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GSS BLOG: SCANNING GENOMIC INFORMATION AND INNOVATION

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Evaluating Genome Sequence Scanning Technology for Use in FDA Public Health and Food Safety Efforts

PathoGenetix has signed a collaborative agreement with the U.S. Food and Drug Administration (FDA) to evaluate the company’s proprietary bacterial identification technology for use in FDA foodborne illness outbreak investigation and response. Collaborative research will assess the effectiveness of Genome Sequence Scanning™ (GSS™) technology in identifying pathogens involved in outbreaks, and shortening decision and response time in public health investigations.

The collaboration will evaluate the GSS instrument, reagents and database on a variety of food samples typically collected by FDA during routine food safety audits or foodborne disease outbreak investigations. As a part of the collaboration, FDA bacterial strains of public health interest such as Salmonella, E. coli and Listeria will be added to the GSS™ pathogen database.

Image PathoGenetix Food Safety Testing resized 600Identifying the specific pathogen causing a foodborne illness outbreak is a critical step in defining the extent of the outbreak, determining the food involved, finding the source of the contamination and defining the scope of a product recall. The ability of GSS™ to derive useful data directly from a complex mixture and to shorten the time for pathogen subtyping may allow for quicker decisions affecting public health.

Other microbial identification systems like PFGE, and even new approaches such as whole genome sequencing (WGS), require a cultured isolate as input. Selecting and culturing a bacterial isolate is a complex and time-consuming process that requires experienced microbiology skills, expensive supplies, and multiple days to complete.

The bacterial strain information provided by GSS™ is comparable to pulsed field gel electrophoresis (PFGE), the current gold standard for pathogen typing in foodborne illness outbreak investigation and response.

The increased automation in preparation, measurement and analysis in the GSS™ system has the potential to reduce the need for advanced laboratory and analysis skills in hospital and public health labs monitoring foodborne outbreaks, and in food industry labs conducting ongoing food safety testing and source tracking. The cultural independence of GSS™ eliminates the selection bias inherent in other molecular epidemiology tools. It also makes GSS™ compatible with newer pathogen detection methods increasingly used in clinical and food industry laboratories. 

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