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Kathleen Glass, distinguished scientist and associate director of the Food Research Institute at the University of Wisconsin-Madison, says whole genome sequencing provides a much more detailed picture of an organism’s DNA, making it far less likely that the source of a bacteria will be misidentified. <b>(Courtesy Wolfgang Hoffmann)</b>

Kathleen Glass, distinguished scientist and associate director of the Food Research Institute at the University of Wisconsin-Madison, says whole genome sequencing provides a much more detailed picture of an organism’s DNA, making it far less likely that the source of a bacteria will be misidentified. (Courtesy Wolfgang Hoffmann)

Whole genome sequencing has gone a long way toward helping scientists track foodborne illness back to the source.

That’s good for consumers who want assurances that food they eat is safe. At the same time, however, it’s causing increasing concern for growers who realize that the technique could potentially implicate a region or any orchard or vineyard, including their own.

Fruit growers have become especially anxious in light of three things:

—The 2014 illness outbreak that was linked to apples.

—The recent use of whole genome sequencing to track not only current disease outbreaks, but also past sporadic clinical cases to their sources as a means of identifying responsibility for low-level but chronic contamination.

—The use of evidence gained from whole genome sequencing to initiate criminal investigations against those connected with illness-causing foods.

Caramel apples

A 2014 listeriosis outbreak tied tainted caramel apples to 34 hospitalizations and three deaths.

Listeriosis is caused by infection with the pathogenic bacterium Listeria monocytogenes. This marked one of the first times that whole genome sequencing had been used to pursue a foodborne-illness outbreak to its origin.

It led to a voluntary recall of Gala and Granny Smith apples, and it showed growers and packers that dangerous illnesses can take root in all kinds of fresh produce, including tree fruit.

The question of who was to blame led to some tense moments, particularly since Listeria is a microorganism that exists just about anywhere in the great outdoors, said Kathleen Glass, distinguished scientist and associate director of the Food Research Institute at the University of Wisconsin–Madison.

“Apple trees grow out in the open. An orchard is not a sterile environment, so you are going to have Listeria show up every once in a while.”

There is no evidence to determine whether apples may have initially been exposed to the bacterium in the orchard, but ample evidence that the specific L. monocytogenes causing illness and death was present in the packing facility.

As a result, the responsibility for the caramel-apple outbreak fell mainly on the packers, she said.

“Ultimately, it was the packer who got into trouble because they didn’t have the next level of cleaning and sanitation that they should have had,” Glass said. The manufacturers also shared the problem. She explained, “When it came to the manufacturers who made the caramel apples out of the contaminated apples, at least one used another sanitation step and assumed it worked, but nobody had a validated sanitation step.”

Validation is key, Glass noted. “This is where we’re really behind the beam. Many packers and processors are doing things they think will be good, but they don’t really have proof that they are.”

Growers may not have been singled out as contributing to this particular outbreak, but Glass said they should nevertheless be cognizant of Listeria and ways they can mitigate it.

“This is an instance where apples, and produce in general, is just a really difficult type of food product, because we don’t have a magic bullet yet to eliminate Listeria. All you can do is try to reduce the level of contaminants that are there.” (See “Protect your customers, protect your orchard” on page 29.)

Cracking cold cases

Trevor Suslow

Trevor Suslow

Besides using whole genome sequencing to track current illness, the U.S. Food and Drug Administration (FDA) has begun using the technique to revisit long-past instances of illness so it can find their source, much as police cold-case squads reinvestigate old crimes to find the culprit.

“A lot of what’s going on in triggering what seems like the weekly product recalls nowadays is the FDA’s, or state public health labs, conducting market-basket surveillance testing,” said Trevor Suslow, extension research specialist in the Department of Plant Sciences at the University of California.

In other words, he explained, regulators are collecting bacterial samples from various foods and food-related locations during their standard or commodity-targeted inspections, and subjecting those positive samples to whole genome sequencing.

When the FDA finds pathogens from those routine inspections or assignments, it is comparing them against the database of illnesses kept by the Centers for Disease Control and Prevention (CDC), and looking for connections between the two.

“We’re talking about going back and looking at past cases, finding indistinguishable isolates associated with your apples or cherries or whatever, and then holding you responsible for those illnesses,” he said. “That’s really how the FDA is using whole genome sequencing — as both a current and as a retrospective assessment of food-safety risks to determine responsibility.”

Although Suslow said the FDA seems confident that whole genome sequencing is an accurate tool for tracing illnesses, he is not so sure.

“We’re starting in my lab to develop data based on environmental testing, and it’s suggesting that such results may not be as ironclad as some might think,” he said, noting that his research group has been conducting this study specifically in tree fruit orchards for about two years.

“We’re now getting the first wave of isolates characterized by whole genome sequencing, in addition to other techniques, and we’re finding that there are isolates that appear to be indistinguishable, yet were collected from regions 100-plus miles apart. So therefore, just because you find a matched whole genome sequencing isolate in one place, that doesn’t necessarily mean it could only have come from one farm or one packing facility.”

In the meantime, whole genome sequencing will continue to be a tool of choice in determining the origin of illness outbreaks, according to Shawn Stevens, a global food-safety attorney and founder of Food Industry Counsel LLC. “As time moves on, we may learn more, but I think the science is good enough to allow the agencies to do what they are trying to do.”

Glass agreed that whole genome sequencing is a high-quality assay, and its use will expand. “It will definitely result in smaller outbreaks in the future, but we’re going to start seeing an increasing number of identified outbreaks,” she said.

Placing criminal blame

Besides looking back in time, the FDA has switched gears in its approach toward the identified sources of contamination, said Stevens, who wrote a white paper on the topic in February (available at bit.ly/22toCA9).

In the past, the FDA tracked foodborne pathogens mainly as a means of learning how they got into the food stream, so it could then determine how to prevent the same thing from happening again.

Following a number of food recalls, however, Congress in 2011 passed the Food Safety Modernization Act, which put the emphasis on preventing contamination rather than on responding to it, Stevens said.

“The Food Safety Modernization Act essentially told the FDA that it was now responsible for overhauling the safety of our food supply,” he said. “As a result, the FDA shifted its policy, and that policy now is one of using criminal sanctions in any circumstance where human illness occurs as a result of contaminated food.”

In fact, an Associated Press article in July 2015 quoted Attorney General Stuart Delery as stating, “We have made a priority holding individuals and companies responsible when they fail to live up to their obligations that they have to protect the safety of the food that all of us eat.”

Stevens pointed to the 2015 Blue Bell ice cream recall as a good example of the altered FDA policy.

In this case, 10 patients over a five-year span — the first in January 2010 and the last in January 2015 — were hospitalized with listeriosis and three died.

In its investigation, the FDA took ice cream samples from retail locations and environmental samples at Blue Bell production facilities, and then was able to match those samples that tested positive for

Listeria to patient samples from the CDC database, he said.

Then, the FDA and Department of Justice served grand jury subpoenas on the company seeking all sorts of documents and records relating to their food safety practices, Stevens said.

“That’s the pattern that I think will be repeated over and over again as we move forward.”

With the FDA’s change in focus and the advent of whole genome sequencing as a means to track foodborne illnesses to their origins, Stevens said anyone involved in the food industry, including growers, should take steps now to scrutinize their operations.

“It’s a very dynamic time for everybody, and I know there’s a lot of apprehension in the industry, but hopefully we can get the word out, keep everybody informed, and look for ways to better protect everyone,” he said. •

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– by Leslie Mertz, Ph.D., is a freelance writer based in Gaylord, Michigan.