Chipotle restaurants in Minnesota experienced a salmonella outbreak on Sept. 11, with 45 cases eventually traced to tomatoes.

Chipotle temporarily closed 43 restaurants on Oct. 31, in Washington and Oregon, after an E. coli outbreak.

In a news analysis on Nov. 4, NRN West Coast Bureau Chief Lisa Jennings wrote that Chipotle's E. coli outbreak was the latest event in a tough year for the chain, as the industry leader grappled with lawsuits, supply challenges, brand attacks and slowing sales.

On Nov. 10, Chipotle said it would reopen restaurants in the Pacific Northwest that closed after an E. coli outbreak, noting that units were sanitized and food replaced.

On Nov. 20, Chipotle said an E. coli outbreak included three new states.

On Dec. 4, Chipotle outlined robust food-safety measures as the illness count tied to an E. coli outbreak at the chain rose and included three more states.

Also on Dec. 4, Chipotle said it expected negative fourth-quarter same-store sales, with an uncertain outlook for 2016 after ongoing E. coli reports.

On Dec. 7, experts expressed mixed opinions on Chipotle’s plans to test produce as part of a strategy to avoid foodborne illness outbreaks.

On Dec. 8, Chipotle closed a restaurant in Boston after illnesses were suspected in a norovirus outbreak unrelated to the chain's E. coli outbreak.

Speaking to Wall Street analysts, Chipotle co-CEO Steve Ells outlined a plan on Dec. 8 for making the chain “the safest place to eat,” and a leader in food safety.

On Dec. 10, Chipotle co-CEO Steve Ells appeared on "The Today Show" to apologize for the foodborne illness outbreaks. Experts said they were unimpressed with Chipotle's crisis management following the incidents.

On Dec. 17, a survey by YouGov Brand Index found that Chipotle’s reputation continued to suffer after an E. coli outbreak at the chain. Consumer perception fell even after a televised apology from founder and co-CEO Steve Ells, according to the survey.

On Dec. 21, Chipotle faced a CDC investigation into a new E. coli outbreak, with illnesses reported in Oklahoma, Kansas and North Dakota.

On Dec. 22, analysts said Chipotle's food-safety crisis would likely take a greater toll on same-store sales.

On Dec. 23, Chipotle outlined new cooking methods in an effort to prevent future foodborne illness outbreaks.

On Jan. 6, a federal court in California served Chipotle with a grand jury subpoena as part of a criminal investigation linked to a norovirus outbreak at a restaurant in Simi Valley, Calif., in August. Company officials updated guidance, saying same-store sales were expected to fall 14.6 percent for the fourth quarter, including a 30-percent dive in December.

On Jan. 8, Chipotle was sued over allegedly misleading shareholders with food safety statements.

On Jan. 13, Chipotle co-CEO Steve Ells said he was "extremely confident" that the chain's food-safety crisis was over. The company plans a marketing push in February to bring customers back to its restaurants.