I.V. NIKOLAEVA¹, E.A. KUPRIYANOVA², S.E. MIFTAKHOVA³

¹Kazan State Medical University, Kazan

²Kazan (Volga region) Federal University, Kazan

³Republican Clinical Hospital for Infectious Diseases named after Prof. A.F. Agafonov, Kazan

Contact details:

Nikolaeva I.V. — MD, Professor, Head of the Department of Infectious Diseases

Address: 83 prospekt Pobedy, 420110 Kazan, Russian Federation, tel.: +7 (843) 267-80-71, e-mail: irina.nikolaeva@kazangmu.ru

The upper respiratory tract microbiota plays an important role in host immune defense against respiratory infections. SARS-CoV-2 infection can alter the respiratory microbiome composition, leading to reduced microbial diversity and overgrowth of opportunistic microorganisms. During the COVID-19 pandemic, cases of SARS-CoV-2 co-infection with fungi and bacteria belonging to the oral microbiota were reported.

The purpose — to investigate the nasopharyngeal microbiota composition in patients with severe COVID-19 using 16S rRNA gene amplicon sequencing. Twelve patients with severe COVID-19 were examined; the mean age was 70.8 (65.5–76.2) years, with 58% females and 42% males.

Candida spp. was detected in nasopharyngeal swabs of 8 (66.7%) patients, predominantly Candida albicans (87.5%). According to 16S rRNA gene sequencing, 18 major bacterial taxa with a high proportion of pathobionts were identified in the nasopharyngeal microbiota. The most abundant taxa were Veillonella dispar (19.7%), Prevotella melaninogenica (11.8%), Streptococcus spp. (11%), Staphylococcus spp. (9%), and members of the Comamonadaceae family (7.4%). Other genera had low relative abundance (<2.0%).

In Candida-negative patients, bacteria of the phylum Firmicutes predominated (59%), whereas Bacteroidetes were more abundant in Candida-positive patients (56%). The mean Shannon diversity index was 4.6 (SD 1.02) in the Candida-positive group and 5.0 (SD 0.99) in the Candida-negative group (p = 1). No statistically significant differences in microbiota composition or diversity were observed between the groups, which may be related to the asymptomatic course of candida infection.

Conclusion. Severe SARS-CoV-2 infection is associated with pronounced dysbiosis of the upper respiratory tract microbiota, characterized by the predominance of opportunistic microorganisms with proinflammatory potential, which may contribute to the development of bacterial and fungal superinfections.

Key words: COVID-19, Candida, microbiota, upper respiratory tract.

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