Russian Journal of Infection and Immunity

The bacterium Francisella tularensis is the etiological agent of tularemia, a natural focal, especially dangerous infection, which, “thanks to” its low infectious dose and ability to be transmitted to humans via all possible routes, is a potential bioterrorism agent. This pathogen has been known to mankind for over a hundred years, but it is still impossible to prevent massive human disease outbreaks and sporadic incidence cases, whereas tularemia diagnosis may be verified within several days-to-weeks. The basis for tularemia causative agent virulence is based on its ability to disrupt phagocyte function. In animals and humans, the various Francisella tularensis systems work together to bypass host immune system, attach to and enter eukaryotic cells, block phagosome-lysosome fusion, multiply in various host cells without being detected, inhibit their destruction and cause host cell death to release bacteria and infect neighboring tissue cells, thus developing an infectious disease in different organs. This is achieved through a unique complement-dependent penetration process into host cell, called loop phagocytosis, and an unusual inert endotoxin as well as variation in diverse forms of “free” lipid A modifications and lipid A in the LPS composition, its dynamic acyl chain length regulation, and specifically combined regulatory factors to induce the “pathogenicity island” protein synthesis. Accumulated point mutations, intragenomic rearrangements, deletions, insertions, duplications, transpositions, gene degradation, variation in the number of copies in repeated DNA sequences, as well as homologous and non-homologous recombinations underlie a markedly expanded potential for existence of the tularemia causative agent: they contribute to the holarctic subspecies strain survival in varying conditions, including osmotic shock, to form multiple resistance to various toxic substances and alter F. tularensis subspecies virulence. Analyzing a whole body of publications on the abovementioned aspects for tularemia causative agent life activity attempts to combine the differences, structural features and “tricks” of the F. tularensis species cells allowing them to be a powerful pathogen, with a high potential to adapt upon low pathogen variability and a limited genome length compared with other specially dangerous bacteria.

Introduction. Taking into account the experience on the new coronavirus infection COVID-19 pandemic, the relevance of studies assessing the cellular processes of SARS-CoV-2 virus assembly and transport to justify the choice of pharmacological action points has now markedly increased. The study was aimed at analyzing morphologically assessed events of SARS-CoV-2 life cycle in neocortical neurons using electron microscopy based on its traced wide prevalence in vivo and ability to penetrate the blood-brain barrier accounts.

Materials and methods. Patient-derived SARS-CoV-2 virus was obtained and accumulated in Vero(B) cell culture. An electron microscopy study (EMR) of the viral particle transport was carried out in male Syrian hamsters. Animals were inoculated intranasally with 26 μl of virus culture in an amount of 4 × 10⁴ TCID₅₀/ml. Animals were euthanized on day 3, 7, and 28 post-infection. The extracted brain was prepared for EMR according to methods previously described in the literature. The results were recorded using an FEI Tecnai G2 Spitit BioTWIN electron microscope.

Results. Using EMR, the morphological equivalents of virus transport variants in neocortical neurons were traced dynamically during infectious process in Syrian hamsters. After synthesis, viral membrane proteins are included in transport vesicles in the endoplasmic reticulum (ER) terminal tubules and enter the intermediate compartment (IC), a collection of smooth-walled membrane vesicles between the endoplasmic reticulum (ER) and the Golgi apparatus (AG). In the first 3 days post-infection, viral copies are included in the Ag in PC membrane-formed transport vesicles. Due to the large size, viral particles are restricted to the expanded ends of the mobile AG tanks. Morphologically, destruction of AG membranes was revealed on day 7 post-infection, which indicates an interaction between PC vesicles and preserved AG membrane elements or the implementation of their independent transport function to deliver SARS-CoV-2 virus to the cell periphery and further into the intercellular space. In the neuronal processes, the transport of mature SARS-CoV-2 viral particles associated with cytoskeletal elements was observed, which was not detected in other loci of virus persistence.

