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New Genotyping System Identifies Pathogenic E. coli Outbreak Strains

WOBURN, MA (PRWEB) May 21, 2013

PathoGenetix, Inc., a commercial-stage developer of an automated system for rapid bacterial strain typing, announced today that it has successfully identified and strain typed a collection of 250 pathogenic E. coli strains obtained from the Centers for Disease Control and Prevention (CDC) using the company’s Genome Sequence Scanning™ (GSS™) technology. The findings are detailed in a poster presented at the General Meeting of the American Society for Microbiology in Denver on Monday.

The 250 E. coli strains, which included the most frequently isolated STEC (Shiga toxin-producing E. coli) serotypes from both sporadic cases and multiple foodborne illness outbreaks, were run on the company’s prototype Genome Sequence Scanning system. The results showed that the system could be used to reliably differentiate and strain type STECs of public health and food safety significance, and aid in epidemiological investigation and response in foodborne illness outbreaks.

The GSS-generated phylogenetic tree clearly delineated the major STEC serotypes, and generally clustered the 250 strains into their appropriate serotype-specific branches. Strains that originated from the same foodborne illness outbreak also clustered together on the phylogenetic tree, demonstrating the system’s ability to differentiate outbreak clusters from each other and from epidemiologically unrelated strains. The strain information provided by GSS was comparable to pulsed field gel electrophoresis (PFGE), the current standard for pathogen typing in foodborne illness outbreak investigation and response.

Genome Sequence Scanning isolates and analyzes genomic DNA from either a complex mixture or a pure culture, provides strain type information and predicts the bacterial serotype in five hours, days faster than current identification methods. The GSS technology will be commercially available in 2014 in PathoGenetix’s RESOLUTION™ Microbial Genotyping System.

Of the numerous types of bacteria categorized as Escherichia coli, or E. coli, some cause disease by producing a toxin called Shiga toxin. Since 1993, when four children died and more than 700 people were infected with E. coli O157:H7 in ground beef, there has been an increasing focus on these “Shiga toxin-producing” E. coli (or STECs) in public health, food safety and regulatory efforts. The CDC lists E. coli STEC O157 in the top five pathogens contributing to domestically acquired foodborne illnesses resulting in hospitalization, estimating that it is responsible for 2,138 hospitalizations each year.

In the past 10 years, other E. coli STEC serotypes have been identified in major outbreaks, as dramatically illustrated in Germany in 2011 when more than 4,000 people became ill and 50 people died due to E. coli O104:H4. In 2012, six additional strains of Shiga toxin-producing E. coli (STECs O26, O45, O103, O111, O121 and O145) were declared adulterants by the U.S. Department of Agriculture Food Safety and Inspection Service (USDA-FSIS), which plans to expand testing for these “Big 6” non-O157 strains next year. Although beef remains the most common source, STECs have been linked to major recalls in numerous other foods including spinach, lettuce, cucumbers, peppers, sprouts and currently, frozen foods.


About PathoGenetix, Inc.

PathoGenetix, Inc. is a commercial-stage developer of an automated system for rapid bacterial identification from complex samples. PathoGenetix is a venture-backed company that has received more than $50 million in technology development funding from the Department of Homeland Security. The core GSS technology isolates and analyzes DNA directly from an enriched biological sample—without the need for a cultured isolate—and provides results in just five hours, days faster than current methods. GSS has broad applicability in food safety, industrial microbiology, and clinical diagnostics and research. The first commercial GSS system will be available in 2014 for use in food safety testing and foodborne illness outbreak investigations. Learn more at

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