Russian Journal of Infection and Immunity

Journal "Infektsiya i immunitet" ("Russian Journal of Infection and Immunity") established by Northwest Branch of RAMS, St. Petersburg Pasteur Institute and the St. Petersburg branch of the Russian Association of Allergologists and Clinical Immunologists, with the participation of the St. Petersburg branch of All-Russian Practical Society of epidemiologists, microbiologists and parasitologists at St. Petersburg and Leningrad region.

The journal is devoted to numerous aspects of the interaction between different microorganisms and the host organism. Journal is of interest for microbiologists, immunologists, epidemiologists and clinicians. The most detailed discussion of the following questions: 

   • molecular basis of infections caused by pathogenic bacteria, fungi and parasites; 
   • mechanisms of pathogenicity of microorganisms; 
   • the impact of microbial virulence factors on host cells; 
   • factors and mechanism to protect the host from infection; 
   • factors of nonspecific and specific immunity; 
   • experimental models of infectious disease; 
   • development of vaccines and nonspecific anti-infectious defense. 

The editorial board of the journal includes leading Russian microbiologists, virologists and immunologists. Among them are 13 full members and 5 corresponding members of RAS, 19 professors. All published in the journal articles, reviews and lectures are subject to mandatory peer review by members of the editorial board. Traditional sections of the journal are: original articles, lectures, reviews, short communications, case studies.

Journal "Infektsiya i immunitet" ("Russian Journal of Infection and Immunity") was registered by the Federal Service for Supervision of Communications, Information Technology and Communications in St. Petersburg and Leningrad region, Registration certificate PI number78-00910 TU 24 June 2011, the International Standard Serial Number (ISSN) - 2220-7619. Journal quarterly (4 issues per year), the log volume - 12-14 conventional printed sheets (96-112 sheets of A4). From the second half of 2011 opened journal subscription, which can be issued through post offices.

Since its inception, the journal began to develop very fast. As a result it is fully meets the criteria for National Certification Comission (VAC) of the Russian Ministry of Education requirements to scientific journals. According the VAC decision №8/13 from 02.03.2012 the journal "Russian Journal of Infection and Immunity" is included in the "List of the leading peer-reviewed scientific journals and publications, in which major scientific results of the thesis for the degree of Doctor of Science or Candidate of Science should be published."

Since April 2014 journal "Russian Journal of Infection and Immunity" is included in the international database Ulrich's Periodicals Directory.

In 2012 the journal "Russian Journal of Infection and Immunity" was supported by grants from the Committee on Science and Higher Education of the Government of St. Petersburg.

In 2015 "Russian Journal of Infection and Immunity" was included in the list of national journals recognized as the most popular both in Russia and abroad and located on the Web of Science platform as part of a separate, but fully integrated with the Web of Science platform data base Russian Science Citation Index (RSCI).

Since 2017 journal "Russian Journal of Infection and Immunity" is included in Web of Science Core Collection (indexed by Emerging Sources Citation Index (ESCI))

Since March 2017 journal "Russian Journal of Infection and Immunity" is included in the international database Scopus

Currently, as of January 2014, according to an analysis of the "Russian Science Citation Index" (RISC) the two-year impact factor for the journal "Russian Journal of Infection and Immunity" was - – 0,676 while the self-citation index is 8% (details on the website: www.elibrary.ru)

 

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MANUSCRIPT CHECKING FOR PLAGIARISM

Posted: 14.03.2019

Dear authors!

Since 2019, all manuscripts received in the Journal "Russian Journal of Infection and Immunity" should be checked using the ANTIPLAGIAT system.

Please note that in case of a high percentage of LOANS and a low percentage of ORIGINALITY, the article cannot be sent for review.


 

PREPRINTS PUBLICATION

Posted: 13.03.2019

Dear authors!

We inform that since April 2019 of the article that has been reviewed and accepted for publication, we begin to publish in the form of preprints in the section "Online First". After the publication of the final version of the article in the next Issue of the Journal, the preprints from the specified section are deleted.


 

Current Issue

Vol 13, No 6 (2023)

Cover Page

Full Issue

REVIEWS

Fulminant invasive group A streptococcal infection in children
Yatsyshina S.B., Mamoshina M.V., Elkina M.A., Polyaeva O.A., Mikhailova Y.V., Shelenkov A.A., Egorova A.E., Maleev V.V.
Abstract

Group A streptococcal infections dominate among invasive streptococcal infections, with the major causative agent, Streptococcus pyogenes, being quite stable in the environment and bearing a large number of chromosome encoded pathogenicity factors or transmitted by horizontal transfer through bacteriophages. Different genetic variants of S. pyogenes can have a different set of pathogenicity factors able to change during pathogen evolution and determine virulence level for specific isolate. With a short incubation period, the disease can proceed with developing invasive infection and toxic shock syndrome with unfavorable outcome within 7 days from disease onset. The purpose of this article is to increase the doctors’ alertness to early recognition and diagnosis, which directly affects adequate treatment in a timely manner and disease outcome. The data on streptococcal morbidity in Russia and worldwide, review of laboratory diagnostic methods and pathogen genetic typing are presented. The maximum number of cases of streptococcal septicemia in Russia was registered in 2022, which accounted for 69% of all cases during the 2014–2022 observation period. The article also describes two clinical cases of fulminant invasive group A streptococcal infection in children with symptoms of acute respiratory viral infections at the onset of the disease. The results of various laboratory diagnostics methods verifying the diagnosis are presented. The genetic characterization of microbial isolates was performed by deep DNA sequencing. In the biological material from patients (including autopsy in one case), S. pyogenes sequence type ST-28, serotypes emm-1.25 and emm-1.0 were identified. The increasing importance of invasive streptococcal infection for health care in Russia and other countries may be associated with a possible change in dominating S. pyogenes genetic variants. In this regard, the study on circulating S. pyogenes genotypes on an ongoing basis as part of surveillance of streptococcal infection and development of vaccine for specific prevention are required.

