Pathogen Detection and Prevention Advice

Despite advancements in food safety, foodborne illnesses haven’t dropped and, in some areas, they’ve increased. While the battle with pathogens is waged from farm-to-fork, there are some back-to-basics best practices food processors can implement and double down on to help the fight.

Shiga toxin-producing E. coli (STEC) infections increased 34% in 2019 compared with 2016-2018, according to data from The Foodborne Diseases Active Surveillance Network.
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The food safety industry still has work to do.

According to a May 2020 report from the Foodborne Diseases Active Surveillance Network (FoodNet), progress on lessening the number of foodborne illness in the United States has stalled. Current estimates from the Centers for Disease Control and Prevention (CDC) are that roughly one in six Americans get sick every year, 128,000 are hospitalized and 3,000 die of foodborne illness.

Based on preliminary data, of the eight pathogens FoodNet tracks, Campylobacter and Salmonella are still the most commonly reported infections. Additionally, infections caused by Listeria remained unchanged, but 98% of reported cases required hospitalization — 21% resulted in death. Shiga toxin-producing E. coli (STEC) infections increased 34% in 2019 compared with 2016-2018.

What all that data means is targets laid out in Healthy People 2020, the Health and Human Services initiative aimed at reducing foodborne illness, will not be met. While some of those cases could be due to consumer mishandling of raw goods such as beef or chicken, the food industry has ground to make up as well.

“Better implementation of known prevention approaches and new strategies is needed to overcome the continued challenges to reducing foodborne illnesses,” the FoodNet report said.

A new year and new decade (and new Healthy People 2030 goals) mean a chance to make more progress. So, we got input from foodborne pathogen experts on back-to-basics best practices on how to understand, detect and prevent four common pathogens: Salmonella, Campylobacter, E. coli and Listeria.


From a consumer awareness perspective, Campylobacter might be the odd pathogen out among this group, but it’s one of the leading causes of illness in the U.S., as the FoodNet report found. 3M Food Safety Pathogen Technical Sales Specialist Luke Thevenet chalks up the lack of consumer knowledge to a couple reasons.

Campylobacter, although it’s not specific to poultry, a large percentage of testing and cases almost exclusively come from the poultry industry,” he said. “It’s not going to be something like Listeria or Salmonella that can be found in a lot of different industries.”

Compared to E. coli, Salmonella and Listeria, it’s also not as hardy, requiring an anaerobic (lack of oxygen) environment to grow. That also makes it more difficult to test for.

“Simplifying the testing protocol with an aerobic enrichment media was difficult up until recently,” Thevenet said.

There’s also not as much regulation around Campylobacter testing, and Thevenet said there’s less prevalence in companies testing their products for it.

“Completely unlike Listeria, unlike Salmonella, [Campylobacter is] a very fragile bug. Yet it causes all this human illness.” Meredith Sutzko, Product Manager, Romer Labs

“There was a lot of buzz about Campylobacter on the Department of Agriculture (USDA) side maybe a year or two years ago,” said Meredith Sutzko, product manager at Romer Labs. “They changed their methods for testing from quantitative to qualitative because direct plating wasn’t detecting it.”

Basically, testers were taking the samples and plating them directly, but the levels weren’t as high as expected considering the number of people getting sick from it. Once the same samples were tested using the enrichment-based methods, more Campylobacter was found.

“They were doing a lot of testing to try to implement new performance standards for poultry, but those haven’t come out yet,” Sutzko said.

It can also be found in raw milk, and subsequently, raw milk cheeses, which Sutzko said leads to a high number of cases in Europe, where a lot of raw milk cheese is consumed.

“It’s a very interesting bug that’s just not focused on as much as Salmonella because it’s not as deadly,” said Sutzko. “Completely unlike Listeria, unlike Salmonella, it’s a very fragile bug. Yet it causes all this human illness.”

While Campylobacter’s stringent growth conditions might make it seem like it wouldn’t be as prevalent, Stan Bailey, senior director of scientific affairs at bioMérieux, said the percentage of chickens with it coming into a facility to be processed could be higher than those with Salmonella.

It is primarily being brought into the plants in the live animals, Bailey said, “unless there happened to be cross contamination from one part [of the plant] to the other.”

E. coli

Although E. coli is one of the most common organisms on Earth, “the vast majority of them are not a problem,” Bailey said. “Your intestinal tract, my intestinal tract, are loaded with E. colis. The one that’s most frequently associated with illness — and it can be really bad because it could cause kidney failure — is E. coli O157:H7.”

While commonly attributed to red meat, E. coli is an issue in a range of products, including leafy greens and flour. In fact, General Mills, Aldi, Pillsbury and King Arthur Flour all recalled flour in 2019 due to E. coli concerns. Bailey said this can be particularly dangerous since batches of flour can be so large, leading to more outbreak risk.

When it comes to E. coli in leafy greens, Sutzko said that the freshness of the products and short shelf life make detection an important challenge to tackle.

“Getting that test result fast is really critical,” she said.

