The effect of positive airway fungal culture and fungal sensitisation on microbial diversity in the lungs of children with asthma.
Introduction: Sensitisation to thermotolerant fungi such as Aspergillus fumigatus and Candida albicans which can colonise the lungs is associated with poor lung function in children with asthma. Dysbiosis of bacteria and fungi in the airway microbiome has been reported between health and asthma but has yet to be characterised for fungal sensitised asthmatic children. We aimed to investigate if microbial diversity of the airways is altered in fungal sensitised school-age asthmatic children.  Methods: Sputum samples from children with asthma who were fungal sensitised (n=22) and non-fungal sensitised (n=17) along with children without asthma (n=15), all aged 5-16 were profiled by bacterial 16S and fungal ITS2 next generation sequencing. Microbiota were compared between groups using alpha/beta diversity and differential relative abundance analysis.  Results: Bacterial alpha diversity was significantly lower in asthma compared to disease controls (P = 0.02) and in stable compared to acute asthma (P = 0.03). Fungal diversity did not change between asthma states and disease controls, but was significantly lower in asthma samples with positive A. fumigatus culture. Samples culture positive for A. fumigatus were higher in Firmicutes and lower in Fusobacteria than culture negative. Children sensitised to both thermotolerant and non-thermotolerant fungi had similar microbial diversity compared to non-sensitised children. However, in children not sensitised to fungi, those with a positive airway fungal culture had significant lower fungal alpha diversity and bacterial beta differences compared to children with negative fungal culture.  Conclusion: Fungal sensitisation did not alter the bacterial or fungal microbiota in the airways of asthmatic children. However, a positive airway fungal culture was associated with significant changes in microbial diversity, particularly in non-fungal sensitised children with asthma.