Those low-grade ingredients are cut from areas of the cow that are more likely to have had contact with feces, which carries E. coli, industry research shows. Yet Cargill, like most meat companies, relies on its suppliers to check for the bacteria and does its own testing only after the ingredients are ground together. The United States Department of Agriculture, which allows grinders to devise their own safety plans, has encouraged them to test ingredients first as a way of increasing the chance of finding contamination.

Unwritten agreements between some companies appear to stand in the way of ingredient testing. Many big slaughterhouses will sell only to grinders who agree not to test their shipments for E. coli, according to officials at two large grinding companies. Slaughterhouses fear that one grinder’s discovery of E. coli will set off a recall of ingredients they sold to others.

“Ground beef is not a completely safe product,” said Dr. Jeffrey Bender, a food safety expert at the University of Minnesota who helped develop systems for tracing E. coli contamination. He said that while outbreaks had been on the decline, “unfortunately it looks like we are going a bit in the opposite direction.”

Food scientists have registered increasing concern about the virulence of this pathogen since only a few stray cells can make someone sick, and they warn that federal guidance to cook meat thoroughly and to wash up afterward is not sufficient. A test by The Times found that the safe handling instructions are not enough to prevent the bacteria from spreading in the kitchen.

Cargill, whose $116.6 billion in revenues last year made it the country’s largest private company, declined requests to interview company officials or visit its facilities. “Cargill is not in a position to answer your specific questions, other than to state that we are committed to continuous improvement in the area of food safety,” the company said, citing continuing litigation.

The meat industry treats much of its practices and the ingredients in ground beef as trade secrets. While the Department of Agriculture has inspectors posted in plants and has access to production records, it also guards those secrets. Federal records released by the department through the Freedom of Information Act blacked out details of Cargill’s grinding operation that could be learned only through copies of the documents obtained from other sources. Those documents illustrate the restrained approach to enforcement by a department whose missions include ensuring meat safety and promoting agriculture markets.

Within weeks of the Cargill outbreak in 2007, U.S.D.A. officials swept across the country, conducting spot checks at 224 meat plants to assess their efforts to combat E. coli. Although inspectors had been monitoring these plants all along, officials found serious problems at 55 that were failing to follow their own safety plans.