Ninety people in 13 states have been infected in a deadly E. coli outbreak linked to McDonald’s Quarter Pounders, the Centers for Disease Control and Prevention said Wednesday, as it continues to investigate the source of the spread.

The outbreak has led to 27 hospitalizations and one previously reported death of an older adult in Colorado. 

Before Wednesday, the CDC last gave an update on the outbreak on Friday, when the agency said it had 75 cases in 13 states. The agency first announced the outbreak on Oct. 22.

Fresh slivered onions served on Quarter Pounders and other menu items at McDonald’s are “the likely source of this outbreak,” the CDC said on its website on Wednesday.

The additional illnesses are from before McDonald’s and Taylor Farms, which supplied onions to the affected region, took action to remove the ingredient from affected locations, the agency added. The CDC believes the risk to the public is “very low” due to the efforts from McDonald’s and Taylor Farms. 

“The likelihood of contaminated onions still being available for sale is low,” the agency wrote. 

Quarter Pounder hamburgers are a core menu item for McDonald’s, raking in billions of dollars each year. The fast-food giant on Sunday said the burgers will return to roughly a fifth of U.S. restaurants this week, or about 3,000 locations, after it pulled the menu item due to the outbreak. 

But around 900 of those locations will serve the Quarter Pounder without slivered onions for the foreseeable future as the CDC and other health authorities continue to examine the source of the outbreak. The change will affect restaurants in Colorado, Kansas and Wyoming as well as parts of Idaho, Iowa, Missouri, Montana, Nebraska, Nevada, New Mexico, Oklahoma and Utah.

McDonald’s Quarter Pounder burgers will return to roughly 900 restaurants this week after the fast-food giant pulled the menu item linked to a deadly E. coli outbreak.

Affected restaurants — roughly a fifth of the company’s U.S. footprint — will be serving the Quarter Pounder burgers without slivered onions for the foreseeable future as health authorities continue their investigation into the source of the outbreak. That change will affect restaurants in Colorado, Kansas and Wyoming and portions of Idaho, Iowa, Missouri, Montana, Nebraska, Nevada, New Mexico, Oklahoma and Utah.

“The issue appears to be contained to a particular ingredient and geography, and we remain very confident that any contaminated product related to this outbreak has been removed from our supply chain and is out of all McDonald’s restaurants,” Cesar Pina, chief supply chain officer for McDonald’s North American operations, said in a letter sent to the company’s U.S. system.

The Colorado Department of Agriculture’s testing did not detect E. coli in samples of the beef patties taken from restaurants in the area, according to Pina. The agency isn’t planning further tests of the company’s beef.

Instead, health authorities have honed in on slivered onions used in the Quarter Pounders as the likely suspect for the outbreak. The Food and Drug Administration is still investigating if onions produced by Taylor Farms are responsible. McDonald’s has stopped using Taylor Farms as a supplier for the ingredient indefinitely.

McDonald’s is now asking its beef suppliers to produce a new supply of the fresh beef patties used in its Quarter Pounders, Pina wrote in a letter sent to the company’s U.S. system. Customers can expect to see the menu item back in all restaurants in the coming week, although it will happen on a rolling basis, depending on delivery and resupply operations.

The Centers for Disease Control and Prevention said Friday that the E. coli outbreak linked to McDonald’s has led to 75 cases across 13 states. Out of 61 patients with information available, 22 have been hospitalized, and two people have developed a serious condition that can cause kidney failure, called hemolytic uremic syndrome. The agency also said previously that an older adult in Colorado died.

Based on reported cases so far, the outbreak took place between Sept. 27 and Oct. 11. Over a two-week period, McDonald’s typically sells roughly one million Quarter Pounders in the affected region, according to company spokespeople.

McDonald’s USA President Joe Erlinger apologized to customers who are feeling “ill, scared or uncertain” in a video posted on the company’s website.

“On behalf of the McDonald’s system, I want you to hear from me: we are sorry,” he said.

McDonald’s is expected to report its third-quarter earnings before the bell on Tuesday. Shares of the company have fallen 7% since the CDC linked the E. coli outbreak to its restaurants.

Burger King and Taco Bell owner Yum Brands have pulled onions from select restaurants following an E. coli outbreak tied to McDonald’s.

“As we continue to monitor the recently reported E. coli outbreak, and out of an abundance of caution, we have proactively removed fresh onions from select Taco Bell, Pizza Hut and KFC restaurants,” a Yum Brands spokesperson said in a statement to CNBC. “We will continue following supplier and regulatory guidance to ensure the ongoing safety and quality of our food.”

Yum did not specify how many of its restaurants are included in the measure.

It comes after restaurant supplier U.S. Foods on Wednesday issued a recall notification for four onion products produced by Taylor Farms. It is unclear if Yum removed the onions from select locations in response to the recall.

Restaurant Brands International’s Burger King is removing onions from 5% of its U.S. restaurants after reviewing its supply chain and determining those onions originated at the Taylor Farms Colorado facility at the center of the recall.

The burger chain said it only uses whole, fresh onions. Its employees cut, peel, wash and slice the onions at its restaurants.

“Despite no contact from health authorities and no indications of illness, we proactively asked our 5% of restaurants who received whole onions distributed by this facility to dispose of them immediately two days ago and we are in the process of restocking them from other facilities,” a Burger King spokesperson said in a statement to CNBC.

U.S. Foods does not distribute onions for McDonald’s restaurants, and the company has not publicly named Taylor Farms as a supplier. Taylor Farms has not responded to CNBC’s request for comment.

Health authorities are currently investigating the source of the E. coli outbreak, which has led to one death and 49 confirmed cases across 10 states, including Colorado, Nebraska and Wyoming. The Centers for Disease Control and Prevention has interviewed 18 people, 14 of whom remember eating a Quarter Pounder burger from McDonald’s, as of Tuesday.

In response to the outbreak, McDonald’s has pulled Quarter Pounders from roughly a fifth of its U.S. restaurants. The investigation has honed in on two ingredients in the burgers: the fresh beef patties and slivered onions.

McDonald’s said the affected restaurants all source onions from a single facility, which washes and slices the onions. Its beef patties, on the other hand, come from multiple suppliers in the region. If cooked according to internal standards, the temperature would kill any E. coli in the patty.

— CNBC’s Kate Rogers contributed reporting for this story.