Russian Journal of Infection and Immunity. 2023;13(6):1009-1017
pages 1009-1017 views

ORIGINAL ARTICLES

Optimized properties of live vaccine influenza reassortant strains obtained by reverse genetics
Larionova N.V., Kiseleva I.V., Bazhenova E.A., Stepanova E.A., Rudenko L.G.
Abstract

Classical reassortment in developing chicken eggs is a well-established technique for obtaining LAIV strains. Naturally generated reassortant vaccine strains are characterized by high reproductive capacity, genetically stable characteristics of temperature sensitivity and cold resistance, which correspond to the characteristics of the MDV involved in crossing with the epidemic virus. Along with antigenic relevance, natural reassortment ensures attenuation of vaccine strains, good reproduction capacity in upper respiratory tract cells and inability to reproduction in the lower respiratory tract. With classical reassortment, the speed and efficiency of obtaining vaccine reassortants largely depend on the properties of epidemic virus, and therefore cannot be stable. The potential of reverse genetics is attractive because it allows to obtain vaccine reassortants quickly and efficiently, reduce the likelihood of spontaneous mutations; however, the vaccine strain is deprived of the advantages of natural selection, in which the most viable clones are selected. This study presents the results of comparatively assessed A(H3N2) LAIVs obtained in parallel by classical reassortment and reverse genetics according to criteria confirming that vaccine strains inherit the necessary properties that guarantee their harmlessness and high reproduction in chicken embryos. Strains for LAIV obtained by both methods retained all attenuating mutations inherited from the MDV, were highly reproductive at the optimal temperature, with temperature sensitivity corresponded to the MDV. However, strains obtained by reverse genetics, was observed to have partial loss of cold resistance in comparison with that of the MDV and classical reassortants. Reduced cold adaptation may negatively affect vaccine effectiveness. It is important that after several additional passages in chicken embryos at low temperature, the cold resistance of the vaccine strain, assembled by reverse genetics, was increased. Credibly that cold resistance is a phenotypic trait, the degree of manifestation of which depends on the temperature conditions of virus multiplication. The selective factor of reduced incubation temperature is missing in reverse genetics. In order for the cold-adapted phenotype to be fully realized, additional passages at low temperature of RG-reassortants are necessary. Thus, the reverse genetics method using plasmid technology allows to effectively prepare reassortant strains for LAIV. An important stage in obtaining vaccine strains using genetic engineering techniques should be the control of their cold-adapted phenotype and its optimization by additional passages at low temperature.

Russian Journal of Infection and Immunity. 2023;13(6):1018-1026
pages 1018-1026 views
The impact of polymorphic variants of interferon receptor genes on COVID-19 severity and antibiotic resistance
Krieger E.A., Samodova O.V., Svitich O.A., Samoilikov R.V., Meremianina E.A., Ivanova L.V., Bebyakova N.A., Ilina E.N., Pavlenko A.V., Esin Y.I., Arkhipova A.L., Kovalchuk S.N., Kudryavtsev A.V.
Abstract

Single nucleotide substitutions in gene sequence associated with conformational changes in protein receptor or in expression of interferon receptors may explain variations in human susceptibility to infection and severity of COVID-19 along with other well-known risk factors. The study aimed to investigate associations between polymorphic variants of interferon receptor genes, COVID-19 severity and prevalence of antibiotic resistance genes in the gut microbiota. Materials and methods. The study was conducted using a random sample of Arkhangelsk population aged 42 to 76 years (n = 305). The research involved gathering COVID-19 data from the Federal Register, conducting blood tests for SARS-CoV-2 antibodies and polymorphic interferon receptor gene variants, and identifying antibiotic resistance genes in stool samples. Results. During the first 12–15 months of the COVID-19 pandemic, 17.4% of the study participants had symptomatic COVID-19, while 32.8% were asymptomatic. By the Autumn of 2022, symptomatic COVID-19 cases rose up to 36.4%, while asymptomatic cases increased to 61.3%. We reveal an association between the CC genotype of the IFNAR1 gene rs2257167 variant, the presence of the T allele of IFNAR2 gene rs2229207 variant, the CCTT haplotype and symptomatic COVID-19. The GCTC haplotype was associated with pneumonia and COVID-19 severity. In November 2022, macrolide resistance genes were observed in 98.4% of cases, whereas those to beta-lactams and glycopeptides — in 26.9% and 13.8% cases, respectively. Resistance to three classes of antibiotics was observed in 4.9% and was more frequently detected in individuals with the ССТТ haplotype. Genes encoding beta-lactamases were more often found in individuals with the GCTC haplotype, those who had COVID-19 with pneumonia and those who received hospital treatment. Glycopeptide resistance genes were associated with the CC genotype of the rs2257167 variant of IFNAR1 gene. Conclusion. We identified genetic determinants of susceptibility, symptomatic infection and COVID-19 severity. The associations between polymorphic variants of interferon receptor genes and COVID-19 severity can be used to identify people with a genetic predisposition to severe infection and to determine priority groups for vaccination, including the prevention of antibiotic resistance in complicated course of viral infections.

Russian Journal of Infection and Immunity. 2023;13(6):1027-1039
pages 1027-1039 views
Molecular and genetic characterization of LEPTOSPIRA spp. collection strains from the St. Petersburg Pasteur institute based on 16S rRNA gene sequencing data
Baimova R.R., Ostankova Y.V., Blinova O.V., Stoyanova N.A., Tokarevich N.K.
Abstract

