Journal article
Characterization of the Upper Respiratory Tract Microbiomes of Patients with Pandemic H1N1 Influenza
PLoS One, Vol.8(7), e69559
2013
Abstract
The upper respiratory tract microbiome has an important role in respiratory health. Influenza A is a common viral infection that challenges that health, and a well-recognized sequela is bacterial pneumonia. Given this connection, we sought to characterize the upper respiratory tract microbiota of individuals suffering from the pandemic H1N1 influenza A outbreak of 2009 and determine if microbiome profiles could be correlated with patient characteristics. We determined the microbial profiles of 65 samples from H1N1 patients by cpn60 universal target amplification and sequencing. Profiles were examined at the phylum and nearest neighbor "species" levels using the characteristics of patient gender, age, originating health authority, sample type and designation (STAT/non-STAT). At the phylum level, Actinobacteria-, Firmicutes- and Proteobacteria-dominated microbiomes were observed, with none of the patient characteristics showing significant profile composition differences. At the nearest neighbor "species" level, the upper respiratory tract microbiomes were composed of 13-20 "species" and showed a trend towards increasing diversity with patient age. Interestingly, at an individual level, most patients had one to three organisms dominant in their microbiota. A limited number of discrete microbiome profiles were observed, shared among influenza patients regardless of patient status variables. To assess the validity of analyses derived from sequence read abundance, several bacterial species were quantified by quantitative PCR and compared to the abundance of cpn60 sequence read counts obtained in the study. A strong positive correlation between read abundance and absolute bacterial quantification was observed. This study represents the first examination of the upper respiratory tract microbiome using a target other than the 16S rRNA gene and to our knowledge, the first thorough examination of this microbiome during a viral infection. © 2013 Chaban et al.
Details
- Title
- Characterization of the Upper Respiratory Tract Microbiomes of Patients with Pandemic H1N1 Influenza
- Authors
- Bonnie L Chaban (Author) - University of Saskatchewan, CanadaA Albert (Author) - Women's Health Research Institute, CanadaM G Links (Author) - University of Saskatchewan, CanadaJ Gardy (Author) - British Columbia Centre for Disease Control, CanadaP Tang (Author) - British Columbia Centre for Disease Control, CanadaJ E Hill (Author) - University of Saskatchewan, Canada
- Publication details
- PLoS One, Vol.8(7), e69559; 11
- Publisher
- Public Library of Science
- Date published
- 2013
- DOI
- 10.1371/journal.pone.0069559
- ISSN
- 1932-6203
- Copyright note
- Copyright © 2013 Chaban et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
- Organisation Unit
- University of the Sunshine Coast, Queensland; Thompson Institute; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99450425202621
- Output Type
- Journal article
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- Domestic collaboration
- Web Of Science research areas
- Microbiology
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