Morriston Hospital said he had a sprained ankle
Richard Donne, 14, of Grange Road, Farnborough, Hampshire, died after becoming infected with a highly antibiotic-resistant strain of staphylococcus aureus .
But the coroner Andrew Bradley was told it was hard to assess how the bug entered his body.
A verdict of death by natural causes was recorded by the coroner at the inquest in Alton.
"I find it very difficult to assess the significance of that injury because the evidence that we have got does not point to that being significant.
"His ankle did get infected with MRSA and that infection started to grow and it presented as a painful area very much in the nature of a sprain."
Richard had been visiting his father, John Poole, in south Wales when he woke up complaining of a sore ankle.
Ankle cut
The next day he was taken to Morriston Hospital in Swansea where he was diagnosed with a sprained ankle and sent home.
Michael McCabe, a consultant at the hospitals accident and emergency unit told the inquest how a small abrasion on Richard's, ankle which he had got while swimming, had been seen but his ankle had not seemed unusually swollen or red.
He said MRSA was extremely rare, especially in a young healthy boy who had not been in hospital.
Two days later Richard was taken back to the hospital on 10 August by his father.
He was seen by a nurse who gave them advice on how to treat the sprain.
Fractured ankle
Richard's condition became worse with him experiencing hallucinations and more pain.
When he returned to Hampshire his mother took him to Frimley Park Hospital, Surrey, on 11 August.
He was seen by Dr John Rollo, who told the inquest he had taken another full medical history.
He said: "I was told on 5 August he had been playing football and awoke with a sore right ankle. I did not think that his ankle was particularly swollen."
It was diagnosed that Richard had fracture his ankle and he was sent home.
In the early hours of 13 August, Richard's step-father, Mark Donne, called out a GP after becoming concerned by the swelling up his entire right leg and into his other leg.
Richard was rushed back to Frimley Park, where MRSA was identified.
The coroner was told MRSA is carried harmlessly by many people, but can cause life-threatening infection.