Russian Journal of Infection and Immunity

In the second half of the 20th century, through the efforts of scientists from many countries, a coherent theory of natural plague foci (sylvatic plague) was formulated, attempted to describe the history of the origin and evolution of the causative agent of plague infection, the microbe Yersinia pestis. But the accumulated knowledge in this regard remained extremely limited. Envisioned by the modern phylogenetics, the methods of phylogenetic constructions in the pregenomic time were rather primitive, “manual”, characteristic of early empirico-intuitive Haeckel phylogenetics. Since the beginning of the 21st century, the introduction of genomic methodologies in the study of the plague pathogen allowed to detail the intraspecific diversity (subspecies, genovariants) of this particularly dangerous pathogen at the level of geographical and local populations (individual natural foci) around the world and to bring the diagnostics and description of intraspecific diversity to a high degree of perfection. Two important discoveries were made. First, the direct ancestor of the plague microbe was reliably established, it turned out to be the causative agent of intestinal infection — Far Eastern scarlet-like fever (Y. pseudotuberculosis 0:1b). Secondly, the evolutionary youth of the plague pathogen was shown, the “molecular clock” showed the time of its divergence from the ancestral population no earlier than 30 thousand years ago. Thus, the root of the phylogenetic tree of Y. pestis was fully characterized. Nevertheless, molecular genetic (MG) achievements do not yet allow to reveal the secrets of its phylogeny, i.e. the origin and sequence of world expansion. The most important reason is the high dependence of the MG of phylogeny reconstructions on the choice of evolutionary model for the analyzed characters: the model of neutral evolution is traditionally accepted, but its adequacy in relation to Y. pestis phylogeny is questioned by many well-known ecological (in the broad sense) facts. At the same time, MG achievements contributed to the creation of an ecological (ECO) approach based on the provisions of the theory of natural plague foci in an updated version, according to which the plague pathogen is an evolutionarily young pathogen descended from a psychrophilic pseudotuberculous ancestor. The presumptive ECO scenario has no obvious natural-scientific and historical contradictions and can serve as a null hypothesis for improving the MG methodology of phylogenetic constructions for plague and other similar microbes. It is suggested that the creation of a real phylogeny of the plague microbe is possible only based on integration of MG and ECO approaches.

Seasonal viral infections of the upper respiratory tract are widespread throughout the world. The SARS-CoV-2 pandemic has revealed the importance of timely personalized prevention of acute viral diseases and related bacterial complications. One of the main directions in the preventing viral infections relies on the development of effective antiseptics to inactivate viruses on the hands and mucous membranes. To effectively destroy SARS-CoV-2, the WHO recommends two antiseptics: a 70% ethanol solution and sodium hypochlorite. The proposed antiseptics are outdated and have an irritating effect on the skin and mucous membranes. In connection with this, a promising research direction includes development of new antiseptics with selective toxicity, low volatility, low coefficients in the oil-water system, weak lipophilic properties, low absorption into the vacuolar skin structures and low content of toxic impurities. One of these antiseptics is anavidin. The development and selection of molecules has been carried out, the next planned stage will be assessment of the effectiveness and safety of new molecules, including preclinical and early phase clinical trials, also analyzing prevention of viral infections, e.g. COVID-19.

