NHS bosses said that five cases in two families around Wigtown and Whithorn had tested positive for the infection but that a six-year old girl who had been treated in Dumfries and Galloway Royal Infirmary (DGRI) had since been released.
Dr David Breen, consultant in public health medicine, said: "The sources of both infections appear to be from contact with cattle and sheep and there is no suspicion of a common source infection such as food.
"Appropriate exclusions from school and work have been made. Appropriate information has been made available and Environmental Standards are helping us with the investigation. All reasonable control measures are in place."
A further outbreak in the Annan and Cannonbie areas of Dumfriesshire has seen many taken ill this week but none of these cases were hospitalised.
In 2006, two-year old Ellie Russell from Ballantrae died after contracting the infection which also saw two other children, both from Wigtownshire, treated at DGRI.
E-coli is a bacterium that can live harmlessly in the gastrointestinal tract of wild, farm and domestic animals (especially cows and sheep) but which can be serious to those under the age of five and over 65.
It has also been linked to unpasteurised milk and dairy products or uncooked meats.
Humans only need to ingest a minute amount to become infected and if hands, food, water, or environmental surfaces are even faintly contaminated this can result in infection.
The advice from NHS Dumfries and Galloway is to be extra vigilant about hand washing at all times and in particular following contact with animals, after changing nappies or using the toilet and after blowing your nose or sneezing.
The bacterium is also quite robust which means it can live in the environment - on things such as railings and gates - for weeks and perhaps months.
In September, Professor Hugh Pennington warned that children under the age of five should not be allowed to touch animals at petting farms because of their succeptibility to the infection.
He said: "Heavy periods of rain can wash manure off fields into water courses, wells and that sort of thing. But by the time the person falls ill, the water may have gone clear."