Utilityman Wilmer Flores has been diagnosed with an infection that could sideline him for two more days as medication is allowed to take effect, Terry Collins said.

Though Collins declined to offer further details, sources said Flores’ infection has affected his left knee and that he might have had to spend Thursday night at a hospital receiving treatment. Flores has dealt with discomfort the last couple of days, Collins said.

Other injuries prompted the Mets to reshuffle the deck before Thursday night’s series finale against the Phillies. It only got worse during the game, as left hamstring cramps forced Yoenis Cespedes to leave after five innings.

First baseman Lucas Duda (hyperextended left elbow) was unavailable and catcher Travis d’Arnaud (bruised right wrist) could be used only as a pinch hitter. “Swelling’s down, the mobilization’s better in his wrist,” Collins said. D’Arnaud grounded out in the ninth.

The Mets might need a few days to get a clearer sense of when Duda can return, Collins said. He was injured in a collision at first base Wednesday night and underwent an MRI exam and other tests Thursday.

“If Lucas is out for an extended period of time, I do not know what the next would be except right now Jay Bruce would play first base,” Collins said. “But that can all change tomorrow.”

Bruce started at first base Thursday night for only the third time in his career and the first time since July 2014. He was charged with a throwing error in the second inning when neither Noah Syndergaard nor second baseman Neil Walker reached out to retrieve Bruce’s toss while covering first.

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Even without the injury, d’Arnaud likely wouldn’t have started Thursday night because backup Rene Rivera has been a personal catcher for Syndergaard. But with d’Arnaud limited to pinch hitting, the Mets needed a healthy catcher, so they promoted Kevin Plawecki, who was hitting .270 with a homer for Triple-A Las Vegas.

The Mets sent down pitchers Rafael Montero and Sean Gilmartin, which restored the bullpen to the standard seven pitchers with the reinstatement of closer Jeurys Familia from his 15-game domestic-violence suspension.

The Mets also sent third baseman David Wright to the 60-day disabled list, a procedural move that was needed to clear a spot on the 40-man roster upon Familia’s return.