Bacterial

The advent of high-throughput sequencing has afforded the ability to examine infectious diseases at a previously unprecedented level. This project takes advantage of ongoing challenge studies with two important human pathogens, Vibrio cholerae, the etiological agent of cholera, and enterotoxigenic Escherichia coli, the etiological agent of severe diarrhea in the developed countries and traveler's diarrhea in individuals from developed countries. Each of these organisms are causes of significant mortality due to diarrheal illness in less economically developed countries leading to hundreds of thousands of deaths each year. Our long-term objective of these studies will be to understand the dynamic interactions between the host, pathogen and microbiota and how these interactions play a role in determining the pathogen population in the host, the development of an immune response, and if these interactions can be assessed and altered in a manner that could be exploited for therapeutic and diagnostic development.

This project will provide a detailed understanding of the virulence mechanisms of these important global enteric pathogens, as well as the complexity of the interactions of the host, pathogen and microbiota. The vast majority of typical pathogenesis studies utilize biochemical assays, tissue culture models, animal models, or non-mammalian models to study virulence mechanisms. The Center for Vaccine Development (CVD) at the University of Maryland School of Medicine (UMSOM) has unparalleled experience in conducting vaccine and pathogenesis studies that utilize human subjects experimentally challenged with a variety of bacterial, viral or parasitic pathogens. The CVD has two upcoming studies that involve human challenge studies with V. cholerae and ETEC strains and clinical specimens from these studies are available for analysis in the proposed University of Maryland Genomic Center for Infectious Diseases (GCID). The combination of state-of-the-art genomic, transcriptomic and metagenomic technologies together with human vaccine challenge studies offers an unprecedented opportunity to generate novel and significant new insights into the interaction of host, pathogen, and microbiota.

Our central hypothesis is that there are as of yet unidentified interactions between host, pathogen and microbiota that impact virulence and clinical outcome during human infection. These interactions will be examined at the pathogen and system levels through pathogen population analysis, community structure as well as metagenomic and metatranscriptomic analyses.

The population diversity of these two enteric pathogens that arises in vivo during the course of human infection will be examined through population analysis. It is anticipated that passage through the human host will select for sub-populations that may arise during infection or may be present within the input population pool. The results will have implications for the basic understanding of the infectious process, but also for applied applications in molecular epidemiology where conclusions are often drawn on the basis of SNP analysis. The inclusion of individuals who have been vaccinated, as well as unvaccinated controls, will provide additional insight into the impact of the immune status on pathogen selection.

The community structure of the human gastrointestinal tract will be examined using 16S rRNA, as well as metagenomic studies. The introduction of a human diarrheal pathogen will likely significantly alter the human microbiome structure. These studies have not been undertaken in this manner before and represent a step forward in the analysis of diarrheal disease. In conjunction with the study of the population structure the methagenomic and metatranscriptomic analyses will provide insight into the potential and the transcriptionally active components of the community structure. It is anticipated that results will provide novel data on how the gastrointestinal microbiome modulates the immune response to the vaccination, as well as what role the gastrointestinal microbiome plays in modulating disease severity. Overall this project will provide an unprecedented view of the host, pathogen microbiome interactions before during and after diarrheal disease.