The purpose of the research: the molecular genetic characteristic of A. baumannii carbapenem-resistant strains, including clonal affiliation, resistome and virulome pattern analysis, description of genetic environment resistance determinants, comparative genetic analysis, and assessment of phylogenetic relationships are presented in the work. The studied A. baumannii strains belonged to sequence types ST2^Pas/ST2062.2063^Oxf (n = 5) and ST78^Pas/ST1757^Oxf (n = 2). The nucleotide sequences of the studied A. baumannii ST2^Pas/ST2062.2063^Oxf strains were grouped into a single cluster according to phylogenetic analysis. And the sequences of the A. baumannii ST78^Pas/ST1757^Oxf strains were combined with the nucleotide sequence of the A. baumannii AbCTX5 strain, isolated in France in 2015. The presence of intrinsic (OXA-51-like) and acquired carbapenemases genes was shown in A. baumannii strains. In particular, blaOXA-23 are identified in members of ST2^Pas/ST2062.2063^Oxf, and in A. baumannii ST78^Pas/ST1757^Oxf strains — blaOXA-72 as part of the plasmid DNA. The A. baumannii ST78^Pas strains possessed additional extended-spectrum beta-lactamase genes. Тhe CTX-M-115 cephalosporinase gene are present in both strains, and the A. baumannii strain NNAb_2023.3 has the blaCARB-16 gene. Most A. baumannii strains are characterized by the presence of acquired genes for enzymatic modification of macrolides (mph(E), msr(E)), chloramphenicols (catB8), aminoglycosides (aadA, aph(3'')-Ib, aph(6)-Id, aac(6')-Ib, aph(3')-Ia, armA). A comparative analysis showed that in A. baumannii ST2^Pas/ST2062.2063^Oxf strains the resistance determinants to macrolides and aminoglycosides are located in the Tn6279-like transposon, and the aminoglycosidases genes aph(3'')-Ib, aph(6)-Id are associated with the IS91-like mobile element. In A. baumannii ST78^Pas/ST1757^Oxf strains, resistance genes to aminoglycosides, macrolides, sulfonamides, and beta-lactamase genes are grouped in a region from 60 to 80 Kb long between the glmS and hutC genes. The presence of mutations in the gyrA and parC genes associated with resistance to fluoroquinolones were characterized in all A. baumannii strains. Thus, new knowledge about the genetic profile of carbapenem-resistant A. baumannii strains representing epidemically significant international clonal lineage has been obtained.

Atopic dermatitis (AtD) is a multifactorial inflammatory skin disease characterized by itching, chronic recurrent course and age-related features of lesions. AtD pathogenesis has not been fully elucidated yet. An important factor for AtD emergence and progression is the imbalance in symbiotic microbiota. The research publications provide a few studies about a role for oropharyngeal microorganisms in AtD immunopathogenesis. The aim of the study is to analyze biological diversity of oropharyngeal microbial communities in varying AtD severity. 97 male patients, aged from 16 to 19 years, with different AtD severity were included in the study. Culture study of oropharyngeal discharge was also performed. Biological material was seeded on the expanded list of growth media and incubated for 5 days at the 37°С. To assess the biological diversity of the oropharyngeal microbiota, the coefficient of constancy (C) was used, in order to classify individual microorganisms as permanent, additional or transient. Statistical data processing was performed using the Stat Tech software (version 4.0.0, Stattech LLC, Russia). While examining biological diversity of the oropharyngeal microbiota in AtD patients, 58 microbial species were isolated and identified. After statistical analysis the significant differences in frequency of isolation, depending on different AtD severity were observed for microbes such as Streptococcus vestibularis and Rothia dentocariosa. When R. dentocariosa is isolated from the oropharynx, the chances of AtD exacerbation emergence decreased by 6 times, whereas in case of S. vestibularis, on the contrary, it increased by 5 times. Therefore, identification of transitions of individual microbes from transient to additional and permanent microbiota and vice versa, depending on the AtD stage and severity, allows to analyze an influence of specific microorganisms in AtD pathological processes and to establish definite new microbiological predictors of AtD exacerbation and remission.

