Abstract
Changes in the airway microbiome may be important in the pathophysiology of chronic lung disease in patients with cystic fibrosis. However, little is known about the microbiome in early cystic fibrosis lung disease and the relationship between the microbiomes from different niches in the upper and lower airways. Therefore, in this cross-sectional study, we examined the relationship between the microbiome in the upper (nose and throat) and lower (sputum) airways from children with cystic fibrosis using next generation sequencing. Our results demonstrate a significant difference in both α and β-diversity between the nose and the two other sampling sites. The nasal microbiome was characterized by a polymicrobial community while the throat and sputum communities were less diverse and dominated by a few operational taxonomic units. Moreover, sputum and throat microbiomes were closely related especially in patients with clinically stable lung disease. There was a high inter-individual variability in sputum samples primarily due to a decrease in evenness linked to increased abundance of potential respiratory pathogens such as Pseudomonas aeruginosa. Patients with chronic Pseudomonas aeruginosa infection exhibited a less diverse sputum microbiome. A high concordance was found between pediatric and adult sputum microbiomes except that Burkholderia was only observed in the adult cohort. These results indicate that an adult-like lower airways microbiome is established early in life and that throat swabs may be a good surrogate in clinically stable children with cystic fibrosis without chronic Pseudomonas aeruginosa infection in whom sputum sampling is often not feasible.
Highlights
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and remains one of the most frequent lethal hereditary diseases in Caucasian populations [1]
Limitations in handling and processing of the samples may account for the differences as some studies showed that a high percentage of the sputum microbiome can be cultured under optimized conditions [27,36,37]
Our results suggest that samples analyzed within a routine setting at a university microbiology laboratory lack a considerable number of bacteria and that next generation sequencing (NGS) analysis may be superior for diagnostic characterization of polymicrobial CF airways infections in the near future
Summary
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and remains one of the most frequent lethal hereditary diseases in Caucasian populations [1]. CF affects various organs, over 85% of the morbidity and mortality of the disease are attributed to an early onset lung disease that is characterized by airway mucus obstruction and intermittent to chronic infection with characteristic pathogens such as Staphylococcus aureus, Haemophilus influenza, Pseudomonas aeruginosa and Burkholderia cepacia complex. This results in and chronic neutrophilic inflammation leading to bronchiectasis and progressive lung damage [2,3,4]. A similar shift from a polymicrobial community to a pathogen centered community linked to disease has already been described in both the gut and oral cavity [13,14,15]
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