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United States Department of Agriculture

Agricultural Research Service

Research Project: Exploring Genomic Differences and Ecological Reservoirs To Control Foodborne Pathogens

Location: Meats Safety & Quality Research

2011 Annual Report

1a. Objectives (from AD-416)
1. Molecular characterization of the genomic and transcriptomic differences present in foodborne pathogens (particularly Shiga-toxigenic Escherichia coil (STEC) and Salmonella spp.) to provide an understanding of genetic variation and how this variation is associated with the ability to cause disease in humans. 2. Survey ecological niches and reservoirs using a systems approach to identify sites for potential interventions to reduce foodborne pathogens. 3. Identify how foodborne pathogens acquire, maintain and transmit genes for antimicrobial resistance and virulence within cattle from production to processing.

1b. Approach (from AD-416)
Prevention and control of foodborne pathogens entering the food chain remain elusive goals, despite intensive research efforts. Information is lacking regarding the genetic variation among these pathogens in terms of the virulence and metabolic genes present, nucleotide polymorphisms, and differences in the transcriptional response and control mechanisms employed when they are exposed to adverse environmental stimuli. The advent of novel, high throughput DNA sequencing methods has revolutionized the fields of microbial genomics and microbial transcriptomics. Herein, we propose to make use of these methods and a systems approach in experiments designed to address three key knowledge gaps: 1. How are foodborne pathogens gaining entry into the food chain? 2. What are the genetic elements that facilitate a foodborne pathogen’s ability to cause disease and how are they acquired and maintained? 3. What are the novel DNA targets that can be exploited for detection, traceback and intervention development of more virulent serotypes? The successful completion of this project will result in the development of methods and techniques to detect, characterize and target foodborne pathogens’ ability to survive in their different environments, cause disease in humans and gain entry into the food supply--which ultimately will provide a microbiologically safer food supply.

3. Progress Report
Progress was made on all three objectives. Under Objective 1, we have made substantial progress identifying genetic variation and how it associates with the ability to cause disease. Progress was made under Objective 1.1 by creating pooled DNA from 200 human and environment strains of Shiga-toxingenic Escherichia coli (STEC) serotypes O26 and O111 to identify genetic variation. Under Objective 1.2, progress was made by sequencing six Salmonella genomes and identifying differences in gene content and transcript abundance. Under Objective 2.2, we have made significant progress demonstrating that biofilm formation and the effectiveness of food-grade sanitizers to remove biofilm is quite variable in STEC strains. Multiple factors, including bacterial serotype and strain, surface materials, and other environmental conditions, significantly affect STEC biofilm formation. Under Objective 3.1, substantial progress has been made in understanding plasmid maintenance and stability in Salmonella. Progress was made by identifying bacteria that are and are not susceptible to transformation with different plasmids containing antimicrobial resistance. Under Objective 3.2, significant progress was made in culturing and identifying antibiotic resistant E. coli. Progress was made toward verifying that antibiotic resistant bacteria persist in the cattle feedlot at low levels in the absence of antibiotic use. This persistence is probably due to the integration of antibiotic resistant plasmids into the chromosome.

4. Accomplishments

Last Modified: 10/18/2017
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