The latest crisis began last month when Chipotle closed 43 restaurants in Washington state and Oregon after health authorities linked an E. coli outbreak to six restaurants in the region. Illnesses contracted at Chipotles have since been reported in seven more states, including Illinois, Pennsylvania and Maryland.
Then this week, at least 80 students at Boston College fell ill after eating at a Chipotle, leading the company to close another restaurant. Boston health officials said the cause was norovirus, a common virus, while citing the restaurant for two health violations: improper handling of poultry and the presence of a sick employee.
After years of strong growth and accolades, Chipotle suddenly is facing the same critical challenge brand names such as Costco and Blue Bell ice cream confronted when serious questions were raised about the quality or safety of one of their products. About a decade ago, Taco Bell's business shrank for more than a year after an E. coli outbreak, even though it rapidly fixed the problem.
In each case, the company recovered, but customers have begun demanding better-quality food without being willing to pay much more for it. That means the pressures on companies to achieve both affordability and quality are greater than ever.
Chipotle's reputation is perhaps more at risk than most in the fast-food industry because the chain has promised that it adheres to more-rigorous standards for procuring and serving its food. Now, industry experts warn it could face a permanent red mark even if the latest spate of setbacks proves temporary.
"The real red flags are repetitive failures," said Arun Lakshmanan, a marketing professor at the University at Buffalo's School of Management. "When there is repetition, that's what really damages credibility. It's a risky position for Chipotle to be in now."
In response to one of its biggest health and public relations challenges in its 22 year history, Chipotle has pledged to sanitize its operations, hired food safety consultants and announced that it would introduce more-stringent testing of its ingredients. Company executives and health officials say they may never know what caused the outbreak, since any contaminated ingredients would now be long gone. Chipotle has about 2,000 locations.
"If there is a silver lining with an incident like this and not knowing for sure what the cause is, it's that it has prompted us to fully reassess our food handling practices, from the farms that produce our food to the restaurants where we serve our customers," said Chris Arnold, the company's director of communications.
On Thursday, Steve Ells, the company's co-chief executive officer, apologized to customers on on NBC's "Today" show, calling the outbreak "a very unfortunate incident" and saying that he is "deeply sorry." He also promised that Chipotle would be a leader in food safety from here on out. "The procedures we're putting in place today are so above industry norms that we are going to be the safest place to eat," he said.
Chipotle, which has publicly reported strong revenue growth for almost a decade, warned recently that it expects significant declines at its flagship stores as a result of the scare. Its stock price, meanwhile, has fallen by nearly 30 percent since the outbreak was first detected.
Even Chipotle restaurants that weren't implicated in the outbreak seemed to be facing a fallout Wednesday. Patrons in the D.C. area, accustomed to lengthy queues at lunch hour, were surprised to find little to no line.
"I can't believe there are actually people in there eating," said Chad Molloy, 29, as he walked past an M Street NW location in the District on his way to District Taco. "There is no way we're even considering going in there today. It's company wide, all over the country, which means it's a problem."
But others said the company's progressive reputation offset any worry about food illness.
"There is more of a chance that I would get sick eating a cheeseburger from a fast-food joint, because they have sick workers coming in and potentially touching the food," said Tim Tagaris, a partner at Revolution Messaging, a digital agency that does work for the Bernie Sanders campaign, as he had a burrito for lunch.
Most E. coli bacteria are harmless. But certain kinds can cause a range of symptoms, including stomach pain, diarrhea, fever and vomiting. E. coli is rarely fatal: For healthy adults, the recovery time is roughly a week. Noroviruses, meanwhile, are a group of viruses that cause what is often called food poisoning or the stomach flu. They are highly contagious.
Chipotle's pledge of higher-quality food is prominent on its website, where it trumpets the core mission of "food with integrity" and emphasizes a respect for animals, farmers, customers and the environment. The company has worked to make good on that promise by seeking out ways to cut its carbon footprint, carefully choose its farmers, source its ingredients locally where it can, and work with farmers known for humane animal practices.
But as the company has grown, it's faced limitations.
In 2013, it began serving "conventionally raised beef" after it became clear that there was no longer enough antibiotic- and hormone-free beef to meet demand. Then this year, it pulled pork from the menus at roughly a third of its restaurants after one of its suppliers violated its standards.
Chipotle anticipated only a brief interruption, but it took more than half a year, a foreign company and two of its most disappointing quarters on record to put carnitas back on the menu.
"They're trying to be local and serve food with integrity, but as you grow it becomes incredibly complex and difficult and challenging," said Darren Tristano, president of industry research firm Technomic. "When you look at what's going on, how they're expanding, the outbreak was almost bound to happen."
Experts say Chipotle's plan to improve food safety will face challenges that reflect deeper problems in the industry.
Mansour Samadpour, a food safety consultant who has been advising Chipotle on the improvements, said the industry is resistant to testing all food before it's sold. The government requires only that a sample of food be tested, and suppliers don't want the expense of going beyond that standard.
"Fast-food companies are 100 percent reliant on their food supply to send them something that is pathogen-free, but the supply chain is still extremely reluctant to test every [food] product it provides," Samadpour said. "Many companies are starting to do it, but the reluctance is real and it's problematic — and that's getting in the way of food safety."
Bill Marler, a lawyer specializing in food-borne illness who represents many of the people who have fallen ill as a result of the outbreak, said people shouldn't assume that just because a company touts certain kinds of food that it has taken all steps to protect them from pathogens.
"I worry that they look at food safety from the organic, non-GMO, sustainability, animal welfare standpoint," Marler said. "And a lot of people in that space, in that agricultural movement, tend to believe that because they do those things their food is automatically safer than food that's served at McDonald's or Jack in the Box or Walmart. But that's just not the case."