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Aim: demonstration of basic molecular biological, metabolic and immunological effects of fecal microbiota transplantation (FMT), on the example of a rare case of acute graft-versus-host disease (GVHD) with intestinal damage in a patient after allogeneic hematopoietic stem cell transplantation (allo-HSCT).Materials and methods. To monitor the basic effects of FMT, we performed targeted DNA sequencing of 16S rRNA gene (V3–V4) using MiSeq platform as well as multiplex real-time PCR, MS/gas chromatography technique, immunophenotyping of blood lymphocytes, histological and immunohistochemical techniques.Clinical case. A 40-year-old female patient diagnosed with myelodysplastic syndrome, with a history of two unsuccessful allo-HSCTs due to graft failure, underwent the third haploidentical HSCT (haplo-HSCT) from her father as ‘salvage’ therapy. Due to early viral/bacterial colitis post-transplant associated with a multidrug-resistant strain of K. pneumoniae and herpes virus type 6, FMT was performed on days 46 and 47 after allo-HSCT. Complete resolution of the enteropathy symptoms was noted following FMT. However, immunosuppressive therapy was canceled on D+106 after haplo-HSCT due to the detection of minimal residual disease causing development of the ‘overlap’-type GVHD with damage skin lesions grade 4, and intestinal mucous membranes grade 3. This complication required resumption and subsequent intensification of immunosuppressive therapy with complete resolution of GVHD symptoms. Following FMT treatment, the patient showed complete resolution of clinical colitis symptoms. According to results of 16S rRNA sequencing, the species-specific diversity of fecal microbiota increased significantly, along with decreased relative contents of opportunistic bacteria (Klebsiella, Enterococcus, Streptococcus genera). A significant growth was revealed for commensal Bacteroidota, and re-emergence of Faecalibacterium, Blautia, Roseburia. Acute gastrointestinal GVHD promoted by tacrolimus withdrawal was associated with repeated depletion of intestinal microbiota. Upon resolution of GVHD and resumed immunosuppression, increased microbiota diversity (Shannon index) was again recorded, and the parameters of patient’s fecal microbiota reached the donor values. The microbiota shifts at all clinical stages (before and after FMT, at the peak of acute intestinal GVHD and intensive immunosuppressive therapy) showed some relations with metabolism of bile and fatty acids in blood plasma and immune parameters.Conclusions. FMT may be a component of complex therapy aimed at early reconstitution of immune system and organic acid metabolism in patients after allo-HSCT. The composition of fecal microbiota, metabolic profile and spectrum of lymphocyte subpopulations may be markers for monitoring complex rehabilitation after allo-HSCT.

Гентамицин является одним из компонентов комбинированной терапии инфекционных эндокардитов, вызванных Staphylococcus aureus, включая метициллинорезистентные штаммы (methicillin-resistant S.aureus, MRSA). Цель исследования — анализ влияния десяти 6-часовых циклов воздействия высоких концентраций (16 мкг/мл) гентамицина in vitro на изменение фенотипа и генотипа аминогликозидочувствительных штаммов S.aureus, относящихся к четырём сиквенс-типам: ST5 (ATCC 29213), ST8, ST97 и ST22 (MRSA). Для всех штаммов, кроме ATCC 29213, после селекции отмечалось увеличение МПК гентамицина до 8–64 мкг/мл. Один штамм (SA0937) диссоциировал на три морфотипа, включая мелкоколониевый вариант (small colony variant, SCV). Вариант производного штамма SA0937 с колониями нормального размера характеризовался ассоциированной устойчивостью к даптомицину за счёт мутации P314L в MprF. Формирование устойчивости не сопровождалось изменением скорости роста, кроме морфотипа SCV. Для штамма ATCC 29213 после селекции отмечалось появление толерантности, проявляющейся в увеличении эффективного киллинга до 14 ч в 24-часовом time-killing эксперименте с концентрацией антибиотика 16 мкг/мл. У штамма ATCC 29213 выявлены мутации в пептидил т-РНК гидролазе (Pth). У трёх штаммов были обнаружены делеции в гене atpG, входящим в состав АТФ-синтазного комплекса. У остальных производных штаммов были выявлены делеции и мутации в генах метаболизма менахинона hepS, menA и трансляционном факторе элонгации G (fusA). Таким образом, использование гентамицина сопряжено с возможным быстрым формированием устойчивости и толерантности, не связанными с приобретением генов аминогликозид-модифицирующих ферментов. Выявление SCV ассоциировано с неблагоприятными клиническими исходами. При использовании комбинированной терапии необходимо учитывать, что существует возможность формирования устойчивости к даптомицину на фоне селекции гентамицином.

