DENVER — Chipotle is not out of the woods yet, but it is trying to reassure customers that its restaurants are safe so it can put a terrible year behind it.

It won’t be easy: There were cases of Salmonella in Minnesota in August; E. coli this fall in nine states; and more recently, norovirus in Boston.

The outbreaks raise legitimate health concerns for customers, and a reputation risk for Chipotle as it becomes the butt of jokes.

Chipotle won’t get to sound the all-clear for a while. The Centers for Disease Control and Prevention says it has not pinpointed the cause of the E. coli, and that it could take another month before it considers closing the case.

But the company says whatever ingredients potentially caused the E. coli outbreak are “long gone” and that it has strengthened its procedures to head off future health problems.

A person familiar with the company’s investigation into the E. Coli outbreak said Chipotle has narrowed the cause down to several foods, though identifying the single source is hard with so many ingredients used across all its menu items.

And that has led Chipotle to examine its protocols. “There is a silver lining of sorts in not knowing for sure what caused this incident in that it prompted us to look at absolutely every ingredient we use, and to reassess our handling practices for each of those ingredients,” Chipotle spokesperson Chris Arnold said.

For example, Chipotle has added an additional layer to testing. Instead of just relying on suppliers to test for possible contaminants, Chipotle will be doing tests as well.

In some cases, it may also change how it washes ingredients. Chipotle had been using whole tomatoes washed and cut inside individual restaurants, but those are now being done in a commissary where they are washed, cut and packaged before they are sent to the restaurants.

Commissaries are large food production facilities that are highly specialized and regulated by the Food and Drug Administration. Using these kitchens helps establish consistent standards, which also makes taking samples for testing easy.

Chipotle will also use a series of DNA-based tests to “ensure the quality and safety of ingredients before they are shipped to restaurants,” according to a statement on its website. The company says it’s a program that far exceeds requirements of state and federal regulatory agencies, as well as industry standards.

“While it is never possible to completely eliminate all risk, this program eliminates or mitigates risk to a level near zero, and will establish Chipotle as the industry leader in this area,” said Mansour Samadpour, who was hired by Chipotle to advise the company on safety procedures.

Still, the E. coli outbreak has garnered national attention and forced the company to warn that sales would suffer.