A5042917299- Antibiotic Resistance in Bacteria
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Vibrio bacteria research studies
- Enterobacteriaceae and Cronobacter Research
- Pneumonia and Respiratory Infections
- Plant Pathogenic Bacteria Studies
- Bacterial biofilms and quorum sensing
- Biochemical and Structural Characterization
- Bacterial Identification and Susceptibility Testing
- Antimicrobial Peptides and Activities
- Salmonella and Campylobacter epidemiology
- Microbial infections and disease research
- Plant Virus Research Studies
- Fractal and DNA sequence analysis
- Carbohydrate Chemistry and Synthesis
- CRISPR and Genetic Engineering
- Bacterial Infections and Vaccines
- Machine Learning in Bioinformatics
- Mycobacterium research and diagnosis
- Antimicrobial Resistance in Staphylococcus
- Infections and bacterial resistance
- Bacillus and Francisella bacterial research
- Cancer Genomics and Diagnostics
Central Research Institute of Epidemiology
2018-2025
Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
2020-2024
Vavilov Institute of General Genetics
2014-2020
Pirogov Russian National Research Medical University
2017
Institute of Bioorganic Chemistry
2014
Russian Academy of Sciences
2006-2012
Bioengineering Center
2012
Fox Chase Cancer Center
2003
Fast and accurate side-chain conformation prediction is important for homology modeling, ab initio protein structure prediction, design applications. Many methods have been presented, although only a few computer programs are publicly available. The SCWRL program one such method widely used because of its speed, accuracy, ease use. A new algorithm presented that uses results from graph theory to solve the combinatorial problem encountered in problem. In this method, side chains represented...
Significance The power of adaptive immunity in humans is realized through the hypervariable molecules: T-cell receptors (TCRs). Each those built from genetically encoded parts with addition random nucleotides finally forming individual TCR repertoire. Despite that repertoire potentially can include 10 11 –10 14 different variants, substantially less molecules are found a single individual. particular genetic impact on final set still poorly understood. In this study, for first time to best...
Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well convergent representatives. It known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, 307 drive their global spread. ST395, was first reported in the context of a carbapenemase-associated outbreak France 2010, less well-characterized, yet emerging lineage.
Abstract Emerging high-throughput sequencing methods for the analyses of complex structure TCR and BCR repertoires give a powerful impulse to adaptive immunity studies. However, there are still essential technical obstacles performing truly quantitative analysis. Specifically, it remains challenging obtain comprehensive information on clonal composition small lymphocyte populations, such as Ag-specific, functional, or tissue-resident cell subsets isolated by sorting, microdissection, fine...
Klebsiella pneumoniae is one of the most important pathogens concerned with multidrug resistance in healthcare-associated infections. The treating infections caused by this bacterium complicated due to emergence and rapid spreading carbapenem-resistant strains, which are associated high mortality rates. Recently, several hypervirulent carbapenemase-producing isolates were reported that make situation even more complicated. In order better understand virulence mechanisms, and, turn, develop...
Acinetobacter baumannii is an opportunistic pathogen being one of the most important causative agents a wide range nosocomial infections associated with multidrug resistance and high mortality rate. This study presents multiparametric correlation analyses clinical multidrug-resistant A. isolates using short- long-read whole-genome sequencing, which allowed us to reveal specific characteristics different CRISPR/Cas systems. We also compared antibiotic virulence gene acquisition for groups...
The type of capsular polysaccharide (CPS) on the cell surface Acinetobacter baumannii can determine specificity lytic bacteriophage under consideration for therapeutic use. Here, we report isolation a phage an extensively antibiotic resistant ST2 A. isolate AB5001 that carries KL3 CPS biosynthesis gene cluster predicting K3-type CPS. As did not infect isolates carrying or KL22 and known to produce K3 CPS, structure isolated from was determined. produced variant form, K3-v1, lacks β-d-GlсpNAc...
Acinetobacter baumannii is a critical priority nosocomial pathogen that produces variety of capsular polysaccharides (CPSs), the primary receptors for specific depolymerase-carrying phages. In this study, tailspike depolymerases (TSDs) encoded in genomes six novel Friunaviruses, APK09, APK14, APK16, APK86, APK127v, APK128, and one previously described Friunavirus phage, APK37.1, were characterized. For all TSDs, mechanism cleavage corresponding A. (CPSs) was established. The structures...