Leptospirosis is a zoonotic disease found virtually worldwide. Microscopic Agglutination Test with live leptospira (MAT) is the reference method for the serological diagnosis of leptospirosis. MAT is based on assessing serum potential to agglutinate live reference serovar Leptospira maintained at a reference laboratory. At some laboratories having own collections of isolated and reference Leptospira strains applicable for serological diagnosis, those microorganisms are maintained for many years by repeated subculturing, that increases markedly a chance of strain cross-contamination. The lack of adequate quality control for reference strains may affect data of epidemiological studies. Control of Leptospira spp. reference strains purity and stability of their antigenic composition is very important for diagnosis of leptospirosis. The study objective was to compare the 16S rRNA gene nucleotide sequences of some Leptospira strains from the collection of the St. Petersburg Pasteur Institute to with relevant sequences uploaded to GenBank. In this study, 38 Leptospira strains were investigated. Nucleotide sequences of 36 strains were deposited in the international GenBank database, inconsistencies were revealed in two strains. The study found that the control Leptospira strains from the collection of the St. Petersburg Pasteur Institute had minimal dissimilarities from international control strains. The analysis of the resultant 16S rRNA sequences has shown the presence of point mutations, transitions, deletions and insertions, regardless of the strain species. The open leptospira pan-genome demonstrates high genomic variability in species due to the capability of leptospira for lateral gene transfer in order to adapt to changing environmental conditions. The massive acquisition and loss of genes give rise to an increased species diversity. The 16S rRNA gene is suitable for screening diagnostics; however, high level of the fragment similarity and close phylogenetic relationship between different species put bounds to its use in genotyping. The presence of point nucleotide mutations is most likely associated with the evolutionary mechanisms of leptospira, their ability to horizontal gene transfer and crossing-over, including ribosomal genes, but this assumption necessitates additional research. For specimen genotyping it is necessary to select alternative genes with high specificity and sufficient level of nucleotide divergence. The study shows a need for genetic analysis of collection strains in order to control the purity of cultures.

Russian Journal of Infection and Immunity. 2023;13(6):1040-1048
pages 1040-1048 views
ESCHERICHIA COLI phenotypic characteristics and antagonistic activity in opisthorchiasis invasion
Kataeva L.V., Karpukhina N.F., Vakarina A.A., Kolotova O.N., Stepanova T.F., Stepanova K.B.
Abstract

Opisthorchis felineus invasion in human causes inflammatory and dyskinetic disorders of the gastrointestinal tract accompanied by altered phenotypic characteristics in colon microbiota. The aim of research — study an impact of the Escherichia coli isolate phenotypic characteristics on Klebsiella spp. bacteria, isolated from colonic contents of patients with diagnosed opisthorchiasis as well as E. coli antagonistic activity. Materials and methods. The phenotypic properties of 54 E. coli isolates and 8 genus Klebsiella isolates obtained from colonic contents of patients with diagnosed opisthorchiasis were assessed. Identification of isolates and analysis of proteomic profiles were performed using Maldi BioTyper 3.0 software. 204 co-cultivation datasets were analyzed investigating antagonistic activity of E. coli isolates with varying properties on Klebsiella spp. E. coli and Klebsiella spp. isolates were examined by whole genome sequencing. Results. E. coli bacteria with typical phenotypic characteristics showed significantly more prominent antagonistic activity against Klebsiella spp. A significantly higher level of antagonistic activity against K. oxytoca bacteria vs K. pneumoniae strains. The proteomic bacterial strain profiles were divided into clusters depending on the level of antagonistic activity. E. coli molecular serotyping for O- and H-antigens revealed the genes of enterotoxigenic, enteroinvasive and extraintestinal pathogens in 60.0% of cases. Strains with the highest antagonistic activity index, which are carriers of the genes typical to enterotoxigenic E. coli sequence serotypes O6:H1 and O6:H5, were identified. The genome of such strains consisted of the largest number of virulence gene complexes: adhesins, invasins, toxins, bacteriocins. Multilocus sequence typing and sequence serotyping of E. coli and K. pneumoniae strains established their heterogeneity; K. oxytoca isolates were identified as ST242 and ST176. All strains were characterized by homology of antibiotic resistance markers (oqxA, oqxB, fosA) and a variety of beta-lactam resistance gene variants. Conclusion. It was found that E. coli isolates with typical phenotypic characteristics and carriers of virulence gene complexes exhibited significantly more pronounced antagonistic activity against Klebsiella spp. isolated from colonic contents of patients with diagnosed opisthorchiasis.

Russian Journal of Infection and Immunity. 2023;13(6):1049-1057
pages 1049-1057 views
Features of baseline and lipopolysaccharide-induced cytokine secretion in mononuclear leukocyte cultures from patients with the erythema migrans form of acute lyme borreliosis based on clinical parameters
Ilyinskikh E.N., Voronkova O.V., Hasanova R.R., Samoylov K.V., Semenova A.V., Esimova I.E., Motlokhova E.A., Yampolskaya O.V., Yampolskaya A.V.
Abstract

Introduction. Features of cytokine production in mononuclear cell cultures from Lyme borreliosis patients based on clinical data remained poorly studied. The study aim was to estimate the patterns of baseline and lipopolysaccharide-induced cytokine-secretory activity of peripheral blood mononuclear leukocytes from patients with erythema migrans form of acute Lyme borreliosis based on clinical parameters. Materials and methods. Groups of 22 and 12 patients with the diagnoses of mild or moderate severity of monoinfection and co-infection with tick-borne encephalitis of Lyme borreliosis with erythema migrans were examined twice: on week 1 after disease onset and day 14. The control group included 17 healthy donors. Basal and lipopolysaccharide-induced IL-6, IL-10, and TNFα secretion levels were assessed in mononuclear leukocyte culture supernatants applying enzyme immunoassay. Statistical analysis was performed by using the Mann–Whitney U-test, Wilcoxon test, and Spearman’s rank correlation. Results. The group of moderate severity patients was clinically distinguished by severer fever and intoxication manifestations. At the disease onset, the basal TNFα, IL-6 and IL-10 secretion levels in the moderate severity patient cultures were significantly higher than in those of the other groups. After antibiotics treatment, the baseline TNFα and IL-10 levels tended to decrease. At the onset, lipopolysaccharide-induced cultures from the moderate severity patients showed significantly suppressed TNFα production and increased IL-10 secretion as compared to the other groups. Lipopolysaccharide-induced IL-6 secretion in the moderate vs. mild severity group supernatants was significantly lower. In dynamics, the induced TNFα levels in the moderate severity patients were increased to the magnitude exceeding that in the controls. Positive correlations between the IL-6 and TNFα basal levels and maximum body temperature or the C-reactive protein serum concentrations were revealed in the patients. Induced TNFα levels showed negative correlations with fever levels or with IL-10 secretion. Conclusions. It was demonstrated that basal TNFα, IL-6 and IL-10 secretion levels in the mononuclear cell cultures of acute Lyme borreliosis patients increased with the increasing disease severity. Suppression of lipopolysaccharide-induced TNFα production in the moderate severity patient cultures was presumably associated with the regulatory cytokine IL-10 effects.

