“It was in both agencies’ netherworld, where neither agency felt they were authorized by law to approve that product,” said Chuck Lambert, a former deputy under secretary for marketing and regulatory programs at the Agriculture Department.
Finally, in March 2005, the Agriculture Department reversed course and said it would take applications. But even as it agreed to review the vaccines, the agency set a high bar for approval.
Officials determined that the vaccines must show at least a 90 percent reduction in the number of cattle carrying the bacteria. And among cattle that still harbored E. coli after being vaccinated, the agency insisted on a 99.9 percent reduction in the number of bacteria shed by the animals.
That was more than the vaccines could achieve — and more than the agency demanded of many other vaccines.
“It was a very high, unrealistic target,” said Dr. David R. Smith, a professor of epidemiology at the University of Nebraska at Lincoln, who has done research on the Bioniche vaccine. Dr. James A. Roth, the director of the Center for Food Security and Public Health at Iowa State University, said that many widely used vaccines, including many for common bovine respiratory ailments, were successful in preventing disease less than 80 percent of the time.
The E. coli vaccines were stuck in limbo. Then, in 2007, the number of E. coli-related beef recalls jumped sharply, alarming food safety advocates and some in the beef industry, who pushed for additional tools.
“I was looking for anything that could help us because people were getting sick and people were dying,” said Dr. Richard Raymond, the Agriculture Department’s under secretary for food safety from 2005 to 2008.
In early 2008, the department told the two vaccine companies that it would relax its requirements. This March, the agency approved sale of the Epitopix vaccine.
“The federal government was slow,” Dr. Raymond said. He called the 18-month lag while the Agriculture Department and the F.D.A. hashed out the jurisdictional dispute “pure wasted time.”
But Dr. John Clifford, the Agriculture Department’s head veterinarian, said the government had acted expeditiously in working through complex regulatory challenges. The two federal agencies “did not slow down the companies’ development of this product,” Dr. Clifford said.
The Agriculture Department said in a statement that it holds all vaccine manufacturers to a high standard and works with them to ensure they meet its requirements.
Dr. Kent McClure, general counsel of the Animal Health Institute, a pharmaceutical industry group, said that while the review took longer than the industry would have liked, the new legal clarity could pave the way for other food safety vaccines.
One possibility, he said, was a vaccine for campylobacter, a bacterium that infects poultry without making them sick, but which causes millions of cases of food poisoning each year.
Today another roadblock stands in the way of the E. coli vaccines: who will pay for them.
Epitopix said it had not yet set a price for its vaccine. In Canada, Bioniche charges about $3 a dose. The vaccines require two or three doses to be effective, meaning the cost could approach $10 an animal.
Farmers and feedlot owners fear that they will be stuck with the vaccine cost and that it will cut into already tight margins. Mr. Timmerman, the feedlot owner, said that in a good year his profit is $25 to $35 an animal.
“The incentive for the vaccine is it’s going to benefit the packer who is vulnerable to recalls and lawsuits,” said Ronald F. Eustis, executive director of the Minnesota Beef Promotion and Research Council, a trade group that represents farmers and feedlot owners. “Unless the farmer, the producers, the rancher is somehow compensated, he’s going to be reluctant to lay out the cash.”
The large-scale study that includes Mr. Timmerman’s calves is being coordinated and paid for by Cargill, the food giant that is the biggest producer of ground beef in the country.
It will include close to 100,000 cattle, with the animals going next summer at Cargill’s Fort Morgan slaughterhouse. Tests will be done on the meat, in particular the smaller pieces, known as trim, that go into ground beef. Researchers will look to see if it contains less E. coli than trim from unvaccinated cattle.
E. coli contamination generally starts when bacteria in feces on a cow’s hide are transferred to the carcass. Cargill has added many steps to keep carcasses clean, including steam pasteurization and hot water washes. But regular tests at the plant still turn up occasional traces of E. coli in trim, underscoring the need for additional steps, like a vaccine.
“It’s definitely a piece of the solution,” said James L. Marsden, a professor of food safety at Kansas State University. “When you combine it with other pieces you may be looking at a real solution, a total solution.”