Jones' father, James Osborne, took him to the hospital on Tuesday, after finding him semiconscious in bed. The teen, who had missed a week of practice and a game because of neck pain, died the same day.
Once seen almost exclusively in hospital patients, MRSA infections have become more common in schools and gyms. Community-associated MRSA is spread most often by direct, skin-to-skin contact, and those who play close-contact sports such as football and wrestling are at particular risk.
Osborne said his son had a turf burn - a common football abrasion - on his stomach but that it seemed to be healing, not infected.
"I don't understand how this could be MRSA," Osborne told the Philadelphia Daily News. "It's supposed to be highly contagious. But I'm fine, my wife is fine, my 5-month-old grandson is fine. ... So how could this have killed my son?"
School officials said any student who came in close contact with Jones will be screened. Two football players with some sort of lesions were referred for medical exams, school district spokesman Fernando Gallard said.
"We have no knowledge of other cases, but we are taking precautions to make sure that everyone who came into close contact with the athlete is getting checked out," Gallard said.
The school canceled a Friday night football game and sent a letter to parents saying officials will follow Department of Public Health requirements for cleaning the school.