Can NGS Be a Replacement for PCR?

(Editor’s Note: This is an online-only article attributed to December/January 2019 issue.)

I don’t think that any of us would work in the food safety industry if we didn’t believe improvement was possible. Through my own work, I hope for a future where foodborne illness outbreaks are virtually eliminated and food recalls are a thing of the past. It’s a big dream. According to the CDC’s July 27, 2018 Surveillance Summaries published in the Morbidity and Mortality Weekly Report, foodborne contaminants cause on average almost 9.4 million illnesses every year. And a recent CDC FoodNet report says that foodborne illness is on the rise, increasing 96 percent in 2017 compared with the 2014-2016 average.

Clearly, it’s a multi-faceted problem that needs an equally complex and complete solution. So how can a safer food ecosystem that takes into account both consumer and food industry needs be achieved? The answer may rest in tech that has been around for quite some time.

Complacent Methods

As the industry becomes complacent with current tools, safety systems are in need of new, intelligent innovation. Polymerase chain reaction (PCR), which has been a popular method for detecting pathogens and adulterations for decades, is thought to be no longer as useful in preventing foodborne illnesses.

In the over 30 years PCR has been on the market, it hasn’t done enough to improve its processes. Instead, the technology has stagnated, especially over the past 10 years. PCR hasn’t kept pace with automation, which in any other industry or tech implementation is now a given. In contrast, PCR still largely relies on hands-on labor. This is problematic for multiple reasons, as it increases the chance of errors in processing and generally creates inefficiencies in a food safety platform.

Unfortunately, this extra effort doesn’t mean extra insight. PCR still just gives binary yes/no answers, meaning that suppliers frequently know the symptom but not the root cause of their problems. Additionally, with high rates of false positives and negatives, even a PCR diagnosis is not the absolute a company would hope for. And yet, this is the current industry standard that has not changed in decades.

PCR as the Canary in the Coal Mine

While foodborne illness should be a preventable problem, it has become prevalent due to the limits of current technology. By the time the scope and specifics of an outbreak are known, it’s often too late for both consumer and company. In a report released in December 2017, the Inspector General of Department of Health and Human Services found it took 57 days on average to recall food.

The industry needs efficiency and knowledge. PCR struggles to meaningfully improve on either vector. Instead, as a tool, it remains a stealthy and serious deficiency in the pursuit of public health.

This problem is reminiscent of another famous public health safety problem, which was also dangerous in its silence: carbon monoxide. For centuries, miners went underground not knowing what they were breathing or how mine conditions would affect their physiology in the wake of their work. What has become a cliché was once peoples’ reality; miners really did take canaries down into coal mines to gauge the safety of the area. If the canary stopped singing, the miners knew they had to get out. While it was industry standard, this methodology was certainly not perfect.

Relying on miners’ observation of a canary is a crude and incredibly fallible mechanism for determining risk. It also frequently left miners with insufficient time to respond to the danger. Sound familiar?

PCR is similarly rudimentary. The living and dying of a canary may be a primitive detriment for safety, but at least it’s an absolute one. In contrast, the false positives and false negatives of PCR in the food safety industry commonly require reevaluations of results, as each uncertainty has huge ramifications from both a food safety standpoint and from a cost consideration standpoint. A false positive means high operational costs, as inventory is held and results are double checked. Meanwhile, when a false negative occurs, it can have ramifications of up to $10 million.

Eventually, the carbon monoxide detector was invented, and mine safety was dramatically improved. However, it took many lives and tragedies for people to force this change and push on inventors for a better solution. The food industry also wants improvement. Companies want to implement whatever protocols that enable them to deliver better and safer food products to customers. Every food safety official, from top to bottom, already recognizes the problem of pathogens and contaminants, as well as their impact.

The Next Safety Revolution

The problem of food safety is even more nuanced than the above example. While the analogy is useful for understanding the prevalence and arch of the problem, it is imperfect. Most notably, with food safety, there isn’t merely one contaminant—like carbon monoxide—to worry about. There are many possible adulterations or issues. That’s why it’s crucial to have technology that is comprehensive in scope and execution.

A promising technology that is thorough and fast enough to speak to these unique challenges of the food safety industry is next-generation sequencing (NGS). NGS looks at the very DNA of foods to discover their composition. It’s a methodology that has revolutionized both the study and application of genomics and molecular biology. Now it’s taking the food safety world by storm.

Unlike PCR, which requires different tests for each pathogen, NGS can ask almost infinite questions about a sample and get the answers all in one test. Additionally, it can sequence hundreds of samples at a time. This amount of data enables companies to identify pathogens at the strain and serotype level even in mixed-ingredient and packaged foods. In addition, all tests go from sample to answer within 24 hours.

The rapid access to in-depth information is something that companies are hungry for. For safety and for consumer satisfaction, having product accuracy that borders on the absolute is not just crucial; it’s a competitive advantage. NGS can provide this certainty with an accuracy of 99.9 percent. PCR’s accuracy is approximately 98 percent, according to a study published in Applied and Environmental Microbiology on accuracy and sensitivity of commercial PCR-based methods for detecting Salmonella enterica in feed.

“Tunable” pathogen profiling is also available from such products as Clear Safety’s Clear Labs NGS platform, which enables companies to set the level of molecular characterization based on the information they need.

This awareness is empowering rather than overwhelming thanks to the complete capabilities of NGS. For every discovery, it offers a solution.

Food safety is a complex, ever-evolving conversation. NGS fits into that conversation with its own complexity of analysis and delivery of results.

Endeavoring Towards a Safer Future

NGS provides an opportunity to enter a new era of safety where companies have unprecedented information about their food products—and consumers have unparalleled peace of mind.

Of course, the obvious benefit to NGS is helping the industry better prevent and react to contamination along the supply chain. However, the key here is not that we’re just better at knowing what happened, we can actually begin to prevent the contamination from making it beyond its first touchpoint along the supply chain. With the speed, accuracy, and affordability provided by NGS, food safety testing can be done early and often, helping brands avoid the consequences of an extensive recall.

The rise of NGS means that we are building a future of food safety that is preventive as well as proactive.

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Ghorashi is co-founder and COO of Clear Labs, where he leads commercial activities, including product, sales, and marketing. Reach him at [email protected].