Here’s why your meal is safer, and why it still may make you sick

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 was 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.

More than 600 people got sick after attending shows at the New Theater Restaurant in Kansas City in January, and tests confirmed infections of the norovirus in at least some.

Upticks in detections of outbreaks of food-borne illness, analysts say, likely reflect our increasing powers to spot them — not a growing danger.

DNA detectives

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. 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. 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, director of the Division of Microbiology at the FDA’s Center for Food Safety & Applied Nutrition.

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.

Poop patrol

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. 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.

Bill Marler is a Seattle attorney who’s made a high-profile career filing lawsuits in food-borne illness cases.

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, Marler 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.

Fresh dilemma

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 has redoubled efforts to track the practices of its suppliers.

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, 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 to keep soiled rain runoff from their vegetable patches. Customers drawn to a restaurant’s 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.”

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.

Experts say the best way to keep it out is to bar sick workers from a restaurant. That’s tough for most restaurants, where workers often barely make minimum wage and struggle from one paycheck to the next. Chipotle has responded by offering sick pay. But paying sick workers to stay home remains highly rare in the industry.

This story was originally published February 24, 2016 at 6:34 PM with the headline "Here’s why your meal is safer, and why it still may make you sick."