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Chipotle reported its first fall in quarterly sales at established restaurants since it went public as the burrito chain operator lost customers after several incidents of food-borne illnesses at its outlets.
The company also said on Tuesday that it received a new subpoena from the U.S. Attorney's office for the Central District of California, broadening the scope of a previously-announced criminal investigation.
Chipotle shares fell about 2 percent to $466 in extended trading.
More than 50 people across 14 U.S. states were sickened in two E.coli outbreaks after eating at the company's outlets. Norovirus outbreaks were also reported in Massachusetts and California last year.
The new subpoena requires Chipotle to produce information related to company-wide food safety matters dating back to Jan. 1, 2013 and supersedes an earlier subpoena that was limited to a single restaurant in Simi Valley.
Sales of established restaurants fell 14.6 percent in the fourth quarter ended Dec. 31.
Chipotle's net income fell 44 percent to $67.9 million, or $2.17 per share, but beat the average analyst estimate of $1.85 per share, according to Thomson Reuters I/B/E/S.
Revenue declined 6.8 percent to $997.5 million, missing analysts' expectations of $1.01 billion.