Influenza and acute respiratory viral infections (ARVI) impose a substantial damage to the population health in the Russian Federation due to their seasonal circulation and predominantly affect young children. A very few data on the cytokine profile, the nonspecific LPO — AOD system and their relationships with clinical characteristics in such diseases in preschool children are available. The aim of this study was to assess the cytokine profile, LPO — AOD system parameters and their relationship with the clinical and laboratory characteristics of diseases in preschool children with influenza and other ARVI. 86 preschool children (3–6 years old) were examined: with an established diagnosis of influenza (n = 31), non-influenza ARVI (n = 28), apparently healthy children (control group (n = 27). All pediatric samples were analyzed by enzyme-linked immunosorbent assay assessing blood serum concentrations of C-reactive protein and cytokines IL-1β, IL-4, IL-6, IL-8, TNFα, IFNα, IFNγ. Spectrophotometric, fluorometric and enzyme immunoassay methods to assess the state of the “LPO — AOD” system were used. In the group of children with influenza vs other ARVI, a higher incidence of intoxication syndrome was revealed. Cytokine profile in children from both clinical groups compared with control cohort was featured with higher indicators of both pro-inflammatory and anti-inflammatory origin. Children with non-influenza ARVI, had increased magnitude of LPO final products in the nonspecific LPO — AOD system along with lowered concentration of fat-soluble vitamins, general antioxidant activity, GSH level, and SOD activity. In the group with influenza, the level of primary and final lipid peroxidation products was increased, whereas that of for retinol, α-tocopherol, and total antioxidant activity was decreased paralleled with higher GSSG and SOD levels. Numerous correlations were noted in the group of children with ARVI: IL-1β/ketones, IL-6/ketones, IL-8/ketones, TNFα/ketones, IL-4/ketones, IFNg/shortness of breath, IFNα/cough, double bonds/fever, double bonds/AST, SO/intoxication, retinol/fever, GSSG/cough. The influenza group differed in the following relationships: IL-4/ketones, IL-4/fever, IFNα/ketones, CDs/AST. It can be concluded that in preschool children with ARVI and influenza, changes in the cytokine profile are accompanied by increased pro- and anti-inflammatory cytokine levels, increased intensity of lipid peroxidation reactions along with reduced magnitude of antioxidant factors. In the group with ARVI, there was a relationship between the final toxic products of lipid peroxidation — Schiff bases — and the intoxication index, as well as the presence of protective mechanisms in the form of connections between interferons and disease clinical manifestations. The group with influenza was distinguished by the presence of protective relations, which may have a beneficial effect in the context of developing pathological process. The data obtained will help expand the understanding of the pathogenetic mechanisms related to immune reactivity and nonspecific lipid peroxidation reactions in preschool patients and formulate appropriate measures for correction.

Laboratory data, especially a general blood test, play an important role in the treatment of infectious diseases, including COVID-19. However, in patients with coronary heart disease (CHD) and COVID-19, a general blood test is rarely analyzed and is insufficient to fully assess an impact of the new coronavirus infection on patients with cardiac diseases. The aim of the study was to analyze a COVID-19 effect on hemogram parameters in the early recovery period of patients with coronary heart disease. The study was performed at the Kursk City Clinical Hospital for Emergency Medical Care in the years 2021–2022, which involved 58 mature-aged patients (45–59 years old) suffering from coronary heart disease who had a new coronavirus infection and 62 elderly patients suffering from coronary heart disease alone. Morning blood sampling was carried out from the forearm superficial veins into Vacutainer test tubes added with a coagulation activator. In elderly patients, 3–4 weeks after recovery, significant changes in red blood parameters persisted — a decline in the level of peripheral blood erythrocytes, hemoglobin and hematocrit. Elderly patients with coronary heart disease comorbid with a moderate new coronavirus infection, 3–4 weeks later had also higher count of leukocytes, neutrophils, segmented neutrophils and ESR level relative to comparison group. It should be noted that in the early convalescence period elderly patients with coronary heart disease and COVID-19 had significantly elevated ESR, which confirms ongoing sustained inflammatory process. After evaluating the information content according to the calculated Kullback informativeness assessment for analyzed general blood test parameters, it was found to peak for platelet and leukocyte counts as well as ESR level. Thus, among the analyzed indicators in the general blood test, it turned out that platelet and leukocyte count along with ESR level were most informative and of prognostic significance during early convalescent period of elderly patients with coronary heart disease comorbid with a new coronavirus infection, which are proposed to be used as biomarkers of early convalescent period.

