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USDA-ARS Evaluating PathoGenetix Technology for Foodborne Pathogen Identification

NEW YORK (GenomeWeb News) – PathoGenetix and the US Department of Agriculture's Agricultural Research Service announced late on Monday the evaluation of PathoGenetix's technology for identifying strains of Shiga-toxin-producing E. coli, or STECs, and Salmonella enterica.

USDA-ARS will provide PathoGenetix the genetic information and bacterial strains of E. coli and Salmonella, and PathoGenetix researchers will analyze the strains as isolates, as well as in mixed cultures using its Genome Sequence Scanning technology.

GSS is currently under development for commercial use as the Resolution Microbial Genotyping System.

USDA-ARS will use the results from the joint analysis to evaluate the Resolution System as a potential platform for the rapid identification of pathogenic Salmonella and E. coli in food samples.

STECs and Salmonella enterica cause an estimated 1.2 million cases of foodborne illnesses each year, PathoGenetix and USDA-ARS said, adding E. coli 0157:H7, the most common of the virulent STECs, has been implicated in multiple foodborne illness outbreaks. Six other STEC serogroups are considered adulterants in certain beef products, but unlike STEC 0157:H7, the "Big 6" virulent strains are not easily differentiated using current molecular testing methods, the partners said.

There are more than 2,500 identified strains of Salmonella enterica, with 1,700 of them classified as human pathogens belonging to subspecies S. enterica I. Twenty of theses serotypes cause more than 70 percent of the illnesses caused by S. enterica subspecies I, pointing to the need for a rapid, cost-effective method of identifying the more virulent strains that may be present in food products.

PathoGenetix's GSS technology identifies DNA from complex mixtures or from isolates, "and automates the process from sample preparation through data analysis to provide actionable information in five hours," PathoGenetix and USDA-ARS said. The technology scans microbial DNA directly from a mixed culture, eliminating the need for pure culture, and reducing time, complexity, skill, and costs associated with molecular identification and strain typing.

They added that the strain type information provided by PathoGenetix's technology is comparable to the current standard for pathogen typing in foodborne outbreak analysis and response, pulsed field gel electrophoresis.

The platform also has been shown to be useful in differentiating virulent Shiga-toxin-producing E. coli, and the Resolution System may be of use as a confirmatory method for "Big 6" STEC screening assays, PathoGenetix and USDA-ARS said.

The deal announced Monday follows a similar evaluation deal in April for PathoGenetix's technology by the US Food and Drug Administration.

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