Jonathan Frye

Our laboratory investigates antibiotic resistance, pathogenicity, genomics, and the evolution of Salmonella enterica. Salmonella is one of the most prevalent foodborne pathogens globally and is estimated to cause over one million infections in the U.S. each year. Antimicrobial resistance is also common in Salmonella and has been increasing over the past few decades. We have pioneered the application of microarrays, next-generation sequencing, and other innovative methods for investigating Salmonella. These studies identified IncA/C and other plasmids that are responsible for much of the multi drug resistance (MDR) in Salmonella isolated from food animals. These plasmids are large (100-250kb), can encode resistance to twelve or more antimicrobials, and are self-transmissible. Our current studies have determined that the resistance genes found in Salmonella isolated from food animals, retail meats, and human infections are genetically similar indicating that some MDR Salmonella likely developed in animals and were transmitted to humans via food. New studies will test this hypothesis and identify points in food production where antimicrobial resistance develops that can be targeted to improve food safety.

Our laboratory’s genomic analysis projects identified genes found in different Salmonella serovars that are responsible for their variability in host range and pathogenicity. We developed assays based on these genetic differences to detect dangerous Salmonella serovars such as Heidelberg and Typhimurium in food. We have also used this data to develop an automated, high-throughput PCR and capillary analysis technique to identify the top 100 clinical Salmonella serotypes (SMART: Salmonella multiplex assay for rapid typing). Testing has shown that SMART is more accurate, easier, quicker, and cheaper than traditional serotyping. Our ongoing investigation of Salmonella genomics has completed the sequencing of 200 Salmonella genomes that represent the genetic diversity found in the most prevalent clinical Salmonella serovars. Our laboratory’s new studies use this database to improve our understanding of Salmonella evolution and enable us to identify genetic markers for pathogenicity, host range, and host specificity. These markers will be used to develop rapid methods for Salmonella outbreak investigations and improve our ability to protect human health. Recently we have expanded our work to address a major data gap by determining what role surface water plays in the development of antimicrobial resistance in bacteria and its spread to humans and animals. This work is a collaboration with Dr. Elizabeth Ottesen, Dr. Erin Lipp., and Dr. Charlene Jackson. Together we are working with the Upper Oconee River Watershed Network (UWON), a group of volunteers that do a quarterly evaluation of the surface waters that feed the Oconee River. We have been sampling the water with their help since Winter of 2015. While Dr. Ottesen focuses on the metagenome of the watershed and Dr. Lipp looks at the ecology of the watershed, Dr. Jackson and I are isolating bacteria, investigating their prevalence, antimicrobial resistance, and genotypes. Our current work is looking at Salmonella, Escherichia coli, and Enterococcus spp. Together we hope to get a comprehensive picture of what is in the watershed and how it changes over time.