How disease detectives' quick work traced deadly E. coli outbreak to McDonald's Quarter Pounders

Silas Mayes rolled into his local McDonald's drive-through at lunchtime on Monday, October 7, and ordered his usual: a Quarter Pounder, fries and a Sprite.

By Thursday morning, he was having waves of stomach cramps so intense that he could hardly stand up to get to the bathroom.

"It was extremely painful. And every time I would use the bathroom, there would be blood," said Silas, 17, who lives in Grand Junction, Colorado. "It was terrifying."

His mom, Lera Davidson, rushed him to the emergency room at St. Mary's Regional Hospital when the bloody diarrhea continued. The doctors took a stool sample and sent it to a lab for analysis, and they gave him IV fluids and painkillers for the cramps. They kept him in the ER nearly all day, he said, but eventually sent him home.

He couldn't keep anything down. Even a small sip of water or one bite of a cracker would send him running for the toilet, and more blood would pour out of him.

His stool tested positive for a strain of E. coli bacteria that is especially dangerous because it produces Shiga toxin, which penetrates and kills cells, causing tissue damage. One of the worst complications of these kinds of infections can behemolytic uremic syndrome, which can lead to kidney failure and may even be deadly, especially for young children and the elderly.

All 50 states require labs to notify their state health departments when they detect these infections, which are called STEC, for Shiga toxin-producing E. coli.

A positive test result for any reportable foodborne illness off a series of routine actions by local and then state public health offices. These steps normally play out quietly, outside the public eye. Without this work, however, outbreaks of foodborne illness might never be spotted or traced back to a tainted ingredient, and more people would get sick and die.

"We look at every case we get like it could be an outbreak. We investigate every case with that mindset of preventing spread of disease and stopping a source of disease," said Julie Hartshorn, a disease surveillance specialist with Mesa County Public Health in Grand Junction.

Scientists at the US Centers for Disease Control and Prevention who worked with the Colorado Department of Public Health and Environment to investigate the latest E. coli outbreak and nail down its cause say the fact that these cases were linked and solved so quickly makes it a noteworthy win.

As part of an outbreak investigation announced by the CDC and the US Food and Drug Administration on October 22, 90 cases of STEC infection from 13 states have been linked to McDonald's Quarter Pounders. More than two dozen people have been hospitalized, and one has died.

Only about 10% of the 6,000 E. coli infections that are genetically sequenced in the US each year are connected to an outbreak, according to Dr. Heather Carleton-Romer, chief of the Enteric Diseases Laboratory Branch at the CDC in Atlanta.

"I feel like I'm in one of the few jobs as a scientist where I can go home and say my work saves people's lives, because it does," she said.

Race to find the root cause

By the time they got the report aboutSilas' case, Hartshorn and two other staffers at Mesa County Public Health had been working full-tilt, trying to figure out exactly why so many people in Grand Junction were getting STEC infections.

"We see maybe one or two of these STEC cases in a month, and we had an unusually large number. So right away, we were all concerned," Hartshorn said.

Mesa County, an early epicenter, has had 11 cases linked to the outbreak, but Hartshorn said they've called more people than that as part of their investigation. Some won't be added to the official count until the bacteria in their stool has undergone genetic sequencing by the state lab to confirm that its DNA fingerprint matches others in the outbreak strain. That process takes time.

Even under the best of circumstances, it's difficult for most people to remember important details about what they ate. So health departments try to work quickly, to catch people while their memories are fresh.

After they get a report of a foodborne illness, a specialist - typically someone who is trained to do these kinds of detailed interviews - calls the person who got sick. They ask people to recall everything they ate for the previous seven days, including all the ingredients in those dishes. People are also asked about recent travel and contact with animals, including what kinds of treats they feed their pets.

The Mesa County team started making calls to people with STEC infections the week of October 7, about three weeks before the CDC announced the investigation.Within two days, it became apparent that most people they were contacting had eaten at McDonald's. The health department dispatched its environmental health team to the local restaurant, but they didn't find any red flags.

"What we realized was that it wasn't a problem with how the food was prepared at the restaurant," Hartshorn said. Employees were washing their hands, food was being cooked to the right temperatures, and surfaces were appropriately cleaned and disinfected.

But still, people were getting sick after eating there, making them wonder whether the food might have been contaminated before it arrived to the restaurant, Hartshorn said. "So we thought this may be wider of an issue."

The investigation widens

They were right.

At the state level, theColorado Department of Public Health and Environment was also getting a deluge of STEC reports from across the state.

Sometimes, local health departments do their own foodborne illness interviews, as Mesa County does, and sometimes cities and rural areas depend on the state health department for that kind of help.

Alayna Younger, an epidemiologist who manages the state agency's four-member Enteric Disease Interview Team, is responsible for assigning those interviews, and she was the first to sound the alarm about an usually large number of STEC cases, according to her supervisor, Rachel Jervis, who calls herself a "scientist ... of diarrhea" on LinkedIn.

"I said, 'OK, can you look at past years' data? I want to have the numbers,' " said Jervis, who manages the Foodborne, Enteric, Waterborne and Wastewater Diseases Program at the Colorado health department.

In the early days of October,the agency had logged as many STEC cases as it would normally see in the entire month, Jervis said.

On October 10, the same day Silas got sick, the agency emailed the CDC to say that it suspected a STEC outbreak and that many of the people who were being interviewed reported eating fast food and ground beef.

Jervis said they also reached out to neighboring states to ask if they were seeing case increases. "Some had similar experiences; some didn't," she said.

