Journal of microbiology, epidemiology and immunobiology

Introduction. In response to the COVID-19 pandemic in the Russian Federation, comprehensive response measures were taken. One of these measures was the development of a viral genome aggregation platform (VGARus) to monitor virus variability.

The aim of this paper is to describe the role of the VGARus platform in tracking genetic variation in SARS-CoV-2.

Materials and methods. VGARus utilizes sequencing data and bioinformatics tools to monitor genetic variations in SARS-CoV-2. The viral genomes were aligned using NextClade, which also translated them into amino acids and identified mutations. The viral variability over time was analyzed by counting the number of amino acid changes compared to the reference sequence.

Results. The analysis of data within VGARus enabled the identification of new virus variants, contributing to improved diagnostic tests and vaccine development. The platform allowed for the prediction of epidemiologic trends, facilitating a rapid response to changes in the epidemiologic situation. For example, using VGARus, an increase in COVID-19 incidence was accurately predicted in the summer of 2022 and early 2023, which were associated with the emergence of Omicron subvariants BA.5 and XBB. Data from the platform helps validate the effectiveness of primers and DNA probes to ensure high diagnostic accuracy and reduce the risk of false negatives.

Conclusion. VGARus demonstrates the growing role of genomic surveillance in combating COVID-19 and improving preparedness for future infectious disease outbreaks. The platform is a powerful tool for generating evidence-based solutions to combat a pandemic and mitigate its health, economic and societal impacts. It provides the ability to promptly obtain information on the epidemiologic situation in a particular region of the Russian Federation, use genomic data for phylogenetic analysis, compare the mutational spectrum of SARS-CoV-2 sequences with foreign samples. VGARus data allow for both retrospective analysis and predictive hypotheses. For example, we can clearly see the dynamics of the change of different virus variants: sequences belonging to the Alpha, Beta, Delta, Omicron lineages and many less common ones, clearly form the upsurges of morbidity, the interaction of which is reflected in the epidemiological picture. It is also currently being expanded to monitor other pathogens, increasing its public health relevance.

Introduction. Uropathogenic Escherichia coli (UPEC) are the dominant bacterial pathogens of urinary tract infections (UTIs). UPEC belong to different phylogenetic groups and have many virulence factors, the study of which, in conjuction with the assessment of their relationship with clinical forms of UTI, is necessary for a better understanding of the pathogenesis of UTI and the development of new diagnostic algorithms.

Aim: determination of the molecular genetic characteristics of uropathogenic Escherichia coli isolated from pregnant women with asymptomatic bacteriuria.

Materials and methods. Clinical isolates of uropathogenic E. coli (n = 70) from pregnant women with asymptomatic bacteriuria were included in the study. The PCR method was used to determine the belonging to phylogenetic groups and detect 15 virulence markers — genes associated with adhesion (fimH, papC, sfa, afa, focG); toxin synthesis (cnf 1, hlyA, sat, vat, usp); siderophores (fyuA, iroN, iuc); capsular antigen (kpsMII). To assess the statistical significance of differences, Fisher's exact test was used. Differences were considered statistically significant at a confidence interval of 95% (p < 0.05).

Results. Most of the UPEC isolates belonged to phylogroup B2 (51,4%) and were characterized by the detection of all UPEC-associated virulence factors included in this study; genes associated with adhesion (sfa, focG), invasins (ibeA), synthesis of toxins (hlyA, cnf1, vat, usp) and capsule (kpsMII), siderophores (fyuA, iroN, hlyA) were detected significantly more frequently (p < 0.05). Two or more virulence determinants were detected in 93% of isolates.

Conclusion. The identification of key determinants of virulence and/or a combination of virulence genes can be a prognostic marker for predicting the course of UTI, especially in pregnant women, and will expand diagnostic capabilities taking into account the virulent properties of the uropathogen.

Aim of the study. Genetic analysis of Streptococcus pneumoniae serogroups 15 and 11 circulating in Russia according to the following parameters: serotype affiliation; clonal complex (CC); presence of resistance and virulence determinants; relatedness to genetic lineages circulating in the world, and justification of inclusion of the actual serotypes of serogroups 15 and 11 in the future conjugate vaccine composition.

Materials and methods. The study included whole genome data of S. pneumoniae serogroups 11 and 15.

Results. Genomes of serogroup 15 strains from Russia are represented mainly by serotypes 15B and 15C, the majority of which belong to CC-1025 and CC-1262. CC-1025 is characterized by a more frequent association with invasive diseases. Representatives of CC-1025 and CC-1262 contain virulence determinants unique to these genetic lineages within the studied population of serogroup 15: oligopeptide transporters, fructose-specific PTS system, unique hydrolase variants, additional iron ion transporters, the gene of zinc metalloprotease ZmpC (activating human MMP9). The genomes of serogroup 11 are represented mainly by serotype 11A, the majority belong to CC-62 and CC-1012. The virulence determinants unique to CC-62 (within the studied serogroup 11) include bacteriocins, components of oligopeptide transport, flavin reductase-like protein (adhesin, also protects bacteria from oxidative stress), fucose processing operon, PsaA (adhesin, also a component of the ATP-binding cassette transporter that imports manganese ions).

