Insights into the Naso-Oropharyngeal Bacterial Composition in Suspected SARS-CoV-2 Cases

Author:

Atencio Librada A.1ORCID,Quintero Indira J.1,Almanza Alejandro1,Eskildsen Gilberto2,Sánchez-Gallego Joel34,Herrera Mellissa5,Fernández-Marín Hermógenes16,Loaiza José R.167,Mejía Luis C.1678ORCID

Affiliation:

1. Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama

2. Departamento de Microbiología Humana, Facultad de Medicina, Universidad de Panamá, Panama City 0819-07289, Panama

3. Department of Marine Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC 27695, USA

4. Coiba Scientific Station (COIBA AIP), Gustavo Lara Street, Bld. 145B, City of Knowledge, Clayton, Panama City 0843-01853, Panama

5. Hospital Luis “Chicho” Fábrega, MINSA, Santiago 0923, Panama

6. Sistema Nacional de Investigación (SNI), Secretaría Nacional de Ciencia, Tecnología, e Innovación (SENACYT), Panama City 0816-02852, Panama

7. Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama

8. Departamento de Genética y Biología Molecular, Universidad de Panamá, Estafeta Universitaria Apartado 3366, Zona 4, Panama City 0819-07289, Panama

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. While research on COVID-19 has mainly focused on its epidemiology, pathogenesis, and treatment, studies on the naso-oropharyngeal microbiota have emerged in the last few years as an overlooked area of research. Here, we analyzed the bacterial community composition of the naso-oropharynx in 50 suspected SARS-CoV-2 cases (43 detected, 7 not detected) from Veraguas province (Panama) distributed across five age categories. Statistical analysis revealed no significant differences (p < 0.05) in bacterial alpha and beta diversities between the groups categorized by SARS-CoV-2 test results, age, or patient status. The genera Corynebacterium, Staphylococcus, Prevotella, Streptococcus, and Tepidiphilus were the most abundant in both detected and not-detected SARS-CoV-2 group. The linear discriminant analysis effect size (LEfSe) for biomarker exploration indicated that Veillonella and Prevotella were enriched in detected and hospitalized patients with SARS-CoV-2 relative to non-detected patients, while Thermoanaerobacterium and Haemophilus were enriched in non-detected patients with SARS-CoV-2. The results also indicated that the genus Corynebacterium was found to decrease in patients with detected SARS-CoV-2 relative to those with non-detected SARS-CoV-2. Understanding the naso-oropharyngeal microbiota provides insights into the diversity, composition, and resilience of the microbial community in patients with SARS-CoV-2.

Funder

British Embassy Panama City

Publisher

MDPI AG

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