Unique molecular identifiers (UMIs) show outstanding performance in targeted high-throughput resequencing, being the most promising approach for accurate identification of rare variants complex DNA samples. This has application multiple areas, including cancer diagnostics, thus demanding dedicated software and algorithms. Here we introduce MAGERI, a computational pipeline that efficiently handles all caveats UMI-based analysis to obtain high-fidelity mutation profiles call ultra-rare...
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 due growing antimicrobial resistance (AMR) acquired transferred various species, especially ones causing healthcare-associated infections, which has become dangerous issue noticed World Health Organization. Numerous reports shown that spread AMR is often driven several species-specific...
Multidrug resistance (MDR) and hypervirulence (hv) have been long considered distinct evolutionary traits for Klebsiella pneumoniae (Kp), a versatile human pathogen. The recent emergence of Kp strains combining these poses serious global threat. In this article, we describe the phenotypic genomic characteristics an MDR hvKp isolate, MAR14-456, representative nosocomial outbreak in Moscow, Russia, that was recovered from postoperative wound patient who later developed multiple abscesses,...
Acinetobacter baumannii is a dangerous bacterial pathogen possessing the ability to persist on various surfaces, especially in clinical settings, and rapidly acquire resistance broad spectrum of antibiotics. Thus, epidemiological surveillance A. within particular hospital, region, across world an important healthcare task that currently usually includes performing whole-genome sequencing (WGS) representative isolates. During past years, dissemination was mainly driven by strains belonging...
The structure of the K141 type capsular polysaccharide (CPS) produced by Acinetobacter baumannii KZ1106, a clinical isolate recovered from Kazakhstan in 2016, was established sugar analyses and one- two-dimensional
1. Introduction: Staphylococcus aureus is a significant infectious agent causing food poisoning. High adaptability and the ability to produce heat-stable enterotoxins make it dangerous pathogen of public health concern. Monitoring antibiotic resistance assessing risk contamination by this microorganism are critical prevent treat foodborne toxic infections. Objective: To assess phenotypic genotypic S. strains isolated from products on territory Republic Tajikistan. Materials methods: The...
Proteus mirabilis is a component of the normal intestinal microflora humans and animals, but can cause urinary tract infections even sepsis in hospital settings. In recent years, number multidrug-resistant P. isolates, including ones producing extended-spectrum β-lactamases (ESBLs), increasing worldwide. However, investigations dedicated to this species, especially, whole-genome sequencing, much lower comparison members ESKAPE pathogens group. This study presents detailed analysis clinical...
Non-typhoidal Salmonella infections remain a significant public health problem worldwide. In this study, we present the first detailed genomic analysis report based on short-read (Illumina) whole-genome sequencing (WGS) of 45 multidrug-resistant (MDR) enterica subsp. serotype Infantis isolates from poultry and meat product samples obtained in Russia during 2018-2020, long-read (MinION) WGS five more representative isolates. We sought to determine whether foodborne S. have acquired new...
Acinetobacter baumannii appears to be one of the most crucial nosocomial pathogens. A possible component antimicrobial therapy for infections caused by extremely drug-resistant A. strains may specific lytic bacteriophages or phage-derived enzymes. In present study, we observe biological features, genomic organization, and phage–host interaction strategy novel virulent bacteriophage Aristophanes isolated on strain having K26 capsular polysaccharide structure. According phylogenetic analysis...
A comprehensive understanding of capsular polysaccharide (CPS) diversity is critical to implementation phage therapy treat panresistant Acinetobacter baumannii infections. Predictions from genome sequences can assist identification the CPS type but be complicated if genes outside K locus (CPS biosynthesis gene cluster) are involved. Here, produced by A. clinical isolate 36-1454 carrying a novel locus, KL127, was determined and compared other CPSs. KL127 differs KL128 in only two...
Whole-genome amplification (WGA) techniques are used for non-specific of low-copy number DNA, and especially single-cell genome transcriptome amplification. There a WGA methods that have been developed over the years. One example is degenerate oligonucleotide-primed PCR (DOP-PCR), which very simple, fast inexpensive technique. Although DOP-PCR has regarded as one pioneering WGA, it only provides low coverage high allele dropout rate when compared to more modern techniques. Here we describe...