Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-CF bronchiectasis patients

Abstract

2Bronchiectasis is accompanied by chronic bronchial infection that may drive disease progression.3 However, the evidence base for antibiotic therapy is limited. DNA based methods offer better 4 identification and quantification of microbial constituents of sputum than standard clinical culture and 5 may help inform patient management strategies. Our study objective was to determine the longitudinal 6 variability of the non-CF bronchiectasis microbiome in sputum with respect to clinical variables. 7 Eighty-five patients with non-cystic fibrosis (CF) bronchiectasis and daily sputum production were 8 recruited from outpatient clinics and followed for six months. Monthly sputum samples and clinical 9 measurements were taken, together with additional samples during exacerbations. 16S rRNA gene 1 0 sequencing of the sputum microbiota was successful for 381 samples from 76 patients and analysed 1 1 in conjunction with clinical data.

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients

“…A version of this manuscript was archived on the pre-print server BioRxiv[ 11 ] and some of the data was presented at the American Thoracic Society Conference[ 10 ].…”

“…Some of this work has been presented before in the form of an abstract and presentation at the American Thoracic Society International Conference 2015 [ 10 ] and pre-print at BioArxiv.org [ 11 ]…”

The Respiratory Microbiome in Chronic Hypersensitivity Pneumonitis Is Distinct from That of Idiopathic Pulmonary Fibrosis

“…Triplicate 10 μl qPCR reactions were set up containing 1 μl of bacterial DNA and 9 μl of Femto™ bacterial qPCR premix (Cambridge bioscience, UK). Each run contained a 10-fold dilution series of the Vibrio natriegens DSM 759 gene cloned into a plasmid of known size and a nontemplate control [14]. For data acquisition, the following cycling parameters were used: 1…”

“…Changes in the respiratory microbiome have been associated with the clinical, physiological and therapeutic aspects of chronic lung diseases such as asthma, bronchiectasis, chronic obstructive pulmonary disease (COPD) and IPF [12][13][14][15][16][17][18]. Studies of the respiratory microbiome in IPF have reported associations between changes in microbial communities, disease progression and mortality [16,17,19,20].…”

Bronchiectasis in the Last Five Years: New Developments

“…The structure of microbial communities is highly individual between patients, and may relate weakly to disease state or antibiotic exposure [21]. The administration of prophylactic treatment with oral erythromycin (macrolide) therapy for one year, for example, demonstrated a decrease in H. influenzae and an increase in P. aeruginosa communities by lung microbiome analysis in patients without culture proven P. aeruginosa at baseline [22].…”