Lipoglycopeptide antibiotics are semi-synthetic derivatives of glycopeptides and are characterized by a pronounced bactericidal activity against gram-positive pathogens. The aim of the study was comparative assessment of the sensitivity of gram-positive clinical isolates to lipoglycopeptide antibiotics (telavancin, dalbavancin, oritavancin). The following isolates were included in the work: methicillin-resistant Staphylococcus aureus (MRSA, n=780), methicillin-resistant coagulase-negative Staphylococcus spp. (MRCoNS, n=163), and vancomycin-resistant Enterococcus faecium (VREf, n=93). Serial dilutions were used to assess sensitivity with the addition of 0.002% polysorbate 80 to the medium. Lipoglycopeptides showed more pronounced antibacterial activity against MRSA compared to vancomycin, teicoplanin, and daptomycin, and had a MIC₅₀/MIC₉₀ (µg/ml): for telavancin — 0.06 /0.125, for dalbavancin — 0.016/0.06, and for oritavancin — 0.06/0.125. A trend towards an increase in the MIC of lipoglycopeptides and daptomycin was established in MRSA with the MIC of 2 µg/ml for vancomycin, the proportion of which was 13%. For MRCoNS, MIC₅₀ and MIC₉₀ of lipoglycopeptides did not exceed 0.06 µg/ml and 0.125 µg/ml, respectively. Oritavancin showed strong activity against VREf at MIC range of 0.03 µg/ml to 0.5 µg/ml, and at MIC₉₀ of 0.25 µg/ml. Thus, lipoglycopeptide antibiotics are a plausible alternative to vancomycin and daptomycin; they are characterized by pronounced activity and can be used to treat severe forms of staphylococcal infections.

The study included 50 isolates of Neisseria meningitidis isolated from patients with generalized forms of meningococcal infection and 48 isolates, which were isolated from carriers. The isolates were identified by MALDI-TOF mass spectrometry using a Microflex LT mass spectrometer (Bruker Daltonics, Germany). Minimum inhibitory concentrations (MICs) of benzylpenicillin, ampicillin, ceftriaxone, meropenem, ciprofloxacin, azithromycin, rifampicin, and chloramphenicol were assessed by the method of serial agar dilution with interpretation of the results according to EUCAST 2021 criteria. Clinical resistance to penicillin was detected in 7% of isolates. However, all isolates with MIC >0.064 µg/ml (n=26) had mutations in the penA gene. Decreased sensitivity to rifampicin was found in four isolates isolated from patients and four isolated from carriers. Seven out of eight isolates with reduced sensitivity to rifampicin had mutations in the rpoB gene. Resistance to ceftriaxone, meropenem, ciprofloxacin was not detected.

The study included 14 isolates of Neisseria meningitidis serogroup W, isolated from patients with generalized forms of meningococcal infection aged 0–17 years at the Pediatric Research and Clinical Center for Infectious Diseases during the period from 2009 to 2020, as well as from carriers. The isolates from carriers (17–18 years old) were isolated in 2016–2019. The isolates were identified by MALDI-TOF mass spectrometry using a Microflex LT mass spectrometer (Bruker Daltonics, Germany). Whole genome sequencing of N. meningitidis was carried out on the basis of the Miseq Illumina platform; it was established that they belong to ST11 (cc11) sequence type. The results of the whole genome sequencing of the studied meningococci showed that there are 2 groups of the subcluster belonging to the Hajj cluster in St. Petersburg. In addition, they show close affinity with meningococci of the Anglo-French and Swedish clusters of the Hajj line.

The rapid spread of gram-negative bacteria resistance to carbapenems due to the production of carbapenemases requires new treatment options. The activity of carbapenem antibiotic biapenem, recently registered in Russia, against producers of various carbapenemases was studied in comparison with other antibiotics of this group. Among NDM-type carbapenemase producers, 77.8% demonstrated clinical susceptibility to biapenem; 50.3% and 21.1% of isolates were susceptible to meropenem and imipenem, respectively. Among the producers of OXA-48-type carbapenemases, 82,6%, 60,9%, and 65,2% of isolates demonstrated susceptibility to biapenem, imipenem, and meropenem, respectively.Producers of KPC-type carbapenemases were 100% resistant to all carbapenems. The introduction of biapenem will significantly expand the possibilities of treating severe infections caused by carbapenemase producers.

