Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis

The early description of cystic fibrosis (CF) was marked by malnutrition and lung infections. The diagnosis and treatment of infection has transformed disease prognosis to a median predicted survival over 50 years. Yet, chronic infections continue to significantly impact morbidity and mortality in CF. Over time, the microbial epidemiology has changed, with a rise of filamentous fungi and yeast recovered by culture from the CF respiratory tract. The pressures of cumulative and chronic exposure to antibiotics in the course of CF likely contributes to the observed changes in fungal detection.Conventional culture-based detection methods are the primary modality to identify microorganisms in CF sputum. However, the adoption of DNA sequence-based analyses has greatly expanded our understanding of bacterial diversity in CF. Unbiased 16S rRNA gene sequencing of CF respiratory samples have yielded insight into age-specific bacterial diversity and resiliency of the bacterial community during pulmonary exacerbations. However, mycologic profiling of the CF airway has remained limited. Our study aimed to molecularly define the fungal composition and community structure in CF sputa and evaluate their associations with clinical characteristics and outcomes.