Relevance. Colorectal cancer (CRC) is the third most common cancer in the world. In the Russian Federation, high rates of neglect in late diagnosis of colon cancer have been established. The study of the complex influence of social, clinical, anamnestic and dietary risk factors in the development of colorectal cancer is valuable in identifying risk groups for effective secondary prevention. Aims. Assessment of the importance of medical and social, clinical and anamnestic, alimentary-dependent factors as risk factors for colon cancer. Materials & Methods. To analyse the regional characteristics of CRC incidence, the database "Cancer diseases in the Northwestern Federal District" for 2010-2023 was used. To investigate the risk factors for CRC, a case- control study was organised in which patients over 18 years of age with or without diagnosed intestinal pathology (colorectal cancer, inflammatory bowel disease) were included. Results and discussion. Among patients with CRC, patients with advanced forms of the disease predominated: the proportion of CRC diagnosed at stage III and IV was 54% and 17% of newly diagnosed cases, respectively. When analyzing the data, no association was found between the risk of developing CRC and the presence of chronic diseases, oncological pathology, including CRC in relatives of the 1st and 2nd degree of kinship, alcohol abuse and smoking, as well as with most alimentary-dependent factors, with the exception of fried and smoked fish. Conclusions. Colon neoplasms are detected in the population of the Northwestern Federal District at late stages and when patients seek medical care independently. Significant attention in epidemiological studies should be paid to such a factor as eating fish after certain types of heat treatment (fried and smoked). prospects for further research, in our opinion, are related to the search for informative markers to identify risk groups, in particular factors associated with altered intestinal microbiota and colonisation of the intestine with potentially oncogenic microorganisms.

Relevance. Escherichia marmotae is a recently described species of Escherichia that is considered a potential new zoonotic pathogen. The geographical distribution of this microorganism in wild animals and its genomic diversity are currently insufficiently studied. Aims. The purpose of the study was to determine the pathogenic potential of the Escherichia marmotae 16guk strain isolated from zoogenic material on Hooker Island (Arkhangelsk Region, Franz Josef Land Archipelago) and its phylogenetic relationships with previously described strains of different origin. Materials and methods. The Escherichia marmotae 16guk strain was isolated from the faeces of an arctic fox (Vulpes lagopus) near a breeding ground. The pathogenic potential of the strain was assessed on the basis of genomic sequencing data using Illumina technology, an estimate of the mean lethal dose when administered intraperitoneally to mice, and an assessment of the antibiotic resistance phenotype using the disc diffusion method. To determine the phylogenetic position of the described strain within the overall structure of the microbial population, genome-wide sequencing data deposited in NCBI GeneBank were used. The phylogenomic analysis was performed based on the distance matrix of single nucleotide polymorphisms in the core genome due Parsnp. Results. The strain is characterized by low virulence when tested on mice (LD50 was 1.3*109 K.O.E.), has resistance to ampicillin and gentamicin. A number of pathogenicity factors have been identified in the genome structure, which includes siderophores of enterobactin and aerobactin operons, fimbria type I genes characteristic of extraintestinal Escherichia strains, amyloid-like protein villi (curli) and capsular genes, as well as the ibeABC invasion factor operon. The resistome is represented by blaEC15 beta-lactamase genes and acrAD-TolC efflux pump genes. According to the results of phylogenomic analysis, the strain under study shows the greatest similarity with the genome sequences of strains circulating in New Zealand and Germany among wild animals (wild boars) and birds. The similarity of the genomes of strains distributed in distant geographical regions and the isolation of the 16guk strain within an ornithogenic ecosystem can be interpreted as a result of the spread of E. marmotae with migratory birds. Conclusions. The discovery of the Escherichia marmotae 16guk strain in one of the most remote Arctic territories demonstrates the possibility of the emergence and circulation of enterobacteria strains with significant pathogenic potential in the island territories of the high-latitude Arctic, which actualizes the need for systematic monitoring studies in this region.

Relevance. Infections caused by methicillin-resistant strains of Staphylococcus aureus are an urgent problem of hospital epidemiology, and control measures involve the development of new antimicrobials. Probiotics based on bacterial strains isolated fro natural habitats are considered promising means of combating MRSA.Aims. To test the possibility of using the Bacillus safensis 440-1 strain isolated from Antarctic soil. as an antibacterial agent for the treatment of experimental staphylococcal infection.Purpose of the study – check the possibility of using the Bacillus safensis 440-1 strain, isolated from Antarctic soil, as a topical antibacterial agent for the treatment of experimental staphylococcal infection.Material and methods. The potential virulence of Bacillus safensis strain 440-1 was studied on a mouse peritonitis model, and its activity against the methicillin-resistant Staphylococcus aureus SA776 test strain was studied on a localized wound infection model.Results and discussion. Our study demonstrated the safety of the tested strain due intraperitoneal use. We found that the use of the studied strain reduces the staphylococci amount in wounds from the third day from the start of the study to the end of the observation period, without aggravating the course of the infection.Conclusion. Bacillus safensis strain is a promising potential probiotic and it can be used as a part of complex antiseptic or disinfectant after additional studies aimed at developing an optimal mode of its use.

