The C difficile 332 strain sparked a national alert earlier this year when three people died after contracting the infection while in hospital. The strain, which has been named ribotype 332, has struck five times since December last year.
The NHS has refused to identify the two hospitals involved on the grounds of "patient confidentiality" but both are in Fife.
NHS Fife's medical director Dr Gordon Birnie revealed that a study by scientists at Cambridge University had found that the strain had been contained to the area.
C.diff is a type of bacterial infection that can affect the digestive system. It most commonly affects people who have been staying in hospital. Symptoms of C.diff include diarrhoea and abdominal cramps. It can also cause life-threatening effects such as swelling of the bowel.
So far, authorities have been unable to find a source.