Composition of oropharyngeal microbiota in patients with COVID-19 of different pneumonia severity
- Authors: Starikova E.V.1, Galeeva J.S.1, Andreev D.N.2, Sokolov P.S.2, Fedorov D.E.1, Manolov A.I.1, Pavlenko A.V.1, Klimina K.M.3, Veselovsky V.A.3, Zaborovsky A.V.4, Evdokimov V.V.2, Andreev N.G.2, Devkota M.K.2, Fomenko A.K.2, Khar'kovskii V.A.2, Asadulin P.O.2, Kucher S.A.2, Cheremushkina A.S.2, Yanushevich O.O.2, Maev I.V.2, Krikheli N.I.2, Levchenko O.V.2, Ilina E.N.1, Govorun V.M.1
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Affiliations:
- Research Institute of Systemic Biology and Medicine
- Yevdokimov Moscow State University of Medicine and Dentistry
- Federal Scientific and Clinical Center for Physical and Chemical Medicine
- Yevdokimov Moscow State University of Medicine and Dentistry, Moscow
- Issue: Vol 94, No 8 (2022)
- Pages: 963-972
- Section: Original articles
- URL: https://journals.rcsi.science/0040-3660/article/view/111814
- DOI: https://doi.org/10.26442/00403660.2022.08.201780
- ID: 111814
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Abstract
Aim. To identify features of the taxonomic composition of the oropharyngeal microbiota of COVID-19 patients with different disease severity.
Materials and methods. The study group included 156 patients hospitalized with confirmed diagnosis of COVID-19 in the clinical medical center of Yevdokimov Moscow State University of Medicine and Dentistry between April and June 2021. There were 77 patients with mild pneumonia according to CT (CT1) and 79 patients with moderate to severe pneumonia (CT2 and CT3). Oropharyngeal swabs were taken when the patient was admitted to the hospital. Total DNA was isolated from the samples, then V3–V4 regions of the 16s rRNA gene were amplified, followed by sequencing using Illumina HiSeq 2500 platform. DADA2 algorithm was used to obtain amplicon sequence variants (ASV).
Results. When comparing the microbial composition of the oropharynx of the patients with different forms of pneumonia, we have identified ASVs associated with the development of both mild and severe pneumonia outside hospital treatment. Based on the results obtained, ASVs associated with a lower degree of lung damage belong predominantly to the class of Gram-negative Firmicutes (Negativicutes), to various classes of Proteobacteria, as well as to the order Fusobacteria. In turn, ASVs associated with a greater degree of lung damage belong predominantly to Gram-positive classes of Firmicutes – Bacilli and Clostridia. While being hospitalized, patients with severe pneumonia demonstrated negative disease dynamics during treatment significantly more often.
Conclusion. We have observed differences in the taxonomic composition of the oropharyngeal microbiota in patients with different forms of pneumonia developed outside hospital treatment against COVID-19. Such differences might be due to the presumed barrier function of the oropharyngeal microbiota, which reduces the risk of virus titer increase.
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##article.viewOnOriginalSite##About the authors
Elizaveta V. Starikova
Research Institute of Systemic Biology and Medicine
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0001-6582-210X
науч. сотр. ФБУН НИИ СБМ
Russian Federation, MoscowJulia S. Galeeva
Research Institute of Systemic Biology and Medicine
Author for correspondence.
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0001-6304-4607
мл. науч. сотр. ФБУН НИИ СБМ
Russian Federation, MoscowDmitry N. Andreev
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0002-4007-7112
канд. мед. наук, доц., доц. каф. пропедевтики внутренних болезней и гастроэнтерологии ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowPhilipp S. Sokolov
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0003-2813-6498
врач-специалист отд-ния микробиологического анализа Клинического центра COVID-19, ст. лаборант каф. ЮНЕСКО «Здоровый образ жизни – залог успешного развития» ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowDmitry E. Fedorov
Research Institute of Systemic Biology and Medicine
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0001-8468-7011
мл. науч. сотр. ФБУН НИИ СБМ
Russian Federation, MoscowAleksander I. Manolov
Research Institute of Systemic Biology and Medicine
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0003-3912-429X
науч. сотр. ФБУН НИИ СБМ
Russian Federation, MoscowAlexander V. Pavlenko
Research Institute of Systemic Biology and Medicine
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0002-9549-0289
науч. сотр. ФБУН НИИ СБМ
Russian Federation, MoscowKsenia M. Klimina
Federal Scientific and Clinical Center for Physical and Chemical Medicine
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0002-5563-644X
канд. биол. наук, ст. науч. сотр. ФГБУ ФНКЦ ФХМ
Russian Federation, MoscowVladimir A. Veselovsky
Federal Scientific and Clinical Center for Physical and Chemical Medicine
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0002-4336-9452
мл. науч. сотр. ФГБУ ФНКЦ ФХМ
Russian Federation, MoscowAndrew V. Zaborovsky
Yevdokimov Moscow State University of Medicine and Dentistry, Moscow
Email: olgagaleeva546@gmail.com
D. Sci. (Med.)
Russian Federation, MoscowVladimir V. Evdokimov
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0001-9281-579X
д-р мед. наук, проф., нач. управления науки ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowNikolai G. Andreev
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0002-5136-0140
канд. мед. наук, доц., доц. каф.пропедевтики внутренних болезней и гастроэнтерологии ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowMikhail K. Devkota
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0002-3736-4196
врач-специалист отд-ния микробиологического анализа Клинического центра COVID-19, преподаватель каф. фармакологии ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowAleksei K. Fomenko
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0002-1794-7263
врач-специалист отд-ния микробиологического анализа Клинического центра COVID-19, преподаватель каф. фармакологии ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowVadim A. Khar'kovskii
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0001-8659-3502
врач-специалист отд-ния микробиологического анализа Клинического центра COVID-19 ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowPavel O. Asadulin
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0001-5236-1770
врач-специалист отд-ния микробиологического анализа Клинического центра COVID-19 ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowSergey A. Kucher
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0001-7981-1786
врач-специалист отд-ния микробиологического анализа Клинического центра COVID-19 ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowAleksandra S. Cheremushkina
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0002-1089-4322
студентка лечебного фак-та ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowOleg O. Yanushevich
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0002-4293-8465
акад. РАН, д-р мед. наук, проф., ректор, зав. каф. пародонтологии ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowIgor V. Maev
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@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 ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowNatella I. Krikheli
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0002-8035-0638
д-р мед. наук, проф., зав. каф. клинической стоматологии ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowOleg V. Levchenko
Yevdokimov Moscow State University of Medicine and Dentistry
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0003-0857-9398
д-р мед. наук, проф. каф. нейрохирургии и нейрореанимации ФГБОУ ВО «МГМСУ им. А.И. Евдокимова»
Russian Federation, MoscowElena N. Ilina
Research Institute of Systemic Biology and Medicine
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0003-0130-5079
чл.-кор. РАН, проф. РАН, д-р биол. наук, гл. науч. сотр. ФБУН НИИ СБМ
Russian Federation, MoscowVadim M. Govorun
Research Institute of Systemic Biology and Medicine
Email: olgagaleeva546@gmail.com
ORCID iD: 0000-0003-0837-8764
акад. РАН, д-р биол. наук, проф., врио дир. ФБУН НИИ СБМ
Russian Federation, MoscowReferences
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