The pathogenic potential of Great Salt Lake dust

The Great Salt Lake (GSL) is rapidly shrinking, exposing a vast lake bed and emitting dust that affects the air quality for the 1.3 million people in the Salt Lake Valley (SLV) with a disproportionate impact on underserved communities. Dust from the GSL contains heavy metals, dangerous for human health. However, the pathogenic content of GSL dust has not been characterized, an urgent gap in our understanding of the health consequences of the drying lake.

To characterize the potential pathogens in the source of GSL dust, we will sample dust from a transect on the exposed lake bed. We will sieve dust and then re-aerosolize it to focus on the respirable fraction of dust that can penetrate deep into the lungs and that poses the most direct infection risk. To characterize the dust microbiome that may more proximally affect people and may contribute to increasing environmental health disparities in SLV, we will collect airborne dust using filter samplers across city transects. For both dust from the GSL lakebed and urban air, we will characterize the dust microbiome, identifying all known human bacterial and fungal pathogens, with next generation sequencing.
This proposal establishes a new multidisciplinary collaboration between researchers in the School of Pharmacy, School of Medicine, College of Mines and Earth Sciences, and College of Engineering, enabling us to collect preliminary data for an NIH proposal to study the epidemiology of GSL dust. By focusing on a major environmental and health justice challenge, our proposal advances the University of Utah’s strategic goals to develop and transfer new knowledge and to engage communities to improve health and the quality of life.

Current Status

2025-02-04
A major obstacle in genomic studies of the Valley fever fungus, Coccidioides, is that fungal DNA comprises only a small proportion of DNA in clinical and environmental samples. Previous genomic sequencing studies have relied on culture of clinical, environmental, or ecological samples, which is resource-intensive and requires a BSL-3 facility. The majority of all sequenced Coccidioides genomes are from cultured human isolates, limiting our understanding of Coccidioides diversity and transmission dynamics in its reservoir(s).
We are working to optimize a hybrid capture approach to bypass culture and directly sequence whole Coccidioides genomes from complex samples for the first time. Specifically, we have designed RNA baits to tile a non-redundant pan-genome of C. immitis and C. posadasii genome sequences. RNA baits hybridize with Coccidioides DNA, allowing us to selectively sequence Coccidioides. In a pilot experiment, we included both soil and small mammal lung DNA samples positive for both C. immitis and posadasii.
We found that hybrid capture significantly increases Coccidioides sequencing efficiency, allowing us to identify Coccidioides reads and assign likely species. However, median sequencing coverage of Coccidioides from both soil and mammal was low (mean: 0.75X).
Together, our results indicate that hybrid capture is an effective tool for the genomics of environmental fungi. However, due to the low copy number of fungal genomes in soil and mammal samples, further optimization is required.