Laboratory for innovative methods of microbiological monitoring

Main tasks:

 The main tasks of the laboratory are related to the implementation of fundamental and applied research aimed at the studying of the processes of formation and distribution of epidemiologically relevant strains of opportunistic and pathogenic bacteria. Currently, the laboratory team is performing these studies within the framework of the scientific project of the National Center for Personalized Medicine ‘Development of approaches of monitoring the formation of epidemic strains of pathogens of multidrug-resistant nosocomial infections in the context of the COVID-19 pandemic and in the post-epidemic period’.

Areas of work

  • development and improvement of technologies for microbiological monitoring of the spread of epidemic clones of pathogens of infectious diseases
  • studying of the fundamental patterns of the formation of a ‘hospital genotype’ for pathogens of infections associated with the provision of medical care
  • development of new technologies for the early detection of strains of pathogens of bacterial infections with multidrug resistance

Project description

The main goal of the project ‘Development of approaches to monitoring the formation of epidemic strains of pathogens of nosocomial infections with multidrug resistance in the context of the COVID-19 pandemic and in the post-epidemic period’ is to develop a set of methods aimed at a rapid identification of epidemic clones of multiantibiotic-resistant HCAI pathogens and predicting the consequences of their spread.

The project involves the creation of a system for the early detection of adverse epidemiological events, including the formation and spread of strains of HCAI pathogens with multidrug resistance. The implementation of this project in the future will increase the efficiency and speed of anti-epidemic measures aimed at curbing antibiotic resistance, and, due to this, reduce the incidence and mortality from infections associated with the provision of medical care, significantly reduce the economic costs of medical organizations associated with the purchase of antimicrobial drugs .

Head of the laboratory – Doctor of Medical Sciences, Associate Professor Goncharov Artemy Evgenievich

Scientific staff of the laboratory

Azarov Daniil Valerievich – researcher

Kuleshevich Evgenia Vladimirovna – researcher

Lebedeva Ekaterina Andreevna – Researcher

Mokhov Aleksey Sergeevich – Researcher

Tkachev Pavel Vladimirovich – junior researcher

Developed and implemented technologies (description)

The laboratory team works on the development of a technology for early detection of the formation of hospital strains in medical institutions of a stationary type based on the use of high-throughput sequencing methods.

Main publications of the laboratories scientific staff

  • Sidorenko, S., Zakharenko, S., Lobzin, Y., Zhdanov, K., Martens, E., Gostev, V., … & Goldstein, A. (2019). Observational study of nasopharyngeal carriage of Neisseria meningitidis in applicants to a military academy in the Russian Federation. International Journal of Infectious Diseases, 81, 12-16. (Q1)
  • Pchelin, I.M., Azarov, D.V., Churina, M.A., Taraskina, A.E., Vasilyeva, N.V. Whole genome sequence of first Candida auris strain, isolated in Russia. Medical Mycology, 2020, 58(3), pp. 414-416 (Q1)
  • Shchepin, O. N., Schnittler, M., Erastova, D. A., Prikhodko, I. S., Dahl, M. B., Azarov, D. V., … & Novozhilov, Y. K. (2019). Community of dark-spored myxomycetes in ground litter and soil of taiga forest (Nizhne-Svirskiy Reserve, Russia) revealed by DNA metabarcoding. Fungal ecology, 39, 80-93. (Q1)
  • Pchelin, I. M., Azarov, D. V., Churina, M. A., Scherbak, S. G., Apalko, S. V., Vasilyeva, N. V., & Taraskina, A. E. (2019). Species boundaries in the Trichophyton mentagrophytes/T. interdigitale species complex. Medical mycology, 57(6), 781-789. (Q1)
  • Pchelin, I.M., Mochalov, Y.V., Azarov, D.V., Vasilyeva, N.V., Taraskina, A.E Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism. Mycoses, 2020 (Q1)
  • Pchelin, I. M., Azarov, D. V., Chilina, G. A., Dmitriev, K. A., Vasilyeva, N. V., & Taraskina, A. E. (2018). Single-nucleotide polymorphism in a local population of Trichophyton rubrum. Medical Mycology, 56(1), 125-128. (Q1)
  • Gupalova, T., Leontieva, G., Kramskaya, T., Grabovskaya, K., Kuleshevich, E., & Suvorov, A. (2019). Development of experimental pneumococcal vaccine for mucosal immunization. PloS one, 14(6), e0218679. (Q1)
  • Popova, A. V., Lavysh, D. G., Klimuk, E. I., Edelstein, M. V., Bogun, A. G., Shneider, M. M., … & Severinov, K. V. (2017). Novel Fri1-like Viruses Infecting Acinetobacter baumannii—vB_AbaP_AS11 and vB_AbaP_AS12—Characterization, Comparative Genomic Analysis, and Host-Recognition Strategy. Viruses, 9(7), 188. (Q1)
  • Grigoriev S.E., Savvinov G.N., Novgorodov G.P., Cheprasov M.Y., Fedorov S.E., Ivanov E.V., Tikhonov A.N., Fisher D.C., Shirley E.A., Rountrey A.N., Obadă T.,Garmaeva D.K., Egorova V.E., Petrova P.P., Egorova E.E., Akhremenko Y.A.,Vasilev S.E., Goncharov A.E., Masharskiy A., van der Plicht J. et al. A woolly mammoth (Mammuthus primigenius) carcass from Maly Lyakhovsky island (New Siberian islands, Russian Federation). Quaternary International. 2017. Т. 427. P. 89-103 (Q1).
  • Kuleshevich, E., Ferretti, J., Sanches, I. S., Balasubramanian, N., Spellerberg, B., Efstratiou, A., … & Shevchenko, V. (2017). Clinical strains of Streptococcus agalactiae carry two different variants of pathogenicity island XII. Folia microbiologica, 62(5), 393-399.(Q2)
  • Azarov, D., Goncharov, A., Karaseva, A., Brodina, T., Lebedeva, E., Taranenko, I., … & Zueva, L. (2017). Draft genome sequence of a multidrug-resistant nosocomial Serratia marcescens strain that persisted in a hospital in Kemerovo, Russian Federation. Genome announcements, 5(10).
  • Panin, A. L., Sboichakov, V. B., Belov, A. B., Kraeva, L. A., Vlasov, D. Y., &Goncharov, A. E. (2016). Natural and technogenic focality of infectious diseases in Antarctic settlements. Biology Bulletin Reviews, 6(4), 320-332.
  • Goncharov, A. E., Krylenkov, V. A., Kolodzhieva, V. V., Khoroshilov, V. Y.,Kraeva, L. A., & Gorbunov, G. A. (2018). Whole-genome sequencing as a tool for comprehensive assessment of the pathogenic potential of ancient arctic microbiomes. Инфекция и иммунитет, 8(4), 512-513. doi: 10.15789/2220-7619-2018-4-2.5  https :// www. iimmun. ru / iimm / article / viewFile /865/472
  • Крыленков В.А. Микробиота земной криосферы. /Крыленков В.А. Гончаров А.Е..- СПб.: Фолиант, 2019. – 448 с.

Patents and inventions

Suvorov A.N., Gupalova T.V., Kuleshevich E.V., Leontieva G.F., Kramskaya T.A., Zolotareva A.D. Live vaccine based on the probiotic strain Enterococcus faecium l3 for the prevention of infection caused by streptococcus pneumoniae. Patent for invention RU 2701733 C1, 01.10.2019. Application No. 2018144657 dated 12/14/2018.