Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients

Maria Paz Ventero; Oscar Moreno-Perez; Carmen Molina-Pardines; Andreu Paytuví-Gallart; Vicente Boix; Isabel Escribano; Irene Galan; Pilar González-delaAleja; Mario López-Pérez; Rosario Sánchez-Martínez; Esperanza Merino; Juan Carlos Rodríguez

doi:10.1016/j.jinf.2021.12.030

Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients

J Infect. 2022 Mar;84(3):329-336. doi: 10.1016/j.jinf.2021.12.030. Epub 2021 Dec 25.

Affiliations

¹ Microbiology Service, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain.
² Endocrinology and Nutrition department, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain; Clinical Medicine department, Miguel Hernández University, Elche, Spain.
³ Microbiology Service, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain. Electronic address: carmenmolinapardines@gmail.com.
⁴ Sequentia Biotech, Carrer Comte d'Urgell 240, 08036 Barcelona, Spain; Open University of Catalonia (UOC), Rambla del Poblenou, 156, 08018 Barcelona, Spain.
⁵ Unit of Infectious Diseases, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain; Clinical Medicine department, Miguel Hernández University, Elche, Spain.
⁶ Pneumology department, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain.
⁷ Unit of Infectious Diseases, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain.
⁸ Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Spain; Microbiology Service, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain.
⁹ Internal Medicine department, Alicante General University Hospital - Alicante Institute of Sanitary and Biomedical Research (ISABIAL), Alicante, Spain.
¹⁰ Microbiology Service, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain; Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Spain.

Abstract

This study aimed to analyse the diversity and taxonomic composition of the nasopharyngeal microbiota, to determine its association with COVID-19 clinical outcome. To study the microbiota, we utilized 16S rRNA sequencing of 177 samples that came from a retrospective cohort of COVID-19 hospitalized patients. Raw sequences were processed by QIIME2. The associations between microbiota, invasive mechanical ventilation (IMV), and all-cause mortality were analysed by multiple logistic regression, adjusted for age, gender, and comorbidity. The microbiota α diversity indexes were lower in patients with a fatal outcome, whereas the β diversity analysis showed a significant clustering in these patients. After multivariate adjustment, the presence of Selenomonas spp., Filifactor spp., Actinobacillus spp., or Chroococcidiopsis spp., was associated with a reduction of more than 90% of IMV. Higher diversity and the presence of certain genera in the nasopharyngeal microbiota seem to be early biomarkers of a favourable clinical evolution in hospitalized COVID-19 patients.

Keywords: Biomarker; COVID-19; Microbiota; Prognosis; SARS-COV-2; Severity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biomarkers
COVID-19*
Humans
Microbiota*
RNA, Ribosomal, 16S / genetics
Retrospective Studies
SARS-CoV-2

Substances

Biomarkers
RNA, Ribosomal, 16S