The subpoena was disclosed in a filing with the Securities and Exchange Commission. It said the company has been required to produce "a broad range of documents" in connection with the outbreak.
County officials were also questioned in October by U.S. authorities, who asked "very general questions about the case," Beach said. He said he was not aware of any activities by Chipotle that might have led to a criminal investigation.
Chiptole said it is cooperating fully with the investigation, which has been jointly carried out 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.
The significance of the subpoena is hard to gauge at this point, said Daniel C. Richman, professor of law at Columbia University:
"It's never good news for a company when federal prosecutors open a grand jury investigation into its operations, but it's far too early to tell how sustained that interest will be here and what, if any, criminal violations will come to light."
One of the most successful restaurant chains in the country, Chipotle has seen its revenue and stock price plunge in recent months. The company revealed today that its same-store sales fell 14.6 percent during the fourth quarter of 2015, a bigger drop than anticipated.
The decline followed a series of outbreaks of food illness that have sickened hundreds of people. As NPR's The Salt blog previously reported, these included two separate outbreaks of E.coli in the past several months:
"The larger one sickened 52 people in October, mostly in Washington and Oregon, according to the Centers for Disease Control and Prevention. A separate outbreak in November sickened five people in Kansas, North Dakota and Oklahoma, the agency said.
"In December, scores of students at Boston College fell ill after eating at a nearby Chipotle, an outbreak the company said was due to a norovirus, which causes vomiting, nausea and diarrhea.
"And in August, a salmonella outbreak in Minnesota sickened 64 people who had eaten at Chipotle. The state's Department of Health later linked the illness to tomatoes served at the chain."
Chipotle has apologized to its customers and closed restaurants where the illnesses occurred. It has also promised extensive changes to its food-handling procedures and enhanced training of its employees in food safety.