Open Access

The upper respiratory tract microbiome of hospitalised patients with community-acquired pneumonia of unknown aetiology: a pilot study

  • Timothy L. Wiemken111, 211Email author,
  • Venkatakrishna Rao Jala311,
  • Robert R. Kelley111, 211,
  • Paula Peyrani111, 211,
  • William A. Mattingly111,
  • Forest W. Arnold111,
  • Patricio W. Cabral111,
  • Rodrigo Cavallazzi411,
  • Bodduluri Haribabu311 and
  • Julio A. Ramirez111, 211
Pneumonia20156:6010083

https://doi.org/10.15172/pneu.2015.6/682

Received: 12 June 2015

Accepted: 31 July 2015

Published: 11 September 2015

Abstract

The composition of the upper respiratory tract microbiome may play an important role in the development of lower respiratory tract infections. Here, we characterised the microbiome of the nasopharynx and oropharynx of hospitalised patients with community-acquired pneumonia (CAP) with unknown aetiology in an attempt to obtain insight into the aetiology of CAP. A random sample of 10 patients hospitalised with CAP previously enrolled in a separate clinical trial (ClinicalTrials.gov registry, Study ID: NCT01248715) in which a complete microbiological workup was not able to define an aetiology were analysed in this pilot study. This larger trial (n = 1,221) enrolled patients from 9 adult hospitals in Louisville, Kentucky, USA. Nasopharyngeal and oropharyngeal swabs were obtained for metagenomic analysis. Polymerase chain reaction (PCR) for Streptococcus pneumoniae was performed in all patients. One patient had a distinct nasophararyngeal microbiome consisting largely of Haemophilus influenzae. This was the only patient with a negative PCR for S. pneumoniae in both nasophararyngeal and oropharyngeal specimens. Overall, substantial differences were found between nasophararyngeal and oropharyngeal microbiomes. The upper respiratory tract microbiome of only one patient suggested H. influenzae as a probable aetiology of CAP. Although this was a pilot study of only 10 patients, the presence of S. pneumoniae in the upper respiratory tract of the other 9 patients warrants further investigation.

Keywords

metagenomics microecology Streptococcus pneumoniae bioinformatics polymerase chain reaction

Notes

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