Vol 100, No 6 (2023)

Introduction. Carbapenemase-producing Klebsiella pneumoniae (CP-Kp), which are international high-risk clones, have become a problem of utmost importance. CP-Kps, adapting to the hospital environment, evolve into convergent pathotypes. Such variants combine traits of two genetic lineages: multidrug resistant (MDR) and hypervirulent. The pathotypes, along with MDR K. pneumoniae, pose an exceptional threat to young patients during systemic infection.

The objective of this study is the detailed molecular genetic analysis of MDR isolates of K. pneumoniae detected during the monitoring of resistant Gram-negative bacteria at the National Medical Research Center for Children’s Health in 2014–2021.

Materials and methods. Whole-genome sequencing with a subsequent bioinformatics analysis of eight MDR isolates from the bloodstream and cerebrospinal fluid.

Results. MDR isolates belonged to 4 sublineages (SL): SL307, SL395, SL29 and SL1198. In the genomes of 6 pangrug-resistant (PDR) isolates, genes associated with resistance to all categories of antibiotics recommended for Enterobacteriaceae therapy were identified. Plasmids were present in all genomes. In 6 isolates, plasmids contained heavy metal ion resistance operons in addition to antibiotic resistance genes. Prophages within the plasmids were also involved in the transfer of resistance genes. The ST395 isolate from the cerebrospinal fluid belonged to the convergent pathotype in terms of resistance and virulence. Comparison of genomes within SLs revealed recombination events in the K- and O-locus regions and the Yersiniabactin operon.

Conclusion. Thus, in a sample of resistant K. pneumoniae isolated from bloodstream and cerebrospinal fluid, 6 PDR isolates were detected, one of which belongs to the convergent pathotype ST395.

Introduction. Diarrheal syndrome is the most characteristic symptom of HIV infection, which occurs in 70% of patients and is often fatal. The severity of diarrheal syndrome, irrespective of immune status, is usually determined by specific microorganisms colonising the gastrointestinal tract.

The objective of this study is to assess the prevalence of classical pathogens of acute intestinal infections in diarrheal syndrome in HIV-infected residents of the Chechen Republic (Grozny).

Materials and methods. Stool samples (n = 191) of HIV-infected patients with a history of diarrheal syndrome were studied by real-time PCR with two kits of reagents: "AmpliSens OKI screen-FL" for the detection of DNA/RNA of Shigella spp./EIEC, Salmonella spp., Campylobacter spp., Adenovirus, Rotavirus, Norovirus and Astrovirus; "AmpliSens Escherichiosis-FL" for the detection of diarrheagenic E. coli (DEC) DNA of five pathogroups: EPEC, EHEC, ETEC, EIEC, EAgEC.

Results. Genetic markers of the acute intestinal infection pathogens were detected in 20.9% of the examined individuals. In patients aged 0–7 years and 18–24 years, DNA/RNA of the tested pathogens were not detected. DNA of bacterial pathogens accounted for 93.9%, RNA of viral pathogens — 6.1%. The etiological structure of bacterial infections was represented by a significant predominance of DEC (84.8%) compared to 10.9% of Campylobacter spp. and 4.4% of Salmonella spp. The structure of viral infections included 66.7% Rotavirus and 33.3% Norovirus. Genetic markers of Adenovirus and Astrovirus have not been identified. In 77.5% of HIV-infected patients, diarrheal syndrome was caused by one pathogen (mono-infection), but in nine examined patients (22.5%) it had a combined etiology.

Conclusion. The etiology of acute intestinal infections in HIV-infected patients of the Chechen Republic includes bacterial and viral pathogens, in every fifth the cause of diarrheal disease was DEC. Due to diarrhea in HIV-infected people being a polyetiological disease, it is necessary to introduce a comprehensive, fast, reliable, and affordable method for identifying a wide range of pathogens that cause secondary infections.

Introduction. H7 subtype avian influenza viruses causing severe epizootics among birds are phylogenetically different in the Eastern and Western hemispheres. Numerous human infections caused by these viruses in the Eastern hemisphere indicate that H7 viruses can overcome the interspecies barrier and pose a potential threat of a new pandemic.The H7N2 viruses with deletion of amino acids 221–228 (H3 numbering) in hemagglutinin (HA) had been circulating among poultry in the Western Hemisphere during 1996–2006, and had once again been detected in 2016 in an animal shelter, where they caused cat diseases.

The objective of this study is to elucidate the mechanism of adaptation to mammals of North American H7N2 influenza viruses with deletion in HA.

Materials and methods. The A/chicken/New Jersey/294598-12/2004 (H7N2) virus was adapted to mice by the lung passages. Complete genomes of original and mouse-adapted viruses were analyzed. The receptor specificity and thermostability of viruses, HA activation pH and virulence for mice were determined.

