Chipotle's nightmare is just beginning

Chipotle's sales and stock price are tanking in the midst of an E. coli scare linked to its restaurants.

The burrito chain has warned that its same-store sales could fall for the first time in company history this quarter, due to the outbreak. The company is expecting a decline in the range of 8% to 11%.

But Chipotle's nightmare is just beginning.

Analysts expect same-store sales to continue declining through at least June of next year.

The slide could extend even longer, however, 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 farther into the future.

Federal health investigators said Friday that the outbreak linked to Chipotle had expanded to nine states, with 47 of the 52 people sickened having reported eating at the chain. The latest date of exposure among those cases was November 7.

Then on Monday, Boston College reported that dozens of students - including members of the men's basketball team - got sick after eating at Chipotle over the weekend.

Chipotle said it has closed the Boston restaurant where the students ate while it works with local health officials investigating the illnesses.

"We do not have any evidence to suggest that this incident is related to the previous E. coli incident," Chipotle spokesman Chris Arnold told Business Insider.

Chipotle says it has strengthened its food safety standards to prevent further contamination.

But the chain will remain more susceptible to food borne illness outbreaks than its competitors regardless, because of its commitment to fresh food and high-quality ingredients.

"We may be at a higher risk for food-borne illness outbreaks than some competitors due to our use of fresh produce and meats rather than frozen, and our reliance on employees cooking with traditional methods rather than automation," the company said in an annual report. "The risk of illnesses associated with our food might also increase in connection with an expansion of our catering business or other situations in which our food is served in conditions we cannot control."

What sets Chipotle apart from its competitors may end up being its greatest weakness, if reports of illnesses continue to dampen sales.

BTIG analysts are betting that the current outbreak won't affect the brand long-term, however.

"We do not believe there will be any longer-term impact to the brand or its customer appeal and expect Chipotle's growth trajectory to remain intact," BTIG analyst Peter Saleh wrote in a recent note.