Chipotle restaurant workers serve customers, April 27, 2015, in Miami. The fast-casual chain has suffered a series of foodborne illness outbreaks in recent months, prompting some critics to say its supply chain is particularly vulnerable due to a heavy reliance on fresh produce and small local growers. Joe Raedle/Getty Images

As if the great carnitas shortage of 2015 wasn’t enough of a supply chain headache for corporate buyers at Chipotle Mexican Grill, the fast-casual chain’s produce purchases are now under intense scrutiny following a string of foodborne illness outbreaks. Critics have accused Chipotle of putting customers in danger by sourcing its food from small-scale local growers who they say can’t provide a consistent supply of safe ingredients for the chain’s famous burritos.

The allegation is a problematic one for Chipotle, which earned its popularity in part by being one of the first American fast-food chains to aggressively pledge to buy organic, locally sourced ingredients whenever possible.

“There's a whole layer of problems that Chipotle is facing and the American people are facing because there's this huge movement that says, 'If I buy locally, I’ll be safe,’ ” Patricia Buck, executive director at the Center for Foodborne Illness Research & Prevention, said. “Pathogens and viruses that cause illnesses — they don't care if [an ingredient is] grown locally or in a big factory farm.”

Chipotle has suffered four significant food safety issues in the past six months. First, a salmonella outbreak that sickened 64 customers in Minnesota last fall was traced to Chipotle’s tomatoes. Then, an E. coli outbreak struck 52 patrons in nine states. Chipotle has yet to name the source of contamination in the second case. In two other instances, restaurant employees or customers came down with norovirus, but those cases are not thought to have resulted from contaminated ingredients because the stomach bug is usually spread by human-to-human contact.

Bill Marler, a leading food safety lawyer at the law firm Marler Clark in Seattle, says the rash of outbreaks that Chipotle has suffered is unprecedented: “I've been doing this for a long time and I can't think of another large-scale or small-scale restaurant chain that had ever had something like that happen,” he said.

Safe or Unsafe?

In the weeks following those outbreaks, economists and commentators wondered aloud whether the 22-year-old company’s business model was fundamentally flawed. Customers fretted over whether their beloved burritos were as safe as they had long assumed. Food safety experts questioned whether Chipotle’s obsession with trendy consumer demands for non-GMO and nonhormonal ingredients compromised its ability to also care deeply about the daily drudgery of basic food safety.

But Chris Arnold, Chipotle’s communications director, said it’s a mistake to assume that the restaurant’s suppliers are inherently more susceptible to outbreaks.

“No source has been identified for this E. coli outbreak, so for people to suggest that it was tied to a smaller supplier is nothing more than speculation,” he said. “We work with suppliers of varying sizes — small to large — so that's not a certainty at all.”

The U.S. Centers for Disease Control and Prevention does not track food safety outbreaks in such a way as to easily determine whether small farmers really do cause a disproportionate share of foodborne illnesses. However, some small studies have found alarming rates of contamination at farmers markets. In 2013, researchers at Penn State purchased 200 chickens, half from local growers and half from supermarkets, and found the local chickens carried the highest levels of salmonella and another harmful bacteria called campylobacter.

Ninety percent of the farmers market chickens were infected with campylobacter as compared with 52 percent of factory-farmed birds bought from supermarkets and 28 percent of organic chickens purchased in stores. About 28 percent of the farmers market chickens carried salmonella while only 8 percent of the factory-farmed ones and 20 percent of the organic ones were infected. In a separate study, Chapman University scientists found that 24 percent of herbs purchased at farmers markets in Seattle and Los Angeles tested positive for E. coli.

Still, Phillip Tocco, a food safety specialist at Michigan State University Extension, says there's no reason to think small producers are inherently less responsible in their food handling and testing. From his experience, outbreaks seem to occur at large and small producers at about the same rates.

“All growers can provide safe produce irrespective of size,” he said. “Local produce and regional produce isn't inherently unsafe, but it's not inherently safe either.”

It’s true that certain small growers that sell food locally are exempt from the Food Safety Modernization Act that governs food safety protocols for the nation’s farmers. One point of contention for Buck is that many small farmers reject any mandate to have even the simplest of protections in place, such as a basic food safety plan.

“A lot of small operations feel that's not necessary. They feel they've been doing things the way they've been doing them for years and they don't need big government to tell them how to run their business,” she said.

Regardless, Jaydee Hanson, a senior policy analyst at the Center for Food Safety, also believes small suppliers are generally no more likely to experience outbreaks than large ones. He says when an outbreak does occur, Chipotle’s preferences could actually work in the company’s favor.

“Where Chipotle will have an advantage is where it tries to source locally,” he said. “Its outbreaks should not be as huge as a company that sources from all over the country and has restaurants all over the country.”

A Fresh Dilemma

Chipotle admits in its own 2014 annual report that the restaurant chain may be more vulnerable to food safety outbreaks because of its heavy reliance on fresh produce, which causes more total cases of foodborne illness than any other source. Harmful bacteria can spread to human food when contaminated animal waste is used as manure to grow fresh produce such as peppers, tomatoes, cucumbers and leafy greens.

“The thing about fresh produce is that no matter what everybody does, if we're all doing everything right, there still could be somebody that's getting sick,” Tocco at MSU Extension said. “There's always a possibility because there's no way to completely sterilize fresh produce when we eat it raw.”

Chipotle’s openness about the risks of its fresh produce applies to both large and small producers. But Buck, of the Center for Foodborne Illness Research & Prevention, thinks the restaurant chain is even more susceptible because the smaller producers it favors tend to not maintain rigorous testing procedures unless required to do so by buyers.

“If you're buying from a larger company, they do testing at all of their facilities before they send it out,” she said. “When you're talking about the local farmers, they don't necessarily all do the same level of testing. Then it is up to the company, whether it’s Chipotle or Walmart, to insist that type of testing is done.”

After the most recent outbreak, the restaurant chain hired IEH Laboratories and Consulting Group to review its food safety protocols and pledged to test all of its produce with “DNA-based tests” for microbes. Though the company didn’t specify which tests it would deploy, the list may include rapid screening for E. coli and salmonella.

In addition to improved testing, the company will route more ingredients through a central preparation facility so employees can consistently prepare and test products together. For example, employees traditionally tested, washed and chopped tomatoes for salsa at each location. Now, staff at a central facility will wash and test them both before and after they are diced.

“It theoretically should improve consistency, it theoretically should improve food safety,” Tocco said.

Buck applauds these changes, but is still careful to caution consumers that purchasing local ingredients does not exempt individual buyers or major restaurant chains from being sticklers for food safety. “I think Chipotle is earnest and trying very hard to make some changes,” she said. “I think it draws more attention to the fact that the general public should not rely on, ‘I know that I bought it from a small farmer so it's going to be safe.’ ”