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Published on: March 17, 2014
Comparison of the upper and lower airway microbiota in children with chronic lung diseases
Bushra Ahmed1,2, Michael J Cox1, Leah Cuthbertson1
1National Heart and Lung Institute, Imperial College London, London, United Kingdom.
Insights
Throat swabs (TS) can reflect lower airway microbiota in children with chronic lung diseases (CLDs). While TS show community structure, they are not suitable for clinical decisions in pediatric respiratory health.
Area of Science:
- Pediatric Pulmonology
- Microbiome Research
- Immunological Development
Background:
- The lower airway microbiota plays a crucial role in immune development and chronic lung diseases (CLDs).
- Limited longitudinal studies exist for pediatric lower airway microbiota due to difficulties in sample collection from young children.
- Uncertainty remains regarding the representativeness of upper airway samples for the lower airway microbiota.
Purpose of the Study:
- To evaluate if throat swabs (TS) and cough swabs (CS) accurately represent the lower airway microbiota in children.
- To determine the utility of non-invasive upper airway samples for studying pediatric respiratory microbiota.
Main Methods:
- Prospective collection of throat swabs (TS), cough swabs (CS), bronchoalveolar lavage (BALF), and bronchial brushings from 49 children with CLDs.
- Bacterial DNA extraction and 16S rRNA gene sequencing (V4 region) using Illumina MiSeq.
- Comparative analysis of microbial community structure (alpha and beta diversity) and relative abundance.
Main Results:
- High-quality sequencing reads were obtained from 168 samples.
- Cough swabs (CS) demonstrated poor sequencing performance.
- Throat swabs (TS) showed no significant difference in alpha diversity compared to lower airway samples.
- Beta diversity variation attributed to sampling method for TS was minimal (<6.31%), significantly less than variation due to pathology or individual patients.
- Strong correlation in the relative abundance of bacterial genera between TS and lower airway samples (r=0.78).
Conclusions:
- Throat swabs (TS) demonstrate community-level correlation with lower airway microbiota in children.
- TS can distinguish between different chronic lung diseases (CLDs) based on respiratory microbiota profiles.
- TS may serve as a valuable non-invasive tool for longitudinal studies of pediatric respiratory microbiota in CLDs, but are not suitable for clinical decision-making.
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.
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