Vaughn S. Cooper, PhD

We aim to understand and eventually forecast the genotypes that enable microbes to colonize hosts, evade antibiotics and/or the immune system, and cause disease. We study evolution in action in the laboratory, in animal models, and in human infections using genome-scale methods to identify mechanisms of adaptation. We focus on how bacterial cells evolve to form communities within biofilms or during a range of chronic infections in collaboration with clinical colleagues. We’ve developed new methods for measuring evolutionary forces acting on mutations, e.g. experimental evolution in biofilms, and cost-effective, high-throughput sequencing methods. Our current work is focused on the evolution of antimicrobial resistance, biofilm-associated adaptations in chronic wounds (in which bacteriophage play a major role), in the airways of persons with cystic fibrosis, and in tracking and forecasting the evolution of viruses like SARS-CoV-2. To enable these studies my lab runs a NIAID-supported core tailored to efficient microbial genome sequencing and bioinformatic analyses that aims to identify genetic causes of adaptation and/or drug tolerance during infections.

A broader goal is to share the wonder and power of evolutionary biology through outreach and mentorship. Thousands of high school students each year participate in our EvolvingSTEM program, which provides authentic research experiences in the classroom that improve student identities as scientists. EvolvingSTEM is ongoing in ~30 high schools and >10 colleges. I also co-founded and direct the Center for Evolutionary Biology and Medicine (CEBaM) to catalyze research at this interface, and am an active leader within the American Society of Microbiology.