First Detect Then Destroy: Fungi in the CF Airway (FUN)

Although significant progress has been made in the approach to cystic fibrosis (CF) lung disease with the development of cystic fibrosis transmembrane conductance regulator (CFTR) modulators, infection and inflammation remain problematic.

The CF scientific community has made great strides in understanding the polymicrobial and dynamic nature of the bacterial communities in the CF airway through the application of next generation sequencing (NGS) techniques; however, CF lung disease is triggered by more than just bacteria. My research team is well-positioned to contribute to the investigation of the fungal communities within the CF airway through the intensive study of a newly developed (and published) NGS technique to determine which airway samples can be used to detect fungi.

Using banked and prospectively collected oropharyngeal (OP) swabs, sputum and bronchoalveolar lavage fluid (BALF) samples, we will leverage the expertise of our longstanding national collaborators at the Cystic Fibrosis Microbiome Analysis Core (CFMAC) at the University of Colorado and an established expert in fungal disease in CF at the University of Pennsylvania to move the field forward. Our work will have the following objectives:

1. Compare fungal detection between culture and NGS in the upper and lower airway to better understand the strengths and weaknesses of NGS compared to standard clinical culture methods.
2. Describe differences in fungal communities detected by airway sample type (OP swab, sputum and BALF) (this is key in the era of CFTR modulators and decreased availability of expectorated sputum).
3. Develop a cohort that can be followed longitudinally for further study of fungi and clinical outcomes.