The fungal diversity in the lungs of children with cystic fibrosis captured by sputum-induction and bronchoalveolar lavage

Weiser, Rebecca ORCID: https://orcid.org/0000-0003-3983-3272, Ronchetti, Katherine, Tame, Jo-Dee, Hoehn, Sven, Jurkowski, Tomasz P. ORCID: https://orcid.org/0000-0002-2012-0240, Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 and Forton, Julian T. ORCID: https://orcid.org/0000-0002-0580-0432 2024. The fungal diversity in the lungs of children with cystic fibrosis captured by sputum-induction and bronchoalveolar lavage. Journal of Cystic Fibrosis 10.1016/j.jcf.2024.07.011

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Abstract

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 bronchoalveolar 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.

Item Type:	Article
Date Type:	Published Online
Status:	In Press
Schools:	Biosciences
Publisher:	Elsevier
ISSN:	1569-1993
Date of First Compliant Deposit:	3 June 2024
Date of Acceptance:	31 May 2024
Last Modified:	05 Aug 2024 08:57
URI:	https://orca.cardiff.ac.uk/id/eprint/169442

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