McDonald’s announced on Sunday that tests in Colorado had ruled out its Quarter Pounder beef patties as the source of a deadly E. coli outbreak, and said that the popular burger would be back on the menu at thousands of locations in a dozen states.

But the company said that in 900 of those sites, Quarter Pounders would not be topped with raw slivered onions — which federal regulators have identified as the likely culprit in the outbreak that health officials said had sickened 75 people and caused the death of one Colorado resident.

In a statement, McDonald’s cited tests conducted in Colorado, the state that had the most cases reported in the outbreak. On its website, the state’s Agriculture Department said that tests were done on “dozens of subsamples from all the lots and all samples were found to be negative for E. coli.”

Colorado health officials tested beef samples from the two beef suppliers that provided patties to the 900 affected locations in a dozen states, McDonald’s spokesmen said.

The company said it was not aware of any other state health agency that was still testing the beef patties for E. coli.

As for the slivered onions, McDonald’s said on Friday it would stop buying onions from the Colorado Springs site of its major regional supplier Taylor Farms, a multistate producer of vegetables and fruits. Last week, Taylor Farms recalled several yellow onion products — among them diced and slivered — because of “potential E. coli contamination.”

Several other fast-food chains, including Taco Bell, KFC, Pizza Hut and Burger King, have stopped offering onions in their menu items as a precautionary measure in the region.

U.S. health officials said they believed that the recall of onions from the region’s food supply chain would lower the risk to consumers.

Among the 75 people who became ill, at least a quarter were hospitalized, according to the most recent data from the Centers for Disease Control and Prevention. Two developed a serious kidney condition associated with E. coli, the agency said. The illnesses were reported between Sept. 27 and Oct. 10.

A McDonald’s spokesman said that the number may rise, as federal regulators process case information, but said that they were “very confident” that they had removed the source of contamination from the supply chain.

Since the C.D.C. first announced the outbreak on Tuesday, McDonald’s shares have fallen roughly 7 percent.