The Laboratory of Metagenomic Research began its work in 2022.

Staff:

Dmitry E. Polev – Head of the Group, Senior Researcher, Ph.D.

polev@pasteurorg.ru

Alina T. Saitova – Junior Researcher

saitova@pasteurorg.ru

Mikhail V. Bezruchko – Junior Researcher

bezruchko@pasteurorg.ru

Sofya E. Platova – Junior Researcher

seplatova@pasteurorg.ru

Ivan A. Gorokhov – Research Assistant

gorohov@pasteurorg.ru

The Laboratory of Metagenomic Research (LMR) was established in March 2025 on the basis of the Metagenomic Research Group, which was formed in 2022 within the Department of Epidemiology. The Laboratory is tasked with implementing modern molecular genetics methods into the Institute's practice. Primarily, this refers to whole-genome sequencing methods and the bioinformatic processing of the obtained data. The group's main partners are the microbiological and molecular genetic laboratories of the Institute, with whom the group works in close cooperation, but certain studies are conducted in collaboration with external scientific organizations.

The main research focus of the laboratory is the sequencing and analysis of bacterial strain genomes from the collections of the Institute's laboratories, conducted within the framework of the federal project "Sanitary Shield – Health Security (Prevention, Detection, Response)" to create a national electronic catalog of microorganisms and biotoxins. In addition, LMR participates in epidemiological investigations of infectious disease outbreaks and in research on bacterial strains of scientific interest.

Selected Publications:

Starkova, D.; Egorova, S.; Suzhaeva, L.; Nguyen, T.Q.; Kaftyreva, L.; Makarova, M.; Zhamborova, S.; Polev, D.; Saitova, A.; Nguyen, V.H.; et al. Antimicrobial Resistance and Phylogenetic Analysis of Multidrug-Resistant Non-Typhoidal Salmonella Isolates from Different Sources in Southern Vietnam. Antibiotics 2025, 14, 489. https://doi.org/10.3390/antibiotics14050489

Starkova D.A., Gladyshev N.S., Polev D.E., Saitova A.T., Glazunova K.A., Egorova S.A., Sarval A.V. Determinants of levofloxacin and metronidazole resistance in Russian clinical isolates of Helicobacter pylori based on whole-genome sequencing // Journal of Microbiology, Epidemiology and Immunobiology. - 2025. - Vol. 102. - No. 4. - P. 465-473. doi: 10.36233/0372-9311-710

Rachina S., Shchendrygina A., de Silva H. Radeesha, Tarasenko S., Mukhina N., Komarova I., Fedina L., Burmistrova E., Martens E., Sidorenko S., Gostev V., Polev D., Saitova A., Kraeva L., Goncharov N., Zvetkova I. A rare case of cardiac and ophthalmic manifestations of meningococcal septicemia // World Journal of Emergency Medicine. - 2024. - Vol. 4, Iss. 15. - pp. 328-330.

Samoilova A.A., Kraeva L.A., Mikhailov N.V., Saitova A.T., Polev D.E. Genomic analysis of virulence and antibiotic resistance of Klebsiella pneumoniae strains // Infection and Immunity. - 2024. - Vol. 14, No. 2. - pp. 339-350.

Dolgova A.S., Kapitonova M.A., Shabalina A.V., Saitova A.T., Polev D.E., Makarova M.A., Kaftyreva L.A., Dedkov V.G. Identification of Salmonella Enterica Serovar Typhi DNA by loop-mediated isothermal amplification with fluorescent detection // Infection and Immunity. - 2024. - Vol. 14, No. 1. - pp. 66-76. doi: 10.15789/2220-7619-IOS-17545.

Repkin, E.A., E.R. Gafarova, M.A. Varfolomeeva, D.S. Kurjachii, D.E. Polev, A.L. Shavarda, G.P. Maslakov, R.I. Mullakhmetov, E.V. Zubova, T.B. Bariev, A.I. Granovitch & A.L. Maltseva Littorina snails and Microphallus trematodes: Diverse consequences of the trematode-induced metabolic shifts. Parasitol Res 123, 229 (2024). https://doi.org/10.1007/s00436-024-08244-8

Kaftyreva L.A., Makarova M.A., Matveeva Z.N., Polev D.E., Saitova A.T., Zhamborova M.Kh., Smirnova M.V., Meltser A.A., Kondratyeva Z.G., Dedkov V.G. First findings of monophasic Salmonella Typhimurium in Saint Petersburg // Problems of Medical Mycology. - 2023. - Vol. 25, No. 3. - pp. 3-9. https://doi.org/10.24412/1999-6780-2023-3-3-9

Gostev V, Sabinova K, Sopova J, Kalinogorskaya O, Sulian O, Chulkova P, Velizhanina M, Pavlova P, Danilov L, Kraeva L, Polev D, Martens E, Sidorenko S. Phenotypic and genomic characteristics of oxacillin-susceptible mecA-positive Staphylococcus aureus, rapid selection of high-level resistance to beta-lactams. Eur J Clin Microbiol Infect Dis. 2023 Sep;42(9):1125-1133. doi: 10.1007/s10096-023-04646-1. Epub 2023 Jul 29. PMID: 37515660.

Gafarova E., Kuracji D., Sogomonyan K., Gorokhov I., Polev D., Zubova E., Golikova E., Granovitch A., Maltseva A. Gut Bacteriomes and Ecological Niche Divergence: An Example of Two Cryptic Gastropod Species// Biology 2023, 12, 1521. https://doi.org/10.3390/biology12121521

Monographs:

Kaftyreva L.A., Balde R., Makarova M.A., Polev D., Saitova A.T., Gladysheva N.P., Boiro M.Y. Characterization of antimicrobial resistance in Escherichia coli strains isolated from the gut microbiota of residents of the Republic of Guinea // In A.Y. Popov, & V.V. Kutyrev (Eds.), Russia - Africa: Experience of the Russian-Guinean Research Center for Epidemiology and Prevention of Infectious Diseases. - Amirit, 2023. - pp. 193-203.