Conclusion. Based on data obtained, it is possible to hypothesize about a cumulative importance for progression and persistence of SARS-CoV-2 infection in cortical neurons. Early signs of neuron infection are represented by characteristic changes in the nuclei, ER hypertrophy and formation of “viral factories” based on the ER, PC and AG. The formation of viral biomass occurs inside neurons; virion exit from target cells is more accompanied by cell death rather than if a virus becomes incorporated in the lysosomal-endosomal system.

Relevance. Due to the large-scale vaccination campaigns against the SARS-CoV-2 coronavirus taking place worldwide, the question arises as to how vaccination may affect complete blood count (CBC) parameters in COVID-19 cases. Research objective: assess differences in complete blood count parameters in COVID-19 patients based on their vaccination status.

Materials and methods. A review of publications was conducted describing and presenting the complete blood count parameters in patients with verified COVID-19, by stratifying them into vaccinated and unvaccinated individuals against the SARS-CoV-2 virus-caused disease. Subsequently, a meta-analysis of the results for each CBC parameter was carried out by describing identified differences among patients with mild and moderate COVID-19, lacking comorbidities affecting CBC indicators.

Results. The analysis conducted allowed to determine that the complete blood count parameters do not exceed the reference range in most cases in both groups, excepting those of individuals with a severe disease course. The exception is the erythrocyte sedimentation rate (ESR) (42 [20.5–63.5] (∑n = 107, Me [Q₁–Q₃])) mm/h in unvaccinated individuals. Also, a slightly lower absolute lymphocyte count is observed in vaccinated individuals (0.95 [0.58–1.62] × 10⁹/L (∑n = 441, Me [Q₁–Q₃])). There is a twofold greater range of leukocyte quartile values in vaccinated individuals compared to unvaccinated individuals: 7.07 [4.07–12.31] × 10⁹/L (∑n = 555, Me [Q1–Q3]) vs 5.68 [4.02–8.34] × 10⁹/L (∑n = 2202, Me [Q₁–Q₃]). A similar pattern is observed for monocytes.

Conclusion. Conducting a meta-analysis of laboratory parameters in COVID-19 cases among vaccinated and unvaccinated individuals allows for determining the effectiveness of vaccination as well as identify the major trends in dynamic changes for essential blood parameters among unvaccinated and vaccinated individuals in general or with certain immunobiological preparations.

Introduction. Real-time PCR may be used along with loop isothermal amplification method (LAMP) allowing to conduct the study in 30–40 minutes to diagnose typhoid fever. Several LAMP assay variations for detecting Salmonella enterica serovar Typhi have been described. The studies report that relevant primers were tested on strains specific for Malaysia and China. We attempted to evaluate the LAMP primers described above for identifying S. Typhi strains specific for the Russian Federation and compare their sensitivity and specificity with each other.

Materials and methods. A comparative in silico analysis of target sequences was carried out both in the open NCBI database and among the genetic sequences of collection strains at the St. Petersburg Pasteur Institute. Several sets of primers for LAMP amplification of various S. Typhi genome regions were tested. The tested primers amplify the following fragments: SalTyp1 — region of the STY1607 gene, SalTyp2 — region of the STY2879 gene, SalTyp3 — region of the STBHUCCB_38510 gene of the PapD chaperone.

Results. In silico analysis of LAMP primers showed that only the SalTyp 3 set has strict specificity for Salmonella enterica serovar Typhi. For the SalTyp 1 and SalTyp 2 an opportunity of false-positive reactions with some E. coli strains was shown. A LAMP method for DNA fluorescent detection of the typhoid fever causative agent was chosen. Assay has been based on a marker gene termed STBHUCCB_38510 and amplification with six specific primers. The detection limit was 20 copies/reaction in reference plasmids and the reaction time lasted for 35 minutes. The specificity of the method was tested on DNA specimens of 20 S. Typhi isolates and 90 strains of other heterologous bacteria from 24 different species. No false positive or false negative results were identified.

Conclusion. The developed method can be used in clinical practice for laboratory confirmation of typhoid fever diagnosis as a part of epidemiological monitoring of environmental objects as well as food products.

