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. Pathogenic strains of Escherichia coli are an important object of surveillance within the One Health concept in the wild, agriculture and human society. Migratory bird colonies and high latitude avian colonies may be points of active intraspecies and interspecies contact between different animal species, accompanied by the spread of pathogens. At the same time, the phylogeography of E. coli in relation to the presence of natural foci of colibacillosis in polar regions remains virtually unstudied. The aim of this study was to assess the pathogenic potential of E. coli strains from the polar regions of the Earth, based on the analysis of the genomes of these bacteria from typical ornithogenic ecosystems of the Arctic and Antarctic. Materials and methods. The study used collections of E. coli isolated from ornithogenic biological material during expeditions to high latitude areas of the Arctic (archipelagos of Novaya Zemlya, Franz Josef Land, Svalbard) and Antarctic (Haswell Archipelago). 16 cultures associated with avian E. coli (12 polar and 4 temperate strains) were selected for genome-wide sequencing using BGI technology. The annotation of the genomes focused on the identification of genes for pathogenicity factors and antimicrobial resistance, as well as the identification of strains belonging to individual genetic lineages using the cgMLST method. Results. The annotation of the genomes allowed their assignment to different sequence types in the multilocus sequencing typing and genome-wide sequencing typing schemes. The analysis of the geographical distribution of the sequence types of polar E. coli strains determined by the cgMLST method showed their global representation in geographically distant regions of the planet. For example, cgST 133718 was observed in Antarctica (strain 17_1myr) and in the UK, and sequence 11903, to which strain 32-1 from the northernmost point of Novaya Zemlya belonged, was previously identified in the USA. All strains studied were characterized by the presence of extensive virulence. Among the pathogenicity factors identified were haemolysins A, E, F, siderophores, including the yersiniabactin gene cluster, a number of adhesion, colonization and invasion factors, as well as the thermostable enterotoxin EAST-1 and genes that characterize enteroaggregative strains of E. coli (the virulence regulator gene eilA and enteroaggregative protein (air)). One of the Arctic strains (33-1) had determinants of antibiotic resistance, in particular the extended-spectrum beta-lactamase gene TEM-1b and the Tn1721 transposon, including tetracycline resistance genes (tetA-TetR), were detected in its genome. Conclusion. The results of the study indicate the circulation of E. coli strains with strong pathogenic potential in high-latitude Arctic and Antarctic ornithogenic ecosystems. The analysis of genomic data indicates the presence of geographically widespread genetic lineages in these regions, which justifies the importance of monitoring epidemic clones of E. coli, along with monitoring for other pathogens, in bird colonies in high-latitude areas.

BACKGROUND: The increasing frequency of cesarean sections and artificial feeding creates a predisposition to allergic diseases, obesity, and diabetes mellitus. Pathogenesis of these involves changes in the gut microbiome of infants. AIM: The aim of this study was to evaluate the impact of the method of delivery and feeding practice on the gut microbiome of infants. MATERIALS AND METHODS: This study included 103 infants aged 4-6 weeks (group 1: 39 infants born vaginally and breastfed; group 2: 10 infants born vaginally and formula-fed; group 3: 31 infants born by caesarean section and breastfed; group 4: 23 infants born by caesarean section and formula-fed), each of whom had stool collected for 16S ribosomal RNA gene sequencing. RESULTS: We found differences in the relative abundance of Akkermansia spp. [34.07 (29.29–38.85)% in group 4 and 0.01 (0.01–0.02)% in group 1; p = 0.011], Bifidobacterium spp. [30.68 (21.65–39.41)% in group 1 and 17.08 (9.86–21.68)% in group 4, (p = 0.002); 31.46 (24,30–52.97)% in group 3 and 17.08 (9.86–21.68)% in group 4 (p = 0.001)], and Enterococcus spp. [4.69 (1.01–8.59)% in group 3 and 0.58 (0.12–1.87)% in group 1 (p = 0.003); 4.29 (2.07–6.96)% in group 4 and 0.58 (0.12–1.87)% in group 1 (p = 0.001)]. The coefficient of correlation adaptometry was maximum for groups of infants who were breastfed. Analysis of the morbidity of infants in the first year of life revealed differences in the incidence of acute respiratory viral infections between infants in groups 1 and 4 (17.9 and 78.3%, respectively; p = 0.0064), as well as groups 3 and 4 (32.2 and 78.3%, respectively; p = 0.018). CONCLUSIONS: The relative abundance of Bifidobacterium spp. depends on feeding practice to a greater extent than on the method of delivery. The method of delivery affects the relative abundance of opportunistic bacteria such as Enterococcus spp. Correlation analysis demonstrated the role of breastfeeding as a mechanism for “learning” and maturing the immune system of children.

