The head of Chipotle Mexican Grill's food safety will step down from his post and retire next year, according to a report by Bloomberg.

James Marsden, a former Kansas State University professor, was hired by Chipotle in 2016 to help the burrito chain rebuild its reputation after it endured a number of setbacks as a result of several very public foodborne illness outbreaks at its restaurants starting in 2015.

While Chipotle is not the only restaurant to struggle with food-safety issues, repeated problems have kept them in the news and made investors and customers wary.

Diners looking for upscale, healthier burritos expect quality and have not been as forgiving of Chipotle's numerous food-safety mishaps. While sales have been improving, a recent outbreak of Clostridium perfringens at a Chipotle in Ohio has once again caused consumers to question the brand's practices. The foodborne disease occurs when food is kept too warm for too long.

In an effort to combat future issues, Chipotle will deploy Zenput at more than 2,400 restaurants. Zenput is a mobile platform that helps restaurants, convenience stores and retailers track their operations using a tablet or phone. The software allows managers to assign a checklist of specific tasks to various jobs, like opening or closing the store, food storage or even new menu item roll-outs.

Shares of the company remained flat after the closing bell Wednesday but are up more than 51 percent since January.

Representatives from Chipotle did not immediately respond to CNBC's request for comment.

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