Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza.
Author(s)
Type
Journal Article
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.
Date Issued
2013-07-02
Date Acceptance
2013-06-10
Citation
PLOS One, 2013, 8 (7)
ISSN
1932-6203
Publisher
Public Library of Science
Journal / Book Title
PLOS One
Volume
8
Issue
7
Copyright Statement
© 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.
License URL
Subjects
Adolescent
Adult
Aged
Aged, 80 and over
Bacteria
British Columbia
Child
Child, Preschool
Female
Fungi
Humans
Infant
Infant, Newborn
Influenza A Virus, H1N1 Subtype
Influenza, Human
Male
Microbiota
Middle Aged
Pandemics
Phylogeny
RNA, Ribosomal, 16S
RNA, Viral
Respiratory System
Reverse Transcriptase Polymerase Chain Reaction
Young Adult
Publication Status
Published
Article Number
e69559