Niese underwent surgery to repair a torn hamstring tendon Aug. 6 and missed the final two months of last season.
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The Mets trainer and manager Jerry Manuel trotted to the mound Sunday after Niese threw a first-pitch strike to Hanley Ramirez with no outs and the Mets trailing 3-0. Manuel signaled for a reliever, and Niese limped slightly as he walked to the dugout.
One pitch earlier, Niese scrambled to barehand a bunt before making an errant throw to first base, allowing a run to score.
The Mets said Niese will return to New York for further evaluation.
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