A closer look at the GenomeTrakr
First off, go ahead and eat out. Or eat in.
Whether you dig into Mom’s casserole, feast on the local diner’s daily special or snarf up something from a mega-corporation’s drive-through, America’s meals may arrive as safe now as mankind has ever known.
Just not 100 percent.
Nearly 50 million illnesses a year in the United States still trace to what people eat. The Centers for Disease Control and Prevention has estimated that more than 120,000 cases lead to hospitalization and roughly 3,000 people die.
So cook that meat. Wash that produce. Thoroughly.
Then realize that you still rely on armies of government regulators slogging against the countless ways germs can poison your food.
People who obsess over food safety believe progress looks steady (even as they say they order their steaks well-done, avoid salads at restaurants and won’t eat a runny egg). Government rules continue to tighten. Various industries, fearful of lawsuits and the lost business that follows bad publicity, put more muscle into keeping things clean.
Yet experts also describe an increasingly elaborate system that tests the power to keep a meal safe.
“The marketplace is probably more complex,” said Charles Hunt, the Kansas state epidemiologist. “The produce that you get in the store today was in Mexico or someplace else just a few days before.”
The Chipotle chain saw multiple, high-profile problems last year. An E. coli outbreak traced to its restaurants in October. In December, the company also was tied to a norovirus incident in Boston, following outbreaks of the pathogen earlier in the year at outlets in California and Minnesota.
In the Kansas City area, more than 600 people got sick after attending shows at the New Theater Restaurant in January, and tests confirmed infections of the norovirus in at least some. The virus can spread by contact with an infected person, through contaminated food or water, or by touching contaminated surfaces. Investigators have not determined how the virus was spread in the New Theater case, nor have they specifically linked it to food service.
Norovirus also struck at least 18 staff and patients at the University of Kansas Hospital’s Marillac Campus that month. And about a dozen people were hit with the same vomiting and diarrhea shortly afterward at a Buffalo Wild Wings in Overland Park.
Upticks in detections of outbreaks of food-borne illness, analysts say, likely reflect our increasing powers to spot them — not a growing danger.
In 1998, the U.S. Food and Drug Administration traced an outbreak of salmonella agona to a Malt-O-Meal processing plant in Minnesota. Ten years later, the same plant again shipped out cereal tainted with salmonella, sickening at least 33 people.
With the two incidents separated by a decade, any link seemed coincidental.
But a few years later, the FDA built a powerful tool for analyzing bacterial strains — Whole Genome Sequencing. It can identify the lineage of any bacterium in its database. In this case it showed the new salmonella was the direct descendant of the earlier one.
It turned out that the first outbreak stemmed from contaminated water used to clean the plant during a renovation. That same water was mixed in with mortar for the construction. Dangerous salmonella had been preserved in that mortar. Over the years, the surface of the mortar turned to dust, got wet and gave new life to that distinct family of salmonella.
Imagine the implications. For starters, the plant could prevent repeats by painting a sealant over the unlikely culprit — mortar in its walls.
But think of the child who becomes sick down the road with salmonella. The source could be any of thousands of ingredients consumed by an American kid in a normal day. But what if a doctor shares the salmonella sample with federal disease trackers? By looking at the particular genetic line, scientists can spot the family tree and the likely source.
“It tells you who’s related to who even over many years,” said Eric Brown, the director of the Division of Microbiology at the FDA’s Center for Food Safety & Applied Nutrition.
He likens the advance to a ship’s captain going from a sextant to GPS. Instead of dispatching investigators across the country to perhaps hundreds of possible sources, they head straight to the most likely culprit.
When, in 2012, 425 Americans fell sick from salmonella, the technology allowed the FDA to quickly trace it to tuna imported from India. So instead of sending investigators across the entire Pacific Rim for a source, they’d narrowed it to a source just five miles from the Indian processing plant.
“When you see a match,” said Marc Allard, a senior biomedical research services officer at the FDA, “it allows you to attack.”
After the tuna case, the FDA created the GenomeTrakr Network, tying together data from state, federal and academic laboratories identifying the DNA of samples from various outbreaks. It also catalogs swabs from factory inspections. Now the agency maintains a database holding more than 10,000 bacteria, adding about one genome every hour.
Technology, food safety experts say, only goes so far.
The bigger payoffs come from diligence. That means, foremost, avoiding contamination from feces.
“Our food safety starts on the farm,” said Doug Powell. A former Kansas State University professor of food safety, he’s now the chief author of barfblog.
“It has to be systemic, repeated and relevant.”
For starters, farmers should not use manure on fresh produce. They need to know where their irrigation supply comes from and whether runoff during heavy rains travels from feedlots or other places where livestock or farm workers defecate. Washing those fruits and vegetables later down the line is necessary, but that often can’t overcome massive exposure to E. coli and other potentially fatal bacteria that thrive in poop.
Increasingly, our meat supply comes from livestock raised in crowded conditions. It’s part of what makes that protein affordable, fatty and tender. Cattle typically spend the last several weeks of their lives penned tightly in massive feedlots with thousands of others headed to slaughter. For pigs and chickens, that close-quarters existence runs from birth to butcher.
