Research

We develop and apply evolutionary approaches to answer open questions about pathogen transmission & epidemiological dynamics with a current focus on M. tuberculosis. Our goal is to directly inform public health in low-income settings.

Locating tuberculosis (TB) transmission

TB kills more people than any other infectious disease. TB is preventable and curable, yet persists in marginalized populations excluded from access to healthcare and other critical social services. It is difficult to identify where the TB bacterium is transmitted and therefore, the best methods to prevent transmission. With researchers in Brazil and Paraguay, we sequence M. tuberculosis genomes to reconstruct transmission chains and identify key locations to focus TB prevention measures.

Investigating multiple scales of pathogen diversity

Pathogens are constantly evolving and individual infections often contain diverse populations of pathogens, within-host variation. Yet most genomic epidemiology studies rely on consensus sequences, generating a single representative genome, discarding potentially valuable epidemiological information. We have integrated deep sequencing and epidemiological data to measure the epidemiological information in SARS-CoV-2 within-host variation. We are currently developing approaches to measure within-host M. tuberculosis use this information to study transmission.

Pathogen emergence linked to climate change in the American West

Climate change has been implicated in the emergence of several fungal pathogens, including Valley fever fungus Coccidioides, a major, environmentally-acquired cause of pneumonia in the American West. The burden of Valley fever disease is expected to dramatically increase under climate change, yet we don’t currently know the current distribution of Coccidioides nor how and where it is expected to spread under climate change. With Coccidioides genomes, we are reconstructing the emergence history of the fungus in Utah in order to inform projections of its future spread.