Klebsiella grimontii is an emerging pathogen associated with multidrug resistance. Although a single recent study reported phages against K. grimontii, their taxonomic diversity and structural characterisation remained limited. Here, we describe the isolation and characterisation of five novel lytic bacteriophages that specifically target K. grimontii strain K15g, originally isolated from a rotting iris rhizome. Phages Silvester, Lyra, Lyris, Mirion, and Helios were isolated from wastewater samples collected in the Moscow region and represent three distinct morphotypes: podovirus (Silvester), siphovirus (Lyra, Lyris, Mirion), and myovirus (Helios). Whole-genome sequencing revealed that Silvester belongs to the genus Przondovirus (family Autographiviridae); Lyra, Lyris, and Mirion are members of the genus Sugarlandvirus (family Demerecviridae); and Helios falls within the genus Slopekvirus (family Straboviridae). All five phages lack genes associated with lysogeny, virulence factors, or antibiotic resistance, indicating their suitability for therapeutic applications. Structural modelling of the receptor-binding proteins revealed diverse architectures of adsorption apparatuses, including a two-depolymerase complex in Silvester, T5-like tail fibres in the Sugarlandvirus phages, and a set of long and short fibres with a structured cell-puncturing device in Helios. This study presents five novel phages active against Klebsiella grimontii and provides a basis for further evaluation of their potential in phage therapy.

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical public health threat because infections caused by this pathogen are associated with high morbidity, mortality, and limited effective therapeutic options. Whilst the majority of studies have concentrated on inter-patient bacterial transmission, within-host genomic analysis offers unprecedented resolution for tracking dynamic clone predominance, plasmid rearrangements, and microevolution under clinical selection pressures. Methods and Results: Whole-genome sequencing (WGS) of nine isolates recovered from oral and rectal swabs revealed an exceptional case of CRKP clonal turnover in an intensive care unit (ICU) patient. Three distinct high-risk clones were identified during the 18 days of surveillance: an initial ST101 (Clonal Group (CG) 101) strain (days 1-7) followed by concurrent colonization with ST395 (carrying blaNDM-5) and ST512 lineages (both CG258, days 11-18). Conclusions: This study describes a rare instance of within-host heterogeneity of CRKP, involving three distinct STs spanning two CGs. Whole-genome analysis revealed potential structural rearrangements of resistance- and virulence-associated plasmids between coexisting lineages. These genomic shifts likely reflect rapid adaptation under the intense selective pressure of broad-spectrum antibiotic therapy, culminating in the persistence of a less virulent yet multidrug-resistant ST512 clone and a favorable clinical outcome with patient recovery.

The blaOXA-1 gene encodes an oxacillin-hydrolyzing beta-lactamase of extended-spectrum beta-lactamase (ESBL)-producing microorganisms. The blaOXA-1 gene is found in the resistomes of some Enterobacteriaceae, Morganellaceae, Pasteurellaceae, Moraxellaceae, Aeromonadaceae, Pseudomonadaceae, Yersiniaceae, and Vibrionaceae. Most ESBL detection methods, including those to detect OXA-1-producing microorganisms, are time-consuming, and require specialized equipment and qualified personnel. Here, we report a new CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats)/Cas12a-based detection assay coupled with polymerase chain reaction (PCR) to sensitively detect OXA-1-bearing microorganisms. The PCR-coupled CRISPR/Cas12a-based fluorescence assay includes (i) a pre-amplification step and (ii) a nucleic acid detection step. The pre-amplification step is based on a commonly used PCR, and the detection step is based on the CRISPR/Cas12a property to nonspecifically hydrolyze single-stranded DNA fluorescent reporter molecules. The pre-amplification step takes 65 min, and the detection step is shortened and takes only 5 min. The developed assay can easily detect single (1.25) copies of the blaOXA-1 gene in a reaction and is efficient not only in the detection of a blaOXA-1 model matrix but also in the detection of blaOXA-1-positive microorganisms. We hope that our assay has the potential to improve the monitoring of OXA-1-producing microorganisms and therefore contribute to mitigating the deadly global threat of antibiotic-resistant microorganisms.

