NEW YORK — Chipotle Mexican Grill Inc., struggling to rebound from multiple outbreaks of foodborne illness, reported a worse-than-expected plunge in fourth-quarter sales and said it was served with a grand jury subpoena in a federal criminal investigation.

Same-store sales — a closely watched benchmark — tumbled 14.6 percent in the period, the Denver-based company said in a regulatory filing on Wednesday. The decline, Chipotle’s first quarterly drop as a public company, was previously projected to be as much as 11 percent. The subpoena, meanwhile, stemmed from a probe by the U.S. Attorney’s Office for the central district of California, which is working with the Food and Drug Administration’s Office of Criminal Investigations.

Chipotle’s reputation has been hammered in recent months by an outbreak of E. coli that afflicted at least 53 people in nine states. That was followed by a norovirus contagion at a Boston location that sickened more than 140 college students. A new spate of illnesses in three additional states was announced by the Centers for Disease Control and Prevention late last month.

The shares fell as much as 3 percent to $435.73 in New York after the filing was released. That followed a 30 percent decline in 2015.

In the wake of the Boston outbreak — and the national news coverage that followed — same-store sales fell 34 percent, the company said on Wednesday. After the CDC report on the additional E. coli cases in late December, the sales dropped 37 percent. They were down 30 percent for the full month of December, Chipotle said.

The company now estimates that fourth-quarter earnings will range from $1.70 to $1.90 a share. Analysts had predicted $2.49, according to data compiled by Bloomberg. Chipotle also expects to record $14 million to $16 million in expenses during the quarter because of the crisis. The company has had to replace food in restaurants, conduct lab tests and boost marketing to cope with the situation.

Chipotle also is making more share buybacks as it tries to placate investors. The board agreed to repurchase $300 million in stock, in addition to $300 million announced on Dec. 4.

The subpoena pertains to a norovirus outbreak at a Chipotle in Simi Valley, California, in August. It sickened more than 200 customers and employees, though it didn’t generate much national publicity before the later E. coli incidents.

“We intend to fully cooperate in the investigation,” the company said in the filing. “It is not possible at this time to determine whether we will incur, or to reasonably estimate the amount of, any fines, penalties or further liabilities in connection with the investigation pursuant to which the subpoena was issued.”

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