The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens
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 microbiota similar to healthy subjects, suggesting a critical role of microbiota in the clinical expression of viruses. These data suggest that the commensal microbiota plays a significant role in susceptibility to viral infection. The frequent co-detection of virus and bacteria raises the question of a strategy to prevent bacterial disease, focusing on the prevention of nasopharyngeal colonization through effective antibiotic treatment. In addition to antibiotics, further studies should test preventive or therapeutic interventions for maintaining or restoring a healthy nasopharyngeal microbiota.
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A recent metagenomics-based study in France reported enrichment of S. aureus, S. pneumoniae, H. influenzae, Moraxella catarrhalis and Klebsiella pneumoniae in nasopharyngeal samples of subjects with confirmed respiratory viral infections compared to healthy controls.
“A recent metagenomics-based study in France reported enrichment of S. aureus, S. pneumoniae, H. influenzae, Moraxella catarrhalis and Klebsiella pneumoniae in nasopharyngeal samples of subjects with confirmed respiratory viral infections compared to healthy controls (100).”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [100]
A French study of nasopharyngeal samples and a South Korean study of oropharyngeal samples from patients with acute respiratory viral infections both displayed decreases in diversity indices during viral infections compared to healthy controls.
“Conversely, a French study of nasopharyngeal samples and a South Korean study of oropharyngeal samples from patients with acute respiratory viral infections both displayed decreases in diversity indices during viral infections compared to healthy controls (71, 100).”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [100]
Both studies included subjects ranging from infants to adults >80 years of age, limiting conclusions about age-related effects.
“Both studies included subjects ranging from infants to adults >80 years of age, limiting conclusions about age-related effects.”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [100]
A recent study of subjects with and without respiratory viral infections demonstrated lower overall bacterial reads from nasopharyngeal samples in virally-infected subjects compared with uninfected controls.
“A recent study of subjects with and without respiratory viral infections demonstrated lower overall bacterial reads from nasopharyngeal samples in virally-infected subjects compared with uninfected controls”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [100]
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Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia.
Hanada, S., Pirzadeh, M., Carver, K. Y., & Deng, J. C. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.02640 · Cited by 495 · see citing works
- Authors
- Edouard, S., Million, M., Bachar, D., Dubourg, G., Michelle, C., Ninove, L., Charrel, R., & Raoult, D.
- Affiliations
- Aix-Marseille Université (FR)
- Inserm (FR)
- Corresponding author
- Raoult, Didier
- Venue
- European Journal of Clinical Microbiology & Infectious Diseases
- Published
- 2018-07-22
- Volume
- 37
- Issue
- 9
- Pages
- 1725-1733
- ISSN
- 0934-9723 (ISSN-L)
- 1435-4373
- OpenAlex
- W2883529746
- Cited by
- 124
- References
- 39
- Citations by year
- 2026: 9 · 2025: 14 · 2024: 17 · 2023: 21 · 2022: 21 · 2021: 21 · 2020: 14 · 2019: 6 · 2018: 1
- FWCI
- 8.46
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- European Journal of Clinical Microbiology & Infectious Diseases (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Funders
- IHU Méditerranée Infection (10-IAHU-03)
- Topics
- Life Sciences › Immunology and Microbiology › Microbiology › Microbial infections and disease research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- nasopharyngeal microbiota, respiratory viral infections, bacterial co-infection, alpha diversity, core microbiome, Prevotella, anaerobic bacteria, Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, Dolosigranulum pigrum, Corynebacterium, influenza, commensal microbiota, infection susceptibility, antibiotic therapy
- MeSH terms
- Acute Disease, Adolescent, Adult, Aged, Aged, 80 and over, Bacteria, Child, Child, Preschool, Disease Susceptibility, Female, Haemophilus influenzae, Humans, Infant, Infant, Newborn, Male, Middle Aged, Nasopharynx, Respiratory Tract Infections, RNA, Ribosomal, 16S, Staphylococcus aureus, Streptococcus pneumoniae, Virus Diseases, Case-Control Studies, Young Adult, Metagenomics, High-Throughput Nucleotide Sequencing, Coinfection, Microbiota
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