Background: Vancomycin-resistant Enterococcus faecium (VREfm), particularly vanA-positive strains, represents a growing threat in hospital settings worldwide. These bacteria are able to survive under severe environmental conditions, including high temperatures and saline concentrations. High genome plasticity and advanced ability of inheriting antimicrobial resistance determinants defined the success of E. faecium as a hospital pathogen. Methods: This study presents the whole genomic characterization of vanA-positive VREfm isolates, analyzing 10 clinical isolates collected from three tertiary care hospitals in Moscow, Russia. Several typing approaches, including two MLST schemes and cgMLST profiles, were used to elucidate the relationship between the isolates. Phylogenetic analysis placed the isolates in context with global VREfm populations, demonstrating both local clonal expansion and possible international connections. Phenotypic and genomic antimicrobial resistance profiles were obtained, as well as data regarding the repertoire of virulence factors and plasmid content. Results: Whole genome sequencing revealed that all isolates belonged to the clinically significant CC17 lineage, specifically sequence types ST80 and ST552. Notably, two isolates possessed truncated Tn1546-type transposons lacking vanY and vanZ genes, representing a potentially emerging variant of the vanA operon in Russian clinical settings. A plasmid carrying a truncated vanA operon was reconstructed using long-read sequencing. Conclusions: The study highlights the utility of genomic investigation for tracking resistance mechanisms and strain dissemination, providing crucial baseline data for epidemiological surveillance of infections caused by VREfm in Russia. These findings emphasize the need for continued genomic monitoring to understand the evolution and spread of antimicrobial resistance in clinically important enterococcal lineages.

BACKGROUND: The dissemination of antibacterial-resistant microorganisms and resistance genes via food products represents a significant threat to global public health. AIM: The study aimed to conduct epidemiological monitoring of antibiotic-resistant bacteria isolated from food products in the Kyrgyz Republic through the study of their phenotypic and genotypic susceptibility profiles. METHODS: It was a cross-sectional observational study. Microorganism species identification was performed using MALDI-TOF mass spectrometry. Phenotypic susceptibility to 35 antimicrobial agents was assessed by minimum inhibitory concentration testing. Genes conferring resistance to antimicrobial agents were detected by whole-genome sequencing. RESULTS: The study subjects were antibiotic-resistant strains of Staphylococcus aureus (n = 16) and Enterococcus faecalis (n = 36) isolated from ready-to-eat food products in the Kyrgyz Republic between 2020 and 2023. The findings indicate a predominance of antibiotic-resistant strains in dairy and meat products as well as in water. The isolates of each species were found to belong to 3 sequence types: S. aureus (ST5, ST15, ST45); E. faecalis (ST21, ST133, ST179). According to the obtained data, all S. aureus isolates carrying the β-lactam resistance gene blaZ were phenotypically resistant to this class of antibiotics. Despite phenotypic resistance to vancomycin, linezolid, and daptomycin observed in 25% of S. aureus isolates, no genetic markers of resistance to these reserve antibiotics were identified. E. faecalis isolates carrying the tetM gene were phenotypically resistant to tetracycline, with the overall proportion of tetracycline-resistant strains reaching 83.3%. A high proportion of E. faecalis carrying the macrolide resistance gene lsaA, accounting for 31.7%, corresponds to the data on the expected phenotypic resistance of this microorganism. CONCLUSION: The studies conducted in the Kyrgyz Republic confirm the need for monitoring the spread of antimicrobial resistance in pathogens through the food chain.

The infections of bacterial origin represent a significant problem to the public healthcare worldwide both in clinical and community settings. Recent decade was marked by limiting treatment options for bacterial infections due to growing antimicrobial resistance (AMR) acquired and transferred by various bacterial species, especially the ones causing healthcare-associated infections, which has become a dangerous issue noticed by the World Health Organization. Numerous reports shown that the spread of AMR is often driven by several species-specific lineages usually called the ‘global clones of high risk’. Thus, it is essential to track the isolates belonging to such clones and investigate the mechanisms of their pathogenicity and AMR acquisition. Currently, the whole genome-based analysis is more and more often used for these purposes, including the epidemiological surveillance and analysis of mobile elements involved in resistance transfer. However, in spite of the exponential growth of available bacterial genomes, their representation usually lack uniformity and availability of supporting metadata, which creates a bottleneck for such investigations. In this database, we provide the results of a thorough genomic analysis of 61,857 genomes of a highly dangerous bacterial pathogen Klebsiella pneumoniae. Important isolate typing information including multilocus sequence typing (MLST) types (STs), assignment of the isolates to known global clones, capsular (KL) and lipooligosaccharide (O) types, the presence of CRISPR-Cas systems, and cgMLST profiles are given, and the information regarding the presence of AMR, virulence genes and plasmid replicons within the genomes is provided. This database is freely available under CC BY-NC-SA at https://doi.org/10.5281/zenodo.11069018 . The database will facilitate selection of the proper reference isolate sets for any types of genome-based investigations. It will be helpful for investigations in the field of K. pneumoniae genomic epidemiology, as well as antimicrobial resistance analysis and the development of prevention measures against this important pathogen.

