Gene Engineering and Immunogenetics, Institute of Physico-Chemical Medicine, Russian Federation Ministry of Public Health, Malaya Pirogovskaya Street 1A, Moscow 119992, Russia e-mail: dhoroshun@nm.ru Tel.: +7-095-2454236 Fax: +7-095-2464501

Staphylococcus aureus - one of the most interesting for clinical studies of microbial species with extensive strain diversity, primarily due to the variability of virulence factors and pathogenicity. The aim of this study was approbation of a method for the rapid strain differentiation of S. aureus on the basis of bacterial cell direct protein profiling approach by means of MALDI TOF MS. Beta-lactamase and alpha-hemolysin productions, cording by the blaZ and hla genes, respectively, were selected as markers for the strain differentiation. Mathematical analysis of MALDI mass spectra from 53 isolates allowed the construction of two independent classification models that can differentiate the strains on the presence/absence of blaZ or hla genes. A number of the most significant peaks (masses), which can be considered as markers of the strain differences in S. aureus, were identified using a statistical contribution of each mass peak in the models. These diagnostic models differ the sensitivity and the specificity, which were 97.5% and 82.5% for the classification of strains on the basis of beta-lactamase production, and 90.0% and 88.7% by the presence of alpha-hemolysin.

β-Carotene inhibits cholesterol production in A-431 cellsin vitro and slightly modifies their growth in a culture. Oxidation of β-carotene increases its biological activity. The main products of β-carotene oxidation are isolated and their biological activity evaluated.