The fungal pathogen and mycobiota diversity in respiratory samples from children with cystic fibrosis
Authors: Weiser Rebecca , Ronchetti Katherine , Tame Jo-Dee , Hoehn Sven , Jurkowski Tomasz P. , Mahenthiralingam Eshwar , Forton Julian T. 
Published: March 2023

ABSTRACTBackgroundThe prevalence of fungi in cystic fibrosis (CF) lung infections is poorly understood and studies have focused on adult patients. We investigated the fungal diversity in children with CF using brochoalveolar lavage (BAL) and induced sputum (IS) samples to capture multiple lung niches.MethodsSequencing of the fungal ITS2 region and molecular mycobiota diversity analysis was performed on 25 matched sets of BAL-IS samples from 23 children collected as part of the CF-SpIT study (UKCRN14615; ISRCTNR12473810).ResultsAspergillusandCandidawere detected in all samples and were the most abundant and prevalent genera, followed byDipodascus, LecanicilliumandSimplicillium. The presumptive CF pathogensExophiala, LomentosporaandScedosporiumwere identified at variable abundances in 100%, 64%, and 24% of sample sets, respectively. Fungal pathogens observed at high relative abundance (≥40%) were not accurately diagnosed by routine culture microbiology in over 50% of the cohort. The fungal communities captured by BAL and IS samples were similar in diversity and composition, with exception toC. albicansbeing significantly increased in IS samples. The respiratory mycobiota varied greatly between individuals, with only 13 of 25 sample sets containing a dominant fungal taxon. In 11/25 BAL sample sets, airway compartmentalisation was observed with diverse mycobiota detected from different lobes of the lung.ConclusionsThe paediatric mycobiota is diverse, complex and inadequately diagnosed by conventional microbiology. Overlapping fungal communities were identified in BAL and IS samples, showing that IS can capture fungal genera associated with the lower airway. Compartmentalisation of the lower airway presents difficulties for consistent mycobiota sampling.What is already known on this topicFungal lung infections in people with CF are poorly described and reports are largely based on conventional culture data from adults, with limited studies on the role of fungal infections in children.What this study addsWe uniquely used culture-independent analysis to interrogate the mycobiota in different respiratory samples (bronchoalveolar lavage and induced sputum) from 23 children with CF aged between 1-18 years.AspergillusandCandidawere detected in 100% of samples at varying levels, and whilst high relative abundances (>50%) of these genera and the emergingExophialawere detected in multiple samples from children over the age of 12, culture-based diagnostics failed to accurately identify them.There were differences in the fungal communities in different regions of the lung from the same individual, suggesting mycobiota compartmentalisation.How this study might affect research, practice or policyFungal prevalence rates in children with CF are underestimated and inaccurately diagnosed by routine culture, which reflects a need for longitudinal respiratory sampling, molecular analyses and improvement in conventional mycology diagnostic practice.