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Enhancing food safety with Next Generation Sequencing

Mahni Ghorashi of Clear Labs in California, USA, describes a new food analytics platform that uses next generation sequencing to analyse the molecular makeup of food samples.

The impact of food product recalls
On May 31, 2016 Golden Valley-based General Mills voluntarily recalled 10 million pounds of Gold Medal flour, Wondra flour and Signature Kitchens flour after a potential E. coli outbreak in its products[1]. The company subsequently expanded the recall dates, first in June and again in July, adding another 20 million pounds to the recall list. Fortunately, the outbreak did not result in any fatalities, but it is expected to have cost the brand tens of millions of dollars[2].

Food recalls cost an average of $15m per incident and cause significant harm to brands’ reputation and credibility. They can also cause significant harm to individuals. In the United States alone, foodborne illnesses make 48 million people sick and are responsible for 3000 fatalities every year[3]

As Bill Marler, a Seattle lawyer specialising in food poisoning lawsuits against food companies, remarked in response to the General Mills E.coli outbreak, ‘We are likely to continue to see ongoing recalls of other products. It looks like the wheels on the bus are coming off, but it's actually a positive thing. I see recalls as a sign the system is operating like it should. Recalls, in the long run, are a positive for food safety.’

Despite the fact that the majority of brands have maintained a strict adherence to food safety protocols and best practices, the negative publicity generated by a rising number of high-profile recalls continues to reinforce consumer scepticism regarding the food industry's ability to ensure safety. 

Food analytics platform
Clear Labs was founded in 2014 by a group of software engineers and genomic scientists to set worldwide standards for food integrity. Its aim is to help customers mitigate risk through data-driven intelligence. It has developed a pioneering new food analytics platform, Clear View, which uses Next Generation Sequencing (NGS) technologies to analyse the composition of DNA in food samples, allowing food manufacturers and retailers to improve the transparency of their supplier network and build stronger food safety programmes. 

The US Safe and Accurate Food Labeling Act of 2015[4] requires the labelling of genetically modified foods, known as GMOs (genetically modified organisms). Clear Labs offers a comprehensive GMO test with coverage of all known GMOs to allow manufacturers to label products as GMO-free.

The NGS-based food tests and software analytics have potential to significantly improve the scalability and accessibility of food safety and quality measures, by comparison with conventional technologies, such as PCR and Elisa-based testing, which have inherent limitations as highlighted by several high-profile outbreaks and recalls in 2016. Compared to 2015, recalls surged by 22%[5].

The food analytics platform can complement food manufacturers’ or retailers’ existing food safety programmes. Laboratories have the option to subcontract NGS testing to Clear Labs or license the technology to conduct their own tests (Figure 1).

Analytical programmes can be up and running with NGS in a matter of weeks. Clear Labs has developed APIs (Application Programming Interfaces) that allow customers to work with food data across various sources and tools so as to not disturb a brand’s existing safety management processes. 

Figure 1: Clear Labs integrates into brands’ existing workflows

In order to provide analytic insights, Clear Labs is building a massive molecular reference database. This would not have been possible a decade before the introduction of NGS in 2005. NGS technologies, developed at Illumina, Roche, Life Technologies, and a number of other firms, have dramatically reduced the time and cost of DNA and RNA sequencing, revolutionising both the study and application of genomics and molecular biology. 
The technology has matured remarkably quickly. Late last year researchers at The University of Toronto launched a massive project to sequence the genomes of 10,000 people per year[6].

This is truly astounding considering that it took 13 years and $3b to sequence the first human genome and that as recently as 2012 there were only 69 whole human genomes that had ever been sequenced. 

Food genomes are far less complex than human genomes, and since establishing Clear Labs in 2014, the company has continued to build its reference database for food. The world’s largest, it currently spans over 2 million entries and tens of thousands of food products and ingredients. 

This database powers a unified, sample-to-answer, analytics platform that connects comprehensive testing results with product metadata: type, origin, ingredients, nutrition data and label claims.

The analytics platform can be leveraged to access the food database, a library of algorithms and customisable reporting tools.

This database powers a unified, sample-to- answer, analytics platform that connects comprehensive testing results with product metadata'

Why NGS?
NGS is poised to replace PCR and Elisa as the standard in food safety testing. The technology is ready for food-industry applications including food safety, food-authenticity, GMO, and food-microbiome testing as well as Whole Genome Sequencing (WGS).

The primary limitation of PCR is that it is targeted, so it is necessary to know what you are looking for in order to test for it. It is also conducted one target at a time, so a separate run is needed for each target chosen. This is costly and difficult to scale up. 

By contrast, NGS-based testing is universal. A single test exposes all potential threats, both expected and unexpected, because instead of testing for one gene at a time, millions of reads are sequenced at once. A single NGS test can reveal the presence and concentration of bacteria, fungi or allergens as well as the precise composition of ingredients in any given sample, helping to guarantee that hazards do not slip through the supply chain. 

