Beef cattle stand in a barn at a feedlot in Illinois April 5, 2011. Next month, the Agriculture Department will begin testing raw ground beef for the “Big Six” in order to keep some pathogens off people’s plates. (Daniel Acker/BLOOMBERG)

On her 14th birthday, Kayla Boner got her driver’s permit and then went home complaining of stomach-bug symptoms that landed her in the hospital two days later.

Antibiotics didn’t work. Kayla’s condition deteriorated. Her kidneys failed. She had a seizure and went on a ventilator. Soon after, her brain activity ceased. Just 11 days after her symptoms surfaced, Kayla’s distraught parents decided not to keep her on life support.

The culprit: E. coli. Not the strain responsible for most serious food-borne illnesses, but a lesser-known one that her parents researched in vain when Kayla died in 2007.

“We were told it was E. coli O111,” said Dana Boner, Kayla’s mother. “Where did it come from? What could it have been? All these years, and we still don’t know.”

And they most likely will never find out.

While most of the outbreaks that have riveted the public for nearly two decades involved one strain of E. coli, the government will soon outlaw another six strains in the same family of bacteria, including the one that killed Kayla.

Next month, the Agriculture Department will begin testing raw ground beef for the “Big Six” at meat plants in order to keep these pathogens off people’s plates. The decision comes four years after scientists and government experts warned of the dangers these germs pose to the nation’s food supply. Since then, the Big Six have been repeatedly tied to multi-state outbreaks and illnesses.

Most of those illnesses were not linked to beef. They were linked to sprouts or lettuce or no source at all. The meat industry argues that it is being unfairly targeted. Only once before — with the notorious E. coli O157:H7 — have regulators banned a pathogen from fresh meat.

If the Food and Drug Administration detects any pathogens in the food it oversees — vegetables, fruits, seafood and just about everything other than meat — it yanks the products. But the resource-strapped agency inspects only a fraction of its plants every year.

By contrast, the law requires the USDA to inspect all meat plants daily.

And the government says it is time to add the Big Six to the daily routine.

“What we’re doing is about prevention,” said Elisabeth Hagen, the USDA’s undersecretary of food safety. “If all we’re going to look at is how many people can we prove have been sickened or killed by contaminated beef before we act, then we miss our opportunity to make a real difference.”

Still, the long and plodding path toward heightened regulation in large part reflects the government’s awareness of another lingering threat: meat industry lawsuits.

Legal challenges on ‘adulterants’

The USDA, consumer groups and the industry have engaged in a fierce and litigious fight that has stretched over decades.

The meat industry has a long history of challenging high-stakes government decisions. The courts have ruled, for instance, that the sale of meat contaminated with salmonella cannot be prohibited. Today, that pathogen is the top cause of food-borne illness resulting in hospitalization and death.

In the 1970s, courts rejected a proposal to put warning labels on poultry about the dangers posed by salmonella on the grounds that salmonella was naturally occurring in meat and posed no risk if the meat was properly cooked.

Then in 2000, the USDA suffered a crushing setback when the industry successfully challenged its effort to shut down a Texas beef plant that had failed a series of salmonella tests.

These legal challenges help explain why the USDA has been weighing action on the Big Six for four years. Only in September did officials feel confident enough about their legal case and the science behind it to declare the strains “adulterants,” requiring the government to test for them. Even then, enforcement was postponed from early March until June 4 to allow the industry more time to prepare for the change.

“The issue for regulators is: What happens if there’s a court challenge?” said Robert Buchanan, a former USDA official who was deeply involved in early discussions about the Big Six. “What you don’t want is to have a good policy that loses in court because it went into effect too quickly.”

A victory for regulators

The first, and so far only, time that the government has banned an E. coli strain from the food supply came after a four-state outbreak linked to Jack in the Box hamburgers, which sickened hundreds of people and killed four children in 1993. It was the largest outbreak ever in North America and sparked consumer outrage.

That decision was announced by Mike Taylor a month after he was tapped to head the USDA’s food-safety branch. Speaking at the American Meat Institute’s annual convention in San Francisco in September 1994, Taylor offered what he later called an “oh-by-the way” moment several pages into the speech. With no warning, he declared the E. coli microbe that caused the outbreak — the O157:H7 strain — to be an adulterant in ground beef and told the stunned audience that the government would start testing for it.

