The fungal pathogen and mycobiota diversity in respiratory samples from children with cystic fibrosis

Background The 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. Methods Sequencing 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). Results Aspergillus and Candida were detected in all samples and were the most abundant and prevalent genera, followed by Dipodascus, Lecanicillium and Simplicillium . The presumptive CF pathogens Exophiala, Lomentospora and Scedosporium were 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 to C. albicans being 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. Conclusions The 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 topic What this study adds How this study might affect research, practice or policy ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was funded by a research project award from the US Cystic Fibrosis foundation grant MAHENT20G0, with additional support from the Health and Care Research Wales-Academic Health Science Collaboration and Wellcome Trust Institutional Strategic Support Fund (Cardiff University). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The South Wales Research Ethics Committee gave ethical approval for this work (11/WA/0334) I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Sequence data are available online at the European Nucleotide Archive under project number PRJEB60511