05/11/2018

Produce Safety Tests Could Use A Refresh

10:18 minutes

rachel noble in a lab using dna and molecular testing equipment
Dr. Rachel Noble examining water samples from a beach near Morehead City using a faster DNA-based test for E. coli. Credit: UNC

The E. coli outbreak linked to romaine lettuce has now spread to 29 states, and it’s claiming more victims. The CDC now reports that 149 people have been infected, more than a dozen have developed kidney failure, and one victim has died. In this segment, Ira talks with Rachel Noble, a molecular biologist at the University of North Carolina, about current methods of testing farm fields for pathogens like E. coli, which can take 24 to 48 hours to show results, and a DNA test Noble has developed that could cut that to less than an hour.


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Segment Guests

Rachel Noble

Rachel Noble is a distinguished professor at the Institute of Marine Sciences at the University of North Carolina, Chapel Hill in Morehead City, North Carolina.

Segment Transcript

IRA FLATOW: The E. coli outbreak linked to romaine lettuce is growing. It’s at 29 states, put half of its 149 victims in the hospital with symptoms like cramps, vomiting, diarrhea, and even kidney failure. And now, one patient has died, according to the latest report out this week from the Centers for Disease Control and Prevention.

The outbreak is now nearly on par with the notorious E.coli spinach outbreak, if you recall, back in 2006. And that déjá vu has made us wonder, is there anything new about how we test our salad greens for disease? Are there ways we could modernize the way we do that to become less reactive and more proactive about the food safety of our salads?

Rachel Noble is here to talk about that. She’s a distinguished professor in the Institute of Marine Sciences at the University of North Carolina in Chapel Hill, based in Morehead City. She joins us by Skype. Welcome back to Science Friday.

RACHEL NOBLE: Thank you very much, Ira. I’m happy to be here.

IRA FLATOW: So how– let’s talk about the ABCs of how our lettuce is tested today. Give us a little thumbnail sketch.

RACHEL NOBLE: Well, the quick sketch is that we have some new legislation that has been put into place. It’s legislation from the FDA and it’s called the Food Safety Modernization Act, which basically requires that water in the fields, particularly agricultural field water, such as irrigation water, and other waters associated with the fields be tested for E.coli. But that’s generic E.coli.

It’s important to remember that those are water samples that are taken, they’re filtered in the laboratory. Those filters are then placed onto Petri dishes, essentially, that contain a concoction of ingredients that are specific only to growing E.coli. And then we basically wait 24 hours for the majority of the tests to count the number of E.coli colonies that appear on that plate. And that’s the way that it’s currently done, but that is only for total E.coli. That is not specific. That’s not a test that’s specific only for the types of E.coli that can make someone sick.

IRA FLATOW: So if you take 24 or 48 hours to test it– some lettuce in the field– they could have harvested and shipped that out by then. Could they?

RACHEL NOBLE: That’s absolutely correct. For a lot of raw products, produce, leafy greens being one of the most important, as we have seen in the past years, we have a situation where freshness and shelf time are optimized. Essentially, it needs to get to the grocery store and be available to the consumer in a pleasing way, as a washed, rinse product.

But these are plants that grow very close to the ground and they often have mixtures of sediment and sand that can be found on that. You can see that just in your salad spinner whenever you spin the salad and ready to eat it for dinner.

IRA FLATOW: And I know you have a patent on a different kind of test, a DNA test that takes much less time. Correct?

RACHEL NOBLE: We have a test, actually, that was developed. Believe it or not, the patent was filed in 2006, the very year of the original outbreak that you just spoke of. And it took some time for it to be completely approved. But we’ve been trying to work to apply this to what we call produce wash. So that’s the water that comes off of the leafy greens as it goes through that washing process that allows a bagged leafy green product to say triple washed, ready for consumption on the front of it.

IRA FLATOW: Would implementing this genetic test be more expensive to farmers and consumers?

RACHEL NOBLE: It’s faster. It takes about 43 minutes for a result. We can get a result completely out in about two hours. And I would argue that the cost is slightly greater, but the way currently that most– a lot of clinical tests are using molecular components these days– DNA, RNA-based tests– that the costs have really come down.

And they’re actually quite close to the cost of the other traditional tests, and that’s because the traditional tests tend to be fairly heavy in the types of preparation to prepare the ingredients and the materials. So it’s a little bit more expensive, but it’s not vastly more expensive.

