Research Strategy: Describe how undergraduate and/or graduate students will be exposed to and supervised conducting hands-on research. Describe how students will participate in research activities such as planning, execution and/or analysis of research. Formal training plans (e.g., non-research activities, didactic training, seminars) should not be provided. A sound rationale should be offered as to why the approach and the research team, including undergraduate and/or graduate students, are appropriate to accomplish the specific aims and to make an important scientific contribution. Drs. Stephens and Hess have developed a 10 week laboratory module, piloted in Spring quarter of 2017, that will expose dozens of students to hypothesis-driven science utilizing whole-genomic sequencing and multidimensional phenotypic data. This portion of the supported research will have the broadest impact on student research and is detailed in multiple sections of the grant including the Introduction to the Resubmission and the Main Proposal. Santa Clara University Department of Biology does not have a graduate program, thus our research groups consist of the P.I., undergraduate researchers and a lab technician when the lab is funded extramurally. Both Dr. Stephens and Hess have a proven track record of recruiting motivated undergraduate students to collect and analyze primary data in both public health and genomics. We each have several undergraduate student co- authors, including first authors, on peer-reviewed manuscripts. We will continue to recruit and train undergraduate researchers using our methods that have proved successful. Importantly these extramural funds will provide our labs with a lab technician. This position is critical to act as primary point of contact for undergraduate researchers, especially during the academic year when the P.I.s have significant teaching responsibilities. We have recruited for these positions from amongst our best graduating research students and have had excellent success in this regard. Recent technicians supported by extramural grants used those positions to further their career paths. Lab technicians supported by previous RUI grants to Stephens have included Lisandra West (who subsequently received her Ph.D. from Stanford University in 2012), Kelly Watanabe (PharmD, UCSF, 2011), Amanda Lieu (M.D., Tufts University, 2014), and Cindy Dick (currently working on her Ph.D. at UC Irvine). In the Hess lab technicians supported by previous grants have included Cindy Dick (currently working on her Ph.D. at UC Irvine), Kiana Espinosa (currently working on her M.D. at Loyola University Chicago), Jillian Gerrity (accepted to medical school at UCSD, working for the non- profit Amigos de Jesus in Honduras) and Farid Tadros (accepted to medical school at Albert Einstein Medical School).
Title: Exploring genomic diversity in commensal Escherichia coli This study will track antibiotic resistance and virulent factors in commensal E. coli in the bay area and compare them to these same factors in bay area pathogenic E. coli. Such studies are needed in public health to understand how dangerous genetic factors such as carbapenem-resistance Enterobacteriaceae (CRE) and colistin resistance are spread among E. coli, a pathogen responsible for almost 2 million deaths annually. Combining whole-genome sequencing with detailed phenotypic characterization of these E. coli isolates, this study will provide crucial insight into how to prevent the spread of these antibiotic resistance factors.