The paper presents optimized methods for PCR and sequence typing of Streptococcus pneumoniae. The serotype composition of pneumococci isolated from children under 5 years of age with infections of the upper respiratory tract was analyzed using optimized methods. Between 2016 and 2021, there was a decrease in the frequency of serotypes included in the pneumococcal 13-valent conjugate vaccine (PCV13) from 94.1 to 25.8%, mainly due to the 6ABCD serogroup and the 19F serotype. The coverage of serotypes circulating in children with PCV15 and PCV20 vaccines was 28.1% and 41.6% in 2021, respectively. During the study period, the number of non-vaccine serogroups 11AD and 15AF, as well as serotypes that are not detected under this capsular PCR typing protocol, increased most significantly.

Glycopeptides are the basis of the treatment of infections caused by MRSA (Methicillin-Resistant Staphylococcus aureus). Previously, it was demonstrated that antibiotic tolerant phenotypes are formed during selection of resistance under the influence of high concentrations of antibiotics. The present study uses a similar in vitro selection model with vancomycin. Clinical isolates of MRSA belonging to genetic lines ST8 and ST239, as well as the MSSA (ATCC29213) strain, were included in the experiment. Test isolates were incubated for five hours in a medium with a high concentration of vancomycin (50 μg/ml). Test cultures were grown on the medium without antibiotic for 18 hours after each exposure. A total of ten exposure cycles were performed. Vancomycin was characterized by bacteriostatic action; the proportion of surviving cells after exposure was 70–100%. After selection, there was a slight increase in the MIC to vancomycin (MIC 2 μg/ml), teicoplanin (MIC 1.5–3 μg/ml) and daptomycin (MIC 0.25–2 μg/ml). According to the results of PAP analysis, all strains showed an increase in the area under curve depending on the concentration of vancomycin after selection, while a heteroresistant phenotype (with PAP/AUC 0.9) was detected in three isolates. All isolates showed walK mutations (T188S, D235N, E261V, V380I, and G223D). Exposure to short-term shock concentrations of vancomycin promotes the formation of heteroresistance in both MRSA and MSSA. Formation of VISA phenotypes is possible during therapy with vancomycin.

The objective of this study was to clarify the intraspecies phylogenetic relationship between pneumococci strains from various geographical locations. Concatenated Multilocus sequence typing (MLST) sequences of six housekeeping genes were chosen for the phylogenetic tree construction. Trees, constructed for concatenated genes, revealed that there is a tendency for a clonal spread of antibiotic resistance. Interestingly, the isolates with novel or circulating mainly in Russia genotypes, described in this study, many are related to successful international clones, with the potential to spread.

The aim of the study was to research the microflora of suppurative complications, its antibiotic resistance, and the molecular genetic features of MRSA in burn patients. Material and methods. The microflora of biopsy specimens, wound fluid from 145 patients with thermal burns was investigated on the first day and on the 10-50th days of stay in the burn center of the Regional Clinical Hospital in 2013-2016. The molecular genetic features of 12 strains of MRSA isolated from different burn patients have been studied. Methods used: bacteriological, PCR, M-PCR, sequencing, PFGE, agglutination reaction. Results. On the first day of hospitalization, when biopsy specimen and wound fluid were taken, microbial growth was detected in 25.5% of cases, gram-positive microorganisms, in particular MSSA (37.8%), dominated. On the 10-50th days of hospitalization, growth was obtained in 93.2% of cases, Gram-negative microflora (53.4%) dominated, with a significant role played by Pseudomonas spp. and Acinetobacter spp. (38.0%), characterized by a high degree of resistance to antimicrobial drugs: XDR - 18%, PDR - 67%. On the 10-50th days of hospitalization, a significant role was played by staphylococci (38.7%), while the proportion of MRSA was 62.2%. Circulation of one MRSA clone in burn patients - ST239/spa3(t037)/a§r//SCCmecIII.1.1.2(IIIA)/CoaIy, characterized by multiple resistance to antimicrobial agents, was established.

