The outbreak has so far sickened 26 people in Washington, 13 in Oregon, two in California, two in Minnesota, one in New York, and one in Ohio.
No one has died from the outbreak so far, but 16 people have been hospitalized.
The outbreak is caused by a strain of E. coli called Shiga toxin-producing Escherichia coli O26 (STEC O26).
It's important to note that not all E. coli bacteria are harmful - all of us have naturally-occurring E. coli in our intestines which help keep us healthy. But some E. coli can make us sick, and these types are often transmitted through contaminated food and water, or through contact with other people.
The strain tied to this outbreak is one of the strains most commonly linked with with foodborne outbreaks.
What made people sick?
Investigators are still working to determine the exact food that caused the recent outbreak.
"The epidemiologic evidence available at this time suggests that a common meal item or ingredient served at Chipotle Mexican Grill restaurants in several states is a likely source of this outbreak," the CDC said on its website.
Of the 45 people who have been sickened, 43 reported eating at a Chipotle restaurant in the week before getting sick.
Investigators are using a technique known as whole genome sequencing to determine the "DNA fingerprint" of the bacteria causing the outbreak.
The CDC recommends that people who get diarrhea after eating at a Chipotle contact their doctor.