Food Safety Research Information Office
Title:Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

1. Molecular characterization of the genomic and transcriptomic differences present in foodborne pathogens (particularly Shiga-toxigenic Escherichia coli(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.

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Approach: 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.

Funding Source:United States Department of Agriculture (USDA), Agricultural Research Service (ARS)
Start Date:2011
End Date:2016
Project Number:5438-42000-015-00
Accession Number:420888
Institutions:USDA/ARS - Northern Plains Area
Investigators:Bono, James
Harhay, Dayna
Schmidt, John
Wang, Rong
Project Reports:2013 Annual Report
2012 Annual Report
2011 Annual Report
Published Journal
Articles USDA
ARS (NP 108):
Prevalence of Escherichia coli 0157:H7 and Salmonella in camel, cattle, goat and sheep harvested for meat in Riyadh
Bosilevac JM, Gassem MA, Al Sheddy IA, Almaiman SA, Al-Mohizea I, Alowaimer A, Koohmaraie M.
J Food Prot. 2015 Jan 1;78(1):89-96.
Lineage and genogroup-defining single nucleotide polymorphisms of Escherichia coli O157:H7
Jung WK, Bono JL, Clawson ML, Leopold SR, Shringi S, Besser TE.
Appl Environ Microbiol. 2013 Nov;79(22):7036-41.
Influence of therapeutic ceftiofur treatments of feedlot cattle on fecal and hide prevalences of commensal Escherichia coli resistant to expanded-spectrum cephalosporins, and molecular characterization of resistant isolates
Schmidt JW, Griffin D, Kuehn LA, Brichta-Harhay DM.
Appl Environ Microbiol. 2013 Apr;79(7):2273-83.
Cross-sectional study examining Salmonella enterica carriage in subiliac lymph nodes of cull and feedlot cattle at harvest
Gragg SE, Loneragan GH, Brashears MM, Arthur TM, Bosilevac JM, Kalchayanand N, Wang R, Schmidt JW, Brooks JC, Shackelford SD, Wheeler TL, Brown TR, Edrington TS, Brichta-Harhay DM.
Foodborne Pathog Dis. 2013 Apr;10(4):368-74.
Dual-serotype biofilm formation by shiga toxin-producing Escherichia coli O157:H7 and O26:H11 strains
Wang R, Kalchayanand N, Bono JL, Schmidt JW, Bosilevac JM.
Appl Environ Microbiol. 2012 Sep;78(17):6341-4.
Association of nucleotide polymorphisms within the O-antigen gene cluster of Escherichia coli O26, O45, O103, O111, O121, and O145 with serogroups and genetic subtypes
Norman KN, Strockbine NA, Bono JL.
Appl Environ Microbiol. 2012 Sep;78(18):6689-703.
Biofilm formation by Shiga toxin-producing Escherichia coli O157:H7 and Non-O157 strains and their tolerance to sanitizers commonly used in the food processing environment
Wang R, Bono JL, Kalchayanand N, Shackelford S, Harhay DM.
J Food Prot. 2012 Aug;75(8):1418-28.
Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans
Bono JL, Smith TP, Keen JE, Harhay GP, McDaneld TG, Mandrell RE, Jung WK, Besser TE, Gerner-Smidt P, Bielaszewska M, Karch H, Clawson ML.
Mol Biol Evol. 2012 Aug;29(8):2047-62.
Non-Journal Publications:
Longitudinal concentrations of antibiotic resistant Escherichia coli in feces do not correspond to the patterns of antibiotic use at a cattle feedlot - (Abstract Only)
Accepted Publication (20-Feb-13)
Prevalence of lactose fermenting coliforms resistant to third generation cephalosporins in cattle feedlot throughout a production cycle and molecular characterization of resistant isolates - (Abstract Only)
Schmidt, J.W., Kuehn, L.A., Griffin, D., Harhay, D.M. 2012. Prevalence of lactose fermenting coliforms resistant to third generation cephalosporins in cattle feedlot throughout a production cycle and molecular characterization of resistant isolates [abstract]. International Association for Food Protection. p. 148-149. Abstract No. P2-95.
Food Safety Categories:Contaminants and Contamination
Government Policy and Regulations
Pathogen Biology
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