Methicillin resistant Staphylococcus aureus (MRSA) is the main pathogen of hospital- and community-associated infections. Methicillin resistance is due to mecA gene located in a mobile complex element, staphylococcal cassette chromosome mec (SCCmec). The structure of the staphylococcal cassettes is diverse. At present eleven types of the cassettes are described. Types I-IV SCCmec are always associated with epidemiologically significant genetic lines of Staphylococcus. Thus, the pandemic hospital-associated MRSA (HA MRSA) belonging to CC5 and CC8 are of the types I-III SCCmec. The prevalence of virulent community-associated MRSA (CA MRSA) in many regions of the world is first of all connected with the characteristics of the type IV SCCmec structure and the presence of a recently described arginine catabolic mobile element (ACME) increasing the colonization activity of Staphylococcus. The review presents the up-to-date data on the origin, genetic structure and classification of SCCmec. Global genetic lines of MRSA are described and the problem of CA MRSA is discussed.

The problem of formation and spread of S.aureus isolates with reduced sensitivity to vancomycin (Vancomycin intermediate S.aureus, VISA) limits the use of this antibiotic for the treatment of infections caused by MRSA. The formation of such a phenotype is complex and is associated with the accumulation of mutations in the genes involved in the biosynthesis of the cell wall. Genomic sequencing of seven isolates with different sensitivity to vancomycin and belonging to the same genetic line was carried out in the study: ST8 - t008 - SCCmec IVc. PAP analysis of isolates with reduced sensitivity to vancomycin did not reveal hVISA/VISA phenotypes, while PAP/AUC was 0.53-0.7. Comparison of 83% of the core parts of isolates’ genomes with MIC = 1 mg/ml and 2 mg/ml, as well as control genomes (NCBI GenBank) with known sensitivity, revealed different clustering, the isolates with MIC=2 mg/ml were localized in one cluster. Comparison of the nucleotide concatenate composed of 44 genes involved in the assembly of the cell wall also showed that the isolates were assembled into one cluster. Unique mutations were identified for isolates with MIC=2 mg/ml in murZ (T353A), rpoB (Y946C), and fdh2 (G446S). Thus, isolates with reduced sensitivity to vancomycin did not have the hVISA or VISA phenotype. However, the identified mutations in the «key» genes of peptidoglycan biosynthesis may indicate the initial stage of selection of resistance to vancomycin with the formation of pre-hVISA.

Prevalence and therapy of infections due to MRSA remain one of the most serious problems in the world. Therefore, correct laboratory identification of the MRSA phenotype based on the use of the marker antibiotic cefoxitine, as a more susceptibile one vs. oxacillin, is of great importance. There is lately being observed a tendency towards emergence of strains with lower susceptibility to the last reserve drugs protecting from MRSA, i. e. vancomycin amd daptomycin. Susceptibility of MSRA to these drugs was not investigated in Russia and there are no data on the prevalence of the VISA and hVISA phenotypes. The results of our study on estimation of susceptibility of 316 MRSA isolates from several regions of Russia to oxacillin, cefoxitine, vancomycin and daptomycin are presented herein. It was shown that the ranges of the oxacillin MIC were extremely wide, i. e. 0.5 to 512 mcg/ml, while 2.2±1% of the isolates was susceptible by the phenotype to oxacillin, in spite of the mecA gene presence. As for cefoxitine, the MRSA isolates were rather resistant to it at the MIC > 16 mcg/ml. The tests with serial microdilutions revealed that 30.7±7% of the isolates had a critical level of susceptibility to vancomycin at the MIC 2 mcg/ml. The E-tests revealed 1.3±1% of the isolates which were susceptible at the MIC 2-4 mcg/ml. The MRSA isolates were highly susceptible to daptomycin, while high levels of the MIC (2 mcg/ml) were characteristic of 2.8±1% of the isolates. Cross reduction of the susceptibility to vancomycin and daptomycin was observed.

Bioinformatic analysis of the data on the genome sequencing of the isolates of the Streptococcus pneumoniae clonal complex SS320 from the Russian Federation, as well as the data on SS320 isolates from public sources in the penicillin resistant isolates resulted in detection of 139 missense mutations in 45 genes. In addition to the mutations in the genes of the main penicillin-binding proteins (PSB - PBP1A, PBP2B and PBP2X) there was detected high frequency of mutations in the genes of the (division and cell wall) dcw-cluster, as well as in RegR protein belonging to the transcription regulators of the LacI/GalR family. Development of resistance to beta-lactams in S.pneumoniae is defined not only by modification of the PSB, but also by adaptive changes in the metabolic pathways involved in the bacterial cell growth and division.

