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ARS Home » Research » Research Project #430182

Research Project: Monitoring and Molecular Characterization of Antimicrobial Resistance in Foodborne Bacteria


Project Number: 6040-32000-009-000-D
Project Type: In-House Appropriated

Start Date: Mar 30, 2016
End Date: Mar 29, 2021

1. Provide data and characterize pathogen prevalence, unique characteristics and trends on antibiotic resistance, subtyping and molecular characterization of foodborne pathogens in food animals. 2. Identify and characterize potential genetic markers within and across serotypes for Salmonella isolated from poultry for rapid identification and diagnosis. 3. Evaluate the role of innovative chemical and/or biological treatments including arsenicals, prebiotics, or ammonium compounds and how they impact the prevalence and type of antimicrobial resistant pathogens or resistance genes. 4. Develop, evaluate and optimize processing treatments to reduce, control and potentially eliminate foodborne pathogens in poultry processing. 5. Evaluate and define the potential role of protozoa in shaping the ecology of bacterial pathogens in controlling foodborne pathogens in poultry processing environments. 6. Develop algorithms for interpreting and handling sequencing data to aid in epidemiological tracking, defining differences in isolates of foodborne pathogens, including antibiotic resistance patterns, and predicting and determining the source of the isolate.

The goals of this project fit into four major approaches: 1) analysis of antimicrobial resistance mechanisms and genetic elements in foodborne bacteria from poultry, 2) analysis of innovative chemical and/or biological treatments used for poultry processing on resistance in foodborne bacteria, 3) development of alternative methods for processing poultry products, and 4) development of methods that accurately monitor the microbial quality of poultry products processed by alternative methods. Studies will focus on the molecular aspects of antimicrobial resistance to identify and characterize new and emerging resistance phenotypes and genotypes of high priority type bacteria from poultry [categorized as urgent and serious threat level antimicrobial-resistant pathogens by the Centers for Disease Control and Prevention (CDC)]. Those high priority bacteria will be evaluated for resistance to biocides. This project will target foodborne pathogens including Salmonella, Campylobacter, and Listeria and commensals including Escherichia coli and Enterococcus, for their role as reservoirs of resistance. The alternative processing methods in this project include testing several novel chemical and physical decontamination procedures. The approach for most of this work is to apply the intervention strategy and compare the microbial quality of the treated poultry product with control product treated by standard methods. Intervention strategies will include studies on the microbial ecology in and around poultry processing and further processing plants, such as floor drains, to determine a particular ecological niche or reservoir for a specific pathogen in the processing environment. These studies will improve understanding of sources and harborage points for human pathogens and how best to combat colonization of a processing plant with those pathogens. A long term objective is to develop systems using protozoa as natural controllers of foodborne pathogens. This will involve studying the ecology of protozoa that feed on the pathogens and determining methods to enrich the processing environment with effective protozoa. Approaches for monitoring microbial quality will include enhancing the sensitivity and specificity of microbial detection. The project will also use genetic typing methods including whole genome sequencing and metagenomics sequencing to characterize antimicrobial and biocide resistance and track specific clones of pathogens in and around poultry processing environments. Data from this research will be used to assist other Federal agencies in assessing antimicrobial resistance in food animal populations as well as to address a direct need outlined by the National Action Plan for Combating Antibiotic-Resistant Bacteria (CARB) in evaluating potential alternatives to antimicrobials. Data generated on biocide resistance and resistance genes active against chemicals specific to poultry production and processing is a specific concern to USDA-FSIS. Development of technologies for detection of microbial contaminants is a critical need for Federal regulatory agencies.