Comparison of the upper and lower airway microbiota in children with chronic lung diseases

Research output: Contribution to journalArticle

Authors

  • Bushra Ahmed
  • Leah Cuthbertson
  • Phillip L. James
  • William O. C. Cookson
  • Jane C. Davies
  • Miriam F. Moffatt
  • Andrew Bush

Colleges, School and Institutes

Abstract

Rationale
The lower airway microbiota is important in normal immunological development and chronic lung diseases (CLDs). Young children cannot expectorate and because of the uncertainty whether upper airway samples reflect the lower airway microbiota, there have been few longitudinal paediatric studies to date.

Objectives
To assess whether throat swabs (TS) and cough swabs (CS) are representative of the lower airway microbiota.

Methods
TS, CS, bronchoalveolar lavage and bronchial brushings were prospectively collected from 49 children undergoing fibreoptic bronchoscopy for CLDs. Bacterial DNA was extracted and the 16S rRNA gene V4 region sequenced using the Illumina MiSeq.

Results
5.97 million high quality reads were obtained from 168 samples (47 TS, 37 CS, 42 BALF and 42 bronchial brushings). CS sequenced poorly. At a community level, no difference in alpha diversity (richness, evenness or Shannon Diversity Index) was seen between lower airway samples and TS (P > 0.05). Less than 6.31% of beta diversity variation related to sampling method for TS (P = 0.001). Variation between pathologies and individual patients was greater (20%, 54% respectively P ≤ 0.001) than between TS and lower airway samples. There was strong correlation in the relative abundance of genera between samples (r = 0.78, P < 0.001). Similarity between upper and lower airway samples was observed to be less for individuals where one sample type was dominated by a single organism.

Conclusions
At the community structure level, TS correlate with lower airway samples and distinguish between different CLDs. TS may be a useful sample for the study of the differences in longitudinal changes in the respiratory microbiota between different CLDs. Differences are too great however for TS to be used for clinical decision making.

Details

Original languageEnglish
Article numbere0201156
Pages (from-to)1-15
Number of pages15
JournalPLoS ONE
Volume13
Issue number8
Publication statusPublished - 2 Aug 2018