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PathoGenetix Identifies E. coli and Listeria for Food Safety; Enables Identification from Clinical Samples

PathoGenetix™ Inc., a commercial-stage developer of an automated system for rapid bacterial identification, presented new research this week demonstrating the use of its Genome Sequence Scanning™ (GSS™) technology to confirm and strain type pathogenic bacteria. The research shows that GSS could be used to identify foodborne pathogens of increasing concern in food safety, in one study identifying STECs (Shigatoxin-producing E. coli) serotypes with the more dangerous "virulence" genes, and in another study not only differentiating L. monocytogenes among the general Listeria species, but even identifying its strains. The study findings were detailed in two posters presented on Monday at the 2014 General Meeting of the American Society for Microbiology in Boston.

The two posters add to a large body of PathoGenetix and independent research demonstrating the capabilities of the GSS technology in providing rapid, culture independent pathogen subtyping and serotype determination from complex biological samples. The GSS technology, which has broad applicability in food safety, industrial microbiology, and clinical diagnostics and research, will be commercially available in the RESOLUTION™ Microbial Genotyping System by early 2015 for use in food industry safety testing and public health foodborne illness outbreak investigations.

Because the GSS technology scans microbial DNA directly from a mixed culture, and does not require a pure culture isolate, it can identify multiple bacteria serovars or strain types in one sample, and greatly reduce the time, complexity and skill level required to confirm the presence of dangerous pathogens. The level of discrimination provided by GSS is comparable to pulsed field gel electrophoresis (PFGE), the current gold standard for pathogen typing in public health laboratories. As a result, GSS could be used to enable quicker decisions affecting food safety and public health.

The first study, entitled "Strain typing of BIG 7 STECs and differentiation from stx- and/or eae- BIG 7 serogroup E. coli by Genome Sequence Scanning" demonstrates that GSS could be used to accurately identify particular strains of pathogenic E. coli that have been identified as "adulterants" in food by the U.S. Department of Agriculture's (USDA) Food Safety and Inspection Service (FSIS). Recent USDA-FSIS regulations require food companies to test for the presence of specific disease-causing organisms (E. coli O157:H7 and STECs of six other serogroups) in combination with certain "virulence" genes (stx+ and eae+), which when present indicate the particularly pathogenic nature of the bacteria. This research shows that GSS could be used as a confirmatory method for Big7 STEC screening assays used to test for these adulterants in food products, and reduce potential loss of product due to high false positive rates among current STEC screening tests.

The second study showed that GSS provides similar insights into the structure of the Listeria species, by rapidly confirming and differentiating the pathogenic L. monocytogenes strains from nonpathogenic Listeria species. In the study, entitled "Rapid Molecular Serotyping of Listeria spp. by Genome Sequence Scanning," GSS was used to examine a collection of 18 strains and 35 genome sequences representing five different species of Listeria. In general, the strains from the different species of Listeria were distinctly separated from each other, with strains belonging to the four major lineages of L. monocytogenes forming individual clusters with each serotype clearly distinguished.

In a separate press release, PathoGenetix, has developed and validated a protocol for the identification and subtyping of bacteria directly from human clinical stool samples without prior cultural isolation. The protocol, which runs on the RESOLUTION™ System, enables public health and microbiome research laboratories to determine serotype and strain type information for multiple bacteria directly from an enriched stool sample, in just five hours.

The new protocol also demonstrates the potential use of the System for follow-up identification to the culture independent diagnostic tests (CIDTs) used by hospital and clinical laboratories in diagnosing foodborne diseases. CIDTs screen for multiple pathogens in stool samples without obtaining a pure culture isolate. But identification methods currently used in public health laboratories to determine if the disease-causing organism is part of a larger foodborne outbreak require a cultured isolate. The PathoGenetix protocol has the potential to enable the public health system to do its important work even when CIDTs are employed and no culture is available.

The fully automated RESOLUTION System, including instrument, bioinformatics software and database, and pathogen-specific assays, will be commercially available by early 2015 for use in both food industry testing and public health foodborne illness outbreak investigations.

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