Chipotle tweaks recipes, ingredient preparation after E. coli scare

After an E. coli outbreak that has sickened more than 50 people across the country, Chipotle is tweaking its cooking methods.

Onions will be dipped in boiling water to kill germs before they're chopped. Raw chicken will be marinated in re-sealable plastic bags, rather than in bowls. Cilantro will be added to freshly cooked rice so the heat gets rid of microbes in the garnish.

Many changes will be implemented in coming weeks, but the company doesn't expect the taste of its food to suffer.

"When you're given a project like this, you look at the universe of hazards," said Mansour Samadpour, CEO of IEH Laboratories, which was hired by Chipotle to tighten its procedures.

The changes mark a dramatic turn in fortunes for Chipotle, which has surged in popularity by touting its "Food With Integrity" slogan. As it expanded to more than 1,900 locations, the company also sought to draw a distinction between itself and other fast-food chains that executives said use "chemical additives" and "cheap artificial ingredients."

Now, Chipotle Mexican Grill Inc. may be suffering from traits that helped define it. In its annual report in February, the Denver company noted it may be at a higher risk for foodborne illnesses because of its use of "fresh produce and meats rather than frozen," and its traditional cooking methods," rather than "automation."

The warning began coming to life this summer when the chain was tied to foodborne illnesses in California and Minnesota, although those cases didn't get as much attention.

The CDC hasn't identified what triggered the E. coli cases, and Chipotle executives say they may never be able to identify what made people sick.

In the meantime, the company  says can't risk waiting to figure out what went wrong.

Chipotle spokesman Chris Arnold said many of changes will be implemented in coming weeks, but that the company doesn't expect the taste of its food to suffer. Among the changes the company is making:

-Cheese will now arrive in restaurants pre-shredded.

-Ingredients like onions will be macerated with lemon or lime juice to kill germs.

-60 samples of every 2,000 pounds of steak will be tested before it's sent to stores. A similar testing program will be implemented for chicken in coming weeks. Pork and barbacoa beef are already delivered cooked in sealed bags.

-Tomatoes, cilantro and other ingredients will be chopped in centralized locations, rather than in stores, so they can be tested. Chipotle has said in the past that tomatoes taste better when freshly diced in restaurants. After the outbreak, Chipotle co-CEO Steve Ells changed tunes: "If I'm eating a burrito that had tomatoes that were chopped in a central kitchen in the salsa or one that was chopped in house, I probably couldn't tell the difference," he said in an interview on CNBC last week.

Not all chopping will be moved to centralized locations. Onions, for instance, would oxidize and smell bad if they were chopped days in advance, Samadpour said. So they will remain chopped in restaurants, along with lemons, limes and jalapenos. All will now be blanched to kill germs.

Still, Chipotle's road to recovery may be long.

Barclays analyst Jeffrey Bernstein has noted Chipotle's recovery may take longer than other chains that have been hurt by foodborne illnesses, because social media has increased people's awareness of such incidents.

And for a chain that has built its brand on a “Food With Integrity” slogan, the E.coli cases could be far more damaging to Chipotle’s reputation.

The Associated Press contributed to this report.