Russian Journal of Infection and Immunity. 2023;13(6):1058-1068
pages 1058-1068 views
Microbial associations for pneumonia causative agents and level of their resistance to antimicrobial drugs during a new coronavirus infection pandemic
Kolotova O.N., Kataeva L.V., Vakarina A.A., Stepanova T.F., Stepanova K.B.
Abstract

Introduction. Bacterial coinfection and secondary bacterial infection are considered critical risk factors for the severity and mortality of SARS-CoV-2-caused pneumonia. The aim of the study was to analyze a pattern of microbial associations between K. pneumoniae and A. baumannii isolated from the lower respiratory tract discharge and sectional material (lung tissue) of patients diagnosed with pneumonia, and to compare resistance level in monoculture and associations during new coronavirus infection pandemic. Materials and methods. A bacteriological study of 2689 sputum and bronchial washing samples from patients at infectious diseases hospitals, and 1411 lung pathological material samples was carried out. Bacterial isolates were identified by mass spectrometry. Antibiotic sensitivity for isolates was determined by the disk diffusion method. Genetic determinants of resistance to beta-lactam antibiotics were detected by PCR. Statistical data processing was performed using SPSS version 22 software. Results. K. pneumoniae and A. baumannii isolates were predominantly found in two- and three-pathogen associations. It was established that the resistance level of K. pneumoniae isolates in association with A. baumannii is significantly higher compared to that in monoculture for all antimicrobial drugs studied. At the same time, K. pneumoniae in combination with Candida spp. vs monoculture showed significantly lower level of resistance to ciprofloxacin, amikacin, cefotaxime, ceftazidime and amoxicillin/clavulanic acid. K. pneumoniae isolates carried resistance determinants to extended-spectrum beta-lactamases: OXA-48 — (22.5%), OXA-51 — (5.6%), OXA-23 — (4.2%), KPC — 70.9%, NDM — 7%. Of these, 14.1% of strains had the ability to co-produce serine carbapenemases OXA-48 and KPC. Sputum and lung tissue A. baumannii isolates exhibited extremely high multiple resistance regardless of their associations with other microorganisms. Microbiome species similarity in the lower respiratory tract and lung tissue discharge was revealed. The proportion of lung tissue vs sputum resistant strains of K. pneumoniae and A. baumannii was significantly higher. Conclusion. The detection of of multiple drug resistant K. pneumoniae and A. baumannii isolates as well as their associations may indicate aggravated pneumonia severity.

Russian Journal of Infection and Immunity. 2023;13(6):1069-1078
pages 1069-1078 views
Influence of long-term antibiotic therapy on gut microbiome composition and metabolic profile in pulmonary tuberculosis
Yunusbaeva M.M., Terentyeva D.R., Borodina L.Y., Zakirova A.M., Bulatov S.E., Bilalov F.S., Yunusbayev B.B.
Abstract

The use of long-term multicomponent antibiotic therapy is the most effective way to treat tuberculosis (TB). However, little is known about the effect of this chemotherapy on the human intestinal microflora. The purpose of this study was to analyze an effect of long-term antibiotic therapy on gut microbiome composition and metabolic profile in TB patients. We used deep sequencing of fecal samples from 23 treatment-naive TB patients to reconstruct the metabolic capacity and strain/species-level abundance in the gut microbiome. Two fecal samples were obtained from each patient: before and after treatment. We showed that TB treatment regimen does not disrupt the overall diversity of the gut microbiome but does have an impact on gut bacterial microbiome composition and metabolic profile. While taking first-line anti-tuberculosis drugs (isoniazid, rifampicin, ethambutol, pyrazinamide), TB patients showed an apparent increase in Actinobacteria abundance. Pairwise comparison of metagenomic data revealed 28 differentially represented bacterial taxa, of which three species Bacteroides cellulosilyticus, Enterocloster aldensis, Clostridium spiroforme were strongly enriched in TB patients post-chemotherapy, whereas 25 species were enriched in TB patients before treatment (Bifidobacterium catenulatum, Enterococcus faecium, Bacteroides salyersiae, Bacteroides xylanisolvens, Bacteroides eggerthii, Lachnospira eligens, Akkermansia muciniphila, Ruminococcus lactaris, etc.) (p < 0.05). The metabolic profile of the gut microbiome was characterized by increased metabolic processes aimed at the growth and division of microbial cells. Iron is the main limiting factor for growth and reproduction. In addition, it is important to note the prevalence of glycolysis and lactate fermentation as the major means for energy production by intestinal microbiota.

