EXPANDING THE CAPACITY TO SEQUENCE BACTERIAL GENOMES AND PERFORM RESISTOME ANALYSIS TO MOST LABORATORIES: BRIDGING THE GAP BETWEEN BIG SEQUENCING CENTERS AND THE DIAGNOSTIC LABORATORY

Project SummarySalmonella accounts for an estimated 1.4 million illnesses, resulting in 16,000 hospitalizationsand 582 deaths in the United States each year. The incidence of salmonellosis within the U.S.varies from state to state and within states. These variations cannot be explained entirely bydifferences in population density, cultural/ethnic customs, or food distribution networks. Theseregional differences in disease incidence are also reflected in Salmonella serovar distribution. Wedo not know or understand what might explain this geographic distribution of Salmonella infectionin the U.S. Part of the answer lies in identifying the role of potential reservoirs such as pet animals.A better understanding of the transmission dynamics of Salmonella in pets will help us understandthe role of these unique companions in the distribution dynamics of Salmonella.The University of Georgia, through its ?One Health? initiative, is committed to promoting, training,and conducting research in all areas of animal, human and environmental health. The College ofVeterinary Medicine and the State Veterinary Diagnostic Laboratory have a duty to the state andto its constituents to not only perform diagnosis but also to monitor trends and report unusualdisease presentations or patterns. Our laboratory takes this responsibility very seriously, and overthe years our faculty members have published articles with such findings. Moreover, the PI hasworked extensively in the study of the chicken gut micro-biome, including the distribution ofantimicrobial resistance, and the epidemiology of Salmonella in wildlife and the environment.The objective of this grant application is to enhance the capacity of our laboratory and other toassist with the FDA's ability to monitor disease in pet animals and pet food products. Wespecifically propose a ?methods comparison? of the newer generation of sequencing platforms byIllumina (Iseq), Oxford Nanopore Technologies (MinION) and SeqStudio (ThermoFisher) topiggyback on the current VET-LIRN Antimicrobial Resistance Surveillance project for which weare a source laboratory.Our laboratory has expertise in the areas of pathology, bacteriology, parasitology, virology,serology, and molecular biology, including high throughput platform testing. Our faculty and staffare highly qualified and are devoted to animal and public health. Our commitment is evident inour participation in many programs at the state and national levels. We are one of the corelaboratories of the National Animal Health laboratory Network (NAHLN) and participate in allNAHLN surveillance testing. In addition, we are have participated in another cooperativeagreement with the FDA assessing the presence of Salmonella in turkey-based pet treats as wellas engaging in an epidemiological study looking at the prevalence of Salmonella in dog and catfeces (1U8FD004318-01) and the potential risk factors for Salmonella carriage. Also,1U18FD004623 completed and currently 1U18FD006157. Therefore, Athens VeterinaryDiagnostic Laboratory and the PI in this application are uniquely positioned to assist the FDA inmeeting the important goals of the project described in this application.