Introduction. Campylobacteriosis is among the leading causes of acute gastrointestinal infections. The severity of campylobacteriosis and the development of long-term complications may be influenced by the genotype of the pathogen, whose biological properties can affect immune response parameters. The aim of the study was to identify common genotypes of epidemic clones of Campylobacter pathogens and to investigate characteristics of the immune response and severity of the disease. Materials and methods. The study included 203 patients aged from 1 month to 17 years with campylobacteriosis who underwent treatment at the clinic of the Federal State Budgetary Institution "DNKCIB FMBA" in 2019–2021. The diagnosis was confirmed using polymerase chain reaction method. Patient samples were also analyzed using culture-based methods. Total DNA was extracted using the QIAamp DNA Mini Kit. Genetic determinants encoding virulence factors and MLST typing were performed using the ResFinder program. The immune status of patients was assessed on days 1 and 7 of the illness. Immunological investigation included measurement of serum immunoglobulin concentrations (IgA, IgM, IgG), C-reactive protein, and cytokines (IL-1β, IL-1, IL-2, IL-4, IL-5, IL-6, IL- 7, IL-8, IL-10, TNF-α, and IFN-γ). Results. When analyzing the frequency of detection of Campylobacter sequence types in children with clinical intestinal infections, it was found that the profile of isolated isolates is most similar to those from countries of North America (USA and Canada), Northern Europe (Great Britain, Holland ) and Scandinavia (Denmark, Sweden, Finland). Identification of a pathogen with the flgE+, cdtA+, cdtC+ genotype was accompanied by a statistically significant increase in the level of IL-8 and a decrease in the content of IgA in the peripheral blood serum, which reflected the low efficiency of the immune response during infection with Campylobacter and predetermined the severe course of the infectious process during the disease.

Bacterial microbiota in stool may vary over a wide range, depending on age, nutrition, etc. The purpose of our work was to discriminate phyla and genera of intestinal bacteria and their biodiversity within a healthy population (North-Western Russia) compared to the patients with type 1 diabetes mellitus (T1DM). The study group included 183 healthy persons 2 to 53 years old (a mean of 26.5±1.0 years old), and 41 T1DM patients (mean age 18.2±1.8 years old). The disease onset was at 11±1.5 years, with a T1DM experience of 7±1.5 years. Total DNA was isolated from the stool samples, and sequencing libraries were prepared by amplifying the V3–V4 region of the 16S rRNA gene sequenced by Illumina MiSeq. Bioinformatic processing of NGS databases was adapted for microbiota evalutaion. Despite the broad scatter, the biological diversity for bacterial microbiota expressed as the Shannon index was significantly increased from younger to older ages in the comparison group, higher in adult healthy persons, with a trend for decrease in the Actinomycetota phylum which includes Bifidobacterium longum species. Similar but non-significant age trends were noted in the T1DM group. Concordant with the Bacillota prevalence in stool samples of diabetic patients, some anaerobic bacteria (Faecalibacteria, Lachnospira and Ruminococcae, Roseburia) were enriched in the T1DM microbiome against controls. Hence, correction of microbiota for Ruminococcus and Lachnospiraceae requires future search for new probiotics. Lower abundance of Actinomycetota and Bifidobacter in T1DM suggests potential usage of Bifidobacter-based probiotics in this cohort.

Summary Fecal microbiota transplantation (FMT), as any other medical procedure, requires standardization of results, approaches, monitoring of its dynamics and microbiota engraftment evaluation. The aim of the present study was to compare efficiency and results of PCR and 16S RNA-based sequencing in order to trace the dynamics of microbiota composition after FMT. Patients and methods The prospective, single-center study included 27 patients with acute intestinal and chronic (overlap syndrome) graft-versus-host disease (GvHD) developed after allogeneic hematopoietic stem cell transplantation (HSCT). FMT in 19 cases was performed, mostly, with ingestible capsules, eight placebo-treated patients were included into control group. Quantitative changes of different bacterial groups in fecal microbiota were assessed by means of real-time multiplex PCR, being compared with16S rRNA sequencing technique at the terms of D+3, D+16, D+30, D+60 and D+120 following FMT. Clinical response was determined by 4 scales evaluating intestinal syndrome and GvHD grade. Results When evaluating stool consistence according to Bristol scale as an index of GvHD therapy efficiency, we have observed complete clinical response by the D+120 after FMT in nine cases (47% with Bristol score of ≤4 points), and nine patients (47%) showed improved stool properties (>4 points). In the placebo group, complete or partial response was revealed, respectively, in one (13%), and four cases (50%) on the D+120. Multiplex PCR of fecal microbiota has shown a different time course in FMT- and placebo-treated patients, when compared to their initial (pre-FMT) levels. Total bacterial mass and copy numbers of distinct microbial species exhibited sufficient increase after FMT. Such shifts were demonstrable on D+30 for total microbial mass (p=0.002); Escherichia coli (p=0.001); Bacteroides fragilis group (p=0.05); Faecalibacterium prausnitzii (p=0.005). Meanwhile, the numbers Lactobacillus spp., and Bacteroides thetaiotaomicron, generally, were not changed over this time period. Moreover, in the control group (placebo) we have not found significant fecal microbiota changes against initial levels during 120 days monitoring period. Over 120 days of observation, we have also found some differences of the microbiota dynamics for the subgroups with complete response and partial/no response: Bifidobacterium spp. (р<0.047), E.coli (р<0.00047), B. fragilis group (p=5.6×10-5), F.prausnitzii (р<0.0062). Conclusions 1. Quantitative PCR of the major bacterial groups of gut microbiota, e.g., Bifidobacterium spp., E. coli, B. fragilis group, F. prausnitzii could be used as microbiological markers for evaluation of changing microbial landscape after FMT as a routine molecular biology technique. 2. The genocopy counts of B. fragilis group correlate with clinical response in the patients with intestinal GvHD after HSCT, either with, or without FMT procedure.