Russian Journal of Infection and Immunity. 2023;13(6):1079-1088
pages 1079-1088 views
Monitoring of coronavirus infection in the kyrgyz population
Popova A.Y., Smirnov V.S., Kasymov O.T., Egorova S.S., Nurmatov Z.S., Drozd I.V., Milichkina A.M., Smolensky V.Y., Nuridinova Z.N., Ivanov V.A., Sattarova G.Z., Ramsay E.S., Dzhangaziev B.I., Zueva E.V., Arabiy U.U., Drobyshevskaya V.G., Zhimbaeva O.B., Razumovskaya A.P., Totolian A.A.
Abstract

Purpose of the study: to study the dynamics of developing herd immunity against SARS-CoV-2 in the population of the Republic of Kyrgyzstan during COVID-19. Materials and methods. The work was carried out using the methodology for assessing population immunity developed by Rospotrebnadzor (Russia) as well as the Ministry of Health (Kypgyzstan) and the St. Petersburg Pasteur Institute. The selection of participants was carried out by questionnaire using a cloud (Internet server) service. To monitor population immunity, a cohort of 2421 subjects was formed, who participated in all stages of seromonitoring. Volunteers were randomized according to age groups (1–17, 18–29, 30–39, 40–49, 50–59, 60–69, 70+ years), regional and professional factors. Antibodies (Abs) against SARS-CoV-2 nucleocapsid (Nc) and the receptor binding domain (RBD) of S-glycoprotein were determined by qualitative and quantitative methods. The study was carried out in 3 stages according to a single scheme: 1st stage — 06/28–07/03/2021, 2nd — 21–25/02/2022 and 3rd — 31/10–04/11/2022. Since 2021, Kyrgyzstan has been vaccinating the population against SARS-CoV-2 mainly using inactivated whole-virion vaccines. Results. Population immunity against SARS-CoV-2 was predominantly accounted for by both Ab types (Nc+RBD+). By the 3rd stage, the percentage of such persons reached 99.2%, NcRBD volunteers — up to 0.8%. At the 1st stage, middle-aged people dominated, but age differences were leveled out by the 2nd stage. The greatest impact on seroprevalence was found among medical workers, the smallest — among businessmen and industrial workers. Populational vaccination significantly impacted on the state of herd immunity that reached 25% by the 3rd stage. The refusals of the population in Kyrgyz Republic from vaccination noted at the 2nd and especially 3rd stages did not significantly affect level of herd immunity, which could probably be associated with asymptomatic cases of COVID-19, against which primary vaccination had a booster effect. Conclusion. The dynamics of population humoral immunity against SARS-CoV-2 included a number of changes in the level of circulating antibodies (Nc, RBD), caused by both primary infection and vaccination. The herd immunity formed in population of Kyrgyzstan allowed to reduce the incidence of COVID-19 to almost sporadic level.

Russian Journal of Infection and Immunity. 2023;13(6):1089-1108
pages 1089-1108 views
Features of ESCHERICHIA COLI samples from patients with diarrheal syndrome in the Republic of Guinea
Makarova M.A., Balde R., Boiro M., Matveeva Z.N., Kaftyreva L.A.
Abstract

Introduction. Diarrheal diseases are a global public health issue and cause 15% of deaths in children under 5 years old, of which about 80% occur in the regions of Africa and Southeast Asia. According to the Global Enteric Multicentre Study (GEMS) conducted in a number of African countries, one of the leading pathogens of high risk of death in infants and young children is diarrheagenic E. coli (DEC). In recent decades, antimicrobial resistance (AMR) has become globally ubiquitous. The Republic of Guinea urgently needs large-scale studies devoted to assessing DEC distribution and antibiotic resistance. The purpose of the study is to assess the pattern of E. coli infections and to test the susceptibility to antibiotics in strains of diarrheagenic E. coli sampled from individuals residing in the Republic of Guinea.

Materials and methods. From 2019 to 2022, we studied 724 samples of faeces of patients with acute diarrhea, among them 72 (9.9%) children aged 1–5 years, 128 (17.7%) children aged 6–17 years, and 524 (72.4%) people aged 18 years and older; a method of polymerase chain reaction (PCR) was applied with the use of the AmpliSense® Escherichioses-FL reagent kit to identify the genetic determinants of DEC: EPEC, EHEC, ETEC, EIEC, and EAgEC (Central Research Institute of Epidemiology of Rospotrebnadzor, Russia). Susceptibility to 15 antimicrobial agents was found by the disc-diffusion method using Mueller–Hinton agar (Russia) and Oxoid discs (UK). Results were interpreted according EUCAST criteria, versions 2019–2022 (https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents).

Results. For the period from 2019 to 2022, the percentage of E. coli infections in the etiological pattern of acute intestinal infections amounted to 51.7%. In the age-related manner, DEC was significantly more common in young children aged 0–5 (96.9%, p < 0.05) as compared to school age children aged 6–17 (53.9%) and adults (45.6%). In all years of observation, EAgEC strains prevailed, accounting for 38.4%. Other DEC pathotypes, EPEC, ETEC, EIEC and STEC, accounted for 27.2%, 17.5%, 11.8%, and 5.1%, respectively. DEC strains are susceptible to meropenem, amikacin, and nitrofurantoin. The activity of other antibiotics ranged from 11.3% for ampicillin, 28.3% for trimethoprim-sulfamethoxazole, and 34.0% for tetracycline to 73.6% for cephalosporins, 84.0% for aminoglycosides, and 98.1% for fluorinated quinolones.

Conclusion. To reduce the burden of diarrheal diseases in the Republic of Guinea, it may be necessary to conduct targeted epidemiological and microbiological studies to identify DEC and monitor the development of antimicrobial resistance of E. coli infection pathogens in the population.

Russian Journal of Infection and Immunity. 2023;13(6):1109-1116
pages 1109-1116 views
Pediatric bacteremia and CNS infections associated with klebsiella pneumoniae: molecular genetic characteristics and clinical features
Sadeeva Z.Z., Novikova I.E., Lazareva A.V., Alyabyeva N.M., Karaseva O.V., Yanushkina O.G., Verschinina M.G., Fisenko A.P.
Abstract

