Composition of oropharyngeal microbiota in patients with COVID-19 of different pneumonia severity

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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.

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, Moscow

Julia 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, Moscow

Dmitry 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, Moscow

Philipp 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, Moscow

Dmitry 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, Moscow

Aleksander 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, Moscow

Alexander 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, Moscow

Ksenia 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, Moscow

Vladimir 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, Moscow

Andrew V. Zaborovsky

Yevdokimov Moscow State University of Medicine and Dentistry, Moscow

Email: olgagaleeva546@gmail.com

D. Sci. (Med.)

Russian Federation, Moscow

Vladimir 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, Moscow

Nikolai 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, Moscow

Mikhail 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, Moscow

Aleksei 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, Moscow

Vadim 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, Moscow

Pavel 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, Moscow

Sergey 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, Moscow

Aleksandra 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, Moscow

Oleg 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, Moscow

Igor 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, Moscow

Natella 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, Moscow

Oleg 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, Moscow

Elena 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, Moscow

Vadim 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, Moscow

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Supplementary files

Supplementary Files
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1. JATS XML
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2. Fig. 1. Distribution of the number of patients diagnosed with COVID-19 by age, gender, degree of lung injury (CT), and need for supplemental oxygen.

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3. Fig. 2. Scheme of bioinformatics processing of 16s rRNA gene amplicon sequences from patient samples.

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4. Fig. 3. Heat map of representation of prokaryotic genera in oropharyngeal samples of 156 patients with varying degrees of lung involvement (indicated in yellow, orange, and purple in the upper panel; CT). The colors of the heat map reflect the representation values of the corresponding bacterial genera after the CLR (centered log ratio transform) transformation.

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5. Fig. 4: a – graph of the similarity of the taxonomic composition (b-diversity) of metagenomes of patients with different degrees of lung damage according to CT: CT-1 (n=77), CT-2 (n=66), CT-3 (n=13) based on NMDS for species diversity (difference metric: Bray–Curtis measure) principal component analysis; b – axonomic diversity (a-diversity) of the microbiota of patients with varying degrees of lung damage according to CT: CT-1 (n=77), CT-2 (n=66), CT-3 (n=13), calculated as an index Shannon.

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6. Fig. 5. The contribution of metadata groups to the variation in the variance of the taxonomic composition of the microbiota of patient samples. Physiological indicators: gender, age. Chronic diseases: chronic diseases of the cardiovascular system, COPD, diabetes mellitus, inflammatory bowel disease. Patients' condition: the severity of pneumonia according to CT, the need for additional O2, taking antibiotics within a month before hospitalization. Dental indicators: dental status, PMA index, PHP index, KUz index.

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7. Fig. 6. Analysis of the differential representation of 16s amplicons of bacteria associated with severe (CT>2, n=79) and mild (CT=1, n=77) degree of lung injury in patients. The analysis was carried out using the DeSeq2 method: a – ASV, reproducible in ≥20 iterations out of 25; b – ASV, reproducing ≥15 iterations out of 25. ASV bacteria that are associated with high lung disease in patients are shown with bars pointing to the right; with a mild degree of lung damage in patients – to the left. To the right and left of the bars is the level of statistical significance (a) calculated from the analysis for each differentially represented ASV.

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