Antibiotic susceptibility of 119 coagulase-negative staphylococci isolated at hospitals of St. Petersburg and Moscow was investigated and estimated at the local laboratories as oxacillin resistant. The following species were identified: Staphylococcus epidermidis, S.haemolyticus, S. hominis, S.capitis, S.simulans, S.pettenkoferi, S.lentus, S.carnosus and S.warneri. The oxacillin resistance was confirmed in 79.8% of the isolates. The frequency of the associated resistance to non-beta-lactams was much higher in the oxacillin resistant isolates vs. the oxacillin susceptible ones. When the CLSI and EUCAST susceptibility criteria were used, 1-3% difference in the resistance levels was recorded. Among the oxacillin resistant isolates the frequency of resistance to gentamicin, ciprofloxacin, erythromycin, moxifloxacin, tetracycline and clindamycin equaled 90, 88, 88, 63, 43 and 26% respectively. Two linezolid resistant isolates of S.epidermidis with lower susceptibility to tedizolid were isolated. Eight isolates of S.epidermidis showed lower resistance to mupirocin. The MIC of ceftarolin for oxacillin resistant coagulase-negative staphylococci varied from 0.5 to 2.0 mcg/ml, while for the oxacillin susceptible ones it was lower than 0.25 mcg/ml. No resistance to tigecyclin and vancomycin was observed.

The results of the multicentre trial on estimation of MRSA antibiotic susceptibility to 17 antibiotics are presented. 474 nonrepeting isolates of MRSA (mecA+), collected in 2011-2014 in 10 cities of the Russian Federation were used in the trial. The antibiotic susceptibility was determined by the method of serial microdilutions in broth with estimation of the MICs in accordance with the international standards CLSI 2014 and EUCAST 2014. The highest levels of the MRSA resistance were stated against ciprofloxacin - 92% (MIC50 32 mcg/ml), gentamicin - 85% (MIC50 128 mcg/ml), erythromycin - 54% (MIC50 32 mcg/ml) and clindamycin - 45% (MIC50 0.03 mcg/ml), as well as against rifampicin - 38% (MIC50 0,06 mcg/ml). The frequency of MRSA isolated at the vancomycin dose of 2 mcg/ml equaled 26%. No correlation of the decrease in susceptibility to vancomycin and rifampicin was observed. In 5% of MRSA isolated from infected surgical wounds in patients with bone infection or sepsis, there was observed a decrease in the susceptibility to ceftarolin (MIC 2-4 mcg/ml). Co-trimoxasole, I'usidic acid (MIC50 0.06 mcg/ml) and mupirocin (MIC50 0.5 mcg/ml) showed high antibacterial activity, 93-98% of the isolates being susceptible to the drugs. No resistance to linezolid and tigecycline was detected. By the associate resistance spectrum, most of the MRSA isolates were characterized by resistance to drugs of 3-7 groups (56%). The phenotypes with simultaneous resistance to drugs of 8-10 groups amounted to 6%. As a whole, 70 variants of associate resistance combinations were detected.

Ceftaroline is a unique cephalosporin with activity against methicillin resistant Staphylococcus aureus (MRSA). It was approved for clinical use in the USA, Europe and Russian Federation since 2010 for the treatment of the skin and soft tissue infection and community-acquired pneumoniae. In the present study there was used molecular typing of 24 isolates of MRSA with reduced susceptibility to ceftaroline. For 8 isolates belonging to different genetic lines (ST8, ST239 and ST228) and requiring MICs there were determined antibiotic concentrations preventing formation of resistant mutants (mutant prevention concentration) and the ranges of the mutant selection window (MSW). The last majority of the isolates with reduced susceptibility to ceftaroline (MIC of 2 mcg/ml) belonged to the clonal line ST228. The whole genome sequencing of two isolates of ST228 showed that they belonged to the epidemic South Germany genetic line and were characterized by the presence of mutations in PBP2a (N146K) and PBP2 (C197Y) responsible for reduced susceptibility. The highest rates of MPC (32 mcg/ml) and MSW (2-16 mcg/ml) were observed in the clinical isolates belonging to the genetic line ST8. The isolates of ST239 and ST228 had the selection window within 2-4 mcg/ml. No dependence of the MIC and MPC/MSW levels was detected.