Aim. To investigate the potential for searching new virulent bacteriophages in the paleontological material extracted from the permafrost zone. Material and methods. The virome structure of the colon content of the wolf pup mummy ( Canis lupus ) from the late Pleistocene was evaluated by means of shotgun metagenomic sequencing. Results. The study demonstrated the predominance of Myoviridae tailed bacteriophages, including PhiKZ-like phages, in the structure of the virome. Conclusion. The results of the study indicate the possibility of using paleontological material preserved in the ancient Arctic permafrost as a resource for searching and isolating new virulent bacteriophages.

Severe course of COVID-19 in inpatients can be caused by a number of reasons, including viral and bacterial superinfections. Empirical use of antibiotics, as well as poor infectious control stimulate the emergence and spread of multidrug-resistant bacteria. Klebsiella pneumoniae is the most common carbapenemase-producing bacterial pathogen causing nosocomial infections. These strains became significantly widespread during the COVID-19 pandemic. Objective. To analyze phenotypic and genetic characteristics of K. pneumoniae strains as the dominant bacterial pathogen in severe COVID-19 patients in the intensive care unit. Patients and methods. This study included 38 COVID-19 patients (including 6 patients with severe disease) treated in the intensive care units of Moscow and Saint Petersburg hospitals for infectious diseases between July 2020 and December 2020. All patients signed an informed consent to participate in the study; patient data was anonymized. The following samples were collected: sputum, bronchoalveolar lavage, and nasopharyngeal swabs. We performed bacteriological identification of isolated bacterial strains, drug susceptibility testing, and whole genome sequencing of K. pneumoniae strains. Results. The majority of K. pneumoniae strains isolated from patients with severe COVID-19 contained clusters of aerobactin and enterobacterin genes. However, some of them (strains 90 and 124) also contained clusters of yersiniabactin genes. These genes are associated with high virulence and ability to form biofilms. The isolated strains belonged to four sequence types (ST874, ST395, ST147, ST15) that are characterized by high virulence and antibiotic resistance. These K. pneumoniae strains can be considered as one of the major causes of severe and lethal COVID-19. Conclusion. Our findings suggest that the detection rate of K. pneumoniae in COVID-19 patients increased from 30% to 70% during the pandemic. Phenotypic tests demonstrated that more than 80% of the strains were resistant to most antibiotics used in patients with complicated COVID-19. The combination of gypervirulence and antibiotic resistance is crucial for nosocomial transmission of these strains and their effect on the disease outcome. The emergence of hyper-resistant pathogens necessitates regular epidemiological monitoring and robust infection control in Russian hospitals, especially in intensive care units. Key words: COVID-19, severe disease, Klebsiella pneumoniae, genome sequencing, carbapenemases, hypervirulence, antibiotic resistance

Relevance. The COVID-19 pandemic has led to significant overloads in the work of health systems in many countries, a shortage of beds and staff, which contributes to a decrease in adherence to measures to prevent and control nosocomial infections, which can significantly worsen the course of viral pneumonia. Aim. To assess the possibility of the formation of hospital strains of multidrugresistant microorganisms in hospitals repurposed to provide medical care to patients with COVID-19. Materials and methods. The study included patients with severe and moderate forms of COVID-19 (ICD codes U07.1, U07.2), who were admitted to two large hospitals repurposed for the treatment of this infection. The data of microbiological studies of the biomaterial associated with the respiratory tract (sputum, bronchoalveolar lavage, tracheal aspirates) obtained from 1101 patients from May to January 2021 were analyzed using a combination of molecular genetic methods (RAPD-PCR, detection of integrons and the carbapenemase gene bla NDM.), and molecular typing of carbapenem-resistant strains of Klebsiella pneumoniae and Acinetobacter baumannii was carried out. Results. It was found that carbapenem resistant gram-negative bacteria predominate in the structure of the nosocomial microbiota of the respiratory tract of patients with COVID-19 in both hospitals. Based on molecular typing made the wide distribution of several genetic lines of integron-positive carbapenem resistant Klebsiella pneumoniae and Acinetobacter baumannii was detected. Conclusions. The COVID-19 pandemic has exacerbated the spread and circulation of bacteria with multiple antibiotic resistance in hospitals. This study has demonstrated the possibility of the formation of hospital strains of nosocomial infections in COVID-19 hospitals, which justifies the need to improve infection control measures in the context of a new coronavirus infection pandemic.

