However, the child has been allowed to remain at his home in central Fife, an indication that the disease has not developed into its life-threatening form. Health officials said the boy was "well" despite the infection.
In May, five toddlers who were all linked to the Careshare nursery in Dunfermline were treated in hospital for kidney failure after an outbreak of the same strain of E coli. A further nine people were also treated for symptoms of illness, but did not require hospital treatment.
Commenting on the latest case, Dr Jackie Hyland, a public health medicine consultant, said: "Initial investigations have not so far found anyone else to be infected, and no obvious source of the bug has been identified."
The incubation period for E coli 0157 is from one to 14 days. Symptoms can include diarrhoea, nausea, vomiting, stomach pain and fever.
Dr Hyland said careful hand-washing before eating or handling food reduced the chance of the infection spreading.