GCID Bacterial Genomics Project

Bacterial diseases kill millions of people worldwide each year, despite the advent of antibiotics 90 years ago. Emergence and spread of new and rapidly evolving pathogens with increased virulence, resistance to antibiotics, and transmissibility is increasingly straining efforts to manage infections and save lives. To combat this trend, we need a comprehensive and systematic understanding of the complex dynamics between hosts (including host microbiota) and pathogens at every level of interaction — cellular, individual, and population. 
Our studies leverage recent advances in sequencing technologies, innovative high-throughput molecular and multi-omic approaches, access to unique patient cohorts, and novel computational methods to characterize the genomes and transcriptomes of bacterial pathogens, as well as their individual strain-level interactions with their hosts and other microbiota. In collaboration with renowned infectious disease researchers, clinicians, and epidemiologists, our aims target critical gaps in our understanding of key infectious disease threats — uropathogenic Escherichia coli (UPEC), carbapenem resistant Enterobacteriaceae (CRE), and multidrug resistant enterococci. 


  1. Determine the gut-to-urinary tract dynamics of UPEC in recurrent urinary tract infections.
  2. Track the multiscale dynamics of antibiotic resistance gene proliferation.
  3. Characterize the dynamic functional reservoir of MDR enterococci.

While our aims focus on ESKAPE pathogens, our goal is to pioneer and disseminate a comprehensive technological framework and resources to empower clinical and research communities working to understand, diagnose, prevent, and treat infectious diseases.

GCID scientists conduct additional work on bacterial genomics, including projects focused on tuberculosis and antibiotic resistance, through the Broad Institute's Infectious Disease and Microbiome Program.