Differences of lung microbiome in patients with clinically stable and exacerbated bronchiectasis

Molecular-based diagnostic techniques can compensate for the inherent limitations of culture-based microbiology and provide a more comprehensive description of an entire community of bacteria at a particular anatomical site. Using culture-independent DNA-based molecular techniques, the aim of the present study was to characterize, differentiate, and compare the composition of lower airway bacterial microbiome between clinically stable and acutely infected patients with bronchiectasis experiencing exacerbation.

Patients with clinically stable bronchiectasis and those experiencing acutely exacerbated bronchiectasis were recruited. All patients underwent bronchoscopy. Paired sputum and bronchoalveolar lavage (BAL) samples were collected for microbiological tests. Molecular analysis was performed for BAL samples using 16S ribosomal RNA (rRNA) gene sequencing.

The mean age of the 14 recruited patients was 60 years (range 42 to 78 years), and nine (64%) were female. Using quantitative culture and 16S rRNA sequencing, the common organisms identified from 14 BAL samples were Haemophilus influenzae, Pseudomonas aeruginosa and Moraxella catarrhalis, and Prevotella. Molecular techniques revealed Prevotella and Veillonella as potentially pathogenic anaerobic species. 16S rRNA gene sequencing yielded similar relative abundances and distributions of taxa in the stable and exacerbated bronchiectasis groups. Alpha diversity with richness, Simpson's and Shannon indices, and beta diversity using principal coordinate analysis revealed no significant differences in lung microbiome between patients with clinically stable and exacerbated bronchiectasis.

Culture-based microbiological and molecular-based techniques did not reveal significant differences in the lung microbiome of patients who were clinically stable and those experiencing exacerbated bronchiectasis. Patient-specific microbial communities were dominated by one or several genera, regardless of clinical status. DNA sequencing could identify potentially pathogenic organisms unable to be identified using microbiological methods.