The Lower Airway Microbiota in Children With Cystic Fibrosis is Captured by Induced Sputum Sampling: Matched Multiple Niche Microbiota Profiles From the CF-Sputum Induction Trial (CF-SpIT)

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. We aimed to assess the ability of induced sputum sampling to characterise the lower airway microbiota.  Methods: Sample sets from Induced-sputum (IS) and three matched bronchoalveolar lavage (BAL) compartments were obtained for microbiota analysis as part of the CF-Sputum Induction Trial. Microbiota profiles and molecular detection of specific pathogens were compared between matched samples. The study is registered with the UK Clinical Research Network (14615) and with the International Standard Randomised Controlled Trial Network Registry (12473810).  Findings: 28 patients, aged 1.1-17.7 years, provided 30 sample sets. BAL microbiota varied from diverse to pathogen-dominated in bacterial composition. Within-patient BAL comparisons revealed spatial heterogeneity in 11/30 (37%) sample sets indicating that the lower airway microbiota is frequently compartmentalised in children with CF. IS samples closely resembled one or more matched BAL compartment in 18/30 (60%) sample sets, and were highly related in composition in a further 5/30 (20%). IS detected 83.4% (SD 17.34) of the Top 5 genera found across matched BAL samples. The sensitivity of IS to detect specific CF-pathogens in any matched BAL sample at a relative abundance >5%, varied between 46-100%, with negative predictive values between 75-100%.  Interpretation: The lower airway microbiota in children with CF is frequently compartmentalised, presenting difficulties in how it should be consistently sampled and highlighting the need for a standardised approach. IS captures a microbiota signature highly representative of the lower airway in 60-80% of cases, and is capable of identifying specific CF-pathogens found on gold standard BAL. IS is a simple, non-invasive and repeatable intervention that may be easily standardised, and is recommended as the sampling approach of choice in future large-scale microbiota studies in children with CF, and for clinical application of microbiota profiling in children.  Funding: Health and Care Research Wales-Academic Health Science Collaboration, Wellcome Trust Institutional Strategic Support Fund, US Cystic Fibrosis Foundation Grant. Declaration of Interest: We declare no competing interests. Ethical Approval: This study is subject to Institutional Review by the Cardiff and Vale Research Review Service CaRRS; Project-ID-11-RPM-5216) and approved by the South Wales Research Ethics Committee (11/WA/0334). This study is registered with the UK Clinical Research Network (14615) and with the International Standard Randomised Controlled Trial Network Registry (12473810).