Chris Collins is a 32-year-old Web developer and photographer who lives in Oregon, just outside Portland. He and his wife are conscientious about their food: They eat organic, local produce and ethically raised animals. Collins liked to have a meal at Chipotle once a week. On Friday evening, Oct. 23, he ordered his regular chicken bowl at his usual Chipotle in Lake Oswego. His dinner was made of 21 ingredients, including toasted cumin, sautéed garlic, fresh organic cilantro, finely diced tomatoes, two kinds of onion, romaine lettuce, and kosher salt. It tasted as good as always.

By the next night, Collins’s body was aching and his stomach was upset. Then he began experiencing cramping and diarrhea. His stomach bloated. “Moving gave me excruciating pain,” he says, “and anytime I ate or drank it got worse.” His diarrhea turned bloody. “All I was doing was pooping blood. It was incredibly scary.” After five days, he went to an urgent-care clinic near his home; the nurse sent him to an emergency room. He feared he might have colon cancer.

On Halloween, the ER doctor called him at home: Collins had Shiga-toxin-producing E. coli 026, and he’d likely gotten it from one of those 21 ingredients in his meal at Chipotle. (This was later confirmed by public-health officials.) The doctor warned him that kidney failure was possible; intensive treatment, including dialysis, could be necessary. His kidneys held up, but it took an additional five days for the worst of Collins’s symptoms to ease and nearly six weeks for him to recover. He still doesn’t have as much physical strength as he used to, and he feels emotionally shaky, too. “Before, I was doing the P90X workouts. For a long time after, I couldn’t even walk a few blocks,” he says. “It made me feel old and weak and anxious.” On Nov. 6, Collins sued Chipotle, seeking unspecified damages.

Collins was among 53 people in nine states who were sickened with the same strain of E. coli; 46 had eaten at Chipotle in the week before they fell ill. Twenty got sick enough to be hospitalized, according to the Centers for Disease Control and Prevention. “I trusted they were providing me with ‘food with integrity,’ ” Collins says, sarcastically repeating the company motto. “We fell for their branding.” Chipotle’s public stance during the outbreak irritated him, too. The company closed all 43 of its restaurants in Oregon and Washington in early November to try to identify the source of the E. coli and sanitize the spaces. Notices on restaurant doors generally referred to problems with the supply chain or equipment. But local media reported that at least one restaurant in Portland put up a note that said, “Don’t panic … order should be restored to the universe in the very near future.” “That felt so snarky,” Collins says. “People could die from this, and they were so smug.”

For a long time, smug worked pretty well for Chipotle Mexican Grill. It’s grown into a chain of more than 1,900 locations, thanks in part to marketing — including short animated films about the evils of industrial agriculture — that reminds customers that its fresh ingredients and naturally raised meat are better than rivals’ and better for the world. The implication: If you eat Chipotle, you’re doing the right thing, and maybe you’re better, too. It helped the company, charging about $7 for a burrito, reach a market valuation of nearly $24 billion. Its executives seemed to have done the impossible and made a national fast-food chain feel healthy.

Fewer people associate Chipotle with “healthy” now. Three months before Collins was infected with E. coli, five people fell ill eating at a Seattle-area restaurant. By the time local health officials had confirmed a link, the outbreak was over, so no one said anything. In August, 234 customers and employees contracted norovirus at a Chipotle in Simi Valley, Calif., where another worker was infected. Salmonella-tainted tomatoes at 22 outlets in Minnesota sickened 64 people in August and September; nine had to be hospitalized. Norovirus struck again in late November: More than 140 Boston College students picked up the highly contagious virus from a nearby Chipotle, including half of the men’s basketball team. An additional 16 students and three health-care staff picked it up from the victims. The source? A sick worker who wasn’t sent home although Chipotle began offering paid sick leave in June. In the second week of December, when Chipotle should have been on highest alert, a Seattle restaurant had to be briefly shut down after a health inspection found that cooked meat on the takeout line wasn’t being kept at a high enough temperature. And in the most recent case, on Dec. 21, the CDC announced it was investigating an outbreak of what seems to be a different and rare version of E. coli 026 that’s sickened five people in two states who ate at Chipotle in mid-November. The company says it had expected to see additional cases. It still doesn’t know which ingredients made people ill.

Almost 500 people around the country have become sick from Chipotle food since July, according to public-health officials. And those are just the ones who went to a doctor, gave a stool sample, and were properly diagnosed. Food-safety experts say they believe with any outbreak the total number of people affected is at least 10 times the reported number. The CDC estimates that 48 million Americans get sick from contaminated food every year.

Read the article “Inside Chipotle’s Contamination Crisis” on bloomberg.com.