Antimicrobial Resistance Profiles of ESKAPE(E) Pathogens Isolated from Retail Fresh Produce in Athens, GA

The overarching aim of this project is to characterize the resistomes and antimicrobial resistance (AMR) phenotypes of ESKAPE(E) group opportunistic pathogens isolated from retail fresh produce. This project has a second overarching aim of supporting the professional development of the Project Director so she may lead interdisciplinary food safety research projects in her future career. To meet these aims, this project has seven specific objectives:Objective 1 of this project is to characterize the resistomes of ESKAPE(E) isolates usingin silicoAMR gene prediction tools, specifically AMRFinderPlus, ResFinder, and RGIbwt. Here, we will extract genomic DNA from isolates using the QIAGEN DNeasy Blood and Tissue kit before fragment analysis with the Advanced Analytical Technologies Fragment AnalyzerTMAutomated CE System, DNA concentration analysis using a QubitTM4 fluorometer, and DNA quality assessment using a NanoDrop One spectrophotometer. Genomic DNA will be sequenced on using a MinION before filtering, assembly, and quality control of assemblies. Assemblies will be annotated using the Prokaryotic Genome Annotation Pipeline, and predicted AMR, virulence, and stress genes will be identified using AMRFinderPlus. The AMR gene prediction pipeline will also involve ResFinder and RGIbwt.Objective 2 of this project is to characterize the antimicrobial resistance phenotypes of the 80 ESKAPE(E) group isolates against first-line antibiotic agents using antimicrobial susceptibility testing. Here, isolates, alongside quality control strains, will be tested against first-line antibiotics using the Thermo ScientificTMSensititreTMGN7F broth microdilution plates, followed by disc elution using the BD BBLTMSensi-DiscTMantimicrobial susceptibility test discs. Susceptibility to agents will be assessed relative to the Clinical and Laboratory Standards Institute (CLSI) M100Enterobacterales breakpoints.Objective 3 of this project is to have two manuscripts pertaining to this project, one being a genome announcement, under peer review by the end of the project period.Objective 4 of this project is for the Project Director (PD) to complete the coursework required to earn the Graduate Certificate in Bioinformatics, offered through the Institute of Bioinformatics at the University of Georgia (UGA). This will directly support the PD's capacity to successfully address Objectives 1 and 3.Objective 5 of this project is for the PD to effectively communicate findings from this project to other scientists and food safety professionals at the annual International Association for Food Protection meeting in July of 2026, which will also serve to assess relevant future directions for such work within the broader food safety microbiology field.Objective 6 of this project is for the PD to communicate relevant findings from this project to UGA Cooperative Extension agents in the summer of 2026 and work with agents to determine feasibility of designing an educational resource based on the project findings that may be useful for the general public.Objective 7 of this project is for the PD to earn her PhD in Nutritional Sciences through having successfully defended an interdisciplinary dissertation project exploring neighborhood food environments, food safety microbiology, and antimicrobial resistance at the end of the project period.