Whole genome sequencing provides insight on the future of food safety

Salmonella

Salmonella

Food production industries continue to make improvements in pathogen reduction and improving public health. One of the ways in which this is accomplished is through improvements in food safety diagnostics.

Next generation sequencing and genomics provides processors with previously unavailable information on strains, sources, and identity of particular pathogens or spoilage issues. Next generation sequencing and whole genome sequencing (WGS) are also key parts of the Healthy People 2020 goals, and the goals of various food agencies.

Sequencing is gaining more traction in the food production arena with the three key food safety agencies, USDA, FDA and CDC, adopting WGS platforms for outbreak investigations, and as a replacement of PULSENET. The additional resolution provided by WGS helps improve the time it takes an agency to identify an outbreak. This reduced amount of time also means the outbreaks become smaller, and less people can become ill from the events.

While the agencies are using WGS as a tool for outbreak identification and resolution, processors can use it for additional purposes. For example, if an organism is present in a manufacturing facility, WGS can help determine some key pieces of information over a given set of isolates.

WGS answers questions such as: Is the pathogen of concern a resident or transient bacteria? If the bacteria is resident, it can start to identify areas within a manufacturing facility that could be harborage areas for the bacteria. This additional resolution, which is not available through traditional subculturing methods or pulse field gel electrophoresis, provides companies with definitive results on potential sources, harborages, and contamination transfer mechanisms.

One example of an improvement in this area is NeoSeek. NeoSeek is a novel platform developed by Neogen that uses next generation sequencing to help processors identify specific pathogen(s). For example, the currently available Salmonella serotyping services provide greater accuracy than traditional labs using anti-sera for serotyping.

Using this novel approach, NeoSeek examines approximately 4,500 bases in the genome over three specific areas including the O antigen, H antigen, and ISR region (identified by Jean Guard at USDA, Athens). Additionally, the samples are not subject to the limitation of traditional serology, such as non-motile Salmonella (i.e. protein expression), or limitations of an anti-sera library.

Next generation sequencing products will continue to be developed through GeneSeek and is a new and exciting area where the power of genomics will provide better insights into the bacteria in a food production facility. This will improve public health, improve food companies supply chains, and provide an additional layer of brand protection.

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