Can NGS Be a Replacement for PCR?

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

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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.