PCR-based tests have high limits of detection and cannot be used to distinguish between closely related species. NGS-based tests, on the other hand, have low limits of detection; the increased sensitivity of NGS produces more accurate results along with much higher levels of specificity. For example, a study conducted by the American Proficiency Institute[7] that analysed the results from 39,500 food proficiency tests conducted between 1999 and 2012 found that routine pathogen testing with NGS detected 100% of target genomes, while PCR or antigen/antibody based methods detected 98%-99% of target genomes. At scales of hundreds of thousands of tests per year, the reduction in number of false negative rates, each a potential recall, is substantial.

There is a concern that adopting new technologies, especially those which promise increased levels of transparency, will increase exposure to regulation and litigation. On the other hand, no stakeholder wants to signal that they are disregarding consumer concerns, especially at a time when consumer vigilance and awareness about food safety and quality are at an all-time high. Millennials are now the largest living generation[8], and, as consumers, they are more likely than their forbears to research what goes into the products they buy and to buy from brands that demonstrate a commitment to social good[9].

There are numerous ways to leverage NGS technologies in food safety applications that empower manufacturers without adding substantial risk. While WGS, for example, provides unprecedented levels of transparency, manufacturers who have access to analytics platforms can maintain control of what they voluntarily test for, customise internal reporting and create private, secure libraries for WGS. In other words, introducing new technologies does not preclude having to make hard decisions that weigh the risk of increased regulation against the risk of product recalls. Brands that have adopted NGS testing will simply be able to execute on these decisions more quickly and at less cost. 

Among other solutions, NGS and WGS are driving the rapid development of microbial strain tracking technology in the food industry to identify persistent or resident pathogen strains and high-risk environments for pathogen growth.

These technologies are also proactively staying a step ahead of new regulatory protocols. The Food Safety Modernization Act (FSMA) (see page 36) now gives the FDA power to access records and conduct on-site ‘swabathons’. Manufacturers using NGS technologies can efficiently engage in intensive internal swabbing to better define microbial ecologies of facilities and take swift corrective actions.

NGS-powered environmental monitoring has been particularly useful in facilities that produce ready-to-eat (RTE) products, which are exposed to the environment and have no kill-step for pathogens after packaging.
Genomics powered environmental monitoring can also verify the effectiveness of routine monitoring programmes and surface insights that inform more effective and more efficient processes. A leading meat and poultry manufacturer, for example, is using Clear Labs to screen plants and houses for resident versus transient pathogens. The company has been able to more accurately identify pathogen strain types and their origin, reduce recall risk through proactive testing, as well as liability through encryption and data matching. 

NGS technologies can also help brands dramatically reduce their exposure to food fraud and third-party contamination.  Food fraud, which occurs in up to 10% of all food types, precipitates serious public-health risks and costs the global food industry $10b-$15b annually. When an NGS-powered authenticity test reveals unexpected ingredients and contaminants, the platform automatically generates an internal report. The report depicted in Figure 2, alerted a Clear Labs customer to the fact that its supplier had engaged in economically motivated adulteration (EMA).

The US FDA (Food and Drug Administration) and FSMA now require food facilities to implement preventative controls to avoid fraud. Deploying traditional PCR-based tests for supplier verification is costly and the results are not reliable since PCR cannot distinguish between closely related species and has high false-positive rates. NGS-powered tests reveal episodes of contamination and adulteration that would be likely to remain undetected. The Clear Labs authenticity test can also be used for undeclared allergen and pathogen identification, which account for more food recalls than any other form of contamination[5]

Figure 3 is a report generated for an existing customer, which reveals both the presence of an undeclared allergen and the absence of listed ingredients. It clearly illustrates the difference between PCR and NGS testing. To detect the presence of an allergen that could easily trigger a recall using PCR-based tests, a brand would have had to specifically test for soy. Rather than wait for an outbreak before conducting a battery of tests to locate the source of an allergen or contaminant, a brand leveraging NGS testing can proactively analyse samples to mitigate risks. 

Figure 2: Economically motivated adulteration (EMA) detected in spice supplier

Figure 3: Presence of undeclared allergen and missing ingredients

Traditional thinking is that adopting high-transparency technologies might expose food products to liability and increased scrutiny, but food brand recalls are so exorbitantly expensive to manage that increased monitoring and transparency of the supply chain is essential. 

The perceived value of food-industry goods is determined by consumer demand and while the food industry’s decisions on operational and process innovation have traditionally been based on legal and regulatory counsel, gaining consumer trust by employing technologies, such as NGS, that enhance transparency, will be increasingly important in the future.

Now, more than ever before, it is the food-industry’s scientists and researchers, those charged with applying new technologies to solve real problems, who can best help endow our products with value.

Mahni Ghorashi, co-founder Clear Labs, 3565 Haven Ave. Suite 2, Menlo Park, CA 94025, US













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