The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations

• Published in: PloS one 2012-09, Vol.7 (9), p.e45001
• Main Authors: Fodor, Anthony A, Klem, Erich R, Gilpin, Deirdre F, Elborn, J Stuart, Boucher, Richard C, Tunney, Michael M, Wolfgang, Matthew C
• Format: Article
• Language: English
• Subjects: Adult; Airway management; Analysis; Anti-Bacterial Agents - pharmacology; Anti-Bacterial Agents - therapeutic use; Antibiotics; Bioinformatics; Biology; Burkholderia; Burkholderia cepacia; Care and treatment; Chronic Disease; Chronic infection; Colonization; Communities; Community composition; Community structure; Complexity; Cystic fibrosis; Cystic Fibrosis - drug therapy; Cystic Fibrosis - microbiology; Cystic Fibrosis - pathology; Disease Progression; DNA, Bacterial - genetics; Drug Resistance, Multiple, Bacterial; Gram-Negative Bacteria - drug effects; Gram-Negative Bacteria - genetics; Gram-Negative Bacteria - isolation & purification; Gram-Positive Bacteria - drug effects; Gram-Positive Bacteria - genetics; Gram-Positive Bacteria - isolation & purification; Health aspects; High-Throughput Nucleotide Sequencing; Humans; Infection; Infections; Inflammation; Lungs; Medical treatment; Medicine; Metagenome - drug effects; Metagenome - genetics; Microbiota; Microbiota (Symbiotic organisms); Microorganisms; Mortality; Patients; Pharmacy; Phylogenetics; Phylogeny; Pseudomonas; Pseudomonas aeruginosa; Recovery of function; Respiratory function; Respiratory System - drug effects; Respiratory System - microbiology; Respiratory System - pathology; Respiratory tract; Risk factors; Species richness; Sputum; Sputum - microbiology; Streptococcus; Studies; Taxa; Viral infections
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0045001

Cystic fibrosis (CF) is characterized by defective mucociliary clearance and chronic airway infection by a complex microbiota. Infection, persistent inflammation and periodic episodes of acute pulmonary exacerbation contribute to an irreversible decline in CF lung function. While the factors leading to acute exacerbations are poorly understood, antibiotic treatment can temporarily resolve pulmonary symptoms and partially restore lung function. Previous studies indicated that exacerbations may be associated with changes in microbial densities and the acquisition of new microbial species. Given the complexity of the CF microbiota, we applied massively parallel pyrosequencing to identify changes in airway microbial community structure in 23 adult CF patients during acute pulmonary exacerbation, after antibiotic treatment and during periods of stable disease. Over 350,000 sequences were generated, representing nearly 170 distinct microbial taxa. Approximately 60% of sequences obtained were from the recognized CF pathogens Pseudomonas and Burkholderia, which were detected in largely non-overlapping patient subsets. In contrast, other taxa including Prevotella, Streptococcus, Rothia and Veillonella were abundant in nearly all patient samples. Although antibiotic treatment was associated with a small decrease in species richness, there was minimal change in overall microbial community structure. Furthermore, microbial community composition was highly similar in patients during an exacerbation and when clinically stable, suggesting that exacerbations may represent intrapulmonary spread of infection rather than a change in microbial community composition. Mouthwash samples, obtained from a subset of patients, showed a nearly identical distribution of taxa as expectorated sputum, indicating that aspiration may contribute to colonization of the lower airways. Finally, we observed a strong correlation between low species richness and poor lung function. Taken together, these results indicate that the adult CF lung microbiome is largely stable through periods of exacerbation and antibiotic treatment and that short-term compositional changes in the airway microbiota do not account for CF pulmonary exacerbations.