Chipotle has been battling the outbreak since late October. More than 50 cases of E. coli have been reported in eight states.
As a result Chipotle’s share price has dropped 18% since October.
The company outlined the changes on its website and said it was taking “aggressive actions”.
“In the wake of recent food safety-related incidents at a number of Chipotle restaurants, we have taken aggressive actions to implement pioneering food safety practices,” a statement on the website said.
Chipotle restaurants will now dip fresh ingredients, like onions, in boiling water to kill off any germs. The company is also preparing ingredients, such as tomatoes, in a centralized kitchen where they can be washed, chopped and tested before being sent to restaurants.
Chicken will be marinated in plastic bags rather than bowls and coriander will be added to hot rice to allow the heat to remove any microbes.
In February, Chipotle warned investors it had a greater risk of exposure to food-borne illness than its rivals.
In its annual report the company said its use of fresh ingredients rather than frozen and traditional stovetop cooking, rather than automated, put it at greater risk than competitors like McDonalds.
The Centers for Disease Control and Prevention (CDC) has been unable to identify the specific cause of the E. coli spread.
Chipotle partnered with food safety consulting firm IEH Laboratories, to come up with the new preparation methods.
IEH also will conduct external assessments of individual branches. These will take place alongside weekly and quarterly food safety audits.
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