The effect of influenza virus on the human oropharyngeal microbiome

Ramos-Sevillano, Elisa; Wade, William G.; Mann, Alex; Gilbert, Anthony; Lambkin-Williams, Robert; Killingley, Ben; Nguyen-Van-Tam, Jonathan S; Tang, Christoph M.

Abstract

© The Author(s) 2018. Background. Secondary bacterial infections are an important cause of morbidity and mortality associated with influenza infections. As bacterial disease can be caused by a disturbance of the host microbiome, we examined the impact of influenza on the upper respiratory tract microbiome in a human challenge study. Methods. The dynamics and ecology of the throat microbiome were examined following an experimental influenza challenge of 52 previously-healthy adult volunteers with influenza A/Wisconsin/67/2005 (H3N2) by intranasal inoculation; 35 healthy control subjects were not subjected to the viral challenge. Serial oropharyngeal samples were taken over a 30-day period, and the V1-V3 region of the bacterial 16S ribosomal RNA sequences were amplified and sequenced to determine the composition of the microbiome. The carriage of pathogens was also detected. Results. Of the 52 challenged individuals, 43 developed proven influenza infections, 33 of whom became symptomatic. None of the controls developed influenza, although 22% reported symptoms. The diversity of bacterial communities remained remarkably stable following the acquisition of influenza, with no significant differences over time between individuals with influenza and those in the control group. Influenza infection was not associated with perturbation of the microbiome at the level of phylum or genus. There was no change in colonization rates with Streptococcus pneumoniae or Neisseria meningitidis. Conclusions. The throat microbiota is resilient to influenza infection, indicating the robustness of the upper-airway microbiome.

Citation

Ramos-Sevillano, E., Wade, W. G., Mann, A., Gilbert, A., Lambkin-Williams, R., Killingley, B., …Tang, C. M. (2019). The effect of influenza virus on the human oropharyngeal microbiome. Clinical Infectious Diseases, 68(12), 1993-2002. https://doi.org/10.1093/cid/ciy821

• Journal Article Type: Article
• Acceptance Date: Oct 4, 2018
• Online Publication Date: Nov 15, 2018
• Publication Date: Jun 1, 2019
• Deposit Date: Nov 26, 2018
• Publicly Available Date: Nov 16, 2019
• Journal: Clinical Infectious Diseases
• Print ISSN: 1058-4838
• Electronic ISSN: 1537-6591
• Publisher: Oxford University Press (OUP)
• Peer Reviewed: Peer Reviewed
• Volume: 68
• Issue: 12
• Pages: 1993-2002
• DOI: https://doi.org/10.1093/cid/ciy821
• Public URL: https://nottingham-repository.worktribe.com/output/1300383
• Publisher URL: https://academic.oup.com/cid/article/68/12/1993/5184302
• Additional Information: This is a pre-copyedited, author-produced version of an article accepted for publication in Clinical Infectious Diseases following peer review. The version of record Elisa Ramos-Sevillano, William G Wade, Alex Mann, Anthony Gilbert, Robert Lambkin-Williams, Ben Killingley, Jonathan S Nguyen-Van-Tam, Christoph M Tang, The Effect of Influenza Virus on the Human Oropharyngeal Microbiome, Clinical Infectious Diseases, Volume 68, Issue 12, 15 June 2019, Pages 1993–2002, https://doi.org/10.1093/cid/ciy821 is available online at: https://doi.org/10.1093/cid/ciy821