CF is a genetic disease associated with debilitating and terminal lung infections. The bacterial lung pathogen Pseudomonas aeruginosa chronically colonizes the lungs of more than 80% of patients with CF, and its presence is strongly associated with worse patient status. However, it is clear that factors other than the presence of P. aeruginosa impact the rate and extent of lung damage in P. aeruginosa-infected patients. More than a dozen studies have found that fungi also inhabit the lungs of the majority of individuals with CF, published clinical data report correlations between the presence of fungi in culture and worse lung function or increased frequency of disease exacerbations. In two studies, researchers found that patients colonized with both P. aeruginosa and fungi, such as Candida albicans or Aspergillus fumigatus, were worse off than those not co-colonized by fungi. Based on published and preliminary data, we hypothesize that the dynamics between airway bacteria and fungi strongly impact CF lung disease in two ways. First, we hypothesize that the suppression of bacteria during periods of antibacterial therapy leads to high fungal loads that can be harmful to airways (tested in Aim 1). As part of these studies, we will develop methods for the analysis of fungal communities in collaboration with Dr. Mitchell Sogin (MBL) and Dr. Jason Stajich, (UC Riverside) using longitudinally collected clinical samples from patients undergoing systemic antibiotic therapy. In addition to analysis of the changes in fungi species, we will determine if specific fungi increase in absolute levels, how the bacterial communities change in conjunction with changes in the fungal communities, and how fungi impact the host over the course of treatment. Second, we hypothesize that molecular interactions between P. aeruginosa and fungi such as C. albicans and other Candida spp. increase P. aeruginosa virulence in mixed bacterial and fungal infections (tested in Aim 2). We will use a combination of cell culture models and clinical studies, in combination with cutting edge RNA analysis methods, in an iterative process to understand the dynamics of bacteria and fungi in the CF lung. Our long term goals are: (i) to determine if CF patients colonized with fungi would benefit from existing antifungal therapies that are currently only routinely administered to a small subset of CF patients, and (ii) to develop strategies for the analysis of other chronic, polymicrobial infections involving fungi and bacteria, and the interactions that occur between microbes within polymicrobial communities.

Public Health Relevance

Chronic respiratory infections often involve long-term polymicrobial infections involving both bacterial and fungal species. Using respiratory infections associated with the genetic disease cystic fibrosis as a model, our goals are to understand i) how specific bacteria and fungi in the lung impact one another, and ii) if commonly used antibacterial therapies are associated with increases in fungal loads that themselves can be damaging to the host. These studies involve the development and use of state of the art technology for the analysis of polymicrobial communities, and this work has the potential to advance our understanding of the interactions between microbes within other host-associated microbial communities in health and disease.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Special Emphasis Panel (ZGM1-GDB-2 (MC))
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Sledjeski, Darren D
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Dartmouth College
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Grahl, Nora; Dolben, Emily L; Filkins, Laura M et al. (2018) Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA. mSphere 3:
Demers, Elora G; Biermann, Amy R; Masonjones, Sawyer et al. (2018) Evolution of drug resistance in an antifungal-naive chronic Candida lusitaniae infection. Proc Natl Acad Sci U S A 115:12040-12045
Grahl, Nora; Demers, Elora G; Crocker, Alex W et al. (2017) Use of RNA-Protein Complexes for Genome Editing in Non-albicans Candida Species. mSphere 2:
Sakhtah, Hassan; Koyama, Leslie; Zhang, Yihan et al. (2016) The Pseudomonas aeruginosa efflux pump MexGHI-OpmD transports a natural phenazine that controls gene expression and biofilm development. Proc Natl Acad Sci U S A 113:E3538-47
Hogan, Deborah A; Willger, Sven D; Dolben, Emily L et al. (2016) Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease. PLoS One 11:e0149998
Hollomon, Jeffrey M; Grahl, Nora; Willger, Sven D et al. (2016) Global Role of Cyclic AMP Signaling in pH-Dependent Responses in Candida albicans. mSphere 1:
Xie, Jinglin L; Grahl, Nora; Sless, Trevor et al. (2016) Signaling through Lrg1, Rho1 and Pkc1 Governs Candida albicans Morphogenesis in Response to Diverse Cues. PLoS Genet 12:e1006405
Hogan, Deborah A; Gladfelter, Amy S (2015) Editorial overview: host-microbe interactions: fungi: heterogeneity in fungal cells, populations, and communities. Curr Opin Microbiol 26:vii-ix
Willger, S D; Liu, Z; Olarte, R A et al. (2015) Analysis of the Candida albicans Phosphoproteome. Eukaryot Cell 14:474-85
Grahl, Nora; Demers, Elora G; Lindsay, Allia K et al. (2015) Mitochondrial Activity and Cyr1 Are Key Regulators of Ras1 Activation of C. albicans Virulence Pathways. PLoS Pathog 11:e1005133

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