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ARS Home » Northeast Area » Frederick, Maryland » Foreign Disease-Weed Science Research » Research » Publications at this Location » Publication #313383

Research Project: Identification, Characterization, and Biology of Foreign and Emerging Viral and Bacterial Plant Pathogens

Location: Foreign Disease-Weed Science Research

Title: Adaptation and validation of E-probe diagnostic nucleic acid analysis for detection of Escherichia coli O157:H7 in metagenomic data of complex food matrices

Author
item BLAGDEN, TRENNA - Oklahoma State University
item Schneider, William
item MELCHER, ULRICH - Oklahoma State University
item DANIELS, JON - Oklahoma State University
item FLETCHER, JACQUELINE - Oklahoma State University

Submitted to: Journal of Food Protection
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/18/2015
Publication Date: 4/1/2016
Publication URL: http://handle.nal.usda.gov/10113/62209
Citation: Blagden, T., Schneider, W.L., Melcher, U., Daniels, J., Fletcher, J. 2016. Adaptation and validation of E-probe diagnostic nucleic acid analysis for detection of Escherichia coli O157:H7 in metagenomic data of complex food matrices. Journal of Food Protection. 79(4) 574-581. DOI: 10.4315/0362-028X.JFP-15-440.

Interpretive Summary: During foodborne illness outbreaks it is critical to have rapid pathogen identification, and efficient trace-back techniques. Use of advanced DNA sequencing techniques allows for the detection of all pathogens present. However, its use is hindered by the time and computational requirements for data analysis. In this paper, researchers from the ARS Foreign Disease-Weed Science Research Unit and the Oklahoma State University describe how a novel diagnostic data analysis tool called E-probe Diagnostic Nucleic acid Analysis (EDNA) was useful for 100 percent precise detection of a dangerous foodborne pathogen, E. coli O157:H7. The adaptation of EDNA provides the capability to simultaneously screen complex food samples for any number of foodborne pathogens while providing rapid and accurate results.

Technical Abstract: Foodborne pathogens are an increasing problem threatening the US food supply. The need for rapid sensitive diagnostic tools that can address multiple types and taxonomic classes of foodbourne pathogens is growing. This paper describes the adaptation of E-probe Diagnostic Nucleic acid Analysis (EDNA) to the detection of foodbourne pathogens. EDNA is a bio-informatic tool that quickly analyses complex metagenomic data to determine if pathogens of interest are present. In this work, EDNA, which was originally developed to detect plant pathogens, was adapted to detect E. coli O157:H7 from food samples. Alfalfa sprouts inoculated with E. coli O157:H7 were used to generate next generation sequencing metagenomes. After analysis by EDNA, E. coli O157:H7 was detected with 100 percent precision. This represents a novel use for an increasingly versatile diagnostic tool.