Characterization of the Upper Respiratory Tract Microbiomes of Patients with Pandemic H1N1 Influenza

被引:49
|
作者
Chaban, Bonnie [1 ]
Albert, Arianne [2 ]
Links, Matthew G. [1 ,3 ]
Gardy, Jennifer [4 ]
Tang, Patrick [4 ,5 ]
Hill, Janet E. [1 ]
机构
[1] Univ Saskatchewan, Western Coll Vet Med, Dept Vet Microbiol, Saskatoon, SK S7N 0W0, Canada
[2] Womens Hlth Res Inst, Vancouver, BC, Canada
[3] Agr & Agri Food Canada, Saskatoon Res Ctr, Saskatoon, SK, Canada
[4] British Columbia Ctr Dis Control, Vancouver, BC, Canada
[5] Univ British Columbia, Dept Pathol & Lab Med, Vancouver, BC V5Z 1M9, Canada
来源
PLOS ONE | 2013年 / 8卷 / 07期
基金
加拿大健康研究院;
关键词
CPN60; DIVERSITY; SEQUENCE; TOOL; REPRESENTATION; COMMUNITIES; IMPROVEMENT; LIBRARIES; TARGET;
D O I
10.1371/journal.pone.0069559
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
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页数:11
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