Assisted reproductive technologies (ART) are one of the most effective ways in fighting infertility, but their effectiveness is influenced by various factors. Our study focuses on examining importance of risk factors underlying ART failure related to altered microbiome pattern in the female reproductive system. The case-control study was based on conducting a laboratory examination of 129 infertile couples applied to the Department of Assisted Reproductive Technologies due to failure of in vitro fertilization (IVF), whereas control group consisted of females with successful progressive pregnancy after ART. Chlamydia, herpes virus and cytomegalovirus were assessed by using PCR and ELISA, whereas culture method was used to detect Trichomonas vaginalis in vaginal swabs and ejaculate applying Trichomonas Modified CPLM Medium (HiMedia, India) followed by microscopy. In addition, the qualitative and quantitative composition of the vaginal biocenosis was studied with multiplex RT-PCR by using Femoflor-16 kit (DNA-technologies, Russia). Serological tests were based on measuring IgG and IgA antibodies against Chlamydia trachomatis in ELISA (diagnostic kits purchased from Vektor Best, Russia; NovaTec, Germany; ImmunoComb, Israel) as well as antibodies against immediate early HSV-1/2 proteins (BioService, Russia) and immediate early HHV-5 proteins (Vector Best, Russia). C. trachomatis and herpesvirus DNA was measured by using PCR diagnostic kits Amplisens (Interlabservice, Russia). It was found that sexually transmitted infection agents were highly prevalent in infertile couples applying to the hospital for IVF. Significant factors for non-pregnancy were vaginal dysmicrobiocenosis (OR = 7.5 (95% CI 1.04—54.1), p = 0.02) and detected T. vaginalis (OR = 2.6 (95% CI 1.12—6.4), p = 0.01). Dysbiosis of the reproductive system, including those occurring due to trichomonas infection is associated with lowered ART effectiveness. It is evident to timely detect urogenital infections and dysbiosis while preparing infertile couples for IVF cycles.

The study of microbial DNA from paleontological and archaeological samples is a powerful tool for estimating the molecular evolution of human pathogens. The paper is a retrospective review of the most significant achievements in medical paleomicrobiology. The subject of the discussion is the genetic diversity of ancient microbiomes including pathogenicity and antibiotic resistance genes. Paleomicrobiological studies of permafrost as a repository of pathogenic microbiota are highly promising.

Pneumococcus and pneumococcal infections are still among actively discussed problems, while there is a lack of information about the population structure in the North-East of Russia. Objective: the identification of microbiological and molecular genetic characteristics of S. pneumoniae strains found during nasopharyngeal carriage in Yakutsk. Materials and methods: we studied S. pneumoniae isolates, obtained from the discharges of nasopharynx in 69 patients from the age of 6 months to 85 years living in Yakutsk and undergoing a survey for acute and chronic diseases of the ENT organs (rhinitis, sinusitis, otitis), repeated acute respiratory viral infections and nasopharyngitis. Identification of the isolated cultures was performed using the time-of-flight mass spectrometry method on a Vitek MS analyzer. For uncertain results, we used test systems to detect S. pneumoniae DNA on PCR-RV. Identification of sensitivity to antimicrobial agents was determined by the disk diffusion method with an interpretation according to the EUCAST recommendations and the Clinical recommendations for determining the sensitivity of microorganisms to antimicrobial agents (version 2018-03). The microbiological analyzer Vitek II Compact was used to specify the phenotype of sensitivity / resistance. Confirmation of species identification was carried out by amplification of the autolysin gene (lytA). Identification of serological types of the isolated S. pneumoniae strains was carried out using multiplex PCR. We were determining presence of genetic determinants of resistance to macrolide antibiotics erm, mef and msr as well as genes associated with the pathogenicity island PPI1 (per, npIT, FtsW). Results: more than 80% of S. pneumoniae strains circulating among the population of Yakutsk are represented by serotypes 6A and 19F. In 50% of pneumococci 6A and 100% of serotype 19F pneumococci were detected all 3 genes associated with the pathogenicity island PPI1. Macrolide resistance was observed in all isolates of serotype 6A, while 80% of serotype 6A and 100% of serotype 19F showed the ermB resistance gene (MLSB phenotype) and 20% of serotype 6A pneumococci had the mef gene (M phenotype). Conclusions: obtained data indicate the prevalence of virulent antibiotic resistant strains of S. pneumoniae among the population of Yakutsk and dictate the need for further epidemiological and microbiological studies of this problem.

