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updated 2/21/2008 8:57:50 AM ET 2008-02-21T13:57:50

It's a Friday night in Missoula, Montana, when my buddy Eric and I walk into the Oxford Café. We make our way through the usual crowd of gamblers, pool players, drinkers, and drunks, and take a seat against the far wall. The waitress looks weary, and we look like work to her. "What'll you have?" she asks. Eric orders a hamburger. I point at the laminated menu and order scrambled eggs and brains, nicknamed "He Needs 'Em."

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"Impossible," the waitress says flatly. "Since mad cow disease, the USDA won't let us serve that."

"I don't know why you'd want to eat brains," Eric says. This from a guy who thinks nothing of gutting an elk.

I've eaten calf testicles and cow hearts and all sorts of things, but I'd never eaten brains before. I'd heard about the Oxford's fabled dish and figured this would be my chance to try something new, to taste something considered a delicacy in many parts of the world. It didn't seem particularly risky. In fact, no one in Missoula (or anywhere else in the United States) had ever been sickened from eating mad-cow-contaminated meat.

"They'll let us sell pig brains," the waitress offers, "but who wants to eat those?"

I follow Eric's lead and order the state-sanctioned part of the cow, though if we're talking food safety, I really should pass. Turns out, the humble hamburger may be the most dangerous item on the menu.

You know there's trouble when your average American carnivore thinks twice about biting into a burger. The appetite-killer in question: Escherichia coliform, a.k.a. E. coli, the bacteria behind the spate of recalls that recently hit the nation's beef supply. From June to September 2007 alone, ground beef contaminated with E. coli sickened 55 people while also shuttering one business and shaking up the USDA.

Not all E. coli are evil. There are actually hundreds of different strains, some of which are residing in your body right now, helping you absorb food and process waste. In fact, it's estimated that the average person excretes 10 billion Escherichia coli bacteria with every bowel movement.

One strain that definitely does not belong inside you is E. coli O157:H7. These bacteria normally live in the guts of cattle. However, if the slaughtering process is sloppy, feces or stomach contents can come into contact with meat and contaminate it with the bug. Next thing you know, you're weathering a weeklong bout of stomach cramps and bloody diarrhea. That is, unless your immune system isn't at full strength, in which case you're facing kidney failure or death.

Prior to 1982, little was known about E. coli O157:H7. That year, the strain was identified as a pathogen after a number of people were sickened by tainted hamburgers. A decade later the bug popped up again, this time in burgers from the fast-food chain Jack in the Box. Hundreds were hospitalized and four children died.

Still, it wasn't until 1994 that the USDA began testing for E. coli in samples of beef in packing plants. Five years after that, the agency added an extra safeguard by implementing a system known as Hazard Analysis and Critical Control Points (HACCP), which placed the main responsibility for testing in the hands of the major slaughterhouses. Theoretically, if they detect a bad batch of beef, it won't be shipped to the smaller "down-line" processors, whose job it is to grind and package bulk beef for the public.

For a while, the system appeared to be working. On April 14, 2005, the USDA, FDA, and CDC released a joint report stating that incidence of E. coli infections decreased 42 percent from 1996 to 2004. In the press release, then–USDA Secretary Mike Johanns proudly noted, "The continued reduction in illnesses from E. coli O157 is a tremendous success story and we are committed to continuing this positive trend in the future."

So you have to wonder, what's going wrong now? In 2007, more than 30 million pounds of ground beef were recalled for possible contamination with E. coli.

Thirty million pounds.

That's 120 million quarter-pound patties that made it as far as our grocery carts and, in some cases, our stomachs.

For most manufacturers, profit is tied to production, and the industry that turns bovines into burgers is no different: The top four meatpacking companies process more than 60,000 head of cattle a day. Given this staggering amount of cow, it makes you wonder how they test all of it for contamination. They don't.

"The biggest plant I've heard of produces about 3 million pounds of trim daily," says John Munsell, manager of the Foundation for Accountability in Regulatory Enforcement. Trim, or beef destined for processing into hamburger, is then put into a "combo," a huge cardboard box that holds, literally, a ton of meat. Each of these 2,000-pound boxes is tested, says Munsell. "They just reach into the top layer and take out less than a pound of trim. They mingle it together and grind it, and that's what they sample for their microbial analysis."

