Chipotle shares have plunged and it's the butt of jokes - can it recover in 2016?

Chipotle's E. coli scare
Chipotle's E. coli scare

Chipotle is having a no good, very bad year.

On Monday, the Mexican restaurant chain reopened a store in Boston that it was forced to close after 141 college students were infected with norovirus earlier this month.

The reopening comes after last week's second E. coli outbreak, which affected five people who had eaten at Chipotle restaurants in Kansas, North Dakota, and Oklahoma.

This is part of a larger trend that has plagued the chain -- it seems no sooner does it reopen a store, then it's forced to close another because of new cases of infection.

In October and November, Chipotle (CMG) was forced to close stores in nine states after 53 customers were infected with E. coli -- the first outbreak.

Before that, in August, a Salmonella outbreak in Minnesota affected 64 people.

But restaurant closures aren't the only repercussion.

Related: E. coli recall affects major retailers across the U.S.

The company has also suffered blows to its reputation -- customers have taken to social media with jokes about getting E. coli from Chipotle's food. One user tweeted "Breaking: Chipotle to begin serving E. coli all day."

And Chipotle's stock has plummeted in recent months. On Tuesday, it was $493 a share -- a 35% drop from its all-time high in August of roughly $759.

Earlier this month, Chipotle announced that its fourth quarter sales would be down between 8% and 11%.

It also estimated that the first E. coli outbreak would cost between $6 million and $8 million. These expenses included the cost of replacing food, conducting lab analyses and environmental swabs and hiring epidemiology and food safety experts.

Chipotle has also had to walk back projections about increased sales in 2016.

In response to the outbreaks, Chipotle CEO Steve Ells issued a public apology on November 20 to affected customers and attempted to reassure the public.

Spokesman Chris Arnold told CNNMoney that Chipotle is focused on developing an improved food safety plan in order to become an "industry leader in food safety."

One such implementation involves the washing and prep of vegetables. Tomatoes used in the restaurant's salsa are now also washed and tested for pathogens after being diced. A consultant for Chipotle said the company's new practices would reduce "risk to a level near zero."

Chipotle said it continues to serve over a million customers a day but the impact of the outbreaks isn't over yet. New cases may come to light and the FDA and CDC investigation is ongoing. Both agencies are still interviewing affected people and working to identify the source of the infection.

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