The surveillance of the serotype pattern and antibiotic resistance of S.pneumoniae in various geographical regions is required for the validity of rational etiotrophic therapy of pneumococcal infections and the choice of the optimal vaccines for their prophylaxis. 250 S.pneumoniae isolates from children with acute otitis or pneumonia and healthy carriers in St.Petersburg in 2010-2013 were investigated. The analysis of the serotype pattern of the pneumococci showed that 13-valent conjugate vaccine was the most active (86.1% of pneumococci causing pneumonia and 86.4% of pneumococci causing acute otitis). The isolates were higly resistant to beta-lactams and macrolides. By the EUCAST criteria, the decrease in the susceptibility to penicillin, cefotaxime, erythromycin and ceftarolin was observed in 32.4%, 14%, 33.2 and 6% of the isolates respectively. 22.4% of the isolates showed associate resistance to penicillin and erythromycin.. No resistance to moxifloxacin was detected. The frequency of resistance to tetracycline, co-trimoxasole and chloramphenicol in various patients ranged within 30-50%. The prevalence of the antibiotic resistance was mainly characteristic of the isolates serotypes 19A, 19F, 14 and serogroup 6.

Coagulase-negative staphylococci (CoNS) are considered as a reservoir of mobile genetic elements and first of all of the staphylococcal cassette chromosome mec (SCCmec), defining staphylococci resistance to beta-lactams. Types II, IV, IVa, V, VII and VIII SCCmec were detected among 95 staphylococcal strains isolated in different regions of the Russian Federation. Subtypes Cla, Clb, Clc and Cl SCCmec were also identified (class B mec complex and two complexes of ccrl and ccr2 genes recombinases). Some other cassette types carrying A, C1 and C2 classes of the mec complexes in combination with various recombinase genes were detected. The S.epidermidis isolates mainly formed cassettes carrying mec complex B, while the S.haemolyticus isolates had cassettes carrying classes C1 and C2 mec complex. Out of 9 isolates of S.hominis 5 isolates carried a new type cassette: class A mec complex in combination with the complex of the recombinase ccrl genes. SCCmec was not identified in S.capitis and S.pasteuri. Their representatives carried either mec complex (1 isolate of S.pasteuri) or the recombinase complexes (2 isolates of S.capitis). The detected SCCmec variants in CoNS could be a source of emergence of new genetic lines of MRSA.

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is an effective method to treat malignancy and some solid tumors which may be accompanied by life-threatening immune and infectious complications refractory to standard immunosuppressive and antibacterial therapy. According to literature data, fecal microbiota transplantation (FMT) may be applied to restore functional activity of microbiota and to overcome antibiotic resistance. Two clinical cases of FMT in critical ill patients who had developed acute graft-versus-host disease (aGvHD) of intestine after allo-HSCT are presented in the article. The aim of the study was to assess FMT efficiency and safety in immunocompromised critically ill patients. Results. Following FMT, a complete regress of aGvHD signs as well as reduction of systemic infectious process were registered, due to probable modulation of the immune response. In one patient, elimination from respiratory ways of carbapenemase-producing Klebsiella pneumoniae positive for NDM- and OXA-48- producing was noted, like as elimination of Pseudomonas aeruginosa synthesizing KRS-type carbapenemase. Conclusions. FMT may be considered an alternative approach to intestinal aGvHD treatment in critically ill patients after allo-HSCT.

The article presents the results of a single study the intestinal microbiota of healthy infants. Study was performed 11 fecal samples, followed by targeted sequencing the amplified sites on the 16S rRNA gene Miseq platform (Illumina, USA), according to standard protocols. Total 600 unique OTU (operation taxonomic units), grouped into 7 bacterial phyla (Phylum) have been identified. Each sample had an average of 190±80 OTU at the species level. Established predominance of gram-positive anaerobic bacteria (71±23%). Quantitative phylum distribution was as follows: phylum Firmicutes – 43±15% (represented by Clostridium spp., Blautia spp., Lactobacillus spp., Enterococcus spp. and Veillonella spp.), The phylum Actinobacteria – 38±10% (of which more than 90% the OTU were represented Bifidobacterium spp.) and the phylum Proteobacteria – 15±8% (represented by the family Enterobacteriaceae). Representatives of phylum Bacteroidetes been identified (7–15%) in only three of eleven samples. All samples characterized by low species diversity, Shannon index and criterion α-diversity were in the range of 1,5–4,2, and 3–20, respectively. Children who are breastfed, observed a higher number of representatives of Proteobacteria, compared with children on artificial feeding. Noted the influence of adverse factors of pregnancy mothers (antibiotics, respiratory infection) on the composition of the intestinal microbiota of children, which reflected in the dominance of Klebsiella pneumoniae in one case, and the dominance of Enterococcus durans otherwise.

