The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens

European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology
Sophie EdouardDidier Raoult

Abstract

The nasopharynx is the primary site of colonization by respiratory pathogen that constitutes the port of entrance in the respiratory tract. The role of mucosal respiratory microbiota in infection has been recently emphasized; therefore, we aimed to assess if a specific respiratory microbiota profile was associated with symptomatic infection and/or with presence of respiratory viruses. We performed a case-control study to characterize the healthy respiratory microbiota and its alteration during acute viral infections. Next-generation sequencing of the 16S rRNA gene was applied to 225 nasopharyngeal samples from 177 patients with viral respiratory infection and 48 matched healthy controls. We evidenced an important decrease of bacterial alpha-diversity in patients with symptomatic respiratory infection and a loss of the healthy core microbiota, specifically anaerobes and Prevotella spp. Moreover, eight respiratory pathogens were enriched in these patients, including Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, Dol osigranulum pigrum and Corynebacterium propinquum/pseudodiphtheriticum, whose role in respiratory infection is unclear. The asymptomatic carrier of influenza harbors a ...Continue Reading

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Citations

Sep 4, 2019·Der Internist·C Malainou, S Herold
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Jun 23, 2021·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Bastiaan W HaakW Joost Wiersinga

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Datasets Mentioned

BETA
PRJEB14780

Methods Mentioned

BETA
PCR
Illumina sequencing

Software Mentioned

fastq
UCLUST
GraphPad Prism
FLASH
QIIME
LEfSe
blast

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