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PLoS One. 2015 Jan 28;10(1):e0116029. doi: 10.1371/journal.pone.0116029. eCollection 2015.

Comparison of microbiomes from different niches of upper and lower airways in children and adolescents with cystic fibrosis.

Author information

1
Dept. of Infectious Diseases-Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
2
Department of Translational Pulmonology, University Hospital Heidelberg, Heidelberg, Germany; Div. of Pediatric Pulmonology & Allergology and Cystic Fibrosis Center, Dept. of Pediatrics, University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
3
Dept. of Infectious Diseases-Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.
4
Institute for Medical Informatics and Biometry, Technical University Dresden, Dresden, Germany.
5
CF & Airways Microbiology Group, Queen's University Belfast, Belfast, United Kingdom.
6
CF & Airways Microbiology Group, Queen's University Belfast, Belfast, United Kingdom; School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom.
7
CF & Airways Microbiology Group, Queen's University Belfast, Belfast, United Kingdom; Centre for Infection & Immunity, School of Medicine, Dentistry & Biomedical Science, Queen's University Belfast, Belfast, United Kingdom.

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.

PMID:
25629612
PMCID:
PMC4309611
DOI:
10.1371/journal.pone.0116029
[Indexed for MEDLINE]
Free PMC Article

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