The study demonstrates the analysis of resistance to antibiotics of clinically common strains of microorganisms that were isolated from open fracture wounds in the patients admitted to our clinic within the period of 2006-2008. It was found that gram-positive bacteria feature a significantly restrained growth of resistance to universally used antibiotics. The increase in numbers of MRSA and MRSE stains was revealed. Enterococci feature a linear growth of resistant stains to most studied antibiotics. Gram-negative bacteria showed an increase in resistance to cephalosporins of generation III-IV. Most strains of non-fermenting bacteria (Pseudomonas, Acinetobacter) were sensitive to amikacin and imipenem.

Generalized meningococcal infection belongs to the group of diseases with a high risk of initiation of life-threatening conditions and death outcomes. There was carried out a retrospective analysis of clinical and epidemiological features of generalized meningococcal infections in children and adolescents of Saint Petersburg in 1995–2014 on the basis of the analysis of 884 medical records of the patients hospitalized at Scientific Research Institute of Children’s Infections. With general prevalence of the children of the first years of life among the patients, there has been revealed the tendency to reduction in the portion of children of the first year of life from 41,4% in 1995 to 22,2% by 2014, and the increase in the number of patients of 1–3 years old from 19,3–30,5% in 1995–1996 to 46,4–46,4% in 2013–2014. Among the number of etiologically identified cases (59,4%) the majority of them has been caused by serogroup B meningococcus (58,5%), in 24,2% – by serogroup C meningococcus, in 11,2% – by serogroup A meningococcus, and in 6,1% – by rare (W135/Y) and unspecified strains N.meningitidis. Within the recent years there has been identified the tendency of rate growth concerning the diseases caused by serogroup C meningococci, remarkable for a severe course and high rate of death cases. Total death indicator for the investigated period has averaged 4,2%, with the variability from 0 to 12,5% for different years.

First in Russia prospective non-interventional hospital-based study on Streptococcus pneumoniae serotypes causing meningitis and acute otitis media (AOM) in children and community-acquired pneumonia (CAP) in children and adults, as well as serotype coverage by pneumococcal conjugate vaccines (PCV’s) of different composition has been conducted. Serotypes 19F, 14 and serogroup 6 are the leading in meningitis; serotype coverage is 70,6% for PCV7, and 76,5% – for PCV10 and PCV13. Among S. pneumoniae serotypes causing AOM 19F, 3, 23F and serogroup 6 have been the most prevalent in Saint Petersburg. PCV7 and PCV10 provide equal serotypes coverage in AOM – 63,2% among children 0–2 years old, and 32,5% among children 5–17 years old. PCV13 covers up to 79% of serotypes in infants. In CAP PCV7 and PCV10 provide 57,1% serotype coverage in children and 56,1% – in adults. Serotype coverage in CAP for PCV13 has been 14,3% and 34,5% higher for children and adults, correspondingly. Obtained data supports PCV inclusion in children immunization program in Saint Petersburg, whereas PCV13 provides the broadest serotype coverage. In the course PCV’s implementation continued pneumococcal infection surveillance is advisable.

It is now a common perception that the vast majority of bacterial life in nature is found in surface-bound communities called biofilms rather than in isolated planktonic cells. Biofilms are implicated in more than 80% of chronic inflammatory and infectious diseases. The biofilm model allows the reconceptualization of multiple chronic diseases as biofilm diseases. The biofilm bacterial community uses secreted pheromones (eg, quorum sensing molecules) and other molecules for cell-cell signaling, even between species. These coordinated activities during formation of biofilms render the bacterial community numerous benefits. Biofilms confer resistance to many antimicrobials, and protection against host defenses. One possible reason for the increased resistance to environmental stresses and antibacterials observed in biofilm cells appears to be the increase in the portion of persister cells within the biofilm.