And after the big processors do what is required of them under HACCP, their products are moved along to the down-line processors, and ultimately our dinner tables, with the USDA mark of inspection.

Though he's never had food poisoning, Munsell's life was still upended by E. coli that a major meat packer had missed. In January 2002, routine tests by the USDA's Food Safety and Inspection Service found evidence of E. coli contamination in meat he was grinding at Montana Quality Foods, the small meatpacking business his father started 56 years earlier in Miles City, Montana.

According to Munsell, the meat he ground that day came in vacuum-sealed packages from two sources, one of which was the huge ConAgra Foods packing plant in Greeley, Colorado. Subsequent tests a month later found more E. coli contamination from ConAgra meat. And though a USDA inspector later testified that he had seen the meat go directly from the ConAgra packages into Munsell's sanitized grinder, there was no way to conclusively prove that the contamination hadn't originated at Montana Quality Foods. USDA officials shut down Munsell's operation, despite his pleas that they send investigators so he could show them documentation verifying the tainted meat's origin.

"I was expecting a whole gang of inspectors to arrive at my plant on Monday, and no one showed up. They didn't even call. "

In the summer of 2002, 5 months after the first positive test results at Munsell's facility, ConAgra voluntarily recalled 354,000 pounds of ground beef from its Greeley plant after numerous tests revealed E. coli contamination. Three weeks later, the recall was expanded to more than 18 million pounds, but it was too late to prevent 46 people across the United States from becoming ill. Of the recalled beef, only 3 million pounds were ever recovered.

Physically and emotionally spent from his one-man fight against the USDA, Munsell sold his plant in 2005. Since then, he's filed a lawsuit against the USDA, maintaining that he was retaliated against for blowing the whistle on what he sees as the agency's refusal to take on the big meat packers.

"They are too formidable a foe," says Munsell. "In the past two large-size litigations that the big packers brought against the agency, the agency lost both, so it lost interest in pressing for corrective action. What we need are people at the USDA who cannot be pressured by the large multi-national companies. We need people who will simply do what is right."

To be fair, the USDA has made some strides in the wake of the latest recalls. It recently announced that it will step up the number of E. coli tests conducted each year. Those tests will focus on plants that produce the largest quantities of ground beef and trim, as well as those that trigger positive results for contaminated meat.

But critics maintain that these moves are just Band-Aids for a testing system that was broken from the beginning. "HACCP was designed to put the onus on the small processor," says Tony Corbo, a legislative representative for Food & Water Watch, a nonprofit consumer-rights group dedicated to holding the government and corporations accountable for food and water issues. "If a sample of meat comes up positive for E. coli or salmonella, the grinder is the one taking the regulatory hit, even though it may have purchased the contaminated trim or coarsely ground beef from a large supplier. The John Munsell situation is a perfect illustration of how badly the regulatory system is set up."

Today, Munsell is a full-time crusader for meat-safety reform, the Ralph Nader of hamburger. He's authored the Traceback Bill, a piece of legislation he hopes will find support in Congress. The bill puts forth four commonsense measures aimed at finding the true origin of contaminated meat. However, he realizes that in the meantime there's still a public that's hungry for beef and reassurance.

"My suggestion would be for people to buy their beef from a small, local, inspected, meat-slaughtering facility," Munsell says. "I no longer have any confidence in meat that comes from these big meatpacking plants. When I go out in public, I don't order hamburger. I just don't trust it anymore."

If 2007 ends up going down as the "Year of E. coli," the USDA has already decided who to blame: the cows.

"The amount of product we test that's positive has gone up about 33 percent this year from the past 3 years," says Richard Raymond, M.D., the USDA's undersecretary for food safety. "I don't think it's that the agency has fallen asleep at the switch. I don't think it's that the industry has gotten sloppy. I think it's the cows."

Specifically, Dr. Raymond cites high corn prices for prompting a switch to cheaper feeds for fattening cattle. "When you change their feed, their intestinal flora change."