1. Introduction: Staphylococcus aureus is a significant infectious agent causing food poisoning. High adaptability and the ability to produce heat-stable enterotoxins make it a dangerous pathogen of public health concern. Monitoring antibiotic resistance and assessing the risk of food contamination by this microorganism are critical to prevent and treat foodborne toxic infections. Objective: To assess phenotypic and genotypic antibiotic resistance of S. aureus strains isolated from food products on the territory of the Republic of Tajikistan. Materials and methods: The study included 50 isolates of S. aureus derived from foods in the Republic of Tajikistan in 2018–2022. Species identification was performed by MALDI-TOF MS. Phenotypic susceptibility to antimicrobial agents was determined by the minimum inhibition concentration method using the Sensititre system. Genetic determinants of resistance and virulence were determined by analyzing data from full-genome sequencing using Illumina NextSeq 2000 system. Results: 44.0 % (22/50) of S. aureus isolates were resistant to at least one antimicrobial drug, of which 34.0 % (17/50) were multidrug resistant. S. aureus with phenotypic and genotypic resistance to beta-lactams were the most common (40.0 %): blaZ resistance genes were detected in 94.0 % (16/17) and mecA in 76.4 % (13/17). The analysis of multilocus sequence typing results revealed 4 different S. aureus sequencing types with ST5 prevailing. A high frequency of virulence genes, including enterotoxins and leukocidins, was also observed. Conclusion: Food contamination with S. aureus poses a significant threat to public health. High antibiotic resistance of the foodborne microorganisms and the presence of multiple virulence genes highlight the need for continuous monitoring and development of strategies to manage the risks associated with the spread of antibiotic resistance through the food chain.

ESKAPE bacteria are a major global threat due to their rapid antibiotic resistance acquisition and severe healthcare-associated infections. Effective countermeasures require epidemiological surveillance and resistance transmission studies, particularly for antimicrobial-resistant (AMR) colonization in intensive care unit (ICU) patients. Whole-genome sequencing (WGS) provides critical information on resistance spread and mechanisms. In the provided protocol, rectal and oropharyngeal swabs, or endotracheal aspirate/bronchoalveolar lavage for intubated patients, are collected at ICU admission and twice weekly. Patient interviews and medical records identify risk factors for resistant microflora. Samples undergo cultivation, species identification, antibiotic susceptibility testing, and DNA extraction. Sequencing is performed using second- and third-generation platforms, with selected isolates subject to hybrid genome assembly. Resistance genes, virulence factors, and typing profiles (MLST, cgMLST) are determined. This protocol characterizes the ICU patient colonization by AMR pathogens, including species distribution, phenotypic and genotypic resistance profiles, clonal structure, and temporal changes. It estimates detection frequency and colonization patterns at each locus, identifies key risk factors, including prior community or inter-facility exposure, and analyzes associations between risk factors and admission colonization. The study aims to estimate AMR infection risk and severity in ICU patients through the comprehensive analysis of colonization dynamics, resistance patterns, and clonal characteristics using WGS data on pathogen composition and AMR trends.

The structure of the K141 type capsular polysaccharide (CPS) produced by Acinetobacter baumannii KZ1106, a clinical isolate recovered from Kazakhstan in 2016, was established by sugar analyses and one- and two-dimensional 1H and 13C NMR spectroscopy. The CPS was shown to consist of branched tetrasaccharide repeating units (K-units) with the following structure: This structure was found to be consistent with the genetic content of the KL141 CPS biosynthesis gene cluster at the chromosomal K locus in the KZ1106 whole genome sequence. Assignment of the encoded enzymes allowed the first sugar of the K unit to be identified, which revealed that the β-d-GlcpNAc-(1→3)-d-GlcpNAc bond is the linkage between K-units formed by the WzyKL141 polymerase.

