The nursery has been cleaned by a specialist cleaning company to comply with the requirements of Fife Environmental Health Department and the nursery group's insurers.
The nursery is holding an open afternoon for parents to discuss any concerns before children return to the nursery.
A letter sent to parents said, 'Following the cleaning, extensive microbial sampling and analysis is being undertaken by an independent laboratory to confirm that all harmful bacteria have been destroyed and that the nursery is completely safe for children to return.'
More than 200 clinical waste bags of items including toys, pictures, rugs and cushions were removed and destroyed.
Nursery staff are also undertaking additional training in infection control procedures.
NHS Fife said the infection did not start in the nursery but was brought in and spread from person-to-person contact.
The last of the five children treated in hospital for kidney failure returned home last week.