Acute COVID-19 is a viral infection caused by a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in dramatically decreased peripheral blood CD3⁺ T cell count apparently due to alterations of thymic T cell maturation, that can persist long term afterwards. Therefore, we analyzed the levels of peripheral blood TRECs (T-cell receptor excision circles), and investigated the main alterations in peripheral blood T cell subsets in COVID-19 convalescents. We performed molecular quantification of TRECs with “TREC/KREC-AMP PS” kit and flow cytometric analysis of peripheral blood lymphocytes from three groups of patients. The first group contained 109 samples from COVID-19 convalescents (6–12 month post-acute COVID-19) with normal levels of TRECs (TRECn); the second was formed from COVID-19 convalescents (6–12 month post-acute COVID-19) with decreased levels of TRECs (TREClow, n = 29), and healthy control group (HC, n = 18). We noticed no significant differences between all three groups in CD3⁺ T cell relative and absolute numbers. However, CD4⁺ T cell frequencies were decreased in TREClow and TRECn groups compared to HC (40.8% (31.6; 50.1) and 46.4% (40.0; 53.0) vs 53.5% (47.36; 56.9), p < 0.001 and р = 0.004, respectively). Furthermore, Th cell levels were decreased in TREClow patients vs HC and TRECn groups (701 cell/1 µL (478; 807) vs 1005 cell/1 µL (700; 1419), р = 0.020, and 876 cell/ 1 µL (661; 1046), р = 0.008, respectively). Finally, both groups of COVID-19 convalescents had increased frequencies of circulating CD8⁺ T cells — 29.4% (20.7; 39.7) in TREClow group, 26.5% (21.1; 32.7) in TRECn group vs 21.3% (17.1; 26.0) in healthy controls (p = 0.024 and р = 0.026, respectively). In TRECn group, CD8⁺ T cell count was elevated vs control range (508 cell/1 µL (372; 622) vs 356 cell/1 µL (247; 531), р = 0.044). Thus, COVID-19 convalescents (6–12 month post-acute COVID-19) showed an imbalance in CD4⁺ and CD8⁺ T cell level even at 6–12 months post-acute SARS-CoV-2 infection, and the observed changes in peripheral blood T cells could be closely related to the alterations in thymic T cell maturation and differentiation. Such a long-term decline in TREC levels in the circulation may have a profound impact on immune system functions and requires immunocorrection therapy.

Background. Vaccines play a critical role in safeguarding public health, particularly for children. It is imperative to proactively address safety concerns to uphold trust in their effectiveness and safety. Skepticism surrounding vaccines can have significant adverse effects on the overall well-being of the entire population, potentially leading to individuals opting out of vital vaccinations, thereby posing risks to public health. Thus, ensuring confidence in vaccine safety remains paramount. Materials and methods. This phase four clinical trial was conducted as a post-marketing study (PMS) on 2 to 7 month old healthy infants (N = 539) to evaluate immunity and safety of Indian pentavalent vaccine containing Diphtheria, Tetanus, Pertussis, Hepatitis B and Haemophilus influenza type b [DTPW-HEP B-HIB (PRP-T)/PENTAVAC] in four different centers at Tehran province. Blood samples were collected from eligible infants before receiving the vaccine (2 months of age) and 1 month after the third dose (7 months of age) to determine antibodies against all antigens in the pentavalent vaccine using ELISA. Results. The results indicated that the immune responses demonstrated seroprotection and protective antibody levels after three doses of the vaccine for Haemophilus influenza b, diphtheria, tetanus, hepatitis B virus and Bordetella pertussis were 99.1%, 98.7%, 99.8%, 99.4% and 69.6%, respectively. Statistical analysis showed that the P-value for all vaccine components was similar (P < 0.001). The five most common side effects reported were mild fever (10%), erythema at the vaccination site (9.1%), inflammation (4.3%), pain at the vaccination site (3.3%), and restlessness (2.6%). Conclusion. This study’s findings demonstrated a significant increase in antibody levels against all five vaccine components. In light of these results, it can be concluded that the Pentavalent vaccine is not only effective in enhancing immunity against multiple diseases but also presents minimal risk of side effects in the study population. These findings contribute to the body of evidence supporting the safety and efficacy of vaccines, underscoring their crucial role in protecting public health.

The HIV-infection continues to be one of the most large-scale epidemics worldwide. Many techniques have been developed to detect this disease, but the Western blot based on the identification of specific viral proteins remains the most commonly used method that allows to monitor ongoing viral processes. Despite discussions regarding the criteria for a positive test assessment and selection of a minimum number of viral proteins to reliably interpret the data, a very few studies on the protein profiles in HIV-infected patients, particularly in the Russian Federation are available. The aim of this study was to assess the prevalence of HIV viral proteins in a group of people with newly diagnosed infections analyzing 2566 blood samples from individuals with newly diagnosed HIV infection for reference testing. The samples were assessed using ELISA and IHL techniques, followed by western blotting. Subsequently, the following viral proteins were analyzed to assess HIV life cycle and the predominance of its different stages: gp160, gp120, gp41, p55, p40, p24, p17, p66, p51, and p31. For comparison, gp110/120 was chosen as the reference protein due to its lowest prevalence frequency among all env gene products comprising 96.06%. A significantly reduced prevalence frequency was found for several protein groups: GAG — p55 (80.91%), p40 (72.14%), nucleocapsid p18/17 (67.37%); POL proteins — p68/66 (89.57%), p52/51 (81.91%), p34/31 (86.02%). Significant differences in frequency of viral proteins between age and sex groups are shown. Hypotheses explaining the obtained data are presented. By aligning anti-viral protein antibody profile with the course of the infection and patient’s condition, it will be possible to identify patterns and take necessary measures for early diagnostics with extended results, such as duration of the infection, viral load, and disease severity.