The challenge with leafy greens and STEC is the size of the growing fields and the ability to take a representative sample.

“How much testing is enough, basically?” she asked. “You’re testing the product itself, or some processors may choose to test [rinsing flume water]. But it’s the scale of the amount of food [you need] in order to find it, because you don’t know how much is contaminated.”

In 2012, the USDA’s Food Safety and Inspection Service (FSIS) identified six more E. coli serotypes for which it said it would “begin instituting a zero-tolerance policy,” but they weren’t as universally tested for until recently, and Bailey expects them to be tested more in the near future.

On the Food and Drug Administration’s side of things, Bailey said the agency’s approach of testing for anything pathogenic comes with its own set of problems.

“That’s good on one level because it’s a broader brush,” he said. “But it’s also difficult because being able to test for all of those things right is not as straightforward — and most people can’t do it.”


Unlike Salmonella, E. coli and Campylobacter, Listeria is so often a process environment problem. Meaning the product can pick it up somewhere in the manufacturing process. While fewer people get sick from Listeria, it can be deadly for pregnant women or immunocompromised individuals.

It’s also a ubiquitous organism that can live virtually anywhere and thrives in unsanitary conditions, such as uncleaned drains or hidden pockets of a facility that attract moisture.

“It gets into the drains and because of the cool nature of processing plants, it will persist,” said Bailey. “Listeria will actually be growing in refrigeration.”

The best mode of prevention for Listeria is a rigorous sanitation routine, paying attention to drains and anywhere with excessive moisture build up.

Bailey said that while Listeria was an issue in processed meats in the 1980s and 1990s, it can really pop up in a number of places such as leafy greens, ice cream, frozen vegetables, hummus and, most recently, an outbreak earlier this year involving El Abuelito Cheese.

[Listeria] gets endemic in a plant if you’re not careful.” Stan Bailey, Senior Director of Scientific Affairs, bioMérieux

“It gets endemic in a plant if you’re not careful,” Bailey said.

As far as testing, Sutzko said it’s not going to be hard to find Listeria if water is used in your facility.

“If you do environmental monitoring and sample the right places, you find Listeria,” she said. “Whenever water is used in a facility to clean and sanitize, you’re always going to have Listeria there. So, it’s really a constant battle to keep that Listeria out.”

She said it’s important to have a robust sampling plan, look in the right places, have proper sanitation and sanitary equipment that’s easy to disassemble and clean every nook and cranny.

Sutzko also said that Listeria is very tolerant.

“It gets into a facility and forms what’s called a biofilm,” she said. “It forms this kind of micro-environment on itself, and if it’s not discovered, then it’s going to take more than just dumping some sanitizer on it to kill it.”

Also, unlike E. coli and Salmonella, Listeria is a slow grower, so it could have a long lag time from when it gets into a plant until it starts showing up in testing. To help in earlier identification, rotate your sampling sites and track where positives are found, then use mapping software to analyze the situation.

Sutzko recalls one company that had Listeria constantly popping up in one spot in a plant. They’d clean it, come back and test the spot later, and get a positive again. What they didn’t know was there was a leak in the roof leading to moisture getting in.

“When they put it in a 3D mapping software, they were like, “that explains it!” she said. “Find the source, and then treat that and sanitize it.”


Historically, Salmonella has been a concern in raw meats, where it’s been more of a contaminant. The idea here is to monitor incoming live animals such as chickens and try to decrease the load of it coming into a plant.

“In the meat industry, it’s really about process controls, and do their interventions help to reduce the load of Salmonella coming out,” Sutzko said. “USDA has been under a lot of scrutiny because they had their Healthy People 2020 goal to reduce Salmonella incidents over 10 years, and basically it has stayed almost the same. There’s kind of a push from these consumer advocate groups and things like that for the USDA to do something different to try to really reduce the levels of Salmonella.”

When it comes to processed foods, Salmonella is a concern in dry-food facilities, especially coming in on ingredients.

“We’ve seen Salmonella in nonfat dry milk, in black pepper,” Sutzko said. “Things that are being used as ingredients for all different kinds of products.”

Of all the pathogens associated with foodborne illness, she also said Salmonella is the most challenging.

“There are over 2,600 [serotypes of] Salmonella, which can get into food and make people sick,” Sutzko said. “They’re all different, and Salmonella is very adaptable.”

Of all the pathogens associated with foodborne illness, Romer Labs’ Meredith Sutzko said Salmonella is the most challenging.
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She said it can survive in a processing facility for many years, citing the 2009 peanut butter outbreak as an example.

“They had Salmonella all over that plant,” Sutzko said. “In ready-to-eat and processed foods, it’s all or nothing because they don’t want to have any Salmonella in there.”

On the detection side, Thevenet advised making sure you’re sampling using the right techniques (and this goes for any pathogen), such as using the right sponge or swab for the job, to make sure you’re properly collecting the samples to begin with.

“If you can’t actually collect the sample that has the pathogen, you have no chance of detecting it,” he said.

March April 2021
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