Klebsiella pneumoniae is one of the most significant and life-threatening pathogen of nosocomial infections. This opportunistic microorganism can cause infections of the bloodstream, respiratory tract, urinary tract, skin and soft tissues, inflammation of meninges of the brain and spinal cord, leading to elevated hospital mortality. The purpose of our study was a retrospective analysis of molecular genetic characteristics of K. pneumoniae isolated from blood and liquor samples as well as to describe clinical features in bacteremia and CNS infections. According to the results of assessed clinical data, K. pneumoniae isolates were selected from 64 children suffered from surgical pathology (congenital heart defects — 30%, abdominal pathology — 39%, severe combined trauma — 12%) and somatic diseases accompanied by antibacterial and/or glucocorticosteroid therapy — 14%. The minimum suppressive concentrations of antibiotics were determined by the broth micro-dilution method. Carbapenemases were detected by real time polymerase chain reaction. Virulence genes and capsule serotypes K1/K2 were assessed by multiplex PCR. Biofilms were grown using flat-bottomed polystyrene plates, followed by coloring, fixation, elution and data detection. The population diversity was assessed by multilocus sequence typing. Bacteremia and CNS infections associated with K. pneumoniae were fatal in 25% of cases. A substantial portion of the isolates demonstrated the phenotype of extremely drug resistance (XDR) — 43%, the phenotype of multidrug resistance (MDR) was shown in 16% of the isolates. The blaCTX-M cephalosporinase gene was found in 85% of the strains. The main determinant of resistance to carbapenems was the blaOXA-48 gene (33%); the blaNDM gene was detected in 9% of strains. The combination of blaOXA-48 and blaNDM was found in 7% of isolates. The study of biofilm production showed that moderate ability to form biofilms was shown in 61%, strong — 21%, and weak — 15% isolates. Two isolates (3%) did not form biofilms. The virulence genes entB and mrkD were detected in 100% of isolates, ybtS — in 78%. The iutA gene was found in 18% of the strains. Two isolates showed the presence of the kfu gene. Seven isolates belonged to the K2 serotype. 27 different genotypes were found in K. pneumoniae isolates examined. The most common were: ST307 — 21%, ST395 — 12%, ST48 — 7%, ST39 — 6% and ST29 — 6%. Infections of the bloodstream and central nervous system associated with K. pneumoniae have great importance in clinical practice. This microorganism is able to long persist on biotic and abiotic surfaces, has a wide natural and acquired resistance to antibiotics.

Russian Journal of Infection and Immunity. 2023;13(6):1117-1128
pages 1117-1128 views
Prevalence of occult hepatitis B infection among blood donors in Saint Petersburg
Ostankova Y.V., Serikova E.N., Shirshova N.Y., Kusevitskaya M.B., Gorskaya O.A., Basina V.V., Mashkov I.A., Zueva E.B., Schemelev A.N., Reingardt D.E., Davydenko V.S., Mukkel D.А., Totolian A.A.
Abstract

The aim of this study was to assess the prevalence of occult hepatitis B infection among blood donors in St. Petersburg, as well as to characterize the identified virus isolates. The study material was represented by 2800 blood plasma samples collected in 2019 from blood donors living in St. Petersburg. The ELISA study for HBV marker rate consisted of HBsAg, anti-HBs IgG, anti-HBcore IgG. HBV DNA was analyzed by nested PCR with real-time hybridization-fluorescence detection on three targets allowing to determine virus DNA at low viral load, including HBsAg-negative chronic hepatitis B. Hepatitis B serological markers were detected in 69.43% of those surveyed, HBsAg was found in 0.43% of individuals, and all of which donated blood first time. A significant excess of the anti-HBcore IgG antibodies occurrence among primary donors (15.1%) compared with repeated/regular donors (7.48%) was shown. The prevalence of virus DNA in the group was 3.14%, including 2.71% of cases in HBsAg-negative CHB. Based on phylogenetic analysis of 88 isolates, HBV subgenotypes were determined in the following order: D1 and D2, 40.91% each, D3 and A2, 9.09% each. While determining the serological subtype in detected isolates, the serotype ayw3 (52.27%) vs ayw2 (46.59%) and adw2 (10.23%) prevailed. Drug resistance mutations, including compensatory ones, were detected in six examined patients (6.82%). In all genotype D isolates, multiple amino acid substitutions were identified in the RT, SHB, MHB, LHB, and Core regions; mutations in the preCore region were detected in 21.59% samples. In the MHR of the HBV genotype D genome, twenty-six positions were identified in which amino acid substitutions occurred, and all isolates showed modifications at positions 113, 114, 131, 134, 159, 161, 168, in 76 — at position 122, in 68 — at position 127, in 36 — at position 118, in 24 — at position 128. In HBV A2 isolates, mutations T113S, S143T, Y161F were identified. Nine isolates in the preCore region showed a polymorphism including a stop codon W28*W; in five isolates the W28S substitution was shown in the same position, and the W28*S variant was found in one more sample. The high incidence of HBsAg-negative CHB cases among blood donors, as well as the predominance of HBV isolates that simultaneously carry mutations resulting in diagnostic failure of HBsAg tests and prophylactic failure of immunoglobulin or vaccines and virus reactivation, mutations that contribute to disease progression obviously pose a threat to health and require to be further examined.

Russian Journal of Infection and Immunity. 2023;13(6):1129-1140
pages 1129-1140 views
The role of Recombinant interleukin-2 in the treatment of patients with chronic hepatitis B.
Novikova A.F., Popova L.L., Konstantinov D.Y.
Abstract

Dysregulated immune response occurring in chronic hepatitis B prevents the virus elimination and contributes to progression of the infectious process. The aim of the study was to evaluate the effectiveness (biochemical, immunological, virological) of combination treatment with tenofovir and Recombinant interleukin-2 in chronic hepatitis B patients.

Material and methods. A comparative analysis of the results from laboratory examination of chronic hepatitis B patients in two comparison groups, comparable in sex, age, stage of fibrosis, viral load, was carried out: group I (n = 27) received tenofovir, according to the accepted recommendations, and recombinant interleukin-2 (rIL-2), group II (n = 25) — tenofovir.