In such tight spaces, they inevitably end up splattered with their own dung and that of the animals next to them.
Those critical of America’s meat industry argue that means a rethinking of livestock practices.
“There are real consumer costs to this,” said Jaydee Hanson, a senior policy analyst at the Center For Food Safety. “But what every feedlot needs to fear is the tort lawyer who will sue them on behalf of the people who get sick.”
Bill Marler, a Seattle attorney who’s made a high-profile career filing lawsuits in food-borne illness cases, speaks with less alarm about the direction of Big Meat.
After years of restaurants and meat packers weathering expensive lawsuits and public relations disasters, he said, they’ve changed.
Take the slaughterhouse. Cattle arrive splattered with barnyard waste. For years, that created problems because the tainted hides would inevitably taint the skinned carcasses. But now, packing operations routinely steam-clean or treat the carcasses with an acid wash.
“You started to see an amazing turnaround and recalls linked to hamburger have fallen like a stone,” Marler said.
Meantime, he said, restaurants better recognize the business risk of not killing pathogens that cling to meat. Marler said big chains, in particular, devote increasing effort to thoroughly cooking beef, pork and poultry.
And federal rules on the required temperature for cooked meat have increased. Some chains, such as Taco Bell, now cook meat at centralized locations before shipping it to franchises. The local teenager preparing that food for customers still needs to be wary of temperature control, but much of the responsibility for safety has been standardized by corporate operations.
Produce, he and others say, poses a more difficult problem. Food that’s not cooked lacks the critical “kill step” to render harmless the bacteria that do slip through.
Many critics of Chipotle like to say its marketing of a more wholesome food chain helps explain its problems. The meat is cooked on site. The company gathers supplies as locally as possible. Much of its ingredient list is fresh produce — lettuce and other add-ons — that isn’t cooked.
That, goes the critique, sets up a corporate culture that valued freshness over safety.
The company has responded by shutting down its restaurants repeatedly for special training days and saying it’s redoubled efforts to track the practices of its suppliers.
(Many have noted that much of Chipotle’s problems related to contamination from sick workers, not from its pursuit of freshness. More on that later.)
But consumers have shown an increasing interest in the source of their food, preferring fresh over processed and local or organic over cheaper commodity ingredients. That’s tied, analysts say, to the belief that food made on a smaller scale and without the use of antibiotics in livestock or pesticides in crops is safer.
Some evidence suggests that such methods provide a more nutritious meal that may avoid long-term health risks. Yet they can pose new challenges in dodging food-borne pathogens in the short term, said barfblog’s Powell and others.
“Natural, organic, sustainable, dolphin-free — those are lifestyle choices,” Powell said. “There’s been no study that has conclusively said one way or another if it’s more likely to make you barf more.”
He worries it might. Smaller farms might not have the resources, or the sophistication, to keep soiled rain runoff from their vegetable patches. The farmer’s market customers or restaurants drawn to their farm-to-plate marketing, he said, might be less inclined to question safety.
“McDonald’s has it covered,” Powell said. “At the boutique places, I say I want my meat cooked to 165 degrees and they look at me like I just came off the turnip truck.”
Some also have worried that the foodie infatuation with food trucks might mean new problems. Wouldn’t a mobile, cramped operation with either no running water or a temporary hookup pose new dangers? One study from the Institute for Justice released last year, however, looked at 260,000 food inspection reports from seven cities and found “food trucks and carts did as well as or better than restaurants.”
Sneezes and sanitizer
One of the most vexing problems comes in maintaining sanitation in the chaos of a restaurant kitchen.
Much of Chipotle’s problems came from norovirus, possibly transmitted by food handlers. That’s a problem that arrives long after a farm or a slaughterhouse. The pathogen, like many other viruses, is highly contagious.
Experts say the best way to keep it out is to bar sick workers from a restaurant. That’s a tough act for most restaurants, where workers often barely make minimum wage and struggle from one paycheck to the next. It’s a dangerous incentive to work rather than skip a shift. Chipotle has now responded by offering sick pay. But paying sick workers to stay home remains highly rare in the industry.
The National Restaurant Association said it urges businesses to be vigilant and encourage workers to swap shifts aggressively when someone gets sick.
“We teach them to look for diarrhea, vomiting, jaundice,” said David Crownover, the director of the association’s ServSafe food safety training efforts. “It’s really important for the managers to be vigilant.”
Naser Jouhari, the manager of Kansas City’s environmental health services division, said he sees far greater detail today than in years past to keeping hot food hot and cold food cold. Gloves used to be rare. Now they’re common. Hand-washing, he said, appears more frequent. Sanitizing gel makes a difference.
He keeps a copy of the city’s food code from 1970. It’s a tiny booklet. Today’s city food is nearly 250 pages drawn mostly from federal rules that have grown over the years.
Enforcing today’s rules may force as many citations and restaurant closures as a generation ago, he said, but only because businesses have more rules to follow.
Take the humble tomato. In past years, it was seen as a harmless part of a dinner. But now the FDA considers tomatoes potentially hazardous food — there’s a possibility of bacterial contamination on the surface.
“Now we’re treating it like meat,” Jouhari said. “That only happened a few years ago.”