Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19

Frontiers in Microbiology

Cynthia B. Silveira¹  Haithem Afli²  Luciana C. A. Regitano²  Bruno G. N. Andrade²  Rafael R. C. Cuadrat³  Mario López-Pérez⁵  Jose M. Haro-Moreno⁵  Felipe H. Coutinho⁵  Juan Carlos Rodríguez⁵  Esperanza Merino⁶  Inmaculada Vidal⁷  Carmen Molina-Pardines⁷  Maria Paz Ventero⁷ 

[1] Department of Biology, University of Miami, Miami, FL, United States;Department of Computer Science, Munster Technological University (MTU), Cork, Ireland;Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany;Embrapa Pecuária Sudeste, São Carlos, Brazil;Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain;Infectious Diseases Unit, Alicante University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain;Microbiology Department, Alicante University General Hospital - Alicante Institute of Sanitary and Biomedical Research (ISABIAL), Alicante, Spain;

关键词: COVID-19;    SARS-CoV-2;    microbiome;    NGS – next generation sequencing;    coronavirus;    Prevotella;   

DOI  :  10.3389/fmicb.2021.637430

来源: DOAJ

【 摘 要 】

BackgroundSARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however, only one study so far focused on the patient’s nasopharynx microbiota. In this study we investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19. We performed 16S ribosomal DNA sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization), and severe (admission to ICU). We compared the microbiota diversity and OTU composition among severity groups and built bacterial co-abundance networks for each group.ResultsStatistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidota (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthermore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms.ConclusionOur study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. Taxa with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results.

【 授权许可】

Unknown