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

Abstract

BackgroundBronchiectasis 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.ResultsMicrobial 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.ConclusionsThe 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 improved by therapy specific to their microbiome, taking into account pathogen load, community stability, and acute and chronic community responses to antibiotics.

The lung microbiome in health and disease

“…The microbiota was quantified by 16S rRNA gene sequencing. 31 Similar to the findings for CF, the subjects were found to have a more complex airway microbiome than that revealed by standard clinical culture. The microbial communities were highly individual in composition and stability and there was a poor correlation with clinical state.…”

Bronchiectasis: Treatment decisions for pulmonary exacerbations and their prevention

“… However, this did not result in a change in pulmonary exacerbation rates. In another hospital‐based cohort, the structure of the airway microbiota was highly specific to an individual, and was generally stable over 6 months of study despite changes in the clinical status and antibiotic usage for a individual patient …”

RESPIRE: breathing new life into bronchiectasis

“…This results in marked differences in outcomes and treatment responses even within groups classified by a single feature, such as the presence of P. aeruginosa [19]. Future clinical trials for bronchiectasis must consider patient stratification and selection more closely including potential delineation based on airway inflammation and/ or specific components of the lung microbiome [11,[20][21][22]. A systems biology and multi-omics approach, now more widely accessible, presents an opportunity for bronchiectasis, an opportunity to combine these measures with existing clinical, immunological, microbiological and radiological data to achieve a clearer endo-phenotype for an individual patient.…”