Foodborne diseases are the serious public health problem. One of the most common food pathogens in the world is Staphylococcus aureus, which is second only to salmonellosis in terms of the frequency of cases. Materials and methods. We studied 146 antimicrobial-resistant S. aureus isolates isolated from ready-to-eat (RTE) food products in the territory of the Republic of Kazakhstan from 2018 to 2019 and from 2021 to 2022. The taxonomic position of the bacteria was identified by MALDI-TOF mass spectrometry. The phenotypic sensitivity of bacteria was determined to 45 antimicrobial drugs by the method of minimum suppressive concentration (MSC) and the disco diffusion method (DDM). Antimicrobial resistance genes in S. aureus multidrug-resistant isolates (MDR) were determined using genome-wide sequencing (WGS). Results. The comprehensive study of the profile of antibiotic sensitivity of S. aureus food isolates was conducted, in which phenotypic sensitivity to antibiotics and the presence of resistance determinants were characterized. As far as we know, this is the first epidemiological study of S. aureus cultures of food origin using WGS in the territory of the Republic of Kazakhstan. The results revealed that the studied S. aureus isolates belong to seven different sequence types based on multilocus sequence typing (MLST), with the predominance of sequence type ST22. The studied isolates may pose a threat to public health, since 33% of S. aureus isolates were resistant to methicillin (MRSA), and the mecA gene associated with a high level of nosocomial MRSA infections was found in 45% of S. aureus isolates. Conclusion. Since food products represent one of the key routes of transmission and distribution of resistance genes, it is necessary to further monitor food products and food raw materials for the presence of antimicrobial-resistant Staphylococcus spp. Key words: Staphylococcus aureus, antimicrobial resistance, WGS

Proteus mirabilis bacteria is a component of normal intestinal microflora of humans and animals, but can also be found in hospital settings causing urinary tract infections and sepsis. The problem of treating such infections is complicated by multidrug-resistant isolates producing extended spectrum beta-lactamases (ESBL), and the number of ESBL-carrying P. mirabilis strains has significantly increased recently. This study presents a detailed analysis of 12 multidrug-resistant P. mirabilis isolates obtained from the wounds of different patients in one surgical department of a multidisciplinary hospital in Moscow, Russia, using the short- and long-read whole genome sequencing. The isolates under investigation divided into two clusters (clones) C1 and C2 based on their genomic profiles and carried antimicrobial resistance (AMR) genes corresponding well with phenotypic profiles, which was the first case of reporting two different P. mirabilis clones obtained simultaneously from the same specimens at one hospital, to the best of our knowledge. Some genes, including ESBL encoding ones, were specific for either C1 or C2 (aac(6')-Ib10, ant(2″)-Ia, qnrA1, bla VEB-6 and fosA3, bla CTX -M-65 , correspondingly). Additionally, the Salmonella genomic islands 1 were found that differed in composition of multiple antibiotic resistance regions between C1 and C2 groups. CRISPR-Cas system type I-E was revealed only in C2 isolates, while the same set of virulence factors was determined for both P. mirabilis clones. Diversity of all genetic factors found in case of simultaneous existence of two clones collected from the same source at one department indicates high pathogenic potential of P. mirabilis and poses a requirement of proper spreading monitoring. The data obtained will facilitate the understanding of AMR transfer and dynamics within clinical P. mirabilis isolates and contribute to epidemiological surveillance of this pathogen.

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.

In recent decades, growing attention has been directed worldwide toward antimicrobial-resistant (AMR) bacterial pathogens causing infections in clinical, environmental, and food chain production settings [...]

