Microbial Genomics and Microbiome Research

The advent of microbial genomics and next-generation sequencing has provided an unprecedented opportunity to study the contribution of discrete microbial genetic traits to pathogenesis, drug resistance, and transmission of single bacterial species as well as of microbial communities. Research in the Division of Infectious Diseases in microbial genomics focuses on:

• Genomics of drug resistance
• Evolution of highly successful bacterial clones
• Transmission of bacterial clones and horizontal transfer of plasmids within communities or the hospital environment
• Impacts of microbiome-pathogen interactions on colonization and infection with multi-drug resistant bacteria

Ongoing cohort studies are incorporating bacterial genomics into pathogen surveillance; for example, in the Neonatal Intensive Care Unit or in solid-organ transplant recipients. While intestinal colonization with carbapenem-resistant Enterobacteriaceae (CREs) has been proposed as a potential risk factor for infections during CRE outbreaks, its actual contribution to infection remains incompletely understood. Dr. Uhlemann's laboratory has established a cohort study of patients undergoing liver transplantation through which they aim to investigate the contribution of colonization to subsequent CRE infection and determine the impact of bacterial adaptations to this transformation. The long-term goal of this project is to elucidate at the bacterial genome level how CRE infections emerge and spread. Understanding these processes is critical to developing intervention and real-time clinical monitoring approaches to limit the impact of CRE infections at an individual and population level.

The division and the Department of Medicine also house the Microbiome Core Facility. The core facilitates all aspects of microbiome studies for investigators across campus and supports a microbiome seminar series.