Twenty-two people have been hospitalised, the Centres for Disease Control and Prevention said.
Two people developed a dangerous kidney disease complication, and one person died.
No source of the outbreak has been identified, officials with the US Food and Drug Administration said.
But investigators have focused on slivered onions used on the burgers, as well as beef patties.
McDonald’s officials have said that a California-based produce grower, Taylor Farms, supplied yellow onions that have been recalled for possible E. coli contamination.
McDonald’s pulled the burger from menus in several states on Tuesday when the outbreak was announced.