Conclusion. In the Russian Federation, serogroups 15 and 11 are the most common non-vaccine serogroups. No antimicrobial resistance determinants have been identified in the genomes of representatives of these serogroups. For each of the genetic lineages prevalent in Russia and associated with serogroups 15 and 11, unique virulence determinants within the studied serogroup have been identified, which may contribute to the success of these lineages. It is advisable to include serotypes 15B and 11A in vaccines promising for the Russian Federation.

Introduction. By fixing on the exposed surfaces of complete removable dentures and oral soft tissues, bacteria form a biofilm, thereby increasing their overall virulence and resistance. The microorganisms that make up the biofilm are often in a symbiotic relationship, which allows them to increase their pathogenic potential and cause the development of denture stomatitis. Accordingly, when a particular strain is present in the oral cavity, the risks of symbiosis are significantly increased.

The aim of the study was to evaluate the effect of symbiotic relationships of oral bacteria on the development of inflammatory changes in the oral cavity in the absence of teeth.

Materials and methods. Two groups of patients belonging to the elderly age according to WHO systematization (60–74 years) with complete absence of teeth (K08.1) were formed, differing in the presence of clinical manifestations of inflammation (82 men and 49 women). Biological material sampled from the oral cavity of patients was studied using the culture method and RT-PCR. To quantify the interaction between members of the microbiocenosis, we used the Jaccard similarity coefficient.

Results. Coagulase-negative and coagulase-positive staphylococci, Neisseria, Candida spp., Enterobacterales and F. nucleatum were more frequently found in patients with complete absence of teeth. Expressed symbiotic relations between microorganisms of the Enterobacterales order, Lactobacillus, Neisseria and Corynebacterium genera, as well as S. salivarius, C. albicans, F. nucleatum were established. The nature of these relations depended on the presence of inflammatory changes in the oral mucosa and, in turn, influenced the development of the latter. Thus, in the absence of inflammation, Corynebacterium, Lactobacillus and S. salivarius showed stable synergism. In case of inflammation, the association between these bacteria was accompanied by the introduction of F. nucleatum and displacement of S. salivarius.

Conclusion. Thus, conditionally pathogenic microorganisms, forming microbial associations with multidirectional symbiotic relations increase their virulence, which allows them to occupy free niches in the oral cavity and subsequently trigger the development of pathological process of inflammatory character of prosthetic bed tissues.

Introduction. The key step in agent-based modeling of epidemics, which allows researchers to take into account individual characteristics of people, is the creation of an artificial population. The main difficulty of this procedure is finding a balance between the detail of the population description and the computational efficiency of the calculations.

The aim and objectives of the review: Critically analyze and summarize the current evidence on how to create artificial populations; evaluate the limitations and advantages of available approaches in solving various problems in epidemiology.

Materials and methods. An analysis of literature sources devoted to agent-based modeling has been performed. The analysis is focused on algorithms for creating an artificial population with a given level of detail for modeling human respiratory infections.

Results. The approaches to the creation of artificial populations are generalized. The main principles of realization of interaction between agents are revealed: by means of networks of contacts between agents and on the basis of taking into account the movement of agents between locations. The first approach is the most computationally efficient and simple; the second approach allows to better take into account the change in the behavior of agents during the development of the epidemic process.

Conclusion. Agent-based modeling is an optimal tool for selecting the best scenario for epidemic control and investigating the role of individual characteristics of people in the development of epidemics. When creating an artificial population, it is important to include in the model factors that can be targeted for control. A significant limitation is the lack of factual data on population structure, but this can be overcome by using indirect data.

Infection caused by Staphylococcus aureus is the most common infection leading to the development of serious complications in humans. S. aureus is among the highly lethal bacteremia-associated pathogens with a mortality rate of approximately 18% in industrial countries; in developing countries, the rate is even higher, up to 27%.

One of the most striking and challenging aspects of clinical manifestations caused by S. aureus is the ability of the bacterium to develop resistance to antibiotics. The development of alternative treatment options for staphylococcal infection is urgently needed. The use of immunotherapy and immunoprophylaxis to activate the anti-infection immune response in patients should be considered as a promising direction.

Objective: to analyze the main trends in the development of vaccines aimed at the prevention of S. aureus infection and its virulence factors.

The present review discusses vaccine development in recent years aimed at preventing infection caused by S. aureus. Particular attention is paid to pathogenicity factors (such as capsule, surface proteins and enzymes) that may be useful for the development of new candidate vaccines or immune therapeutics. In recent years, numerous clinical trials of candidate vaccines based on different antigens, taking into account particularly relevant S. aureus pathogenicity factors that influence morbidity, have not been successful due to their low efficacy or insufficiently substantiated safety (development of adverse events). One of the most important factors constraining vaccine development is the lack of successful translation of vaccine protective activity, which is observed in preclinical studies in experimental models but not confirmed in clinical trials.

Therefore, according to numerous researchers, the use of multiple antigens in vaccine formulations should be considered with the focus on different mechanisms of S. aureus pathogenicity and the use of adjuvants.