Could an increase in the cost of corn have had such gut-wrenching consequences? Perhaps. First you have to understand that the reason corn prices have skyrocketed is because of the recent increase in domestic ethanol production, which uses corn to produce a relatively clean alternative to fossil-based fuels. Consequently, more feedlots have resorted to using distiller's grains, a cheap but nutritious supplemental feed left over when corn is turned into ethanol. But research shows that the monetary savings may come at a hidden cost to the consumer.

"We found that cattle consuming distiller's grains as 25 percent of their diet had about a twofold higher incidence of E. coli O157:H7," says T.G. Nagaraja, Ph.D., a professor of microbiology at Kansas State University and the leader of a team of researchers targeting ways to decrease levels of E. coli in cattle before they reach the slaughterhouse. "Our observation is preliminary, but we've done three studies that show a positive association between this feed and increased levels of O157."

The USDA's Dr. Raymond points to another possible reason for the increase in E. coli levels: "We have seen some pretty severe environmental extremes this summer. There's been a lot of rain in the Midwest from Nebraska down to Texas--flooding, in fact. When feedlots flood, that puts stress on cattle. And when they're stressed, their E. coli numbers go up."

His flooded-feedlot explanation may hold some water. "One factor associated with cattle shedding the E. coli organism is wet and muddy pen conditions," says David Smith, D.V.M., Ph.D., a professor of veterinary and biomedical science at the University of Nebraska. "I suspect the slaughterhouses may have had cattle arrive this summer with a higher probability of shedding E. coli, or the cattle had it present on their hides, which led to greater opportunities for ground-beef contamination than during droughts."

Of course, this only explains why there may have been more E. coli than usual in cattle bound for slaughter, not why the bug ultimately ended up contaminating so much of the beef supply.

Michael Doyle, Ph.D., director of the center for food safety at the University of Georgia and one of the world's leading authorities on E. coli and other foodborne pathogens, has a theory: "There is often an increase in bacterial contamination when experienced workers on the slaughter line are replaced with less-experienced workers, such as before and after holidays," he says, "and raids this year on illegal slaughterhouse workers by the INS led to replacement with less-experienced line workers."

Still, you could argue that if an adequate testing system had been in place at the slaughterhouses during this uptick in tainted meat, little to none of it would have gone out the door. And yet some experts say that it's simply unrealistic to expect that the big meat packers will ever be able to catch all the contaminated beef, no matter what new testing procedures are ultimately instituted.

"You're not going to eliminate E. coli O157:H7," says Doug Powell, Ph.D., an associate professor of pathobiology and scientific director of the International Food Safety Network. "Down-line processors have to be operating under the assumption that they're going to get some E. coli just like we expect consumers to operate under the assumption that they're going to have some in their product, which is why we tell them to cook it."

And really that basic assumption could be the most important lesson we can learn from the recalls. Forget the fact that 70 percent of the cattle in America are slaughtered by just four companies, and that those companies may have managed to intimi-date the USDA into inaction. Put aside theories that cattle are loaded with more E. coli because of stress or due to diet changes arising from our rush to utilize alternative fuels. What you as the consumer need to keep in mind is that beef is being contaminated in slaughterhouses and that you are your own last line of defense.

To put it another way, remember that fecal contamination will continue to occur and shit always flows downstream.

Back at the Oxford, the waitress brings our hamburgers just as the first bets of the night are laid on the poker table in the front room. Eric dolls up his burger with mustard and ketchup and takes a big bite.

It's impossible to tell where the meat for my burger originated, but odds are it came from one of the big packing plants. An old man walks away from his video keno machine, discouraged at having lost his money. I cut into my hamburger patty and stare at it. It looks done, but it's impossible to tell what temperature it was cooked to. A collective groan goes up from the poker table.

"What?" Eric asks, his mouth full of half-chewed meat.

I shrug my shoulders. I'm an unapologetic carnivore. I love beef and I can't imagine giving it up. Besides, until the USDA gets data back from its new measures, until the agency begins cracking down on packing plants that consistently produce contaminated beef, and until the beef industry figures out a way to keep fecal matter from coming into contact with meat in the slaughterhouse, it's all a crapshoot anyhow.

"Pass the ketchup," I say.

© 2012 Rodale Inc. All rights reserved.

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