In the context of the antimicrobial therapy crisis, the significance of studying and implementing alternative treatment methods, particularly phage therapy, is increasingly evident. This study aimed to investigate the resistance of clinical Staphylococcus aureus ST239 strains to Herelleviridae phages through comparative genomics, transcriptomics, and proteomics. Analysis of resistant and sensitive S. aureus strains showed that resistant strains form a separate cluster on the phylogenetic tree, suggesting unique genetic traits underlying their phage resistance. Further in-depth analysis of the resistant SA191 strain infected with Herelleviridae phage, compared to an uninfected control, unveiled significant changes in the transcription of 462 genes (271↑ 191↓) at 5 min and 504 genes (276↑ 228↓) at 30 min post-infection. Proteomic analysis identified 184 differentially abundant proteins (41↑ 143↓) at 30 min. Functional analysis highlighted changes in the glycolysis, the tricarboxylic acid cycle, and transport systems; notable, changes were also observed in the transcription of prophage genes. Despite the observed metabolic shifts, classical resistance mechanisms related to teichoic acid synthesis, restriction-modification, and toxin-antitoxin systems were not identified, suggesting the existence of other mechanism. Our study contributes to the elucidation of S. aureus resistance mechanisms against Herelleviridae phages, highlighting the intricate nature of bacterial defense mechanisms., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

COVID-19 is caused by an airborne virus, SARS-CoV-2. The upper respiratory tract (URT) is, therefore, the first system to endure the attack. Inhabited by an assemblage of microbial communities, a healthy URT wards off the invasion. However, once invaded, it becomes destabilised, which could be crucial to the establishment and progression of the infection. We examined 696 URT samples collected from 285 COVID-19 patients at three time-points throughout their hospital stay and 100 URT samples from 100 healthy controls. We used 16S ribosomal RNA sequencing to evaluate the abundance of various bacterial taxa, α-diversity, and β-diversity of the URT microbiome. Ordinary least squares regression was used to establish associations between the variables, with age, sex, and antibiotics as covariates. The URT microbiome in the COVID-19 patients was distinctively different from that of healthy controls. In COVID-19 patients, the abundance of 16 genera was significantly reduced. A total of 47 genera were specific to patients, whereas only 2 were unique to controls. The URT samples collected at admission differed more from the control than from the samples collected at later stages of treatment. The following four genera originally depleted in the patients grew significantly by the end of treatment: Fusobacterium, Haemophilus, Neisseria, and Stenotrophomonas. Our findings strongly suggest that SARS-CoV-2 caused significant changes in the URT microbiome, including the emergence of numerous atypical taxa. These findings may indicate increased instability of the URT microbiome in COVID-19 patients. In the course of the treatment, the microbial composition of the URT of COVID-19 patients tended toward that of controls. These microbial changes may be interpreted as markers of recovery.

Ever decreasing efficiency of antibiotic treatment due to growing antibiotic resistance of pathogenic bacteria is a critical issue in clinical practice. The two generally accepted major approaches to this problem are the search for new antibiotics and the development of antibiotic adjuvants to enhance the antimicrobial activity of known compounds. It was therefore the aim of the present study to test whether alkylresorcinols, a class of phenolic lipids, can be used as adjuvants to potentiate the effect of various classes of antibiotics. Alkylresorcinols were combined with 12 clinically used antibiotics. Growth-inhibiting activity against a broad range of pro- and eukaryotic microorganisms was determined. Test organisms did comprise 10 bacterial and 2 fungal collection strains, including E. coli and S. aureus, and clinical isolates of K. pneumoniae. The highest adjuvant activity was observed in the case of 4-hexylresorcinol (4-HR), a natural compound found in plants with antimicrobial activity. 50% of the minimal inhibitory concentration (MIC) of 4-HR caused an up to 50-fold decrease in the MIC of antibiotics of various classes. Application of 4-HR as an adjuvant revealed its efficiency against germination of bacterial dormant forms (spores) and prevented formation of antibiotic-tolerant persister cells. Using an in vivo mouse model of K. pneumoniae-induced sepsis, we could demonstrate that the combination of 4-HR and polymyxin was highly effective. 75% of animals were free of infection after treatment as compared to none of the animals receiving the antibiotic alone. We conclude that alkylresorcinols such as 4-HR can be used as an adjuvant to increase the efficiency of several known antibiotics. We suggest that by this approach the risk for development of genetically determined antibiotic resistance can be minimized due to the multimodal mode of action of 4-HR., Competing Interests: The authors have declared that no competing interests exist.