Analysts negative on Chipotle after CDC launches new E.coli investigation

More E. coli cases linked to Chipotle
Chipotle responds to CDC report after new E. Coli case
Analyst keeps 'buy' on Chipotle amid E. coli testing
CDC investigating different E. coli strain at Chipotle

Shares of Chipotle Mexican Grill dropped more than 4 percent Tuesday morning after the stock was dinged by prominent analysts.

JPMorgan's John Ivankoe downgraded the stock to "neutral" after the Centers for Disease Control and Prevention (CDC) announced Monday it is investigating another, more recent outbreak of a different strain of E. coli linked to the restaurant chain.

Five ill people were identified in Kansas, North Dakota and Oklahoma as part of the new investigation, on dates ranging from Nov.18 to Nov. 26, 2015, the CDC said Monday.

Chipotle restaurant workers fill orders for customers in Miami, Florida.
Poll: Are you scared of eating at Chipotle?

"At this point, even rational and informed consumers could potentially be given reason to pause when choosing Chipotle over the plethora of fast-casual competition in the marketplace," Ivankoe wrote. "This new case was not contemplated in our previous investment thesis."

The CDC does not know yet if the more recent cases are tied to a larger outbreak that began at the end of October. On Oct. 31, an outbreak of E. coli was first linked to the chain, mostly in Washington and Oregon. Illnesses started on dates ranging from Oct. 19 to Nov. 13.

Twenty ill people were hospitalized during that outbreak, according to the agency. The new Illnesses are not included in the current case count, which is now at 53, the CDC report said.

Chipotle metric drops to lowest level ever

Bank of America Merrill Lynch analysts Joseph Buckley and Gregory Francfort lowered sales and EPS estimates for Chipotle on the latest E. coli news, factoring in a 25 percent decline in same-store sales in the month of December.

"The new CDC report has potential to derail the early damage control/recovery actions," they wrote. "We think there are significant near-term risks to Chipotle's business and our concerns about these risks underlie our rating."

As of midmorning Tuesday, 52 percent of more than 9,000 CNBC readers polled said they've stopped eating at the restaurant based on E. coli fears, while 23 percent said they weren't concerned. The remainder either never ate at the fast-casual chain (17 percent) or are still eating there (8 percent).

A Chipotle restaurant in Federal Way, Washington.
Chipotle slashes guidance on E. coli news; stock drops

Chipotle announced it would revise its standards after reports of illnesses, with measures like high-resolution testing of ingredients, end of shelf-life testing of ingredients, continuous improvement in the supply system based on testing data and enhanced food safety training for team members.

"I will say though, that we can assure you today that there is no E. coli in Chipotle," founder and co-CEO Steve Ells told CNBC's Jim Cramer last week. "We have thoroughly tested our food, we have thoroughly tested our surfaces and we are confident that Chipotle is a safe place to eat."

The way Chipotle keeps records could make it more difficult to trace the source of the disease, according to William Schaffner, a professor of preventive medicine at Vanderbilt University.

"This series of outbreaks with one chain has everyone, including my friends at the CDC, scratching their heads," Schaffner told CNBC's "Squawk on the Street" on Tuesday. "They're trying to figure out what the common denominators here are."

Schaffner said he would recommend patients with underlying conditions exercise caution around the restaurant. But a Chipotle spokesman told CNBC on Monday that the company is "confident" it can achieve a level of food safety risk that is near zero.

"We have indicated before that we expected that we may see additional cases stemming from this, and CDC is now reporting some additional cases," the spokesman said. "Since this issue began, we have completed a comprehensive reassessment of our food safety programs with an eye to finding best practices for each of the ingredients we use."

Source: FactSet

Shares of Chipotle fell to a 52-week low Monday before rebounding slightly to close at $522.01, a drop of 3.5 percent. The stock was down more than 4 percent to $499.50 midmorning Tuesday.

William Blair analyst Sharon Zackfia told CNBC on Monday she has a "buy" rating on the shares, and is not rethinking it because of the recent outbreak issues.

"I think they're doing everything realistically that they can," Zackfia said. "Again, given the lag between when the illness is contracted and when the symptoms arise, and how quickly they turn over their produce, it may be impossible to actually link it to a specific item. I mean, that might just be the truth of the matter. And I think that's part of the reason why their new food safety protocol that they will be implementing and have started to implement kind of goes above and beyond anything that you might expect."

— CNBC's Katie Little, Ritika Shah, Evelyn Cheng and The Associated Press contributed to this report.