The aim of our work was to assess prevalence in the HCV drug resistance mutations in the NS3, NS5A, NS5B genes in HIV-infected patients. The material of the study was 157 blood plasma samples collected from HIV patients living in the Leningrad Region, with virological inefficiency of antiretroviral therapy. Samples were examined for the presence of anti-HCV antibodies and HCV RNA using commercial test systems in accordance with the manufacturer’s recommendations. In the case of detecting HCV RNA, amplification reaction was carried out using a set of primers co-flanking the NS3, NS5A, and NS5B genes. After sequencing the nucleotide sequences of the above genes, the virus subtype was determined. To assess HCV drug resistance mutations to direct-acting antiviral agents (DAAs), the Geno2pheno HCV resistance software (https:// hcv.geno2pheno.org) was used. The age of the patients varied from 18 to 65 and averaged 34.3±7.27 years. The number of males vs females prevailed comprising 71% and 28%, respectively. Antibodies against HCV were detected in 94.2% cases, whereas HCV RNA — in 98 (61.7%) HIV-infected persons. The distribution of HCV genotypes in this group was as follows: 1a — 7% (n = 7), 1b — 53% (n = 52), 2 — 2% (n = 2), 3a — 38% (n = 37). The results of determining the viral load varied from 5.3 × 10³ to 2.3 × 10⁸ IU/ml. The nucleotide sequence of all three regions NS3, NS5A, NS5B was determined in 73 samples. Analysis of drug resistance mutations in the NS3 region was performed for 82 HCV isolates of genotypes 1b (n = 46), 3a (n = 31), 1a (n = 4), 2 (n = 1). In total, the proportion of strains containing mutations in the NS3 region was 9.8%. The presence of significant amino acid substitutions in the NS5A region was tested for 83 HCV isolates of genotypes 1b (n = 47), 3a (n = 30), 1a (n = 6). The percentage of strains containing mutations in the NS5A region was 19.3%. Resistance mutations in the NS5B region were analysed for 87 HCV isolates of genotypes 1b (n = 48), 3a (n = 32), 2 (n = 2), 1a (n = 5). The proportion of strains containing mutations in the NS5B region was 11.5%. In the study group, mutations associated with hepatitis C virus resistance to DAAs in all regions were found in 16.6% (95% CI: 11.11–23.32%) cases (n = 26). In the NS3, NS5A and NS5B, there have been identified 6, 15 and 10 significant amino acid substitutions, respectively.

Klebsiella pneumoniae is one of the main causative agents of healthcare-associated infections (HAI) worldwide. The study was aimed at molecular characterization of beta-lactam antibiotic resistance in K. pneumoniae isolated in the cardiac surgery hospital, identify hypervirulent isolates and assess isolate genetic relatedness. K. pneumoniae isolated from the clinical material of patients (n = 50) at cardiac surgery departments as well as anesthesiology and reanimation department treated at the cardiovascular surgery hospital in Perm from July 2021 to December 2022 were analyzed. Bacteriological studies were performed on an automatic analyzer WalkAway-96Plus (Beckman Coulter, USA). The sensitivity to thirteen antimicrobials, production of extended-spectrum beta-lactamases (ESBL) and multidrug resistance (MDR) phenotype were assessed. The string test was used to screen hypermucoviscous K. pneumoniae. Isolate relatedness (ERIC-PCR), presence of beta-lactamase genes (bla_TEM, bla_CTX-M, bla_SHV, bla_OXA, bla_KPC, bla_VIM-2, bla_IMP-1, bla_NDM-1), as well as genes associated with hypervirulence (prmpA, iucA, peg-344, wzyK2, magA) were analyzed by PCR. Amplifications were performed in a DNA Engine Dyad Thermal Cycler (Bio-Rad, USA). Gel documentation system Gel-Doc XR (Bio-Rad, USA) was used for band visualization and data documentation. According to the study results, it was found that carbapenem-resistant isolates accounted for almost 76% of all isolates, the ESBL-phenotype had 90%, and MDR-phenotype — 88% of studied isolates. According to the string test results, 8% of K. pneumoniae isolates had a hypermucoviscous phenotype. As for genes associated with hypervirulence, it was shown that the iucA gene was the most common, amplified in 54% of isolates, prmpA was detected in 38% of isolates, 48% of isolates had wzyK2 or magA genes encoding capsular type K1/K2. Almost a third of K. pneumoniae samples contained a combination of the rmpA and iucA genes, and they were isolated more often in the group of patients with active infection. Only carbapenem-sensitive microorganisms had hypermucoviscous phenotype, K1 capsular type, and a combination of prmpA, iucA, peg-344 genes, whereas the K2 capsular type was most common among carbapenem-resistant K. pneumoniae. Based on molecular genetic typing, it was found that 24% of K. pneumoniae isolates were assigned to four genome groups of identical cultures, 76% of the isolates had individual profiles. Closely related isolates were found among patients from different departments that indicates a potential pathogen circulation in the closed circuit “surgery department–department of anesthesiology” and “reanimation–surgery department”.

