In the sample preparation room of Menlo Park startup Clear Labs, research associate Abhishek Hegde carefully injects a series of tiny test tubes with fluid. Each tube contains a different food sample — and the transparent solution extracts DNA from the sample so it can be sequenced and analyzed.
Looking at food at the molecular level helps Clear Labs answer questions that plague retailers, manufacturers and consumers: Was the most recent batch of beef contaminated with E. coli? Is this soy burger patty actually vegan? Is that “GMO-free” sticker accurate?
Food safety is about more than checking bureaucratic boxes. A food-borne illness outbreak can create lingering damage to a brand’s image, as burrito chain Chipotle proved in 2015. As DNA extraction becomes easier and the world stores more information on computers, new technologies are emerging to pinpoint safety issues.
DNA sequencing allows the food industry to determine exactly what is (and isn’t) in a food sample, which is particularly useful when tracing a food illness. If a person is diagnosed with a particular strain of salmonella, sequencing the genome of that bacteria makes it possible to narrow the source to, for example, nut butters.
“You can tune questions to that epidemiological data you have,” said Jesse Miller, director of public health and safety organization NSF International’s Applied Research Center.
The level of precision that comes from looking at DNA is transformative, according to Mahni Ghorashi, co-founder and chief commercial officer at Clear Labs. “You’re able to sequence everything and see threats you would never think to test for,” he said. Ghorashi quotes Eric Brown, director of the Food and Drug Administration’s division of microbiology: “It’s like upgrading from an old backyard telescope to the Hubble.”
Since 2008, the cost of sequencing a human genome fell from around $10 million to about $1,000, according to the National Human Genome Institute. Routine tests at Clear Labs — where only targeted sequences of DNA are analyzed — cost tens of dollars per sample, Ghorashi said. An authenticity test or a GMO screening would cost in the low hundreds of dollars, because they require looking at all genetic markers on every ingredient, not just at selected areas of DNA. Still, that’s far less than they would have cost a decade ago, a benefit of the fast progress of sequencing technology.
Founded in 2013, Clear Labs recently announced it had raised $16 million from investors. The company says it works with about a dozen major food brands, including half of the top 10 U.S. food manufacturers and retailers. Clear Labs declined to name any customers, though Walmart’s vice president of food safety, Frank Yiannas, confirmed that the company has worked with Clear Labs. “Genetic techniques are the way of the future,” he said.
Clear Labs’ technology has been on the market for a little over a year, and the company has conducted hundreds of thousands of tests so far. Ghorashi says Clear Labs has built the largest molecular food database in the world, with millions of genomic markers in it. But the entire process of getting a sample and figuring out what unexpected elements are in it still takes three to four days.
Clear Labs and others are working to drive the time to sequence and analyze DNA from days to hours. That would significantly shorten the length of government food advisories and reduce retailers’ losses.
Research scientist Pollard works on developing novel food safety technologies that involve DNA extraction and sequencing to determine what is and isn’t in food products.
Another option that will be available to grocers in the coming years is blockchain, a distributed digital ledger shared among a network of computers. With this technology, every time a food product moves through the supply chain, it is recorded, creating an immutable digital record of where the food has been. (Blockchain technology was first developed to track the movement of digital bitcoins.)
As tools like DNA sequencing and blockchain technology become faster, the lag time between observing an outbreak of food-borne disease and pinpointing its source — which currently can take weeks — could shrink dramatically. Following an announcement in October, Walmart and IBM began a collaborating on a blockchain system to track pork in China and sliced mango in the U.S.
In a demonstration last month, Yiannas of Walmart was able to trace a pack of sliced mango to a particular farm and packaging date in just 2.2 seconds. The same task would have taken the company a week without a blockchain. Walmart is reaching out to other food companies and retailers, and plans to test blockchain technology on multi-ingredient foods later this year.
Omar Oyarzabal, a food safety specialist at the University of Vermont, said the main caveat with blockchain is that it would require the global supply chain — from stores in the U.S. to farms in Mexico and beyond — to digitize. “It’s not very common to have electronic information that is created and entered in an electronic way,” he said. “There’s a lot of paper documentation.”
But Yiannas is more optimistic, given the rapid spread of smartphones.
“If we were trying to do it 10 years ago,” he said, “it would’ve probably been an idea before its time.”
Isha Salian is a San Francisco Chronicle staff writer. Email: firstname.lastname@example.org