A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations

Abstract

Acute exacerbations of chronic obstructive pulmonary disease (COPD) are a major source of morbidity and contribute significantly to healthcare costs. Although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in COPD airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. The aim of this study was to comprehensively profile airway bacterial communities using a culture-independent microarray, the 16S rRNA PhyloChip, of a cohort of COPD patients requiring ventilatory support and antibiotic therapy for exacerbation-related respiratory failure. PhyloChip analysis revealed the presence of over 1,200 bacterial taxa representing 140 distinct families, many previously undetected in airway diseases; bacterial community composition was strongly influenced by the duration of intubation. A core community of 75 taxa was detected in all patients, many of which are known pathogens. Bacterial community diversity in COPD airways is substantially greater than previously recognized and includes a number of potential pathogens detected in the setting of antibiotic exposure. Comprehensive assessment of the COPD airway microbiota using high-throughput, culture-independent methods may prove key to understanding the relationships between airway bacterial colonization, acute exacerbation, and clinical outcomes in this and other chronic inflammatory airway diseases.

FIG. 1.

(A) Phylogenetic tree exhibiting family level bacterial diversity detected in COPD airways despite antimicrobial administration. (B) Bacterial richness detected in individual patient samples.

FIG. 1.

(A) Phylogenetic tree exhibiting family level bacterial diversity detected in COPD airways despite antimicrobial administration. (B) Bacterial richness detected in individual patient samples.

FIG. 2.

NMDS analysis demonstrates that bacterial community composition is highly influenced by the duration of intubation (red isotherms). Subjects COPD 5 and COPD 6 are superimposed on the right side of the figure, indicative of highly similar bacterial community composition.

FIG. 3.

Phylogenetic tree illustrating core bacterial taxa detected in COPD airways samples in this study. Known pathogens are denoted with an asterix; distinct bacterial families are indicated by different colors.