Results. Before the onset of antiviral therapy all patients with chronic hepatitis B had increased hepatic transaminases, alkaline phosphatase and gammaglutamyl transpeptidase from 1.2 to 5 norms as well as dysregulated cellular immunity factors with significantly decreased absolute count of CD4+, CD8+, CD16+ and increased CD20+ lymphocytes. After 12 months of treatment, patients in observation groups showed normalized cytolysis and cholestasis with insignificant intergroup differences. The level of absolute count of CD4+, CD8+ T-cells and CD16+ lymphocytes in the I group increased (by 24.7%, 24.1%, 34.5%, respectively, all p < 0.001 relative to the initial values), not observed in comparison group. The level of CD20+ lymphocytes in group 1 was decreased by 35.9%, and in group 2 — by 7.9% (pI–II < 0.001). In group 1, the level of HBsAg after 12 months of treatment became lower by 52% (p < 0.001).

Conclusion. The conducted pilot study showed that the combination etiopathogenetic therapy of patients with chronic hepatitis B using tenofovir and rIL-2 improves liver functional state, restores the disturbed balance of immunocompetent cells: by increasing level of CD4+, CD8+ T-lymphocytes, CD16+ lymphocytes and reducing the count of CD20+ cells, and also allows to steadily reduce blood serum HBsAg level.

Russian Journal of Infection and Immunity. 2023;13(6):1141-1149
pages 1141-1149 views
Side effects following administration of the Gam-COVID-Vac in Montenegro
Dabanovic V.
Abstract

Introduction. In Montenegro, vaccination against COVID-19 infection began with the use of Gam-COVID-Vac, which was not approved for emergency use before the end of clinical trials, by the Food and Drug Administration and the European Medicines Agency. Therefore, it is necessary to emphasize the adverse effects.

Materials and methods. For the purpose of this study, there were collected data from national adverse events reporting form for Gam-COVID-Vac obtained from the Health Institution Pharmacy of Montenegro — Montefarm, as the holder of permits for these vaccines. Results. For the period March 1, 2021 to February 13, 2022, after administration of 16 756 doses of vaccine Gam-COVID, a total of 220 case reports, or 716 adverse effects were recorded. The mean age of vaccinated individuals who reported adverse effects was 40.79±11.35 years. Totally, 79.55% females versus 20.45% males reported side effects post-vaccination. The most common adverse reaction was pyrexia (79.55%). Other very common adverse effects were as follows: injection site pain (38.18%), headache (33.18%), myalgia (32.27%), malaise (31.82%), fever (30.45%), arthralgia (22.73%) as well as swelling and redness at the site of application (15.91%). Less common adverse effects were nausea, pain in extremity, diarrhea, dizziness, fatigue, sore throat and labial herpes. Serious adverse effects were recorded in 8 cases including tinnitus, thrombophlebitis, hypotension, chest pain, palpitations and peripheral cyanosis related to specific comorbidities.

Conclusions. After the administration of Gam-COVID vaccine, the population in Montenegro experienced mild to moderate adverse effects, with rare serious transient adverse effects related to specific comorbidities. The data presented here on investigating Gam-COVID-Vac caccine verified good safety profile and high tolerability evidenced by the statistics analysis as lacked COVID-19-associated hospitalizations or deaths.

Russian Journal of Infection and Immunity. 2023;13(6):1150-1160
pages 1150-1160 views
Effect the pre-exposure prophylactic of hydroxychloroquine on severe COVID-19 disease: a randomized controlled trial
Valizadeh M., Tarjoman T., Farhoudi B., Chouhdari A., Mesgarian M., SeyedAlinaghi S., Zangeneh M., Hanifezadeh Z., Adain Atashi H., Massumi-Naini H., Abolghasemi S., Dezfulinejad M., Haghani S.
Abstract

Background. In vitro studies have shown some effects for Hydroxychloroquine (HCQ) against SARS-CoV-2 virus. Despite effective vaccination program, relatively large proportion of population remains unvaccinated. So, there still remains a need for other prophylactic measures. The present study aims to evaluate whether HCQ can prevent severe COVID-19 outcomes among health-care workers.

Materials and methods. In this randomized, double blind placebo-controlled clinical trial 334 healthcare workers aged 18–65 years old were included of whom 278 individuals completed the study. Participants were randomly assigned to the HCQ group (800 mg at day one, followed by 400 mg weekly for the next 7 weeks); or the placebo group. Participants were followed three weeks after the last dose of drug or placebo (10 weeks from the first dose of drug or placebo). The primary outcome was hospitalization or death from COVID-19. Results. Of 148 people who received HCQ, none were hospitalized or died from COIVD-19, while of 130 people who received the placebo, 2 (1.5%) were hospitalized for COIVD-19 (p-value: 0.26). And, 22 (14.9%) people in the HCQ group and 15 (11.6%) people in the placebo group contracted COVID-19 (p-value: 0.99). Adverse reactions were reported by 5 (3.4%) of participants in the HCQ group and 5 (3.9%) of participants in the placebo group (p-value: 0.99).

Conclusion. We found that HCQ has no significant prevention effect on the incidence of mild COVID-19. However, the low rate of hospitalization (the primary outcome) in this trial like most of the other clinical trials with HCQ would have required increasing the sample size considerably to be able to comment on the effectiveness of HCQ in prevention of severe forms including death rate. This justifies systematic reviews to include similar studies to further investigate the issue.

Russian Journal of Infection and Immunity. 2023;13(6):1161-1168
pages 1161-1168 views
Monkeypox: a systematic review of epidemiology, pathogenesis, manifestations, and outcomes
SeyedAlinaghi S., Afsahi A., Afzalian A., Shahidi R., Tamehri Zadeh S., Varshochi S., Dashti M., Ghasemzadeh A., Pashaei A., Paranjkhoo P., Parmoon Z., Parikhani S.N., Shamsabadi A., Pezeshgi P., Ahmadi S., Arjmand G., Javaherian M., Ebrahimi H., Karimi A., Mehraeen E., Jahanfar S.
Abstract

Introduction. Since May 2022, an unusually large number of new monkeypox infections-a previously rare viral zoonotic disease, mainly reported from central and western Africa has been reported globally, and the World Health Organization (WHO) declared a global health emergency in July 2022. We aimed to systematically review the monkeypox virus epidemiology, pathogenesis, transmission, presentations, and outcomes.

