Molecular Methods to Detect and Quantify Fungal Communities in Cystic Fibrosis Airway Specimens

Area of Science:

• Medical Mycology
• Genomics
• Infectious Diseases

Background:

• Fungal presence in cystic fibrosis (CF) airways is common, but current culture methods have limitations.
• Novel next-generation sequencing (NGS) offers a more comprehensive approach to fungal identification.

Purpose of the Study:

• To compare NGS with traditional culture for identifying fungal taxa in airway samples from CF patients and controls.
• To evaluate the effectiveness of different sample types (bronchoalveolar lavage fluid, oropharyngeal swabs, expectorated sputum) for fungal detection.

Main Methods:

• Collected bronchoalveolar lavage fluid (BALF), oropharyngeal (OP) swabs, and expectorated sputum (ES) from CF patients and controls.
• Quantified total fungal load (TFL) using quantitative polymerase chain reaction (qPCR).
• Determined fungal communities using NGS, assessing relative abundance, diversity, and richness; compared results using Wilcoxon rank-sum tests.

Main Results:

• NGS successfully identified a more diverse fungal community compared to culture across 76 samples from 52 individuals (69% CF).
• Predominant fungi included Agaricomycetes, Aspergillus, Candida-Lodderomyces-clade, and Cladosporium; Aspergillus was ubiquitous in sequenced samples.
• While fungal richness and diversity varied by sample type, oropharyngeal swabs showed potential for reliable fungal detection, similar to expectorated sputum.

Conclusions:

• NGS provides a more detailed profile of airway fungi in individuals with CF.
• Oropharyngeal swabs are a viable alternative to expectorated sputum for airway fungal detection in CF patients.
• Future research will explore fungal-bacterial interactions and their impact on clinical outcomes in CF.