Escherichia coli is a commensal and opportunistic bacterium widely distributed around the world in different niches including intestinal of humans and animals, and its extraordinary genome plasticity led to the emergence of pathogenic strains causing a wide range of diseases. E. coli is one of the monitored species in maternity hospitals, being the main etiological agent of urogenital infections, endometriosis, puerperal sepsis, and neonatal diseases. This study presents a comprehensive analysis of E. coli isolates obtained from the maternal birth canal of healthy puerperant women 3–4 days after labor. According to whole genome sequencing data, 31 sequence types and six phylogenetic groups characterized the collection containing 53 isolates. The majority of the isolates belonged to the B2 phylogroup. The data also includes phenotypic and genotypic antibiotic resistance profiles, virulence factors, and plasmid replicons. Phenotypic and genotypic antibiotic resistance testing did not demonstrate extensive drug resistance traits except for two multidrug-resistant E. coli isolates. The pathogenic factors revealed in silico were assessed with respect to CRISPR-element patterns. Multiparametric and correlation analyses were conducted to study the interrelation of different pathoadaptability factors, including antimicrobial resistance and virulence genomic determinants carried by the isolates under investigation. The data presented will serve as a valuable addition to further scientific investigations in the field of bacterial pathoadaptability, especially in studying the role of CRISPR/Cas systems in the E. coli genome plasticity and evolution.

The infections caused by various bacterial pathogens both in clinical and community settings represent a significant threat to public healthcare worldwide. The growing resistance to antimicrobial drugs acquired by bacterial species causing healthcare-associated infections has already become a life-threatening danger noticed by the World Health Organization. Several groups or lineages of bacterial isolates, usually called ‘the clones of high risk’, often drive the spread of resistance within particular species. Thus, it is vitally important to reveal and track the spread of such clones and the mechanisms by which they acquire antibiotic resistance and enhance their survival skills. Currently, the analysis of whole-genome sequences for bacterial isolates of interest is increasingly used for these purposes, including epidemiological surveillance and the development of spread prevention measures. However, the availability and uniformity of the data derived from genomic sequences often represent a bottleneck for such investigations. With this dataset, we present the results of a genomic epidemiology analysis of 17,546 genomes of a dangerous bacterial pathogen, Acinetobacter baumannii. Important typing information, including multilocus sequence typing (MLST)-based sequence types (STs), intrinsic blaOXA-51-like gene variants, capsular (KL) and oligosaccharide (OCL) types, CRISPR-Cas systems, and cgMLST profiles are presented, as well as the assignment of particular isolates to nine known international clones of high risk. The presence of antimicrobial resistance genes within the genomes is also reported. These data will be useful for researchers in the field of A. baumannii genomic epidemiology, resistance analysis, and prevention measure development.

Capsular polysaccharide (CPS) is a heteroglycan that coats the cell surface of most isolates of the important Gram-negative bacterial pathogen, Acinetobacter baumannii. Strain MAR 15-4076, a clinical isolate recovered in Russia in 2015, was found to carry the KL129 sequence at the CPS biosynthesis K locus. The CPS was isolated from the strain and studied by sugar analysis, Smith degradation, one- and two-dimensional 1H and 13C NMR spectroscopy. It was composed of branched pentasaccharide units that include a →3)-α-l-Rhap-(1 → 3)-α-l-Rhap-(1 → 3)-β-d-GlcpNAc-(1→ mainchain and α-d-ManpNAc-(1 → 3)-l-Rhap side branch. Though the pentasaccharide units are identical to those that make up the K84 CPS produced by A. baumannii LUH5540, the units are linked differently via the substitution of an alternate l-Rhap residue, resulting in a difference in the overall topology of the CPS. This was due to the replacement of the Wzy polymerase gene encoded at the K locus.

Environmental bacterial species Raoultella ornithinolytica is an emerging pathogen becoming increasingly important in causing human infections. Thus far, the clinical isolates of this species have not exhibited multidrug resistance very often, but some reports underline the necessity for continuous monitoring of this potentially dangerous pathogen. Currently, epidemiological surveillance and antimicrobial resistance investigations of any bacterial pathogen usually rely on whole genome sequencing, which is becoming more affordable while providing increasingly important data in the recent years. However, R. ornithinolytica genomic information is scantily presented in public databases. Here, we report, to the best of our knowledge, the first whole genome sequence and corresponding raw data for a clinical R. ornithinolytica isolate from Russian Federation, which carried antimicrobial resistance (AMR) genes, virulence factors, one plasmid, and CRISPR-Cas system of type I-F. The data provided will facilitate epidemiological surveillance and antimicrobial resistance monitoring of this emerging pathogen.