Results. The non-pathogenic H7N2 avian influenza virus became pathogenic after 10 passages in mice. Amino acid substitutions occurred in five viral proteins: one in PB2 (E627K), NA (K127N), NEP (E14Q), four in HA and six in NS1. Mutations in HA slightly changed receptor specificity but increased the pH of HA activation by 0.4 units. The NS1 protein undergone the greatest changes in the positions (N73T, S114G, K118R, G171A, F214L and G224R), where amino acid polymorphisms were observed in the original virus, but only minor amino acid variants have been preserved in the mouse adapted variant.

Conclusion. The results show that H7N2 viruses have the potential to adapt to mammals. The increase in virulence is most likely due to the adaptive E627K mutation in PB2 and possibly in HA.

Background. The ongoing cholera pandemic determines the relevance of the development and improvement of methods for analysis of data on genome-wide sequencing of the cholera pathogen. This is of particular importance in the light of the challenges of import substitution of foreign products, including software.

The aim of the study was to develop a methodology for molecular genetic monitoring for the cholera causative agent using online geographic information system (GIS) and analysis with its help of strains isolated in Russia earlier.

Materials and methods. Data from genome-wide sequencing of 2598 toxigenic (ctxAB⁺tcpA⁺) strains of V. cholerae O1 El Tor, both obtained by the authors on the MiSeq (Illumina) platform, and retrieved from the NCBI database were used in the study. The SNP analysis software was developed in the Java and Python programming languages. Cytoscape program was used to visualize the dendrogram. The development of online GIS was carried out using the programming languages HTML, JavaScript and PHP. The freely distributed Leaflet library written in JavaScript was used as the core. Maps obtained from the OpenStreetMap community were used as cartographic data.

Results and discussion. A universal set of SNPs and software have been developed to analyze the data of genome-wide sequencing of cholera vibrio strains. It was shown that the majority of strains were distributed among several large clusters. The most closely related strains for cholera vibrions isolated in Russia since 2001 have been identified. An online GIS "Molecular genetic monitoring for V. cholerae" has been created, which allows the recognition of closely related strains directly on an electronic map.

Introduction. Periodontal diseases are a common pathology with chronic periodontitis (CP) being the most severe form. This polymicrobial disease has become a problem of great importance in recent years due to the possibility of development of systemic effects associated with this condition. CP is often combined with type 2 diabetes (T2D). The main cause of the occurrence and development of periodontal pathology is played by the bacteria Filifactor alocis, the least studied and most recently discovered periodontal pathogen.

The objective of this study was to identify bacteria of genus Filifactor as part of the periodontal microbiome associated with CP and T2D and to clarify the mechanisms of their possible influence on associated metabolic processes according to comparative metagenomic analysis.

Materials and methods. A metagenomic study of the microbiome of periodontal pocket samples from 28 patients with CP associated with T2D and 22 patients with CP, as well as the microbiome of dental gingival sulcus samples from 19 clinically healthy individuals was performed. 16S-sequencing of the ribosomal RNA gene was used to determine the taxonomic composition of the microbiome. Prediction of metabolic pathways involving the microbiome was performed with the help of the shotgun method.

Results. Filifactor bacteria were the one of the most frequent microorganisms only in patients with CP associated with T2D. The rate of identification of these bacteria was correlated with low predicted metagenomic levels of fatty acid biosynthesis and pyrimidine metabolism in the affected area.

Conclusion. The detection frequency of Filifactor bacteria in patients associated with CP and T2D is negatively correlated with the selected features of putative metabolic pathways of the microbiome, which include fatty acid biosynthesis and pyrimidine metabolism.

Nowadays, an estimated more than 300 million people live with hepatitis B virus (HBV) infection globally. One of the main goals of the World Health Organization (WHO) is to eliminate viral hepatitis by the year 2030. The study of the pathogenic and immunologic properties of HBV, as well as therapeutic substances and treatment regimens, is significantly complicated by the insufficient number of susceptible biological test subjects (animal models) and the lack of zoonotic reservoirs of the virus. In this regard, researching the properties of HBV and related hepadnaviruses provides invaluable material for understanding the biology of the pathogen and the developing methods of prevention and control of this chronic infectious disease, leading to severe hepatopathies (cirrhosis and hepatocellular carcinoma).

Furthermore, prolonged HBV viremia leads to depletion of the immune system, reducing resistance against pathogens of other infections, especially those with a chronic course and socially determined spread.

The aim of this research is to evaluate existing animal models of HBV infection in the context of pathogenesis, immunologic and pathomorphological features. For the first time, the hypothesis of the possible use of certain models for the research of HBV-associated socially significant infections is considered from the point of view of the development of pathomorphological features.

To complete this review, we analyzed the information about the features of HBV infection models in vivo, published over the last 25 years in open sources (Web of Science, PubMed, Scopus, ScienceDirect, Springer). The main criteria for literature selection were the type of infecting agent, the observed immunologic features of the course of the infectious process and the availability of a description of the pathomorphological features in model organisms.