Do You Know What’s in Your Salad’s DNA?

New technology promises to tell us everything about the food we eat.

Photo: Suzifoo/Getty Images/iStockphoto
Photo: Suzifoo/Getty Images/iStockphoto
Photo: Suzifoo/Getty Images/iStockphoto

To read it in the news, last year was not gentle on our nation’s stomachs. McDonald’s salads gave 500 people Cyclosporiasis. Two hundred million eggs were recalled. In July, Chipotle faced its umpteenth food-safety problem when 650 customers in Ohio fell sick with clostridium, a pathogen that was new to the chain. Multidrug-resistant salmonella infected turkeys just in time for Thanksgiving, and the country’s supply of romaine lettuce was pulled off shelves not once but twice. All told, the FDA issued food-safety warnings nearly every two days in 2018, and the Centers for Disease Control investigated 24 foodborne disease outbreaks, more than in any other year this decade. Eater recapped the year in food recalls under the headline “11 Foods That Tried to Kill You in 2018.”

There is plenty of debate about what is actually causing these outbreaks, and FDA commissioner Scott Gottlieb argues that better technology simply makes it “easier and faster” to detect contaminants. Our food, Gottlieb contends, isn’t any less safe than in the past, but at least some people disagree. Bill Marler is the country’s most prominent food-safety attorney: he’s won over $600 million for victims of almost every major food outbreak in the last 25 years, and is the founder of Food Safety News. Marler tells Grub Street that, in 2018, he hired four new attorneys; they were his first hires since 2010. “It’s been a very bad year for foodborne illness outbreaks,” he summarizes before adding, in the third person, “it’s a bad sign for food safety if Bill Marler is hiring lawyers and paralegals.”

It might, however, be a good sign for the people who are starting companies to ostensibly fix our food, because even if our food isn’t more dangerous, the case can be made that it at least feels that way, and there are plenty of ideas about what can be done to help everyone believe their food is a little less frightening. Some people want to use blockchain technology to create tamper-proof logs of our mind-bogglingly complex food-supply chain. USDA researchers, meanwhile, are experimenting with “cold plasma,” a pathogen-annihilating technology that looks as futuristic as it sounds. And the most promising idea for everyday retailers and consumers just might be DNA sequencing.

In 2015, a Bay Area start-up called Clear Labs made headlines when it revealed that its tests found some kind of human DNA in hot dogs, and animal DNA in 10 percent of veggie dogs. The goal was to demonstrate that if things like stray hair follicles can enter our food supply undetected, the same is true for microscopic organisms like E. coli (which was responsible for five deaths this past spring after it tainted the country’s romaine supply and which, according to one recent report, can replicate at speeds that push “the limits of what is thermodynamically possible”). “Every week it’s the same stuff, the same recalls,” says Mahni Ghorashi, a co-founder of Clear Labs. “It speaks to the magnitude of problem.”

Clear Labs was able to generate its data using its own DNA-sequencing platform, a breakthrough in the food industry that uses a technology called NGS. If you think this sounds like the food version of 23andMe, it is — sort of — but NGS, which stands for next-generation sequencing, generates far more complex results than what you’ll get with an at-home DNA test. It also generates far more data than what has traditionally been used to test our food. “The food industry is stuck using legacy technology,” Ghorashi explains. He says that, with his company’s sequencing technology, testers can generate “over 100 million data points,” meaning, “you can look blindly into a thing and know everything, everywhere about it.”

Practically speaking, this advanced DNA sequencing is the same type of test that’s used to screen for cancer, only for finding salmonella instead of melanomas. Clear Labs can install a robotic sequencer at a food-processing facility that analyzes whatever sample is loaded into a test tube (a sliver of lettuce, bits of raw pork, a dab of peanut butter), then cross-checks the results against a massive molecular database. The platform can handle hundreds of samples in parallel, plowing through terabytes of data per test run.

The tests are also extremely accurate. There is a less-than-one-percent chance that the test will generate a false positive (reporting that something uncontaminated is tainted) or a false negative (the opposite, where a tainted product gets the all-clear). This is big, because traditional surveys have found food-industry lab tests return false positives as much as 50 percent of the time. To give an example, Ghorashi at least partially blames Chipotle’s food-safety disaster on the fact the chain was only screening for one type of E. coli, so it simply missed another. The tests are fast, too, taking mere hours, as opposed to the days or weeks that older processes take. All of this is to say that, if ground beef or leafy greens are making consumers sick, NGS data can quickly identify the strain and even specific subtype of the bug to see if it came from a farm, a factory, or someplace else.

Martin Wiedmann, a food-science professor at Cornell and a regular on the food-safety lecture circuit, is an advocate for NGS and says that its advanced sequencing “can be 100 times better at detecting outbreaks than what was possible 20 years ago.” Clear Labs’ big breakthrough was to apply this technology to food. Now other companies, like NSF International and Genewiz, offer similar services.

Some of the biggest names in food are starting to notice. Frank Yiannas is the FDA’s deputy commissioner for food policy and response and, before that, was the head of food safety for Walmart. While there, he once pointed out that “people today are further removed from how food is grown, produced, and transported than at any other time in human history.” Plus, he added, the public increasingly mistrusts food companies “due to the food outbreaks and scares we have faced in recent years.” Genetic techniques, he said, “are the way of the future.”

As with any new technology, one of the biggest hurdles to clear before mass adoption has been cost. Ghorashi, however, is quick to point out that prices for NGS are dropping quickly. In 2008, it would have cost $10 million to sequence a person’s genome; today it costs less than $1,000. At Clear Labs, the cheapest tests now run at just $10 per sample.

Those low costs will be crucial, since the benefit of NGS technology is only really felt if everyone along the supply chain has the correct tools. Ghorashi, for one, is particularly excited about the next step: handheld genomic scanners that he predicts will arrive in just a few years. “You’ll be able to catch things as they flow through the supply chain in near real-time,” he says. “Just watch: It won’t be long before this is all over the food market.”

With a food system that is so complicated and massive, it’s something of a miracle that more serious outbreaks don’t occur, and there will never be a way to eliminate contamination completely. But if or when we get to a point where we can easily and instantly identify everything that’s really in our food, it could possibly be one more way for us all to at least feel a little safer next time we sit down for a salad.

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