Introduction. Influenza virus poses significant risks to immunocompromised individuals such as those who have received organ transplants and are undergoing immunosuppressive treatment to prevent transplant rejection. Therefore, annual influenza vaccination is recommended for these individuals. This study aimed to comparison of safety and effectiveness of single- versus double-dose of seasonal influenza vaccine in kidney transplant recipients.

Materials and methods. This randomized clinical trial involved 50 kidney transplant recipients at Imam Khomeini Hospital. Participants were randomly assigned to two groups: those receiving a single dose (standard dose) and those receiving a double dose of the seasonal flu vaccine. Serum samples were collected before and 4 weeks after vaccination to measure influenza A&B-related antibodies. Sixteen patients were excluded from the study. The trial focused on evaluating the vaccine safety and immunogenicity, as well as documenting any local and systemic side effects following vaccination.

Results. The results indicated no significant difference in gender, age, and type of immunosuppressive drug used between the single- and double-dose groups (p > 0.05). No significant difference in post-vaccination adverse effects, such as injection site pain (p = 0.21) between the two groups. The seroconversion rates (change from IgG < 9 IU/µL to IgG >11 IU/µL) for IgG Influenza A were 12.5% (n = 2) in the single-dose group and 26.7% (n = 4) in the double-dose group, and for IgG Influenza B, they were 11.8% (n = 2) and 21.4% (n = 3), respectively.

Conclusion. A double dose of the influenza vaccine slightly enhanced the immune response in kidney transplant patients without causing any adverse side effects.

Background. Saudi Arabia, a large country in terms of population size and geographical area, is divided into administrative areas and governorates. It has metropolises, cities (large, medium sized, and small), towns, villages and rural neighborhoods, classifiable into well equipped, rapidly expanding, and others. The COVID-19 epidemics spread all over the country with differentials in infection rates, percentages, and affected persons, alongside daily increases. This analysis, focused on administrative areas, aimed to comprehend the spread and escalation of the epidemic, in addition to highlighting the distribution of the infected population with a special emphasis on geographical spread and seasonal variations.

Materials and methods. This analysis of data compiled from COVID-19 daily reports published by the Saudi Arabian Ministry of Health considers into account administrative areas and localities (neighborhoods) to demonstrate the distribution of spread, increase in infection, and the proportion of population infected between March 21, 2020 and May 4, 2023.

Results. A large majority of the infected cases were reported in three major administrative areas including Riyadh, Makkah, and the Eastern Region. Other regions had a smaller number of infected cases. However, some locations, especially medium-sized upcoming towns and neighborhoods experienced greater number of people seriously affected at a rapid pace, with seasonal differentials, in medium sized upcoming cities — the governorate headquarters and promising future cities, apart from the major cities.

Conclusions. COVID-19 spread in the country followed a certain regional pattern. Beyond the populous administrative areas, upcoming cities in fast changing areas had a high impact. Thus, having a categorization of major, medium or low spread is necessary. Such detailing of COVID-19 infection would be useful not only to develop combating strategies but also to create epidemic and emergency preparedness.

