Study of the resistome of human microbial communities using a targeted panel of antibiotic resistance genes in COVID-19 patients
- Authors: Yanushevich O.O.1, Maev I.V.1, Krikheli N.I.1, Levchenko O.V.1, Galeeva J.S.2, Starikova E.V.2, Andreev D.N.1, Sokolov P.S.1, Fomenko A.K.1, Devkota M.K.1, Andreev N.G.1, Zaborovsky A.V.1, Evdokimov V.V.1, Tsaregorodtsev S.V.1, Ilina E.N.2, Govorun V.M.2, Bely P.A.1, Sabelnikova E.A.1,3, Solodov A.A.1, Cheremushkin S.V.1,4, Shaburov R.I.1,4, Kebina A.L.1
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Affiliations:
- Russian University of Medicine
- Research Institute for Systems Biology and Medicine
- Loginov Moscow Clinical Scientific Center
- Central Clinical Hospital «Russian Railways Medicine»
- Issue: Vol 95, No 12 (2023)
- Pages: 1103-1111
- Section: Original articles
- URL: https://journals.rcsi.science/0040-3660/article/view/258737
- DOI: https://doi.org/10.26442/00403660.2023.12.202490
- ID: 258737
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Abstract
Aim. To study overall drug resistance genes (resistome) in the human gut microbiome and the changes in these genes during COVID-19 in-hospital therapy.
Materials and methods. A single-center retrospective cohort study was conducted. Only cases with laboratory-confirmed SARS-CoV-2 RNA using polymerase chain reaction in oro-/nasopharyngeal swab samples were subject to analysis. The patients with a documented history of or current comorbidities of the hepatobiliary system, malignant neoplasms of any localization, systemic and autoimmune diseases, as well as pregnant women were excluded. Feces were collected from all study subjects for subsequent metagenomic sequencing. The final cohort was divided into two groups depending on the disease severity: mild (group 1) and severe (group 2). Within group 2, five subgroups were formed, depending on the use of antibacterial drugs (ABD): group 2A (receiving ABD), group 2AC (receiving ABD before hospitalization), group 2AD (receiving ABD during hospitalization), group 2AE (receiving ABD during and before hospitalization), group 2B (not receiving ABD).
Results. The median number of antibiotic resistance (ABR) genes (cumulative at all time points) was significantly higher in the group of patients treated with ABD: 81.0 (95% CI 73.8–84.5) vs. 51.0 (95% CI 31.1–68.4). In the group of patients treated with ABD (2A), the average number of multidrug resistance genes (efflux systems) was significantly higher than in controls (group 2B): 47.0 (95% CI 46.0–51.2) vs. 21.5 (95% CI 7.0–43.9). Patients with severe coronavirus infection tended to have a higher median number of ABR genes but without statistical significance. Patients in the severe COVID-19 group who did not receive ABD before and during hospitalization also had more resistance genes than the patients in the comparison group.
Conclusion. This study demonstrated that fewer ABR genes were identified in the group with a milder disease than in the group with a more severe disease associated with more ABR genes, with the following five being the most common: SULI, MSRC, ACRE, EFMA, SAT.
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##article.viewOnOriginalSite##About the authors
Oleg O. Yanushevich
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0002-4293-8465
акад. РАН, д-р мед. наук, проф., ректор, зав. каф. пародонтологии
Russian Federation, MoscowIgor V. Maev
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0001-6114-564X
акад. РАН, д-р мед. наук, проф., зав. каф. пропедевтики внутренних болезней и гастроэнтерологии лечебного фак-та
Russian Federation, MoscowNatella I. Krikheli
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0002-8035-0638
д-р мед. наук, проф., зав. каф. клинической стоматологии
Russian Federation, MoscowOleg V. Levchenko
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0003-0857-9398
д-р мед. наук, проф., зав. каф. нейрохирургии и нейрореанимации
Russian Federation, MoscowJulia S. Galeeva
Research Institute for Systems Biology and Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0001-6304-4607
мл. науч. сотр.
Russian Federation, MoscowElizaveta V. Starikova
Research Institute for Systems Biology and Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0001-6582-210X
науч. сотр.
