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Updated: Oct 5, 2025
Design and Development of a Model to Study the Effect of Supplemental Oxygen on the Cystic Fibrosis Airway Microbiome
Published on: August 3, 2021
The lung microbiota in children with cystic fibrosis captured by induced sputum sampling
Rebecca Weiser1, Juliette Oakley2, Katherine Ronchetti3
1Microbiomes Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Sir Martin Evans Building, Park Place, Cardiff, UK.
Insights
Induced sputum (IS) sampling effectively represents the lower airway microbiota in 80% of children with cystic fibrosis (CF). This non-invasive method aids in pathogen diagnosis and understanding CF lung microbiota evolution.
Area of Science:
- Microbiology
- Pediatrics
- Pulmonology
Background:
- The spatial distribution of the cystic fibrosis (CF) lung microbiota in children is not well understood.
- Optimal respiratory tract sampling methods for pediatric microbiota analysis and the clinical utility of profiling in early infection are unclear.
Purpose of the Study:
- To compare induced sputum (IS) sampling with bronchoalveolar lavage (BAL) for characterizing the lower airway microbiota in children with CF.
- To assess the utility of IS for pathogen detection and microbiota profiling in pediatric CF patients.
Main Methods:
- Collected matched sample sets from IS and BAL compartments from 28 pediatric CF patients (aged 1.1-17.7 years).
- Performed microbiota profiling and compared pathogen detection between matched IS and BAL samples.
Main Results:
- Spatial heterogeneity was observed in 27% of BAL samples, indicating compartmentalization of the lower airway microbiota.
- IS samples closely resembled BAL microbiota in 50% of cases and were compositionally related in another 30%.
- IS detected 86.2% of the top 5 genera in BAL and showed variable sensitivity (43-100%) for specific CF-pathogens.
Conclusions:
- Induced sputum (IS) sampling captures a representative lower airway microbiota signature in 80% of pediatric CF cases.
- IS is a non-invasive, feasible method for frequent sampling to aid pathogen diagnosis and monitor microbiota changes in CF.
- Observed spatial heterogeneity in BAL highlights challenges in consistent lung sampling, reinforcing the value of IS.
Background:
Spatial topography of the cystic fibrosis (CF) lung microbiota is poorly understood in childhood. How best to sample the respiratory tract in children for microbiota analysis, and the utility of microbiota profiling in clinical management of early infection remains unclear. By comparison with bronchoalveolar lavage (BAL), we assessed the ability of induced sputum (IS) sampling to characterise the lower airway microbiota.
Methods:
Sample sets from IS and two or three matched BAL compartments were obtained for microbiota analysis as part of the CF-Sputum Induction Trial (UKCRN_14615, ISRCTNR_12473810). Microbiota profiles and pathogen detection were compared between matched samples.
Results:
Twenty-eight patients, aged 1.1-17.7 years, provided 30 sample sets. Within-patient BAL comparisons revealed spatial heterogeneity in 8/30 (27%) sample sets indicating that the lower airway microbiota from BAL is frequently compartmentalised in children with CF. IS samples closely resembled one or more matched BAL compartments in 15/30 (50%) sets, and were related in composition in a further 9/30 (30%). IS detected 86.2% of the Top 5 genera found across matched BAL samples. The sensitivity of IS to detect specific CF-pathogens identified in matched BAL samples at relative abundance ≥5% varied between 43 and 100%, with negative predictive values between 73 and 100%.
Conclusions:
Spatial heterogeneity of the lower airway microbiota was observed in BAL samples and presents difficulties for consistent lung sampling. IS captured a microbiota signature representative of the lower airway in 80% of cases, and is a straightforward, non-invasive intervention that can be performed frequently to aid pathogen diagnosis and understand microbiota evolution in children with CF.
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