Is it now safe to eat at Chipotle? After a series of food-safety incidents that began in the latter half of 2015, including outbreaks related to E. coli, norovirus, and salmonella, once loyal customers of the Mexican-inspired restaurant chain still have their doubts.

Throughout my research for our new feature on Chipotle, which charts the company’s internal struggles as it attempts to revive sales and consumer trust, I encountered countless numbers of people who wondered whether they could return to eating the restaurant’s food without worry of getting sick. This lingering concern can be seen in the company’s financial performance: Chipotle lost nearly a third of its sales after the food-safety crisis. Morgan Stanley surveyed customers in January 2016, in the immediate aftermath of Chipotle’s E. coli outbreaks and before the CDC closed its investigation, and found that just 41% of customers considered the chain a safe place to eat. That percentage ticked up in a subsequent study in June but not enough to resemble anything close to a full recovery. “When 50-some-odd people contract E. coli, and you realize that you were responsible for that, it really—shooooooo,” says Chipotle co-CEO Steve Ells, deeply exhaling. “Justifiably, people really question our trust. You lose that trust. For how long? We’re working really, really hard to get that trust back.”

Multiple industry experts tell me that Chipotle did not take food safety seriously enough or invest sufficient resources into quality assurance (QA). “When this [outbreak] first broke, the leadership at Chipotle, and I include Steve and [co-CEO] Monty [Moran], were completely sideswiped and didn’t know what the hell they were doing,” says one source familiar with Chipotle’s food-safety measures. “They had not really considered food safety at the level that they should have.”

Making Safety A Higher Priority

Before its E. coli incidents, a slew of sources tell me that the food safety and QA team overseeing the company’s entire supply chain included just four people, a low number for a chain of Chipotle’s scale and complexity. The company also split its safety teams, which some suggest created arbitrary divisions of responsibility within the organization. Heidi Wederquist, then Chipotle’s director of QA and food safety, oversaw supply-chain issues, but had little visibility into restaurant operations. Conversely, Tim Spong, who knew Moran in college and served as outside counsel for Chipotle before joining the company, managed safety, security, and risk at the restaurant level. “There is no way a team that small could properly manage all the food coming into that system,” says one former analyst at the company, who now works for a chain much smaller than Chipotle but with a QA team that’s twice its size. Chipotle spokesperson Chris Arnold disputes the visibility claims but confirms the rest, adding that the team was “strengthened” with additional hires after February 2016 and that the two groups have now been merged under Spong’s leadership. (Additionally, Jason Von Rohr, Chipotle’s executive director of supply chain, who was responsible for sourcing all of Chipotle’s ingredients, departed shortly after the E. coli outbreaks. Multiple sources indicate he had been planning to leave Chipotle and his departure was not a result of the outbreaks. He has since joined Amazon.)

Originally, Chipotle followed the guidance of food-safety scientist Mansour Samadpour, who runs the Seattle-based consultancy IEH Laboratories. He’d initially focused the company’s food-safety program on a mix of supply-chain testing and what are called “interventions” or “kill steps,” which work to eliminate pathogens from ingredients. For example, he introduced blanching produce to Chipotle, a kill step whereby Chipotle workers put lemons, limes, onions, avocados, and jalapeños into 185-degree water for five seconds before preparing them for customers.

When Chipotle hired James Marsden in February 2016 to be its director of food safety, he shifted the company to adopt more of these interventions, while winding down Samadpour’s testing system. He expanded the company’s blanching system, for example, to include bell peppers.

One of Marsden’s first acts was to create an ordered list of the riskiest ingredients on the restaurant’s menu. At the top of his list? Chipotle’s beef. Though there likely wasn’t one smoking gun that caused the outbreaks, in terms of particular ingredients, sources indicate Chipotle had narrowed its investigation to a select few items, including onions, cilantro, and beef. Cross-contamination was likely, but because the company’s E. coli outbreaks were limited to around 60 infected people, some food-safety sources suggest it was more than likely Chipotle’s beef was the original culprit that carried the E. coli, since it is a cooked item (unlike, say, cilantro), which may have reduced how widespread the outbreak could have been.