Aim. To give epidemiological assessment of potential risk factors for prevalence of antibiotic resistant strains of upper airways and ENT-organs infectious pathogens in children. Materials and methods. The study included children (165 persons) aged 1 to 17years, who asked for ambulatory-polyclinic medical care in connection with upper airways and ENT-organs diseases and formed the group of “cases” (75 persons) - patients, colonized by Streptococcus spp. and Staphylococcus aureus strains with antibiotic resistance not less than one of three classes (beta-lactams, macrolides, lincosamides) and the control group (90 persons) - patients without the facts of colonization by antibiotic-resistant strains of the studied microorganisms. During doctor’s reception, parents of all patients were surveyed. Results. According to the results of a survey carried out, there was estimated connection of 18 potential risk factors with carriage of antibiotic-resistant strains. Pneumococcal vaccination in the investigated population was a factor, rendering preventive effect on the colonization rate of antibiotic-resistant strains Streptococcus spp. and Staphylococcus aureus ( OR = 0,40 [95 %DI 0,19-0,86]). At the same time, no ties between colonization by antibiotic-resistant microorganisms and risk factors, connected with previous use of antibiotics, especially without doctor’s administration, was noted. Conclusions. Vaccination with pneumococcal vaccines in the studied population is a factor, controlling prevalence of resistance to antimicrobial drugs

Background. Vancomycin-resistant enterococci (VRE) have become one of the leading cause of health care-associated infections. Data on occurrence and spread of these pathogens in different types of hospital units are needed to develop effective surveillance and control measures to prevent dissemination of VRE. Aim. The aim of this study was to define hospital units with high risk of VRE dissemination in health care facilities of St. Petersburg. Materials and Methods. Point-prevalence study of colonisation and infection in patients and contamination of the environment was conducted during 2013 - 2014 in 8 hospital units of different types: neonatal intensive care, newborn pathology, general paediatric surgery, bone marrow transplantation (BMT for adolescents), cancer surgery of the gastrointestinal (GI) tract and breast cancer, haemodialysis (three units). In each unit microbiological testing of clinical (N=857) and environmental (N=508) samples was conducted three times a months during the study period. Verification of vancomycin resistance in enterococci was conducted by amplification of vanA and vanB cassettes according to the technique developed by S. Dutka-Malen et al. Molecular genetic typing of enterococci by random amplification of polymorphic DNA (RAPD-PCR) was performed with universal primer R5 (5’-AACGCGCAAC-3’) in the concentration of 50 pmol/^L, according to the protocol proposed by B. Martin et al. VNTR analysis was performed according to the technique published by J. Top et al. Results. Colonization of patients and contamination of environment by VRE were detected only in haemato-oncologyunits (21,6 per 100 patients, 2,6 per 100 environmental swabs), neonatal intensive care (16,7 per 100 patients, 8,5 per 100 environmental swabs), and newborn pathology (34,6 per 100 patients, 3,3 per 100 environmental swabs). VRE were detected on the related to patient care environmental objects in common use for all patients (scales, changing tables, procedure tables, sink faucets) in the neonatal intensive care units and non-medical objects shared by all patients (tables in patient rooms, microwave oven and refrigerators shelves) in the haemato-oncology unit. The molecular genetic typing showed that strains of VRE isolated from patients and the environment were identical. Vancomycin resistance due to presence of vanA was dominating. Conclusion. Neonatal and haemato-oncology departments were identified as high risk hospital units. The most common mode of transmission of VRE is contact transmission via hands of health care workers in neonatal units and via environmental objects in haemato-oncology. To contain dissemination of VRE in the high risk units, development of microbiological monitoring of VRE and measures to control their transmission is needed.

Enterococcus faecium 58m is a putative ancient nonpathogenic strain isolated from the intestinal content of an adult woolly mammoth (Mammuthus primigenius). Here, we report its draft genome sequence, consisting of 60 contigs. In silico genomic analysis was performed to determine the genetic features and pathogenic potential of this microorganism.

Investigation and description of viable bacteria isolated from ancient permafrost are an essential part of modern paleomicrobiology ([1][1], [2][2]), despite the difficulties with evidence of autochthony of isolates. In our work, we have described the draft genome of an unusual strain of