A5064757806- SARS-CoV-2 and COVID-19 Research
- Animal Virus Infections Studies
- Gut microbiota and health
- Viral gastroenteritis research and epidemiology
- Helicobacter pylori-related gastroenterology studies
- Viral Infections and Vectors
- Clostridium difficile and Clostridium perfringens research
- Bacteriophages and microbial interactions
- Respiratory viral infections research
- Mycobacterium research and diagnosis
- COVID-19 Clinical Research Studies
- vaccines and immunoinformatics approaches
- Plant Virus Research Studies
- Plant Diversity and Evolution
- Leptospirosis research and findings
- SARS-CoV-2 detection and testing
- Bat Biology and Ecology Studies
- Yersinia bacterium, plague, ectoparasites research
- Rabies epidemiology and control
- CRISPR and Genetic Engineering
- Enterobacteriaceae and Cronobacter Research
- Viral Infections and Outbreaks Research
- COVID-19 diagnosis using AI
- Genomics and Phylogenetic Studies
- Vector-borne infectious diseases
InSysBio (Russia)
2022-2024
Saint Petersburg Pasteur Institute
2022-2023
Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
2020-2022
Institute for Systems Biology
2022
Central Research Institute of Epidemiology
2020-2021
State Scientific Center of the Russian Federation - Federal Medical Biophysical Center named after A.I. Burnazyan
2021
Federal Medical-Biological Agency
2018-2019
Federal Research and Clinical Center of Physical-Chemical Medicine named after Y.M. Lopukhin
2017-2018
Moscow Institute of Physics and Technology
2017
Microbiome spectra serve as critical clues to elucidate the evolutionary biology pathways, potential pathologies, and even behavioral patterns of host organisms. Furthermore, exotic sources microbiota represent an unexplored niche discover microbial secondary metabolites. However, establishing bacterial functionality is complicated by intricate web interactions inside microbiome. Here we apply ultrahigh-throughput (uHT) microfluidic droplet platform for activity profiling entire oral...
Abstract Background The dual infection with SARS-CoV-2 is poorly described and currently under discussion. We present a study of two strains detected in the same patient during disease presentation. Case presentation A their 90 s was hospitalised fever. Oropharyngeal swab obtained on next day (sample 1) tested positive for SARS-CoV-2. Five days later, transferred to ICU (intensive care unit) hospital specialising treatment COVID-19 patients, where patient's condition progressively worsened...
Being diverse and widely distributed globally, bats are a known reservoir of series emerging zoonotic viruses. We studied fecal viromes twenty-six captured in 2015 the Moscow Region found 13 26 (50%) samples to be coronavirus positive. Of P. nathusii (the Nathusius' pipistrelle), 3 6 were carriers novel MERS-related betacoronavirus. sequenced assembled complete genome this betacoronavirus named it MOW-BatCoV strain 15-22. Whole phylogenetic analysis suggests that MOW-BatCoV/15-22 falls into...
Human gut microbiome plays an important role both in health and disease. Use of antibiotics can alter microbiota composition, which leads to various deleterious events. Here we report a whole genome sequencing metagenomic/genomic study the intestinal changes caused by Helicobacter pylori (HP) eradication therapy. The analyzed dataset included 80 metagenomes from 40 patients before after HP obtained SOLiD 5500W technology, 10 ones 4 Illumina HiSeq 2500 19 genomes Enterococcus spp. recovered...
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...
Amaryllidaceae is a large family with more than 1,600 species, belonging to 75 genera. The largest genus— Allium —is vast, comprising about thousand species. species (as well as other members of the ) are widespread and diversified, they adapted wide range habitats from shady forests open like meadows, steppes, deserts. genes present in chloroplast genomes (plastomes) play fundamental roles for photosynthetic plants. Plastome traits could thus be associated geophysical abiotic...
Introduction Bats are considered the natural reservoirs of several viruses including coronaviruses (CoVs), two genera which, alpha- and betacoronaviruses, infect humans. Despite widespread screening bat samples for novel viruses, information on diversity in bats inhabiting Russian territory remains scarce. Here, we analyzed presence alphacoronaviruses (Alpha-CoVs) from European Russia. Methods Fourty three fecal 8 species: P. nathusii, kuhlii, M. brandtii, daubentonii, N. noctula, V....
Members of the jingmenviruses group have been found in arthropods and mammals on all continents except Australia Antarctica. Two viruses this were isolated from patients with fever after a tick bite. Using nested RT-PCR assay targeting jingmenvirus polymerase gene fragment, we screened ticks collected seven regions Russia that abundant jingmenvirus-positive Ixodes ricinus species, prevalence ranging 19.8% to 34.3%. In cases, DNase/RNase treatment suggested detected molecule was DNA...
Bats are natural hosts for a wide variety of viruses and could therefore be the reservoir, source spillover several mammalian viruses, including adenoviruses. We examined faecal samples from 12 bats (five species family Vespertilionidae) central Russia (Moscow Region) found that two them (16%) were positive mastadenoviruses. One identified was isolated faeces Nyctalis noctule named BatAdV/MOW15-Nn19. The genome BatAdV/MOW15-Nn19 37,915 bp in length. Comparative studies have shown significant...