On October 11, the CDC received the first genetic sequences from Colorado through its PulseNet system. The DNA fingerprint from the cases was remarkably similar, with only one gene change difference between them, Jervis said, a clear sign that the cases were related.

PulseNet is a system that collects and analyzes more than 60,000 genomes collected from people who get foodborne illnesses each year. Each genome contains every letter of the instructions needed to build the bacteria or virus that's causing the illness, and collectively, they represent a huge amount of information. Each month, the PulseNet system sifts through enough data to fill the Library of Congress.

"Imagine you're putting together a 5,000-piece puzzle, and then you're comparing that puzzle across multiple cases to see if there's even one part, one piece difference, because that will tell us things," Carleton-Romer said.

Traditional methods crack the case

Normally, the scientists who monitor the PulseNet system will be the first to connect cases that become an outbreak investigation.

In the case of the STEC outbreak linked to McDonald's Quarter Pounders, however, it was Younger and her team of epidemiologists manning the phones in Colorado who first linked the cases, a testament to the tried-and-true methods of epidemiology.

This type of case investigation dates to the mid-1800s, when Dr. John Snow, who is often credited as the father of modern epidemiology, stopped a cholera outbreak in London by tracing it to contaminated water from a single pump that was making people sick.

As more E. coli sequences came into PulseNet, the team at the CDC could see genomes with the same DNA fingerprint popping up in other states, suggesting that a common food being widely distributed was making people sick.

The CDC team worked with the Colorado health departmentto develop a second set of questions asking specifically about certain fast-food restaurants, menu items at those restaurants and the consumption of beef or onions. The supplemental questionnaire was 13 pages long.

"The best practice for these supplemental outbreak questionnaires is to have as few interviewers as possible conducting them, because it just helps people pick up on commonalities," Jervis said, "and so these additional interviews are centralized at the state health department."

Davidson tried to answer the Mesa County workers' questions for Silas because his condition had gotten worse, with episodes of bloody diarrhea every minute or so, and he was too sick to help much. But when she was initially interviewed, she didn't know that her son had eaten at McDonald's.

"You're really thinking about every single thing you've eaten in a week's period," Davidson said. "I kind of could piece together the meals I had cooked, but piecing together where he'd been with his girlfriend, out eating and stuff like that, was where the challenge was."

When state investigators called back to do the supplemental interview on October 12, they asked her to look for receipts for ground beef that she had purchased and to check bank statements for any information that might help fill in the gaps.

It wasn't until there were reports on the news about the connection to McDonald's that Silas remembered his lunch there.

Later, they found a line on the bank statement noting a purchase at McDonald's on October 7.

"Your memory is jogged when you're asked for something specific," Jervis said. "We absolutely had cases who called us back and said, 'You know what, after I talked to you, I went back and looked at my credit card statement, and I went to McDonald's on this date.'"

Still, the number of official cases is an undercount. There will be people who got sick but not sick enough to go to the doctor, so they were never tested. Or perhaps they were treated without getting a stool test.

McDonald's said that in any two week period, in the region where cases had been reported, it sells over 1 million Quarter Pounders.

Because the sick people overwhelmingly reported eating Quarter Pounders, investigators were able to ask what made that particular menu item different fromothers. It turns out that Quarter Pounders are made with fresh beef that is cooked to order, as well as fresh slivered onions. Only one other thing on the menu - a breakfast item - used the slivered onions, McDonald's said.

McDonald's temporarily stopped selling Quarter Pounders in about one-fifth of its restaurants until testing ruled out beef patties as the E. coli source.

Taylor Farms, the supplier of the fresh onions, recalled onions sent to McDonald's and other restaurants and institutions. Testing of the onions is ongoing, and the CDC and the FDA said Thursday that they were the likely source of the E. coli bacteria that made people sick.

Because scientists were able to narrow the scope of the investigation so fast, companies were able to remove the suspect ingredients from restaurants quickly. Carleton-Romer said they don't think they'll have new illnesses going forward, but the investigation may grow as lab testing shows that historical cases are linked to the outbreak strain.

Lasting impacts

McDonald's said in a statement that "the health and safety of our people and our customers is our top priority."

"While McDonald's removed all slivered onions produced from this facility as of October 22, 2024, due to broad concern and our unwavering commitment to food safety we have made the decision to stop sourcing onions fromTaylor Farms' Colorado Springs facility indefinitely," the statement says.

"At McDonald's, food safety is something we will never compromise on. Customers can count on McDonald's to do the right thing, and public health authorities can count on McDonald's continued close partnership. We thank health authorities for all they are doing.'

Silas' family has hired an attorney, Ron Simon, to represent them in a case against the fast-food chain.

Even though they're sure that Silas ate at McDonald's and that he was diagnosed with E. coli, they don't know whether his case has been officially connected to the outbreak. They've requested his lab test results from the state health department but haven't received them, Simon said.

Silas is still recovering from his infection. He says he lost 10 pounds while he was sick, which was a lot for his already-slender frame.He's still experiencingextreme fatigue and has to take frequent breaks when he exercises or works at his job installing tile. He says it's a struggle to get anything done.

Silas is off IV fluids and back at work with his dad. But he says he won't be eating McDonald's or any other kind of fast food anytime soon.

"I don't trust fast food now because of how sick it made me," he said.

Jervis, of the Colorado health department, said it was professionally satisfying to crack the case.

"It's always this feeling of, 'Wow, this is fascinating. It's so exciting. I really want to solve this,'" she said.

"But at the same time, these are people who are getting very sick," she said.

Over the next few weeks, she expects case numbers to tick up as more test results match the outbreak strain.

"It's hard to see the numbers and know that those are individuals who have been quite sick, and they and their families have been impacted," she said.

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