The Adult Cystic Fibrosis Airway Microbiota Is Stable over Time and Infection Type, and Highly Resilient to Antibiotic Treatment of Exacerbations

Anthony A Fodor,Matthew C Wolfgang,Richard C Boucher,Deirdre F Gilpin,Erich R Klem,J Stuart Elborn,Michael M Tunney,Suzanne Fleiszig

doi:10.1371/journal.pone.0045001

Abstract

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.

Highlights

Cystic fibrosis (CF) is a hereditary disease characterized by defective mucociliary clearance and airway obstruction by dehydrated, mucopurulent secretions [1]
Traditional aerobic culture-based studies, of spontaneous expectorated sputa, indicate that CF airway infection involves a relatively small collection of opportunistic pathogens that are typically acquired in a temporal succession, beginning early in life with Haemophilus influenzae and Staphylococcus aureus and culminating in chronic infections dominated by Pseudomonas aeruginosa or Burkholderia cepacia complex species [5]
The taxa reported here are well represented in Sangerbased sequencing and culture-based CF studies, suggesting that the adult CF microbial community has a distinct signature that can be successfully detected with multiple technologies [8,9,12,29]

Summary

Introduction

Cystic fibrosis (CF) is a hereditary disease characterized by defective mucociliary clearance and airway obstruction by dehydrated, mucopurulent secretions [1]. Traditional aerobic culture-based studies, of spontaneous expectorated sputa, indicate that CF airway infection involves a relatively small collection of opportunistic pathogens that are typically acquired in a temporal succession, beginning early in life with Haemophilus influenzae and Staphylococcus aureus and culminating in chronic infections dominated by Pseudomonas aeruginosa or Burkholderia cepacia complex species [5]. The observation that the mucous obstructing CF airways is hypoxic [7] has led to multiple studies in which CF respiratory specimens have been analyzed under strict anaerobic culture conditions [8,9,10]. These studies have shown that anaerobic bacterial species are present within CF airways in high numbers. High throughput sequencing efforts indicate that the CF microbiome consists of more than 60 different bacterial genera, while interrogation of bacterial 16S ribosomal RNA (rRNA) gene-based phylogenetic microarrays has placed the estimate at as many as 43 different bacterial phyla and over 2,000 different taxa [11,12,13]

Methods

Results

Conclusion