Imperial College London


Faculty of MedicineNational Heart & Lung Institute

Research Associate



+44 (0)20 7594 7974michael.cox1 Website




413Guy Scadding BuildingRoyal Brompton Campus






BibTex format

author = {Cox, MJ and Turek, EM and Hennessy, C and Mirza, GK and James, PL and Coleman, M and Jones, A and Wilson, R and Bilton, D and Cookson, WOC and Moffatt, MF and Loebinger, MR},
doi = {10.1371/journal.pone.0170622},
journal = {PLOS ONE},
title = {Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients},
url = {},
volume = {12},
year = {2017}

RIS format (EndNote, RefMan)

AB - Background:Bronchiectasis is accompanied by chronic bronchial infection that may drive disease progression. However, the evidence base for antibiotic therapy is limited. DNA based methods offer better identification and quantification of microbial constituents of sputum than standard clinical culture and may help inform patient management strategies. Our study objective was to determine the longitudinal variability of the non-cystic fibrosis (CF) bronchiectasis microbiome in sputum with respect to clinical variables. Eighty-five patients with non-CF bronchiectasis and daily sputum production were recruited from outpatient clinics and followed for six months. Monthly sputum samples and clinical measurements were taken, together with additional samples during exacerbations. 16S rRNA gene sequencing of the sputum microbiota was successful for 381 samples from 76 patients and analysed in conjunction with clinical data.Results:Microbial communities were highly individual in composition and stability, usually with limited diversity and often containing multiple pathogens. When compared to DNA sequencing, microbial culture had restricted sensitivity in identifying common pathogens such as Pseudomonas aeruginosa, Haemophilus influenzae, Moraxella catarrhalis. With some exceptions, community characteristics showed poor correlations with clinical features including underlying disease, antibiotic use and exacerbations, with the subject showing the strongest association with community structure. When present, the pathogens mucoid Pseudomonas aeruginosa and Haemophilus influenzae may also shape the structure of the rest of the microbial community.Conclusions:The use of microbial community analysis of sputum added to information from microbial culture. A simple model of exacerbations driven by bacterial overgrowth was not supported, suggesting a need for revision of principles for antibiotic therapy. In individual patients, the management of chronic bronchial infection may be imp
AU - Cox,MJ
AU - Turek,EM
AU - Hennessy,C
AU - Mirza,GK
AU - James,PL
AU - Coleman,M
AU - Jones,A
AU - Wilson,R
AU - Bilton,D
AU - Cookson,WOC
AU - Moffatt,MF
AU - Loebinger,MR
DO - 10.1371/journal.pone.0170622
PY - 2017///
SN - 1932-6203
TI - Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients
UR -
UR -
UR -
VL - 12
ER -