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ERJ Open Res. 2017 Aug 30;3(3). pii: 00019-2017. doi: 10.1183/23120541.00019-2017. eCollection 2017 Jul.

Protected sampling is preferable in bronchoscopic studies of the airway microbiome.

Author information

1
Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway.
2
Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway.
3
Dept of Microbiology, Haukeland University Hospital, Bergen, Norway.
4
Computational Biology Unit, Dept of Informatics, University of Bergen, Bergen, Norway.

Abstract

The aim was to evaluate susceptibility of oropharyngeal contamination with various bronchoscopic sampling techniques. 67 patients with obstructive lung disease and 58 control subjects underwent bronchoscopy with small-volume lavage (SVL) through the working channel, protected bronchoalveolar lavage (PBAL) and bilateral protected specimen brush (PSB) sampling. Subjects also provided an oral wash (OW) sample, and negative control samples were gathered for each bronchoscopy procedure. DNA encoding bacterial 16S ribosomal RNA was sequenced and bioinformatically processed to cluster into operational taxonomic units (OTU), assign taxonomy and obtain measures of diversity. The proportion of Proteobacteria increased, whereas Firmicutes diminished in the order OW, SVL, PBAL, PSB (p<0.01). The alpha-diversity decreased in the same order (p<0.01). Also, beta-diversity varied by sampling method (p<0.01), and visualisation of principal coordinates analyses indicated that differences in diversity were smaller between OW and SVL and OW and PBAL samples than for OW and the PSB samples. The order of sampling (left versus right first) did not influence alpha- or beta-diversity for PSB samples. Studies of the airway microbiota need to address the potential for oropharyngeal contamination, and protected sampling might represent an acceptable measure to minimise this problem.

Conflict of interest statement

Conflict of interest: Disclosures can be found alongside this article at openres.ersjournals.com

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