WASHINGTON -- Whole Foods Market has pulled fresh ground beef from all of its stores, becoming the latest retailer affected by an E. coli outbreak traced to one of the nation's largest meat packers. It's the second outbreak linked to Nebraska Beef in as many months.

The meat Whole Foods recalled came from Coleman Natural Foods, which unbeknownst to Whole Foods had processed it at Nebraska Beef, an Omaha meat packer with a history of food-safety and other violations. Nebraska Beef last month recalled more than 5 million pounds of beef produced in May and June after its meat was blamed for another E. coli outbreak in seven states. On Friday it recalled an additional 1.2 million pounds of beef produced on June 17, June 24 and July 8, which included products eventually sold to Whole Foods.

Whole Foods officials are investigating why they were not aware that Coleman was using Nebraska Beef as a processor, spokeswoman Libba Letton said.

The chain's managers took action after Massachusetts health officials informed them on Aug. 1 that seven people who had gotten sick from E. coli O157:H7 had all bought ground beef from Whole Foods. Two people in Pennsylvania who shopped at Whole Foods also became ill.

The same strain has sickened 31 people so far in Pennsylvania, the District of Columbia and Canada.

In addition to Pennsylvania, the products have been linked to illnesses in California, Colorado, Connecticut, Idaho, Illinois, Massachusetts, New Jersey, New Mexico, New York, Ohio and Virginia.

So far, tests have not found contaminated Whole Foods beef, Ms. Letton said.

This latest outbreak was first identified in late July among customers of Dorothy Lane Market, a small Ohio grocery chain. Dorothy Lane also bought meat from Coleman Natural Foods, which bought primal cuts -- meat intended for steaks and roasts -- from Nebraska Beef. The E. coli strain found in the Massachusetts Whole Foods customers matches that Ohio strain.

Nebraska Beef, which continues to operate, had already been under close scrutiny by the Department of Agriculture since late June.

William M. Lamson Jr., a Nebraska Beef spokesman, said the company and the USDA had increased testing of its meat since then. It has found no E. coli O157:H7 in products made since July 8.

He said since June, Nebraska Beef has hired food safety consultants and undertaken an in-depth review of its processes. USDA is doing the same.

"We will continue to investigate to see what is happening at the plant to see what they have to do to get a handle on their food safety issues," said agency spokeswoman Laura Reiser.

Nebraska Beef has a contentious history with USDA. Over the past six years, federal meat inspectors have written it up repeatedly for sanitation violations. And the company has fought back in court.

From September 2002 to February 2003, USDA shut down the plant three times for problems such as feces on carcasses, water dripping off pipes onto meat, paint peeling onto equipment, and plugged up meat wash sinks, according to agency records.

Whole Foods Market said customers who bought ground beef between June 2 and Aug. 6 should throw it out. They can return the packaging or receipt to the store for a refund.