Chipotle Mexican Grill is facing a supply chain nightmare in the wake of a recent E. coli outbreak in Washington state and Oregon. The company's woes began as initial reports on Oct. 31 counted 22 illnesses connected to the chain. The company closed nearly 43 Chipotle sites in both states to help stop the spread of the outbreak. Not long after, a Washington woman filed a lawsuit against Chipotle claiming that a burrito bowl made her sick with E. coli.

Two days later, the number of illnesses spiked to 35, with additional illnesses reported in both states. The company also began deep cleaning and fully sanitizing the temporarily shuttered restaurants and replacing all food in them, testing the food in its Oregon and Washington restaurants and distribution centers, and hiring two food safety consulting firms to assess and improve its food safety standards in an attempt to retain consumer trust.

Meanwhile, scientists identified the specific microorganism responsible for the illnesses. The scientists believe it is entering the food supply chain through fresh produce such as lettuce, tomatoes, cilantro or onions, but did not rule out spices as a cause.

The outbreak follows earlier, unrelated outbreaks in Minnesota and California. In the Minnesota case, salmonella was linked to tomatoes used by the restaurant. According to a lawsuit in the Minnesota case, "a total of 64 illnesses and 22 locations were tied to this outbreak. The Minnesota Department of Health (MDH) has reported that 9 individuals have been hospitalized due to the severity of their symptoms."

Chipotle made a splash earlier this year when it noted that it had completed an initiative started in 2013 to remove GMOs from its food. The company was sourcing GMO soybean oil for cooking chips and taco shells, in addition to a number of products. Overall, the reception seemed to be positive. It's somewhat ironic that this shining anti-GMO supply chain, a widely popular initiative, is now taking a backseat to the foodborne illness outbreak.