“There was a lull for a day or two before I heard much,” Taylor recalled in an oral history recorded several years later. “And then the industry’s lawyers began to focus and the industry was on edge, shall we say, and they kind of started making phone calls.”

Not long after, the meat industry and a group of supermarkets sued the USDA to overturn the ban. The government, in this case, ultimately prevailed.

But the court battle left its mark on federal regulators and industry representatives, who all became more vigilant about the efforts to restrict contaminants.

Infections from other strains rise

Hagen, who assumed her current USDA post in 2010, was one of the first regulators to flag the risks posed by the Big Six in raw meat.

Hagen was head of the department’s outbreak response division in 2006 when she learned from her staff about infections apparently related to beef, she recounted. Several states had detected infections linked to E. coli strains other than O157:H7.

By then, the USDA’s food-safety chief, Richard Raymond, was also hearing concerns. Over dinner in Omaha with a friend who ran Nebraska’s public health laboratory, Raymond learned that the lab was seeing as many infections from these other strains as the one that had been banned. Calls to labs in other states revealed a pattern.

When Hagen and Raymond compared notes, they realized they had a problem. “I told her that we needed to have a conference to discuss what we know about these bugs,” Raymond said.

That day-long event took place in October 2007, the same month Kayla was hospitalized.

At the meeting, Patricia Griffin, a senior scientist at the Centers for Disease Control and Prevention, reported that six strains of E. coli — other than O157:H7 — were responsible for about 70 percent of the country’s E. coli infections. The infections tended to be less severe than those linked to the prohibited strain. But some some caused bloody diarrhea and kidney failure, Griffin reported.

After soliciting input from more than two dozen scientists, government experts, industry groups and consumer advocates that day, the USDA concluded that it needed more information before it could act.

Bill Marler, a Seattle lawyer who had represented victims of the Jack in the Box outbreak, was not satisfied. He petitioned the USDA to ban dozens of E. coli strains from the food supply. In support, he detailed the case of Maryland woman who died after eating bagged baby spinach, a Utah woman who suffered permanent kidney damage after eating a fast-food meal, and an Oklahoma woman who also suffered kidney failure. Marler said each victim had been infected by a different E. coli strain.

The government’s own evidence was also mounting as more public health laboratories started testing the stool samples of people with diarrheal illness. In 2010, for the first time, the reported illnesses from E. coli O157:H7 were outnumbered by the total from all other E. coli strains combined.

Since then, four multi-state food-borne outbreaks tied to other strains of E. coli have been reported, including one this year linked to raw clover sprouts at Jimmy John’s restaurants.

And, for the first time, an outbreak from one of the Big Six was linked to beef.

The case for and against testing

The meat industry has remained unconvinced.

The American Meat Institute points out that nearly all the known infections tied to the six strains do not involve beef and that the government should have done more testing of ground beef and more research before deciding the strains were adulterants.

Industry representatives also object to proposed testing. Companies do not want to wait for the result from government-run tests because this could take days, shortening meat’s shelf life. And tests that some companies now use for quick screening have a notoriously high level of false positives when trying to detect the Big Six.

Also, the mere presence of these strains does not mean they will cause illness.

“Why put in place a policy where a significant percentage of the meat could have to be destroyed when it’s perfectly safe?” said Mark Dopp, the AMI’s senior vice president of regulatory affairs.

Nor can anyone point to an outbreak on the scale of Jack in the Box to justify barring these six strains. More than one microbiologist has questioned whether the USDA should use its scant resources on these six strains when it has more menacing pathogens to tackle.

Dana Boner doesn’t see it that way. She has always wondered whether her daughter ate a contaminated hamburger at school or maybe got some ground beef under her nails while helping shape patties at home. After all, she said, “We’re meat people. We’re from Iowa. That’s what we eat.”

And that, she says, is what makes government testing so critical.

“If the government isn’t testing, how do we know that [the pathogens] are not in the beef?” Boner said. “If these tests save just one life, isn’t it worth it?”