CHIPOTLE ANALYST: I don't know how much more of this I can take

JP Morgan has downgraded Chipotle in the wake of a second outbreak of E. coli tied to its restaurants.

Analyst John Ivankoe dropped the company from "overweight" to "neutral," saying consumers are going to think twice before eating at Chipotle after the latest outbreak.

"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 writes.

JP Morgan had previously thought a downgrade would be rash, calling the recent outbreak of norovirus - which sickened more than 150 people who ate at a Boston Chipotle - a "phenomenally unlucky coincidence."

But the latest E. coli outbreak, which has sickened five people in three states, changed everything. The company's shares, which have lost one third of their value since mid-October, were down another 4% on Tuesday.

"The new news flow shows the impact continuing and more importantly a management team that seems to be scrambling for answers," Ivankoe writes.

He cited a customer comment on Chipotle's website as perfectly summarizing JP Morgan's feelings about the company now: "I've been so supportive lately, but just don't know how much more of this I can take."

In an effort to restore public trust, Chipotle CEO Steve Ells has stressed in multiple TV appearances over the last couple weeks that no E. coli cases were contracted by customers eating at stores after November 7.

"We can assure you today there is no E. coli in Chipotle," Ells said on CNBC's "Mad Money" last week.

On Monday, the CDC announced that a different strain of E. coli sickened five people from three states. The customers all reported illnesses from November 18 to November 26 and had eaten at Chipotle in the week before their illnesses started.

Chipotle said it is in the process of implementing new measures to improve food safety.

"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," Chipotle spokesman Chris Arnold said Monday. "We are confident that we can achieve a level of food safety risk that is near zero."

Unprecedented outbreaks

Dr. William Schaffner, a professor of infectious diseases at Vanderbilt University's School of Medicine, says this number of outbreaks tied to a single chain is somewhat unprecedented.

"This series of outbreaks with one chain has everyone, including my friends at the CDC, scratching their heads," he said on CNBC Tuesday.

So far, 53 people have been sickened in nine states as a result of the dual E. coli outbreaks, and 47 of those people have confirmed eating at Chipotle before their illnesses started. Chipotle was also recently hit with a norovirus outbreak at a restaurant in Boston that sickened more than 150 customers.

Chipotle's sales are tanking in the midst of the illness scares.

The burrito chain has warned that its same-store sales could fall for the first time in company history this quarter because of the outbreak. While the company is expecting a decline of between 8% and 11%, JP Morgan expects same-store sales to fall as much as 13%.

Analysts expect same-store sales to continue declining through at least September 2016. The slide could extend even longer, if history is any indication.

A similar outbreak of E. coli illnesses linked to Taco Bell restaurants in 2006 sent same-store sales into negative territory for five straight quarters, Quartz reports.

As long as new E. coli cases linked to Chipotle keep popping up, the chain's estimated recovery time will continue to stretch further into the future.

"The Chipotle foodborne illness case will now be studied by restaurant PR officials for years if not decades to come," Ivankoe writes.