Hard to Swallow: Outbreaks at Chipotle Restaurants Mimic Broader Patterns of Foodborne Illness in the United States

It’s been a rough year for Chipotle Mexican Grill.


Over the course of the past year, the fast food chain that has built its success on a local, non-GMO, “food with integrity” ethos has experienced a constant wave of foodborne illness at many of its locations nationwide. The first of these surfaced in July 2015 at a single location in Seattle, where two customers were hospitalized as a result of E. coli infection [1]. One month later, Chipotle suffered two outbreaks, with a Norovirus epidemic affecting at least 80 customers and 18 employees at a Simi Valley location and a Salmonella outbreak stemming from 22 locations in the Minneapolis area that resulted in 64 customers falling ill and 9 hospitalizations [2,3]. October was perhaps the toughest month of 2015 for Chipotle, with an E. coli outbreak emerging in 11 states, affecting 55 customers and resulting in 21 hospitalizations [4]. Another unrelated strain of E. coli affected Chipotle customers in Kansas and Oklahoma a month later. Finally, in December, a Norovirus outbreak at a single Chipotle location near Boston College saw 141 people (mostly students) fall ill [5]. All told, more than 500 Chipotle customers were affected by foodborne illnesses in 6 months.

Graphic by Jeff Maloy

Graphic by Jeff Maloy




These highly publicized outbreaks have taken a major toll on the company, with Chipotle’s profits tumbling 44% in the fourth quarter of 2015 [6]. Despite the media’s focus on Chipotle’s shortcomings in these outbreaks, the varied nature of the different outbreaks and Chipotle’s response to them illustrates some important points about patterns of outbreaks from foodborne pathogens in the United States.


Graphic by Jeff Maloy

Graphic by Jeff Maloy

Each year, roughly 48 million people get sick, 128,000 are hospitalized, and 3,000 die as a result of foodborne illness in the United States [7]. Foodborne illness in the U.S. comes in a variety of flavors. By far the most common foodborne pathogen encountered by Americans is not a bacterium, but a virus called Norovirus.


Infection with Norovirus leads to nausea, vomiting, abdominal cramps, and diarrhea within 24-48 hours of exposure, and symptoms usually last between 2-3 days [8]. During this time, infected individuals are highly contagious, which explains why the two largest outbreaks at Chipotle in 2015 were caused by Norovirus. As little as 10 virus particles can cause disease in a new host, and any contact with fecal matter or vomit of infected individuals can result in spreading of Norovirus. Oftentimes, spreading occurs because of unsanitary conditions in restrooms or poor hygiene practices such as insufficient handwashing by food handlers who then go on to contaminate prepared food product with the virus. The current recommendation from the United States Centers for Disease Control (CDC) to prevent the spread of Norovirus in restaurants is that workers who have been sick stay home from work for 48-72 hours after symptoms resolve, and that restaurants practice routine sterilization of utensils and surfaces as well as effective handwashing by employees.


Although Norovirus is the most common cause of foodborne illness in the United States, it is not the most common pathogen spread by fast food restaurants, where food is less likely to be prepared fresh and handled by employees. That award goes to Salmonella, which struck Chipotle patrons in the Minneapolis area last year. Symptoms of Salmonella infection include diarrhea, fever, and abdominal cramps that begin within 12-72 hours after infection and last for 4-7 days [9]. Salmonella is most commonly associated with animal products, particularly poultry, eggs, and dairy. However, in the past few decades more and more Salmonella contamination has been associated with fresh produce such as sprouts, leafy greens, and vine-stalk vegetables like the tomatoes that were identified as the source of the Chipotle outbreak. Although the reason for this shift is not entirely clear, much of the vegetable contamination has been attributed to the use of manure from infected animals to fertilize crops, as well as the use of irrigation water that has been contaminated by feces of infected animals [10]. Because vegetables are often consumed fresh, contaminated produce is likely to cause disease in consumers, leading to regional or national outbreaks in restaurants that use single large suppliers for their produce.


Much like SalmonellaE. coli is a bacterium normally present in the gut of farm animals that has become increasingly associated with fresh produce in recent years. Many strains of E. coli are harmless, and in fact some are part of the good bacteria normally present in our own guts. However, some strains of E. coli have acquired toxins such as Shiga Toxin that can cause severe disease in humans. These strains are generally referred to as Shiga Toxin-producing E. coli, or STEC. The unlucky individuals infected by certain harmful strains of E. coli such as STEC may experience stomach cramps, vomiting, fever, and bloody diarrhea within 3-4 days of exposure [11]. In some serious cases, infection can lead to severe damage to the kidneys or other organs. Individuals infected with STEC, like those with Salmonella, may spread the disease through fecal-oral transmission, making routine handwashing an important prevention method for person-to-person spread. However, unlike Chipotle’s highly localized Norovirus outbreaks, the STEC outbreaks at Chipotle restaurants, like the Salmonella outbreak in Minnesota, affected broader regions, with an October outbreak affecting 55 customers across 11 states. This discrepancy highlights differences in the major transmission routes between the pathogens. While Norovirus tends to spread mostly by person-to-person transmission, STEC and Salmonella can be transmitted both by person-to-person spread and by contamination in the food supply, suggesting different kinds of control and prevention measures such as more frequent testing and stringent control of the food supply chain.


In response to its disastrous 6 months in 2015, Chipotle took the unprecedented step of closing all of its stores nationwide on February 8 this year for 4 hours to hold a virtual town hall meeting addressing food safety issues [12]. During the meeting, Chipotle founder and CEO Steve Ells announced a series of measures aimed at increasing the safety of Chipotle’s food supply in the wake of the recent Salmonella and E. coli outbreaks. Perhaps most notably, Ells discussed a new $10 million program to help small farmers who supply Chipotle’s produce to put in place new food safety policies including increased testing of food items prior to shipping as well as food safety training for their workers. Additionally, Chipotle has announced that it will begin blanching many of its fresh produce ingredients prior to serving them, to reduce the risk of bacterial contamination on the surface of fresh produce.


In addition to addressing concerns with the safety of their food supply chain, Ells discussed a number of policies that Chipotle is putting in place to prevent the spread of pathogens such as Norovirus from infected workers to customers. For example, a newly announced paid sick leave program will encourage sick employees to stay home from work, a policy whose importance is underscored by the finding that a Chipotle employee who showed up at work sick may have been the source of the Boston College Norovirus outbreak. This new policy, along with enhanced sanitation techniques and more frequent health inspections at their individual restaurants, should go a long way toward preventing the more localized outbreaks that have plagued Chipotle in recent months.


Although Chipotle has had an unfortunate 2015, the outbreaks represent a microcosm of the larger problem of foodborne illness in the United States. Some of Chipotle’s changes to food preparation policies in response to their food safety woes represent a new acquiescence to the realities of maintaining food safety standards in the context of a large international fast food chain. Although many of these new policies represent welcome steps toward a safer food supply, whether or not Chipotle will be able to increase the safety of their increasingly globalized product while maintaining a “fresh and local” ethos remains to be seen.


-Jeff Maloy (@JeffreyMaloy)

Signal to Noise Staff Writer

PhD Candidate, Microbiology


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[12] Strom, S. Chipotle Meeting Outlines Food Safety to Workers and Message for Public. New York Times. http://www.nytimes.com/2016/02/09/business/chipotle-meeting-outlines-food-safety-to-workers-and-message-for-public.html?_r=0 (2016).