IRA FLATOW: In my own thinking about this– of course, if you weigh the safety of people’s lives in shipping out something that might be contaminated– the cost may be worth it.

RACHEL NOBLE: That’s exactly right. If people are interested and willing to support a move towards a more proactive system, we will, in general, as a public, as a community, we will need to absorb some of these additional costs, because if we want to be more proactive about the monitoring, currently most of the monitoring that is done, is done out on the samples from the field, but there’s no way to sample every single bit of water that comes in contact with a batch of lettuce.

The wash process, you just don’t know where to sample. You would have to take a lot of different types of water samples in order to describe exactly the type of contamination that any single head of lettuce had experienced.

IRA FLATOW: So how do you then sample the lettuce with a DNA test? Can you get to a lot more lettuce?

RACHEL NOBLE: Well, we actually are just using the water that it’s washed with. Or irrigation water in the field. So we have two choices. We can take a water sample out in the field with the water that’s actually being used to provide water to the lettuce itself. Or when it’s brought to a packing house, basically what happens is that it’s put on a belt and it’s processed through a series of baths. And we sample those baths.

IRA FLATOW: I see, I see.

RACHEL NOBLE: So, of course, it makes the most sense to only sample the very last bath because it doesn’t make much sense to sample the very first bath that it goes through. So you can visibly see the amount of material coming off of the leafy greens as you watch them in these huge systems.

IRA FLATOW: I’m Ira Flatow. This is Science Friday from WNYC Studios, talking with Rachel Noble about lettuce testing. You know, every time we talk about whether it’s lettuce testing, it’s vaccination, or whatever, and there are these other more efficient, better methods available that are never being used. Why don’t we already use genetic testing across the board? It’s pretty standard in the medical field, why not agriculture?

RACHEL NOBLE: It is standard in the medical field. In the medical field you’re often targeting a certain set of symptoms to someone who’s actually coming to the doctor. So you have a good feeling from that particular person, that physician, what you’re already expecting to test for. When we’re out in the field it’s very difficult because there’s a whole range of organisms that actually could be causing a problem.

And so the test that has been put in place by the FDA– that’s now required due to new legislation– calls for testing of generic E.coli, and I think that’s really a good start. That’s really the best way to go because there’s no possible way to test for all of the different types of E.coli or even other things that could get on lettuce and make people sick, like noroviruses or like other organisms, like salmonella or listeria.

So it’s very important that we get a feel for what might be out there from a more generic perspective. But the other answer to your question is that getting change and new rules adapted through the process of legislation and also having different groups of people that are in the produce-growing field, that’s somewhat difficult because these are not rules that have been in place for a long period of time.

And so these are requiring not only training of individuals, training for hygiene for people that are working out in the fields, but also training of a new mode of trying to test the material using a different way. And it just ends up being a little bit difficult. But I truly believe that we’ll get there. It’s just taking a little bit of time to make the jump from one to the other.

IRA FLATOW: Well, speaking of getting there, are you not working with some farms to test the DNA method? How is that going?

RACHEL NOBLE: We have been working with some farms and the interesting thing is that it works well. The data that we are able to produce– what we’re doing now is we’re trying to see how well it compares to the existing methods. Those existing methods that take 24 hours, they are what are considered the gold standard.

And so what we are trying to do is we’re trying to hone our method of quantification, our way of counting the E.coli so that it matches exactly what’s been done previously, so that we know what to do with the data, so that we don’t get a data set that’s apples and oranges. That’s what takes a little bit of time. But that’s a matter of just optimizing some of the details. It’s not a matter of changing the basic components of the test that was patented.

IRA FLATOW: So can we convert our food safety system to be proactive instead of reactive?

RACHEL NOBLE: I think that we can. I think that just the fact that people are more aware from media representation of outbreaks is a start. The FDA legislation is an excellent start. People are insisting that food safety is important. They don’t care for the types of risks that are being posed. People are trying to eat healthier and they want to be able to eat raw foods.

And so I think as this transition takes place, the ability to translate these tests to a faster molecular test, it will take some time, but I believe that we’re on the path. And we also have some examples that show us that that path is vital. So I think that this is a transition that will take place. It’s just a matter of time.

IRA FLATOW: Dr. Noble, thank you for taking time to be with us today.

RACHEL NOBLE: Absolutely. Thank you so much.

IRA FLATOW: You’re welcome. Rachel Noble, distinguished professor in the Institute of Marine Sciences at the University of North Carolina in Chapel Hill. She’s based in Morehead City.

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