McDonald’s Corp.’s decision to yank one of its most popular menu items from a fifth of its restaurants started with a curious set of stool samples in Colorado.

Patients with seemingly little in common began growing ill from E. coli in late September, prompting doctors to send samples for testing to health officials. When Colorado’s health department began probing further in early October, one unifying detail emerged: The sickened patients had all recently eaten at different McDonald’s.

It would be a number of weeks before the state and federal investigations would result in a notice sent Tuesday from the Centers for Disease Control and Prevention about a multistate outbreak that infected at least 49 people, leading to 10 hospitalizations and one death. Now, an investigation that started with McDonald’s has led to a broader recall that has affected multiple distributors and restaurants across the US.

McDonald’s hasn’t yet confirmed the source of the outbreak but has said that the likely culprit of the contamination was the slivered raw onions that go into its popular Quarter Pounder burger. The chain pulled the Quarter Pounders from 20% of its more than 13,000 US restaurants. One of McDonald’s yellow onion suppliers, Taylor Farms, said late Wednesday that it would recall some of its batches “out of an abundance of caution.” Restaurant distributors US Foods Holding Corp. and Sysco Corp. notified customers of the recall as well.

The burger chain said it acted quickly to address the issue.

“After being notified by the CDC last week, we were in daily contact and worked in lockstep to investigate,” McDonald’s said in a statement Thursday to Bloomberg News. “As soon as we identified that a subset of illnesses may be linked to slivered onions used in the Quarter Pounder, we made the decision to remove product from restaurants in affected regions. Instructions for product to be removed were sent early this week, ahead of the CDC’s public advisory notice.”

‘Active Investigation’

Health authorities including the CDC and the Food and Drug Administration are still investigating the incidents and have said the numbers of illnesses could grow. McDonald’s shares had erased most of their year-to-date gains as of Thursday at 12:20 p.m. New York as investors tried to determine the impact of the food-safety issues on the burger chain’s business.

“This is absolutely a very active investigation, meaning that we do expect additional cases to be identified and reported,” Rachel Herlihy, the state epidemiologist for Colorado’s Department of Public Health and Environment, said in an interview.

Herlihy said it’s hard to determine who patient zero is because of the lag time from when someone eats contaminated food and when they report being sick, a process that can take weeks.

It was late September when the first customers to be infected with E. coli ate at McDonald’s locations in Colorado, she said. It took some time for those people to get sick, go to their health-care provider, get tested — and for those results to come back to health officials.

By mid-October, Colorado health officials began seeing an elevated number of cases and started working with the CDC and health officials in other states “to figure out if something unusual is happening,” Herlihy said. Initially, the CDC said only Colorado was reporting an unusually high number of cases.

Herlihy’s team interviewed customers who got sick, at first asking them general questions about where and what they’d eaten recently, hoping to identify the source of the outbreak. Meanwhile, laboratories were conducting full genome sequencing of the bacteria to see if the cases were closely related.

Then, Herlihy’s team started asking patients more specific questions: “We’ll want to know more detail,” she said. “Did you eat a McDonald’s Quarter Pounder, specifically? What were the ingredients that you excluded from your burger?”

The Colorado health department worked with the CDC, which first reached out to McDonald’s about the outbreak on Oct. 16. At the time, the CDC wasn’t able to link the outbreak to a single menu item. The agency said results from whole genome sequencing of the bacteria from Colorado and other states showed the illnesses had the same DNA fingerprints and were part of an outbreak. When the CDC got a list of cases, it saw that an unusually high number of people were getting sick from E. coli after eating at McDonald’s.

The CDC worked with McDonald’s to discuss sales data and what unique ingredients were used in various menu items before they came upon the Quarter Pounder, which uses the particular kind of slivered onions the health officials suspect was the culprit. The FDA is working with McDonald’s to identify the supplier of those ingredients.

McDonald’s onion supplier Taylor Farms, based in Salinas, California, said on Wednesday that it was pulling batches of its yellow onions. Best known for ready-made bagged salad kits found in grocery aisles, Taylor provides the raw, slivered onions that are cut and washed before being sent to McDonald’s and placed atop millions of Quarter Pounders around the US. Other McDonald’s burgers use diced onions, which weren’t implicated in the contamination.

More Illnesses

McDonald’s said it jumped into action as soon as it was contacted by health officials. Instead of waiting until it could confirm the exact source of contamination, the company said it decided to strike the popular Quarter Pounders from its affected stores altogether with hopes of containing the outbreak. While the company hasn’t ruled out the beef patties, it said it believes the culprit was the onions because they all originated from one supplier.

“As many have noted, including CDC, we have acted swiftly to do the right thing,” McDonald’s said Thursday. “Our entire company has been committed to and focused on swift and decisive action, and transparent communication.”

Now that McDonald’s has stopped selling Quarter Pounders in the impacted areas, “the risk today to the public is low,” said Laura Gieraltowski, an epidemiologist with the CDC’s foodborne-diseases division. “That will prevent more people from getting sick.”

Gieraltowski praised Colorado health officials for spotting the cases quickly. Because of that, “we were really able to jump on this earlier than we typically would,” she said.

Still, there’s always a lag of two to four weeks from when someone eats contaminated food to when they’re considered part of an outbreak. “We do expect to see more illnesses,” she said. If the CDC can identify the specific contaminated ingredient at fault, it will need to look at what other restaurants that ingredient has gone to, she added.

Another brand supplied by Taylor Farms, Illegal Pete’s, has already pulled the onions from its products.

McDonald’s US President Joe Erlinger said Wednesday on NBC that it’s likely any contaminated products already worked their way through the company’s supply chain. The chain sells a million Quarter Pounders during a typical two-week period and onions have a fairly short shelf life.

“I want to say to our consumers that you can confidently go to McDonald’s today,” he said.

— With assistance from Deena Shanker.