The problem of biological safety is extremely relevant today for all countries of the world because of the real and potential threats caused by biological agents that are dangerous to public health and the environment. Modern microorganisms are becoming increasingly aggressive towards humans, as clearly demonstrated by the COVID-19 pandemic, which has affected all aspects of people's lives and exposed the vulnerability of the healthcare system. According to the Decree of the President of the Russian Federation «On the Fundamentals of the State policy of the Russian Federation in the field of chemical and biological safety for the period up to 2025 and beyond» and the Federal Law «On Biological Safety in the Russian Federation», the main objectives of state policy are to reduce the risks of negative effects of biological factors on the population and the environment. Antimicrobial resistance, the emergence of new infections and the overcoming of interspecific barriers by microorganisms are of particular concern. Infectious disease agents with epidemic potential, such as Ebola, Zika, Marburg, Lassa, MERS-CoV and SARS-CoV viruses, continue to pose a high threat. To counteract new biological threats, Russia has created a scientific concept of future biosafety, focusing on the development of genomic epidemiological surveillance, digital transformation and mobile technologies. Effective management of epidemic processes requires constant monitoring of genetic changes in infectious agents and prompt response to new threats, which allows the VGARus platform created in Russia to monitor virus mutations. Thus, genomic epidemiological surveillance is becoming a key element of ensuring biological safety and scientific and technological development in Russia.

The K239 type capsular polysaccharide (CPS) isolated from Acinetobacter baumannii isolate MAR19-4435 was studied by sugar analysis, one- and two-dimensional 1H and 13C NMR spectroscopy. K239 consists of branched heptasaccharide repeats (K-units) comprised of five residues of l-rhamnose (l-Rhap), and one residue each of d-glucuronic acid (d-GlcpA) and N-acetyl-d-glucosamine (d-GlcpNAc). The structure of K239 is closely related to that of the A. baumannii K86 CPS type, though the two differ in the 2,3-substitution patterns on the l-Rhap residue that is involved in the linkage between K-units in the CPS polymer. This structural difference was attributed to the presence of a gtr221 glycosyltransferase gene and a wzyKL239 polymerase gene in KL239 that replaces the gtr80 and wzyKL86 genes in the KL86 CPS biosynthesis gene cluster. Comparison of the two structures established the role of a novel WzyKL239 polymerase encoded by KL239 that forms the β-d-GlcpNAc-(1→2)-l-Rhap linkage between K239 units. A. baumannii MAR19-4435 was found to be non-susceptible to infection by the APK86 bacteriophage, which encodes a depolymerase that specifically cleaves the linkage between K-units in the K86 CPS, indicating that the difference in 2,3-substitution of l-Rhap influences the susceptibility of this isolate to bacteriophage activity.

Relevance . Listeria monocytogenes is a ubiquitous bacterium that causes listeriosis, which represents a widespread infectious disease currently inflicting great damage to livestock production and posing a serious threat to human health. Aim. To analyze the population structure and assess the pathogenic potential of Listeria monocytogenes isolates isolated on the territory of the Russian Federation. Materials and methods. A total of 79 listeria isolates were isolated from food products. Species identification and phenotypic analysis for antibiotic resistance were performed using VITEK MS system (bioMerieux, Marcyl’toile, France). Thirty-five antibiotic-resistant isolates were characterized by analysis of whole-genome sequencing data. Results. Whole genome sequences of thirty-five antibiotic-resistant Listeria monocytogenes isolates of food origin were analyzed. We determined clonal structure of this population and revealed a small number of antibiotic resistance determinants (fosX, tetM и сlpL), extensive set of virulence factors, as well as the presence of CRISPR/Cas systems. Most of the isolates belonged to phylogenetic line II and were divided into nine clonal complexes with the prevalence of CC121, which was one of the epidemiologically significant genetic clones. Two CC2 isolates belonging to the most pathogenic phylogenetic lineage I were also found. Thirteen isolates were characterized by the presence of putative CRISPR/Cas systems of IB and IIA types. All ST 121 isolates contained two types of identified adaptive immunity systems simultaneously in their genomes. Correlation analysis confirmed their functionality. Conclusion. We believe that the whole genome data obtained for the foodborne Listeria monocytogenes isolates will facilitate and complement further epidemiological studies of this pathogen, as well as the investigations of its genome variability in terms of the acquisition of various genetic elements associated with adaptation, antimicrobial resistance, and virulence. Moreover, the results of such studies will help to develop preventive measures to effectively solve problems associated with the bacterial contamination of animal products and ensure food safety in production conditions and the «farm-to-table» chain.