But Warthen, based upon his conversation with Mejia, indicated that the injury was in "a completely different area."
The final answer should come from an MRI taken late Wednesday night at the Hospital for Special Surgery in Manhattan. Mejia, en route to the hospital, was not available for comment.
"I'm not a doctor," Manuel said. "You have to wait and see what exactly the MRI says. If it's anything that is serious, obviously, he won't be pitching."
Catch Henry Blanco and Warthen were the first to notice the injury, running out to the mound after Mejia landed awkwardly on his final pitch to McCutchen. Initially, both thought Mejia had suffered a leg injury, until the right-hander motioned to the back of his shoulder.
According to Blanco, Mejia said that the problem was actually with his back.
"I knew something was not OK," Blanco said. "The look on his face, he was in a little pain."
That was enough for the Mets to walk Mejia off the mound without even throwing a test pitch. Raul Valdes, who earned a win in the Mets' 8-7 victory over the Pirates, entered in relief.
Not long after the Mets made an announcement calling Mejia's injury an "acute strain of a muscle in the back of his right shoulder," Mejia left Citi Field for the hospital. The team expects to have results of the test by Thursday morning, at which point it can begin discussing Mejia's future. But with 16 games and less than four turns of the rotation remaining, it is extremely unlikely that Mejia will pitch again this season.
"We'll find out as we go along," Warthen said.
By far the organization's top pitching prospect, Mejia was preparing to play winter ball in the Dominican Republic. Details regarding that plan should surface along with the test results.
"The kid works pretty hard," Blanco said. "You can't tell when stuff is going to happen. I'm not sure what the problem is, but hopefully he's going to be all right."
Enamored with Mejia's upper-90s fastball in Spring Training, the Mets opted to break camp with the rookie right-hander, initially using him in low-leverage situations out of the bullpen. But after Mejia struggled for a time, the organization's next move became clear. In June, the Mets demoted Mejia to Double-A Binghamton to stretch him out as a starter.
Eight days later, pitching on three days' rest, Mejia exited a game in Binghamton with shoulder discomfort, which the organization's medical staff later diagnosed as a muscle strain in the back of the shoulder. Mejia missed six weeks.
At least initially, Wednesday's injury appeared to be in the same area.
"Any injury to a young guy like that, who has a bright future, is real scary," Mets outfielder Angel Pagan said. "But I'm sure he'll be all right. He'll work his way back, and hopefully it's nothing bad. We're just looking forward to having him back healthy as soon as possible."
Assuming Mejia misses his next turn in the rotation, the Mets have several options. They could call upon Pat Misch or Valdes, both of whom pitched in relief in Wednesday's game, to make a spot start. They could turn to Oliver Perez, who has pitched sporadically in relief. But with two off-days next week, Manuel indicated that the Mets most likely will skip Mejia's turn in the rotation altogether, opting to proceed with Mike Pelfrey on regular rest.