Aim of the study: to characterize the integration and implementation of the main components of infection prevention and control (IPC), defined by the World Health Organization (WHO), in psychoneurological hospitals in Armenia.

Materials and methods. The study was conducted over the period from 2019 to 2022 in all 8 psychoneurological hospitals in Armenia. The research tool was based on using the IPCAF (Infection Prevention and Control Assessment Framework) questionnaire translated into Armenian, consisting of 8 sections. In accordance with the WHO scoring methodology, each possible answer to the question was scored. The maximum total score for each core component could be 100 points, and the final score — 800. Descriptive epidemiology was used during the study.

Results. The average final score for all IPCAF components for all neuropsychiatric hospitals in Armenia over the entire study period was increased by 1.46 times (from 345.0±10.7 points in 2019 to 502.5±32.5 in 2022; р < 0.01) and in 2022 was characterized as an “intermediate level”. Analysis by individual IPC core components (CC) found that the highest average scores in 2022 were obtained for components CC2 (IPC guidelines) — 81.6 points, CC8 (Built environment, materials and equipment for IPC at the facility level) — 72.8 points, and CC5 (Multimodal strategies) — 70.0 points. The lowest average scores were obtained for the key components: CC4 (Health care-associated infection (HAI) surveillance) — 45.0 points, and for CC3 (IPC education and training) — 56.3 points and CC7 (Workload, staffing and bed occupancy) — 56.9 points.

Conclusion. Our study demonstrated for the first time an opportunity for using the IPCAF questionnaire to evaluate IPC programs in neuropsychiatric hospitals and identify gaps in various areas of IPC. Information was received regarding the state of key IPC component implementation in psychoneurological hospitals in Armenia. Analysis by individual core components identified gaps that need to be addressed. It is recommended to implement continuous monitoring of compliance with various aspects of IPC in order to prevent weakening of control and deterioration of epidemiological situation.

The aim of the study was to determine the sensitivity of the bacteria of the biovar Acinetobacter baumannii bv. tryptophandestruens to antibiotics used to treat Acinetobacter-infection. The object of the study was 86 primary clinical isolates of A. baumannii, of which 34 strains of A. baumannii bv. tryptophandestruens isolated in the microbiological laboratory of the Military Medical Academy in 2021–2022. Species identification of bacteria was carried out by MALDI-ToF mass spectrometry. The biovar tryptophandestruens of A. baumannii was determined on a dense chromogenic medium. The sensitivity of A. baumannii isolates to antibiotics was determined by a “Vitek 2 compact” microbiological analyzer (bioMerieux, France). Clinical categories of isolates sensitivity to antibiotics (S) were identified based on the boundary values of minimum suppressive concentrations (MSC, mg/L) established by the European Committee for the Determination of Sensitivity to Antimicrobial Preparates (EUCAST), version 11.0. Isolates of A. baumannii bv. tryptophandestruens and groups of isolates of other A. baumannii very rarely sensitive to meropenem (8.8±4.6%; 3.8±2.6%, respectively, p > 0.05), ciprofloxacin (5.8±4.0; 9.6±4.1%, p > 0.05). Strains sensitive to gentamicin are rarely represented in both groups (26.7±7.55; 19.3±5.5%, p > 0.05) trimethoprim/sulfamethoxazole (38.8±8.3%; 23.6±5.3%, p > 0.05). Sensitivity to polymyxin B was preserved in all strains of both groups (100%). Strains of the tryptophandestruens biovar A. baumannii group surpass strains of the other strain of A. baumannii group in the frequency of isolates with MSC50% tigecycline (MSC50% — 0.5 mg/l; MSC50% — 2 mg/l, respectively), and also have significantly more strains with MSC 0.5 mg/l (52.9% and 15.4%, respectively, p < 0.01 ). Thus, the clinical isolates of the biovar A. baumannii bv. tryptophandestruens have no significant differences with isolates of other strains of A. baumannii in the frequency of strains sensitive (S) to meropenem, ciprofloxacin, gentamicin, trimethoprim/sulfamethoxazole, polymyxin B, but they differ in terms of sensitivity to tigecycline — a higher frequency of strains with an MSC of 0.5 mg/l (p < 0.01) and an MSC of 50%.