The article analyzes statistical data on the 2020 vs 2019 opisthorchiasis incidence rate on the territory of the Russian Federation and in foreign countries, provides absolute and intensive morbidity indicators across entire the Russian Federation and specifically in its subjects — republics and regions, general prevalence of helminthiasis, and opisthorchiasis particularly overall pattern of parasitic diseases, as well as contribution of opisthorchiasis to general pattern of biohelminthiasis, its dynamics, and prevalence of relevant causative agent. A comparative analysis for incidence rates in the regions where opisthorchiasis was recorded and mean country-wide statistical parameters was carried out. As a result, it was concluded that despite a decline in the Russia-wide overall parasitic morbidity, an excess of mean indicators, sometimes significant, was noted in some regions. Thus, compared to Russia-wide magnitude of intensive indicator, it was higher by 4-fold in the Komi Republic, whereas in the Kurgan, Vologda, Arkhangelsk Regions and the Nenets Autonomous Okrug — by 3-fold. The article provides an analysis of the population age groups as well as percentage of opisthorchis-affected urban and rural populations. In addition, the special clinical and epidemiological significance of opisthorchiasis remains urgent due to severity of its course, affected various body systems and organs, emergence of serious complications leading to disability, and in some cases to fatal outcomes, the presence of natural foci, most of which are located in the Russian Federation. Almost all territories adjacent to the basins of the Ob, Irtysh, Tom rivers and their tributaries pose special concern regarding opisthorchiasis. The data related to prevalence of helminthiasis larvae detected in fish in 2020 and 2019 since 2010 are presented. Based on the data shown above, strict adherence to preventive measures plays an important role in reducing opisthorchiasis incidence rate and preventing its spread.

Monitoring of humoral immunity in 3–4 year-old anti-pertussis vaccinated children is one of the approaches for pertussis epidemiological surveillance. It’s a predictive indicator for comprehensive assessment of morbidity in the region. The agglutination reaction (RA) used earlier has been displaced with enzyme immunoassay (ELISA). So, two questions arose: regarding i) a relevance of using ELISA in whole-cell vaccinated individuals, and ii) correctness of large-scale data interpretation without applying a unified IgG reference value. Study aims were to assess humoral anti-pertussis population immunity by ELISA, to determine features of humoral protection in vaccinated subjects after using various vaccine types, to identify age features, to make recommendations for evaluating seromonitoring data. Blood serum samples from anti-pertussis vaccinated children in Samara region (n = 1729) were examined in 2016–2020; children were divided into 4 age groups (< 3, 3–4, 5–7, ≥ 7.1 years) and into 3 type vaccines groups: cellular, acellular and combined. We used two ELISA kits, which are designed to assess post-vaccination immunity, according to the manufacturer’s instructions, quantifying IgG against B. pertussis, which differ in units and reference values. Statistical analysis was performed using StatTech program v.2.6.2. The largest and smallest percentage of seronegative children was in the cellular-vaccinated and acellular-vaccinated group, respectively. Seronegative percentage in the “indicator group” reaches 55.2% being significantly higher than acceptable 10.0%-level, and differs from the literature data (30–40%), which were obtained mainly with RA. This may suggest about an incorrect interpretation of post-vaccination immunity data evaluation strictly according to manufacturers’ reference criteria, especially for whole-cell vaccinated subjects. A method for calculating the seronegative percentage is proposed that relies on the prognostic negative data level as a correction factor. The required values were obtained during comparison studies of random serum samples from 3–4-year-old children (n = 70) using two ELISA kits (“RIDASCREEN^® Bordetella”, “SeroPertussis™ IgG”) and intra-laboratory comparison panel. It should be given preference for sets with a greater prognostic negative data level, if population seronegative percentage is assessed.