Chipotle's recent norovirus outbreak was the result of lax sick-policy enforcement

• A self-identified Chipotle employee alleged in a Reddit post last month that a manager required them to work while sick.
• A Chipotle employee from a different state told CNBC that it was only after the norovirus outbreak last week that their manager began enforcing the sick policy.
• Chipotle's sick policy may not be the only one that managers are overlooking.

Chipotle Mexican Grill's recent norovirus outbreak in Virginia was the result of lax sick policy enforcement by store managers, the company confirmed on Tuesday.

It has been two years since a string of food safety incidents first battered sales and scared away diners. While the beleaguered burrito chain was able to return to profitability and its same-store sales have begun trending in a positive direction, its successes have been overshadowed by a recent series of incidents.

Chipotle's reputation took a hit last week after reports surfaced that customers were sickened bynorovirus at a location in Sterling, Virginia. Then, a few days later, a viral cellphone video was released that showed rodents falling from the ceilingat a restaurant near Dallas.

Both restaurants have addressed these issues, with the Virginia location shuttering briefly to sanitize, and the Texas restaurant sealing up the rodents' entry point.

But by that point, the damage was done. Chipotle shares have fallen nearly 12 percent since last Tuesday, when the news broke, and Chipotle's food safety policies are once again up for debate.

"If another chain had a norovirus outbreak, I am pretty sure that it would not have gained the national exposure the way that Chipotle had in this last outbreak," Martin Bucknavage, senior food safety extension associate at The Pennsylvania State University, told CNBC via email. "So yes, we are hyperaware of their issues. That being said, the entire system of retail operations should have been hyperaware of employee health issues."

The company said Tuesday in their earnings conference call that they believe an employee was the cause of the outbreak.

"We conducted a thorough investigation, and it revealed that our leadership there didn't strictly adhere to our company protocols," CEO Steve Ells said during the call.

Discussions among Reddit users had suggested that some Chipotle locations are not adhering to the company's safety guidelines.

By not following guidelines, conditions are created that would make a norovirus or similar outbreak seem "eminently predictable," Stuyvesant Square Consultancy Managing Director J.G. Collins, who writes frequently about the restaurant industry, told CNBC via email.

A self-identified Chipotle employee alleged in a Reddit post last month that a manager required them to work while sick.

"My boss has told me that I have no option but to come in tomorrow, and it's been heavily implied that my job will be in jeopardy if I don't come in," the user wrote last month.

"Isn't it against company policy to work with a fever anyway? Today I was told I was not allowed to blow my nose during peak for about an hour and a half. If I'm dripping snot, shouldn't that constitute too sick to work with food anyway?"

This Reddit user, who is from Missouri, wished to remain anonymous but told CNBC by email Friday that they did not lose their job, but their absence was "frowned upon."

"I've since had one of my managers tell us that they only abide by the sick policy about 40 percent of the time," this person said. "Apparently since the sick policy worked for two years its 'no longer necessary' to make sure sick employees stay home."

Chipotle has a paid sick-leave policy to ensure employees stay home when they are ill.

"We have policies that preclude people from coming to work sick, and are one of few restaurant companies that provides paid sick days for our employees (including hourly employees)," Chris Arnold, a Chipotle spokesman, told CNBC by email.

"We have added a HACCP (hazard analysis critical control points) program to all of our restaurants, and that program begins with a daily wellness check where employees in our restaurants are asked screening questions to be sure no one is working while sick. If any employees report symptoms of illness, [they] are excused from work until they are feeling better."

However, not all managers seem to abide by this standard. A Chipotle employee who works in a Virginia location — not the Sterling location — told CNBC by email that it was only after the norovirus outbreak last week that their manager began enforcing the sick policy.

"Two weeks ago [I] came to work, felt like I was going to puke, just felt awful," they said. "One of my managers told me if I don't find someone to cover my shift, I'm going to have to stay. Mind you, my position was on line working with food."

Chipotle's sick policy may not be the only one that managers are overlooking. Collins said that a few Reddit users who reported working for Chipotle said that management within their restaurants had not complied with the company's safety protocols. Collins first wrote about these posts in a Seeking Alpha article published last month.

One user alleged that their manager "makes us pretend we're doing things the right way when Ecosure [the company's food safety auditor] is there," but doesn't blanch the produce when the inspector is not present. Another one said that their general manager had them falsify food safety sheets.

The Virginia employee told CNBC that his location blanches their avocados, onions, peppers, lemons, limes and jalapenos every morning, as specified by Chipotle's food safety guidelines.

Chipotle has taken a number of measures to prevent foodborne illnesses, including shifting some preparation to its central kitchens, blanching ingredients, and making modifications to how it marinates steak and chicken.

"Clearly, they have hired some well-known food safety experts to help with their programs, so I would expect that their programs would not be drastically different than what occurs at other operations," Bucknavage said. "Their size is not much different than any other large foodservice operation (McDonald's, Panera, Chick-fil-a, etc)."

However, Chipotle's commitment to locally sourced ingredients, a defining part of their business model, is what poses one of the largest threats to the chain.

"[It] creates problems with tracability and consistency of supply," David Henkes, principal at Technomic, told CNBC via email.

Despite these food safety initiatives Henkes said that there is always a risk of employees "short cutting the system."

"You're asking an 18- or 19-year-old kid to replicate the recipes of a [Culinary Institute of America]-trained chef in a kitchen — chopping, cooking, serving, — with very limited supervision and to maintain some fairly stringent food safety standards," Stuyvesant's Collins told CNBC via email.

Collins said that Chipotle's food safety practices are hard to replicate in its more than 2,200 restaurants nationwide, especially as the brand continues to grow. And he's not the only one to see scale as a major issue for Chipotle.

"Chipotle is damaged goods," Dana Blankenhorn, an analyst at InvestorPlace.com, told CNBC via email. "There's a reason why McDonald's freezes its meat. This is the reason. Fresh food prep like this does not scale."

Chipotle reports second-quarter earnings on Tuesday afternoon.

WATCH: Chipotle shares plummet on report of norovirus in Va. restaurant