The Cleveland Circle Chipotle Mexican Grill in Brighton, Massachusetts, is a popular late-night spot for Boston College students.

In early December, Griffin Carney’s roommate ate there and got sick with what was first diagnosed as E. coli. Once he began feeling a bit better, the roommate began socializing with others in their dormitory.

“Then they [student health services] told him it was the norovirus,” Carney told Healthline. “When we heard that, we scrubbed everything.”

But norovirus — the leading cause of illness and contaminated food outbreaks in the United States — had already spread and infected three of the eight men in the same dorm room, causing intense bouts of vomiting.

“It was the Wednesday before finals and I was deathly sick,” Carney, a sophomore studying biology, said. 

Carney was one of the 141 Boston College students who contracted the norovirus related to the Chipotle restaurant near the college. The norovirus, which kills an estimated 200,000 people worldwide each year, is passed by an infected person, contaminated food or water, or by touching contaminated surfaces.

Following the outbreak, the Massachusetts Department of Public Health closed the Chipotle location on Dec. 7. It reopened more than two weeks later.

While he ate at that particular restaurant many times, Carney said he hasn’t gone back, although other students continue to eat there. 

“After all this, I’m sure it’s the cleanest and safest location,” Carney, who has eaten at a different Chipotle since being sick, said. “They’re on a tight leash.”

But experts told Healthline contaminants such as the norovirus can be easily transmitted in restaurants by workers as well as customers, even with safety precautions in place.

Read More: Get the Facts on Food Poisoning »

Chipotle Linked to 500 Cases

The Brighton outbreak was the latest of six separate outbreaks of norovirus or E. coli to infect customers at the burrito chain restaurant. About 500 people have been sickened since July at various Chipotle restaurants.

According to the latest report from the U.S. Centers for Disease Control and Prevention (CDC), 53 of the victims have been sickened in nine states from a form of E. coli that produces a toxin that can cause kidney damage. While 20 were hospitalized, no one has died.

The CDC is also investigating another outbreak of E. coli 026 at other Chipotle locations in November. The five sickened customers say they ate at Chipotle in either Kansas or Oklahoma.

While the outbreak is considered over, the company continues to deal with the fallout.

In the aftermath of dozens of locations being closed, cleaned, and reopened, Chipotle is under criminal investigation by the U.S. Attorney’s Office for the Central District of California and the U.S. Food and Drug Administration’s Office of Criminal Investigations following the norovirus outbreak in Simi Valley, California. 

The criminal case stems from how the company handled its food, which spurred debate about the safety of Chipotle’s ingredients sourced from smaller local farms. Because of the outbreaks, Chipotle announced new safety measures to be included in their supply chain, including safety testing, food handling, and contaminant screening.

Chipotle founder and co-CEO Steve Ells has been accused of allowing the chain to grow too quickly for food safety measures to keep up. Ells has defended Chipotle’s mission to use local and sustainable ingredients when possible.

“I don’t think so. If you look at the quality of our ingredients over time, we’ve made great strides in sourcing better quality foods: meats without antibiotics or growth hormones, more organics, more local, and sustainably raised foods,” he told Today’s Matt Lauer last month. “This was a very unfortunate incident and I’m truly sorry this happened, but the procedures that were put in place today are so above industry norms that we are going to be the safest place to eat.”

Chipotle’s stocks dropped by 40 percent over the last three months of 2015. The company’s investors filed a lawsuit accusing company leaders of failing to implement sufficient safety measures, causing huge shareholder losses.

‘Lots of Opportunities for Contamination’

Points of possible contamination in the food chain start at the farm and continue to food handling at the restaurant.

While Chipotle has cleaned up their restaurants, neither the company nor health investigators have determined the source of the contamination.

Experts are quick to point out the potential holes in food safety when using farm-to-table practices, a cornerstone of the company’s marketing campaign that differentiates

Chipotle in the fast food realm.

Dr. Amesh A. Adalja, an infectious disease physician at the University of Pittsburgh Medical Center, says smaller farms often don’t have the same kind of quality control as larger farms, which makes quality control “a risk factor in locally sourced ingredients.”

“That type of practice needs to be examined,” Adalja told Healthline. “Just buying from a local farmer, clearly the food wasn’t safe.”

These practices, as well as assembling food directly in front of the consumer, may seem healthier and more socially conscious. But they can come with certain risks.

Tom Webster, chair of chemical engineering at Northeastern University and president of the U.S. Society for Biomaterials, said restaurants similar to Chipotle that prepare food in front of customers open up their food to increased chances of contamination.

“People may think it’s neat and healthy, but that plexiglass protection is nothing,” Webster told Healthline. “Viruses can travel great distances.”

When it comes to protecting themselves while dining out, customers have little control. Food safety, on the whole, rests with the food preparers. Patrons of the Cleveland Circle Chipotle often cited the “dirty” conditions of the restaurant when reviewing it on Yelp.

Dr. Stephen G. Baum, professor of medicine, microbiology, and immunology at Albert Einstein College of Medicine, said outbreaks like the norovirus are caused by restaurant employees.

“There are lots of opportunities for contamination. It’s a very contagious virus,” he told Healthline. “The whole idea of washing your hands would make the biggest impact, mainly after going to the bathroom. That sounds simple, but it would make a difference.”

Another major step in slowing the spread of preventable infectious diseases is making sure food workers stay home when they are sick. But, as most fast food jobs pay low wages, few can afford to miss a day of work.

It’s up to the employers to incentivize workers to stay home when they’re ill to prevent contaminating food and sickening others, Baum said.

“Food is a problem,” he said. “It needs to be prepared right, served right, and stored right.”