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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Research Project #429923

Research Project: Assessment of Genotypic and Phenotypic Factors for Foodborne Pathogen Transmission and Development of Intervention Strategies

Location: Meat Safety and Quality

2016 Annual Report

Objective 1. Determine the genotypic and/or phenotypic factors associated with the levels and persistence of pathogens and antibiotic resistance in the host animal and the livestock production environment. Sub-objective 1.1 - Determine genotypic or phenotypic factors associated with persistence of E. coli O157:H7 in cattle production. Sub-objective 1.2 - Determine animal host genotypes that confer resistance/susceptibility to pathogen infection. Sub-objective 1.3 - Evaluate the influence of spatiotemporal, environmental, and wildlife factors on pathogen and antibiotic resistance occurrence and transmission dynamics in cattle and waterways in a pasture-based production system. Objective 2. Develop and evaluate intervention strategies that reduce or eliminate the occurrence, transmission or persistence of foodborne pathogens in host animals, including cattle and swine, and the environment. Sub-objective 2.1 - Develop a high-throughput procedure to identify and measure antibiotic resistance genes. Sub-objective 2.2 - Identify alternatives to antibiotics for use as growth promoters in production animals. Sub-objective 2.3 - Determine the effect of calcium hydroxide application to feedlot pens on E. coli O157:H7, total E. coli, and antibiotic resistance on feedlot pen surfaces and in cattle.

The overall goal of this project is to reduce the risk of human foodborne illness, by providing information that can be used to reduce the transmission of zoonotic pathogens and antibiotic resistance from cattle and swine production to food, water, and the environment. Primary targets of the work include Escherichia coli O157:H7 and other Shiga-toxigenic E. coli (STEC), Salmonella, Campylobacter, and antibiotic resistant bacteria in cattle and swine. Approaches for reducing these organisms include reduction of colonization and shedding by livestock, as well as reduction of pathogens and antibiotic resistant bacteria present in the manure and production environment. Persistent shedding, shedding in high numbers, and environmental persistence have been identified as important reasons for the prevalence and maintenance of zoonotic pathogens in livestock, and therefore are intervention targets to reduce these organisms. This project will focus on determining microbial, host, and environmental factors that contribute to these persistence mechanisms, and identify potential strategies for reduction of persistence. Furthermore, this project will develop molecular approaches to assess antibiotic resistance genes in cattle and swine production, and utilize these strategies to evaluate their distribution and abundance. In addition, understanding the potential sources and transmission dynamics of pathogens in livestock production environments is critical for identifying management strategies to reduce their introduction and dissemination. Expected outcomes are scientific information and procedures that will be used to reduce or eliminate foodborne pathogens and antibiotic resistance in livestock production, thus contributing to a safer food and water supply and a lower risk of human foodborne illness.

Progress Report
Reducing pathogens in livestock and their production environment will require identification of genotypic and/or phenotypic factors that are associated with their occurrence, levels, or persistence (Objective 1). In 2016, we initiated studies to determine genotypic or phenotypic factors associated with persistence of the pathogen E. coli O157:H7 in cattle production. In addition, microbial DNA has been extracted from repository bovine fecal samples and sequencing to determine bacterial populations associated with E. coli O157:H7 shedding has been initiated. Bioinformatic pipelines have been developed and are being validated for these sequence analyses. Also in 2016, experiments were designed and procedures currently are undergoing review that will determine associations between swine pathogen shedding and host genotypes. Additionally, studies have been initiated to examine the relationship between bovine genotypes and chronic Salmonella colonization. Reducing pathogen persistence and transmission from host animals will require the development of intervention strategies that reduce their prevalence and persistence in manure and the production environment (Objective 2). In 2016, we completed studies to determine if the use of hydrated calcium hydroxide (lime) can be used to reduce the prevalence and levels of E. coli O157:H7 and antibiotic resistant bacteria on feedlot pen surfaces. Assessing intervention effects on antibiotic resistance genes will require the development of novel approaches to assay those genes that are of concern to both animal and public health. In 2016, research was conducted to develop a high-throughput sequence-based assay for detecting and quantifying the broad spectrum of bacterial antibiotic resistance genes. In addition, studies have been initiated to explore the use of Lactobacillus fermentation extracts as alternatives to antibiotic growth promotants in swine.