One of the children is in a stable condition in Yorkhill Hospital
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Three cases of E.coli O157 have been confirmed in the Borders.
The cases of the strain, involving children, have been reported to NHS Borders during the last week.
Two of those affected are members of the same family, one of whom attends a nursery in Melrose. The third child attends the same nursery group.
One of the children is currently being treated at Yorkhill Hospital in Glasgow and is said to be in a "stable" condition. The other two are at home.
Investigations ongoing
Dr Tim Patterson, consultant in public health at NHS Borders, said: "The first two cases are thought to have contracted the disease at home.
"As a precautionary measure, all close contacts from the same nursery group as the cases have been excluded from the nursery until they have been screened for E. coli 0157.
"They will be able to return once negative results are obtained. All other children can attend the nursery as normal."
Dr Patterson investigations were ongoing and that there had been excellent co-operation from nursery staff.
"Appropriate public health measures have been taken and public health staff at NHS Borders will continue to work with the nursery and parents to manage the situation and minimise any further risk," he said.
All the parents had been given information and they were urged to take simple precautions such as careful hand-washing.