Chipotle Mexican Grill's long-term strategy to woo customers back to the troubled burrito chain won't do much to ease its near-term woes, according to Wedbush.

Analyst Nick Setyan downgraded the stock to underperform from neutral on Monday and slashed his 12-month price target, citing weaker-than-expected same-store sales growth so far in the third quarter and increased pressure on profits margins through 2020.

Setyan said Chipotle's comparable store sales won't grow as fast during the third quarter as what analysts expect, based on his preliminary research. Analysts forecast an average of 5.7 percent growth for same-store sales, but Setyan said he thinks they will come in at growth of 4.5 percent. He previously forecast comparable store sales growth of 5.5 percent during the third quarter. He also cut his price target to $445 from $450 a share.

Shares of Chipotle fell 4.8 percent Monday, last changing hands at around $496.

Setyan attributed the slowdown to an outbreak of Clostridium perfringens, a foodborne disease that occurs when food is kept too warm for too long, that was traced back to a Chipotle in Ohio, according to the Centers for Disease Control and Prevention. Almost 700 customers reported gastrointestinal problems, including nausea, diarrhea and fever, after eating at the Chipotle restaurant, according to local health officials.

The incident dealt another blow to Chipotle, which has spent years trying to convince diners and investors it has improved its food safety practices. The company said it will start retraining all restaurant employees on food safety and wellness protocols this week.

Setyan said Wall Street's same-store sales estimate of 4.2 percent for full-year 2019, might not be out of reach, but there are several "underappreciated" risks. He said menu price increases from 2017 and early 2018 will have less of an impact on sales growth and new menu items could be pushed back further than expected.

In addition, CEO Brian Niccol's compensation and bonus package is tied to achieving several financial targets in 2020, including $20 in earnings per share and same-store sales growth at a rate of more than 6.5 percent, Setyan said.

However, these incentives might not be as meaningful as some bullish investors believe, Setyan said. He noted that Niccol will be well-compensated even if 2020 numbers are not as robust as desired.

While Chipotle shares shed value on Monday, the company's stock is still up more than 70 percent since January, the result of investors' renewed confidence after former Taco Bell CEO Niccol was brought in to run the company.