Publication Q&A: Molecular Methods to Detect and Quantify Fungal Communities in Cystic Fibrosis Airway Specimens
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Summary
Latest research from the Center for Respiratory Biology and Therapeutics shows that our newer DNA-based testing can detect and identify more fungi in the lungs of people with and without cystic fibrosis (CF) compared to traditional culture-based approaches, and that throat swabs may provide useful information about airway fungi.
Theresa Annette Laguna, MD, MSc, and Matt Fought, MS, share insights from their latest research.
Is this cystic fibrosis research a first in any way?
Our study expands upon previous work that looks at the different types of fungus that is present in the airways using a newer DNA-based method [called next generation sequencing (NGS)] to measure the total amount of fungal DNA to give a more complete picture of how much fungus is present, not just whether it grows in a lab. Applying NGS to oral swabs to detect bacterial communities in CF, particularly children, has yielded impactful data; however, it has not yet been applied to fungal communities. Our study addresses this gap.
How can this research lead to better ways to diagnose fungal colonies in cystic fibrosis patients? What is the potential impact?
Currently, doctors rely on culture-based tests to identify infection, where they try to grow fungi from patient samples in the lab. However, fungal culture often misses fungi that are present but do not grow well.
This study shows that a DNA-based detection method detects more types of fungi, even in patient samples that tested negative by culture. With better methods for detecting fungi in the airways, doctors may be able to identify infections earlier, through less invasive methods and better understand which fungi are present in the lungs, and make more informed decisions regarding treatment, particularly in pediatric patients.
What are the next steps and long-term goals for this research?
The next steps are to better understand how these fungal communities that reside in the airways affect patient health. For example:
- Do certain fungi make lung disease worse?
- How do fungi interact with bacteria that are also in the lungs?
- Which fungi are harmful, which are harmless?
The long-term goal is to better understand the role that fungi play in CF lung disease. Improving fungal testing methods so they can be used more easily in clinical care is the first step to help monitor lung infections and create more targeted treatments, possibly including antifungal therapies tailored to each patient’s microbiome.
Is there any other information we should know about your research (e.g., Children’s research resources leveraged, how this research was funded, partner institutions to credit, etc.)?
This was a multicenter study with our collaborators at the Perelman School of Medicine at the University of Pennsylvania, Colorado School of Public Health and the Colorado School of Medicine, and included respiratory samples from children with and without CF and adults with CF. All samples were sent to Cystic Fibrosis Microbiome Analysis Core for next generation sequencing. Funding for the study was awarded by the Cystic Fibrosis Foundation and National Institutes of Health.
This work was previously presented at the 2025 American Thoracic Society meeting as well as at the 2025 North American Cystic Fibrosis conference here in Seattle.
Further Reading
Decades of Discovery: World Clinical Trials Day Q&A With Dr. Margaret Rosenfeld
Developing Monoclonal Therapies to Treat Serious Lung Infections
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About the Center for Respiratory Biology and Therapeutics
Unifying basic, translational, clinical, epidemiologic and global health research, the physician-scientists at Seattle Children’s Center for Respiratory Biology and Therapeutics are leading transformative “bench to bedside and back” efforts to drive the next phase of discoveries and novel therapeutics for pediatric respiratory diseases.