The potentially fatal strain of the bacteria was found on 13 babies at the premature baby unit at Queen Elizabeth Hospital in Woolwich, south-east London. Five of the newborns have now been discharged.
A spokesman for the South London Healthcare NHS Trust has revealed that the neonatal unit remains shut after being closed down to avoidable admissions when the E Coli 0157 discovery was made in November.
He said."The trust's other two neonatal units at the Princess Royal Bromley and Queen Mary's Sidcup remain open as normal.
"None of the babies are clinically affected by the bacteria. Babies who appear to carry the bacteria have been isolated.
"The trust is working with the Health Protection Agency to ensure that the correct measures are being taken to prevent any further spread of the infection and we can assure our patients that the rest of the hospital is not affected."
An investigation is currently under way to determine how the rare outbreak happened, the trust added.
Since the bacteria was found the unit has undergone a thorough clean, with hand hygiene stressed to parents and staff, while visiting hours have been restricted.
Newborn babies are more vulnerable to infection because the body's normal defences are not yet fully formed.
A HPA spokeswoman said: "Most infections caused by ESBL-producing E.coli occur in people with other underlying medical conditions - who are already very sick - and in elderly people. Patients who have been taking antibiotics or who have been previously hospitalised are mainly affected."