Despite the stable decline in SARS-CoV-2 virus-caused COVID-19 incidence in most countries worldwide by the end of 2023, spreading of this infection on a global scale remains relevant. Among all known SARS-CoV-2 genovariants, within the last about two years Omicron remains dominant. The distinctive properties of this genovariant are presented by short incubation period (1–5 days), high contagiousness, and a relatively mild disease course due to largest number of genomic mutations among all SARS-CoV-2 genovariants. The first case of Omicron genovariant-caused infection in Russia was recorded in early December 2021. Over many month-monitoring after active spread of the genovariant in Russia, it is obvious that in a number of key characteristics it differs profoundly from previous SARS-CoV-2 genovariants. Analyzing major patterns inherent in COVID-19 epidemic process particularly uncovering geographic features is one of the most crucial activities in COVID-19 surveillance. Here, we provide a comparatively analyzed pattern of Delta and Omicron SARS-CoV-2 genovariant dominated COVID-19 incidence in the population of the Saratov region. For this, there was used statistical reporting from the Office of Rospotrebnadzor for the Saratov Region. The main research method is based on epidemiological analysis. The study data showed that upon Omicron genovariant dominance, an increased percentage in COVID-19 cases among children of varying age, increased rate of infected subjects with unknown source of infection as well as improved clinical disease course were recorded. Regardless of the circulating genovariant, elderly people remain to be in risk group. Thus, after three years of the COVID-19 pandemic, the mutual adaptation for SARS-CoV-2 and human population can be observed, which is accompanied by altered biological properties of the former and the accumulation of herd immunity. Alleviated disease symptoms and decreased mortality rate among Omicron genovariant-infected individuals evidence in favor of further COVID-19 transformation into a seasonal infection.

Burkholderia cepacia is a motile, aerobic, non-fermentative, gram-negative bacillus and has been widely documented as a lung pathogen in patients with cystic fibrosis and chronic granulomatous disease. It is documented as an important emerging cause of multi-drug resistant nosocomial infections, and an important cause of morbidity and mortality. A 64-year-old male patient visited the Nikea Primary Healthcare Center, Piraeus, Greece, referred by the family doctor (GP), for follow-up due a history of prostate cancer (patient on immunosuppression) and recurrent UTIs with subsequent admission to the hospital. Patient history revealed diabetes mellitus type 2, arterial hypertension, hypercholesterolemia, hypertriglyceridemia, history of recurrent UTIs, with 4 hospitalizations in a tertiary hospital during the last 2 years, prostatic hypertrophy, 2 episodes of prostatitis before the diagnosis of prostate cancer Gleason score 6, at the end of 2019, with subsequent total prostatectomy, and radiotherapy. Patient history also revealed dysuria, frequent urination, pain and burning sensation during urination and erectile dysfunction. Urinalysis showed intense pyuria, abundance of micro-organisms and abundance of red blood cells. The urine culture grew monomicrobial Burkholderia cepacia > 10⁵ CFU/ml. The bacterium was identified by the RapID™ REMEL ONE identification system (Thermo Fisher Scientific). Antimicrobial susceptibility testing revealed susceptibility to antibiotics such as, Ceftazidime, Ciprofloxacin, Norfloxacin, Levofloxacin and Imipenem.The patient received treatment with Levofloxacin. Burkholderia cepacia infections outside the respiratory system are rare. Moreover, recurrent UTIs with B. cepacia is a rare finding, which highlights the importance of our study. UTIs with B. cepacia have been associated with bladder irrigation or use of contaminated hospital objects and liquids. B. cepacia is one of the most antimicrobial-resistant organisms and treatment options are limited. The patient was treated with Levofloxacin (3rd generation fluoroquinolone — Tavanic) 500 mg daily per os for 2 weeks, due to his history.