Materials and methods. Our aim is to systematically review the epidemiology, pathogenesis, manifestations, and outcomes of Monkeypox disease. We searched the keywords in the online databases of PubMed, Embase, Scopus, and Web of Science and investigated all English articles until December 2022. In order to ascertain the findings, this study adheres to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist. In order to optimize the quality, this review study benefits from the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist. To minimize any probable bias risk, we utilized the Newcastle-Ottawa Scale (NOS) risk assessment tool.

Results. The most prevalent symptoms were rash and fever. The infection was accompanied by different complications such as, but not limited to, encephalitis (mainly in children), septicemia, bacterial cellulitis, retropharyngeal and parapharyngeal abscesses, etc. A wide range of hospitalization from 3.7% to 100% has been reported. The mortality rate ranged from 0% to 23%, which mainly occurred in infants and children. High mortality of the monkeypox rate was reported among pregnant women. The mortality rate of monkeypox is lower among women and those who received the smallpox vaccine compared to men and those who did not receive the vaccine. A wide range of the overall second-rate attack was reported, which is more pronounced in unvaccinated patients.

Conclusion. In our systematic review of 35 studies on monkeypox, we cast light on the existing evidence on its epidemiology, pathogenesis, manifestation, and outcomes. Further studies are needed to elucidate the natural history of the disease in various patients’ population, as well as detailing the monkeypox attack rate.

Russian Journal of Infection and Immunity. 2023;13(6):1169-1186
pages 1169-1186 views

SHORT COMMUNICATIONS

Chronobiological approach to study microsymbiont catalase activity in female reproductive tract
Nikolenko M.V., Vaseva E.M., Baryshnikova N.V., Malishevskaya O.I.
Abstract

Catalase is a heme-containing enzyme belonging to protection factors that destroys peroxide compounds. The presence of catalase activity is an important ability of microorganisms that allows them to be protected from unfavorable factors as well as adapt to macroorganism conditions. Catalase along with superoxide dismutase plays an important role in pathogen resistance to phagocyte oxygen-dependent bactericidal mechanisms. The aim of the study was to investigate microsymbiont catalase activity from female reproductive tract in normocenosis and candidiasis dysbiosis using the chronobiological approach. The study was conducted on clinical isolates, isolated from female reproductive tract microsymbiocenosis. The catalase activity was determined by spectrophotometry based on 24 hour-long hydrogen peroxide reduction with 3-hours interval in winter season. Dynamic hydrogen peroxide was assessed in 3–5 experiment replicates. In some Lactobacillus spp., catalase was found containing no heme group — pseudocatalase. Chronobiological approach allowed to reveal enzyme activity from all microsymbionts. The dominant and associative microbiota isolated from healthy females was characterized by circadian (24 hours) rhythms of catalase activity early in the morning — 5 a.m. (р < 0.05). Hydrogen peroxide decomposes spontaneously or via non-enzymatic catalysts, and microorganisms cope with this situation under such conditions. In microsymbionts characteristic of female reproductive tract dysbiosis, and usually found in large numbers along with decreased Lactobacillus spp. ultradian rhythms with 12- and 8-hour harmonics of catalase activity with acrophase were recorded in the morning (8 a.m.) and evening hours (8 p.m.). The minimum values of enzyme production in all cultures were recorded at 12 p.m. and 5 p.m. Therefore, the contribution of the rhythm of the studied parameter at varying degree of vaginal sterility reflects the adaptive pathogen capabilities to the conditions of existence and can be the basis for studying related regulatory mechanisms. Mesor and amplitude phase stability are universal rhythmometric parameters used to evaluate patient’s condition independent of species assignment.

Russian Journal of Infection and Immunity. 2023;13(6):1187-1191
pages 1187-1191 views
Immunological aspects of vaccination in HIV-infected patients
Zhestkov A.V., Zolotov M.O., Kadantseva E.V., Nikitina T.R., Protasov A.D.
Abstract

Until recently, HIV infection does not lose its relevance. In 2022, 630 000 people died and 1.3 million people became infected with the human immunodeficiency virus (HIV). HIV-positive persons develop more infectious diseases than healthy people do; the causative agents are mainly opportunistic microorganisms. Streptococcus pneumoniae is the main causative agent of infection in the lungs in HIV-infected persons. In order to prevent the development of severe pneumococcal infections and to overcome antibiotic resistance, vaccines have been developed. There are polysaccharide (PPV) and conjugate (PCV) vaccines. According to clinical recommendations, vaccination of previously unvaccinated HIV-infected patients is carried out regardless of T-helper cell level. However, no data were found on the effect of PCV13 on immunological memory cells. The purpose of this study is to assess an effect of PCV13 vaccination on the immune system in HIV-infected subjects.

Materials and methods. The study included 200 patients with HIV infection, which were divided into two groups: I — received a dose of PCV13 (n = 100) and control group (n = 100). During the first visit, immunological and microbiological studies were carried out. On the second visit, a PCV13 was injected into the deltoid muscle. The third visit was made a year later, where immunological and microbiological studies were repeated. Participants were divided into 4 subgroups depending on CD4+ T cell level. The microbial study was done using a swab collected from the back of the throat.

Results. During the immunological examination at visit 1, abnormalities were detected in all examined populations and immune cell subsets. At 12 months post-vaccination, the median levels of CD3+CD4+ and CD45RO+ T lymphocytes in the immunized group were higher than pre-vaccination levels compared to control group, in which the values changed insignificantly. Our data confirm the immunological effectiveness of PCV13 administration in HIV-infected patients. In patients with peripheral blood CD19+ lymphocyte deficiency, had increased microbial detection rate (p = 0.003).

Conclusion. As a result, due to the high risk of pneumococcal pneumonia, HIV-infected patients should be immunized with a 13-valent pneumococcal conjugate vaccine.

Russian Journal of Infection and Immunity. 2023;13(6):1192-1196
pages 1192-1196 views


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