Russian Federation, MoscowDmitry N. Andreev
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0002-4007-7112
канд. мед. наук, доц., доц. каф. пропедевтики внутренних болезней и гастроэнтерологии лечебного фак-та
Russian Federation, MoscowPhilipp S. Sokolov
Russian University of Medicine
Author for correspondence.
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0003-2813-6498
преподаватель каф. фармакологии лечебного фак-та НОИ «Высшая школа клинической медицины им. Н.А. Семашко»
Russian Federation, MoscowAleksei K. Fomenko
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0002-1794-7263
преп. каф. фармакологии лечебного фак-та
Russian Federation, MoscowMikhail K. Devkota
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0002-3736-4196
преп. каф. фармакологии лечебного фак-та
Russian Federation, MoscowNikolai G. Andreev
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0002-5136-0140
канд. мед. наук, доц., доц. каф. пропедевтики внутренних болезней и гастроэнтерологии лечебного фак-та
Russian Federation, MoscowAndrew V. Zaborovsky
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0002-7923-9916
д-р мед. наук, доц., зав. каф. фармакологии лечебного фак-та
Russian Federation, MoscowVladimir V. Evdokimov
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0001-9281-579X
д-р мед. наук, проф. каф. клинической функциональной диагностики
Russian Federation, MoscowSergey V. Tsaregorodtsev
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0002-0254-0516
преп. каф. фармакологии лечебного фак-та
Russian Federation, MoscowElena N. Ilina
Research Institute for Systems Biology and Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0003-0130-5079
чл.-кор. РАН, проф. РАН, д-р биол. наук, гл. науч. сотр.
Russian Federation, MoscowVadim M. Govorun
Research Institute for Systems Biology and Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0003-0837-8764
акад. РАН, д-р биол. наук, проф., дир.
Russian Federation, MoscowPetr A. Bely
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0001-5998-4874
канд. мед. наук, доц. каф. пропедевтики внутренних болезней и гастроэнтерологии лечебного фак-та
Russian Federation, MoscowElena A. Sabelnikova
Russian University of Medicine; Loginov Moscow Clinical Scientific Center
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0001-7519-2041
д-р мед. наук, проф. каф. пропедевтики внутренних болезней и гастроэнтерологии лечебного фак-та ФГБОУ ВО «Российский университет медицины», зам. дир. по научной работе ГБУЗ «МКНЦ им. А.С. Логинова»
Russian Federation, Moscow; MoscowAleksandr A. Solodov
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0002-8263-1433
д-р мед. наук, дир. НОИ «Высшая школа клинической медицины им. Н.А. Семашко»
Russian Federation, MoscowSergei V. Cheremushkin
Russian University of Medicine; Central Clinical Hospital «Russian Railways Medicine»
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0002-0982-2006
канд. мед. наук, доц. каф. пропедевтики внутренних болезней и гастроэнтерологии лечебного фак-та НОИ «Высшая школа клинической медицины им. Н.А. Семашко» ФГБОУ ВО «Российский университет медицины», зам. гл. врача по терапевтической деятельности ЧУЗ «ЦКБ "РЖД-Медицина"»
Russian Federation, Moscow; MoscowRafik I. Shaburov
Russian University of Medicine; Central Clinical Hospital «Russian Railways Medicine»
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0001-9741-0150
канд. мед. наук, доц. каф. пропедевтики внутренних болезней и гастроэнтерологии лечебного фак-та НОИ «Высшая школа клинической медицины им. Н.А. Семашко» ФГБОУ ВО «Российский университет медицины», гл. врач ЧУЗ «ЦКБ "РЖД-Медицина"»
Russian Federation, Moscow; MoscowAnastasia L. Kebina
Russian University of Medicine
Email: phlppsokolov@gmail.com
ORCID iD: 0000-0002-7570-9650
зам. глав. врача НОИ «Высшая школа клинической медицины им. Н.А. Семашко» Университетской клиники, ассистент каф. терапии, клинической фармакологии и скорой медицинской помощи
Russian Federation, MoscowReferences
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