McDonald’s yanked Quarter Pounders from about a fifth of its U.S. locations after a deadly E.Coli outbreak was linked to the popular burger, the company said Wednesday.

Federal agencies announced Tuesday that one person had died in Colorado and 49 others had fallen ill in 10 states in the Midwest and West.

The nation’s largest fast-food chain said Wednesday it is confident the outbreak’s culprit is chopped onions on top of the Quarter Pounder.

A single, unnamed supplier of the onions no longer supplies vegetables to McDonald’s restaurants, the company added.

It has not cut ties with any beef suppliers, but officials said they could not rule out contaminated ground beef was to blame.

Nevertheless, McDonald’s removed Quarter Pounders from about 2,700 locations in 12 states, according to a Wednesday update from the Centers for Disease Control.

The FDA and CDC warned McDonald’s late last week about illnesses linked to their food, a spokesperson said.

But the first reported case linked to McDonald’s was on September 27 – almost a month ago – leaving some food safety experts scratching their heads as to why it took so long to alert the public.

“The flow of information is unfolding more slowly than normal,” food safety expert James Marsden told The Post on Wednesday.

“Normally, in reported cases, the recording would cause alarm and the (government) would warn the public sooner.”

The CDC had interviewed 18 people with confirmed cases and 12 of them said they ate a Quarter Pounder before becoming sick, a McDonald’s spokesperson said.

A spokesperson for the CDC told The Post that the “Colorado Department of Health notified the CDC on 10/10 of an increase in E. coli illnesses in their state and the CDC began investigating on 10/15 after lab tests confirmed that it was a multi-state outbreak and not just a local outbreak in Colorado. Investigators are working as quickly as possible to identify a contaminated ingredient.”

Meanwhile, McDonald’s franchisees are bracing for a sales slump, exacerbating the sales slowdown that has led McDonald’s to push Value Meals this year.

The stock fell more than 5% on Wednesday.

“This will affect all of us as people are hesitant to visit,” one franchisee, who did not want to be identified, told The Post.

A McDonald’s spokesperson declined to say whether the company’s foot traffic has been affected by the outbreak.

McDonald’s sells more than two million Quarter Pounders a day, the franchisee said, adding that if the outbreaks were “widespread, there would be tens of thousands of cases.”

The company is “very, very, very careful” in removing Quarter Pounders from its restaurants, the franchisee added.