Antibiotic therapy can lead to the disruption of gut microbiota community with possible negative outcomes for human health. One diseases which treatment scheme commonly included antibiotic intake is Helicobacter pylori infection. The changes in taxonomic and functional composition patients be assessed using "shotgun" metagenomic sequencing. Ten stool samples were collected from 4 infection before directly after H. eradication course. Additionally, two subjects, 1 month end treatment. subject...
Abstract The majority of emerging infectious diseases are caused by pathogens with zoonotic origin, and most these emerged from wildlife reservoirs. Bats diverse, widely distributed globally, the known or hypothesized reservoir a series viruses. Analyses bat viromes have been used to identify novel viruses potential cause human infection. We characterized fecal virome 26 samples collected six species captured during 2015 in Moscow Region. Of 13/26 (50%) were found be coronavirus positive....
Summary Background The effect of SARS-CoV-2 mutations and viral load on the severity COVID-19 is not well understood. possibility reinfection with has already been reported, but dual infection poorly described currently under discussion. We describe a study two strains detected in same patient during disease presentation. Methods Two nasopharyngeal swabs were obtained eight days apart from their 90s, diagnosed lobar pneumonia (J18.1). Both tests positive for high (Ct = 13). have performed...
Abstract The microbiota of the respiratory tract remains a relatively poorly studied subject. At same time, like intestinal microbiota, it is involved in modulating immune response to infectious agents host organism. A causal relationship between composition and likelihood development severity COVID-19 may be hypothesized. We analyze biomaterial from nasopharyngeal smears 336 patients with confirmed diagnosis COVID-19, selected during first second waves epidemic Russia. Sequences similar...
The aim of the work was to study interaction Yersinia pestis with soil nematodes isolated on territory Gorno-Altai high-mountain plague focus. Materials and methods . We used fluorescent Y. strain KM2083, a derivative natural 4.ANT phylogenetic line, antique biovar main subspecies, nematode culture in same area taxonomy determined by region 18S rRNA gene; analysis performed using Maximum Likelihood method based Tamura-Nei model Mega 7.0 software. KM2083 studied during cultivation solid NGM...
ABSTRACT Here we provide technical data for amplifying the complete genome of SARS-CoV-2 from clinical samples using only seventeen pairs primers. We demonstrate that СV2000bp primer panel successfully produces genomes when used with residual total RNA extracts positive following diagnostic RT-PCRs (with Ct in range 13 to 20). The library preparation method reported here includes amplification ~1750-2000 bp fragments followed by ultrasonic fragmentation combined introduction Illumina...
Abstract Background Delta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution led to emergence multiple sublineages, many which are well-mixed between countries. Aim Here, we aim study and spread in Russia. Methods We use a phylogeographic approach infer imports sublineages into Russia, phylodynamic models assess rate their spread. Results show that nearly entire epidemic Russia probably descended from...
Bats are natural hosts of a wide variety viruses, including adenoviruses. European bats known to carry mastadenoviruses categorized as species B (widespread in Vespertilionidae bats) and whose taxonomy has not been clarified. We examined fecal samples from (five species) captured central Russia found that 2/12 (16%) were positive for mastadenoviruses. The partial genome the mastadenovirus was assembled
The abundance of Enterococci in the human intestinal microbiota environment is usually < 0.1% total bacterial fraction. multiple resistance to antibiotics opportunistic Enterococcus spp. alarming for world medical community because their high prevalence among clinically significant strains microorganisms. are able collect different mobile genetic elements and transmit wide range Gram-positive Gram-negative species microorganisms, including transmission vancomycin methicillin-resistant...
This article describes a lethal case of leptospirosis that occurred in Southern Russia. The Leptospira strain was isolated and characterized using microscopic agglutination test, MALDI-TOF mass spectrometry, targeted PCR, high-throughput sequencing. We show molecular mass-spectrometry methods can be an alternative to conventional diagnostics study, which require highly qualified staff performed only at specialized laboratories. also report the first whole genome L. interrogans
Currently, a lot of attention is given to SARS-CoV-2 subpopulations and their coexistence with different genomic variants within the same patient. In this study, we performed next-generation whole-genome sequencing assembly viruses from samples representing swabs or autopsy specimens obtained patients diagnosed СOVID-19, which were initially confirmed by real-time polymerase chain reaction (Ct = 10.4–19.8). Samples prepared for using SCV-2000bp protocol. The data checked presence more than...
Abstract The human gut microbiome plays an important role both in health and disease. use of antibiotics can alter microbiota composition, which cause complications various kinds. Here we report a whole genome sequencing metagenomic study the intestinal changes caused by Helicobacter pylori eradication therapy. We have found decrease taxonomic alpha-diversity due to observed were more extensive for patients with duodenal ulcer female ones. As well across under therapy detected shifts...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for over two years of the COVID-19 pandemic and a global health emergency. Genomic surveillance plays key role in overcoming ongoing despite its relative successive waves continuous emergence new variants. Many technological approaches are currently applied whole genome sequencing (WGS) SARS-CoV-2. They differ stages process, they feature some differences genomic coverage, depth, accuracy variant-calling...