Genomic Testing in Food Safety
Genomic testing of food products or environmental surfaces for food safety has been around for a number of years now. Whereas PCR-based tests still dominate as the standard for pathogen detection and identification, genomic testing (next gen sequencing and whole genome sequencing) offers the opportunity to provide much more information, which can be critical in tracing a contamination back to the source. Absolute cost is still high compared to PCR methods; however, there is value equated to the additional information provided with genomic identification.
When discussing genomic testing related to food safety, it’s important to clarify the difference between next-generation sequencing (NGS), and whole genome sequencing (WGS), as they are sometimes used interchangeably, and they are two distinct technologies. NGS is an umbrella term for various sequencing technologies, including whole genome sequencing, 16S analysis, targeted panel sequencing, and others.
Whole genome sequencing is a subset of next gen sequencing, and as its name implies, it involves sequencing the whole genome of an organism. For example, some NGS applications use a targeted PCR step to isolate the DNA targets of interest, while WGS does not use a targeted PCR step. Using currently available bioinformatic tools, regulatory agencies such as the FDA, USDA and CDC now use NGS and WGS technologies to sequence foodborne isolates within the timeframe of an outbreak (3+ days). And 16S sequencing is an efficient method of identifying bacteria by targeting a specific region of the genome.
Sequencing can uncover genetic markers which can track and trace foodborne pathogens back to the source, as well as identify virulence factors. The FDA led the way in the United States for NGS deployment and standardization as a test method, beginning in 2013, as part of its GenomeTrakr project.
Genome Trakr deployed sequencers to FDA labs and was designed to create a database of the genetic makeups of thousands of foodborne disease-causing bacteria for use in cross-referencing and identifying future outbreaks. In 2014, the FDA labs started using WGS for Shiga toxin-producing E. coli (STEC), salmonella, and listeria monocytogenes detection and confirmation. The FDA sequences all routine samples for pathogenic bacteria using WGS, and has done so since 2016.
As explained above, from a regulatory perspective, WGS is a great tool. A pathogenic food outbreak can be identified in its early stages, minimizing illness. The pathogen can even be traced back to the source, preventing future contamination and illness. The result is that we are seeing more frequent outbreaks being reported as they are identified, but the impact is smaller.
But the perspective of the processor or producer of the food product differs. Food producers and processors are reluctant to implement WGS in food plants for several reasons:
- Too much information makes it difficult to determine response levels. Because of the high-volume nature of food production and the lag time of testing, plants need faster tests rather than the higher resolution that WGS offers.
- Genetic information is useful for tracking outbreaks. However, the value of genome identification of pathogens within a food processing environment is dubious, because the focus there is eliminating all pathogens, irrespective of subtype or species.
- There is a significant cost associated with equipping a lab to implement NGS. In addition to the lab equipment and consumable expenses, there are also costs such as: IT infrastructure; staffing of personnel trained to process the samples and interpret the bioinformatics, and training/hiring staff to apply the genomic testing information into an actionable strategy for pathogen control.
Marketing Genomics for Food Safety
We are at a crossroad with this technology. While it has a high level of maturity for specific applications, there are still significant barriers to widespread adoption in the food processing and production markets. Predictably, there will be some adoption by companies that can afford the investment in resources, as well as intermittent projects and studies, either related to research or outbreaks.
- A broad-perspective analysis was published recently in Food Safety Magazine: “The Benefits and Barriers of Whole-Genome Sequencing for Pathogen Source Tracking: A Food Industry Perspective,” which goes into detail on the situation and explains the challenges of using this technology.
- As suggested, decreasing the amount of information and increasing the speed of analysis would offer the industry the product it needs and increase adoption of the technology. One company focused on evolving NGS technology to make it faster and more user-friendly is Clear Labs, with their Clear Safety Service, as well as Similarity Analysis used for environmental monitoring.
WGS brings a lot to the food safety table. While this technology has proven instrumental in reducing the severity of food safety outbreaks in the field, its potential as an analytical tool to be used at the plant level has yet to be fully realized. Other NGS technologies hold more promise as practical tools for use in food production and processing environments. As with any product, customers will look for the product that offers the best fit-for purpose. Further development will reduce complexity and create products which fit the market requirements for a broader audience within food safety.
In the Spirit of SWAT (Sell What’s Available Today), How Do You Address the Market with Your NGS Products and Services?
- Focus on the needs of your audience. Facility mapping or installation qualification of new equipment using NGS are viable services if positioned correctly.
- Evaluate the go-to-market strategy of your NGS offering. Prospective customers for NGS will need proof in the form of data, reference customers, and key opinion leaders. This is a product that will have to be sold using a personal approach — not from an internet order (at least initially). Sell the benefits and build the relationships.
- Consider blending in NGS services as a compliment to other products, or collaborating with a partner leveraging their products or services. NGS services could complement cleaning chemicals, packaging, capital equipment, or contract lab services.
Remember, every product can be sold. It’s just a matter of finding the right customer!
If you need help with a food safety marketing strategy, contact us for a 30-minute consultation.