Enteric pathogenesis and vaccine development
We explore the multifaceted roles by which Vibrio cholerae, enterohemorrhagic Escherichia coli, Shigella, Salmonella, and Listeria monocytogenes cause disease and colonize the host. We have pioneered the development of novel small animal models and applied next generation sequencing technologies, such as Tn-Seq, to decipher the interplay between these pathogens and the host (Kuehl et al 2019, Warr et al 2019, Ritchie et al 2010). Additionally, we are interested in vaccine development and understanding the mechanisms by which our live-attenuated cholera vaccine can prevent cholera-like disease. (Hubbard et al 2018, Sit et al 2019, Fakoya et al 2020).
Host responses to bacterial infection
We are interested in deciphering the host factors that influence the outcome of infection. We have performed genome-wide CRISPR screens, developed proteomic approaches, and pioneered other next-generation sequencing techniques to uncover these factors (Park et al 2019, Pacheco et al 2019, Blondel et al 2019, Abel et al 2014). We are currently expanding our interest from the enteric mucosal surface to other sites of dissemination in the host.
Major on-going projects include:
I. Use of infant rabbit models of diarrheal disease to study host-pathogen interactions. Studies of the biology of enteric pathogens during infection have been hampered by the lack of non-surgical small animal models of diarrheal disease. We found that infant rabbits orally inoculated with EHEC, V. cholerae or V. parahaemolyticus develop diarrheal diseases that mimic the respective human infections. We are taking advantage of these models to gain insights into bacterial physiology during growth in the host as well as host-pathogen interactions.
II. Development and implementation of new approaches to comprehensively identify pathogen and host factors critical for virulence using high throughput transposon- and CRISPR-based screens.
III. We developed an approach (STAMP) that utilizes high-throughput sequencing data to characterize pathogen population dynamics within an infected host. Such analyses reveal the extent and sites of host barriers to infection, as well as pathways by which pathogens disseminate within hosts. We are using STAMP to investigate V. cholerae transmission and to define the factors that control V. cholerae population dynamics. STAMP analyses are particularly interesting for pathogens that disseminate to secondary sites of infection through uncharacterized bottlenecks; e.g., we are using STAMP to investigate passage of Listeria monocytogenes from the GI tract to secondary infection sites. These studies will also identify pathogen and host factors that modulate dissemination routes and founding population sizes.
IV. Spatiotemporal genetic determinants of Vibrio cholerae fitness during infection. We use MultiCAST, an in vivo transposon sequencing approach, to screen thousands of Vibrio cholerae mutants during intestinal infection and sample bacterial populations across multiple GI tract sites and time points. By mapping gene fitness in both space and time, we aim to identify genetic programs that control colonization, metabolism, motility, and virulence, and to reveal how V. cholerae adapts to distinct host environments during infection.
V. Applying single molecule real time DNA sequencing to assess the extent, diversity and functional consequences of DNA modifications (e.g. methylation) in enteric pathogens.