Since July 1 2018, 11 babies were found with Klebsiella in their blood and six of them have died.
The NICD said that 20 other babies had the bacteria in their gut but it was not making them sick, what is medically known as colonised.
He said to address the challenge, babies would be moved, especially those with low risks, to Nelson Mandela Children's Hospital in Parktown.
"We know that the hospital has recently opened and is progressively admitting new patients but still has unused space.
"This is the space that we are planning to use to decant neonates from Thelle Mogoerane."
Charlotte Maxeke Academic Hospital in Johannesburg will also be used to decant the babies.
"We are concerned about the design of the neonatal, antenatal, postnatal, labour ward and theatre [of Thelle Mogoerane Hospital]. The passage from these wards to theatre passes through the neonatal ward adds to the risk and this is undesirable situation.
"Thus decanting these patients and their mothers to Nelson Mandela Children's Hospital and Charlotte Maxeke will give us an opportunity to scrub down and decontaminate the environment and address the structural issues without any disturbance."
Klebsiella pneumoniae is a bacterium that normally lives inside human intestines, where it doesn't cause disease.
However, if Klebsiella pneumoniae gets into other areas of the body, it can cause a range of different illnesses. Motsoaledi said the bacteria was every neonatal ward's nightmare. It has been reported in other hospitals across the country before as the country struggles to deal with overcrowding in public health facilities.
Gauteng needs six new hospitals urgently - minister
The Gauteng province is in dire need of six new hospitals to deal with its extreme overcrowding problem in public health facilities.
According to health minister Aaron Motsoaledi, overcrowding in Gauteng hospitals is a big problem as the population has grown from 7-million in 1999 to about 14-million.
"We need six new [public] hospitals Gauteng," Motsoaledi said on Sunday.
The minister was speaking at the Thelle Mogoerane Hospital in Vosloorus, where six babies died as a result of antibiotic-resistant bacteria in the neonatal ward.
Sowetan broke the story of the babies' deaths in August.
Motsoaledi confirmed our report when releasing preliminary findings by the National Institute for Communicable Diseases (NICD).
He said extreme overcrowding has been identified as the main factor that resulted in anti-drug resistant bacteria Klebsiella that killed the babies at Thelle Mogoerane.
He said overcrowding is a national problem as 84% of the population uses public health facilities.
"Going to Treasury and telling them about new hospitals in this economic climate? . I started long ago with Treasury, knocking at their door.
"I am becoming a pest. We need a new George Mukhari Academic Hospital. We need it urgently. We need a new King Edward VII Hospital."
Motsoaledi said the NICD gave health MEC Gwen Ramokgopa the interim report on the case, which revealed among others that:
Due to overcrowding, infection control measures were compromised; and
This is a multi-drug resistant strain, which means that prognosis was poor.
"The issue of overcrowding is of particular concern because all neonatal wards in the province were found to be overcrowded - on average 132% bed utilisation.
"In this hospital, the NICD found that there were 90 neonates in a 61-bed capacity unit. We cannot turn any patient away because of overcrowding."
Since July 1 2018, 11 babies were found with Klebsiella in their blood and six of them have died.
The NICD said that 20 other babies had the bacteria in their gut but it was not making them sick, what is medically known as colonised.
He said to address the challenge, babies would be moved, especially those with low risks, to Nelson Mandela Children's Hospital in Parktown.
"We know that the hospital has recently opened and is progressively admitting new patients but still has unused space.
"This is the space that we are planning to use to decant neonates from Thelle Mogoerane."
Charlotte Maxeke Academic Hospital in Johannesburg will also be used to decant the babies.
"We are concerned about the design of the neonatal, antenatal, postnatal, labour ward and theatre [of Thelle Mogoerane Hospital]. The passage from these wards to theatre passes through the neonatal ward adds to the risk and this is undesirable situation.
"Thus decanting these patients and their mothers to Nelson Mandela Children's Hospital and Charlotte Maxeke will give us an opportunity to scrub down and decontaminate the environment and address the structural issues without any disturbance."
Klebsiella pneumoniae is a bacterium that normally lives inside human intestines, where it doesn't cause disease.
However, if Klebsiella pneumoniae gets into other areas of the body, it can cause a range of different illnesses. Motsoaledi said the bacteria was every neonatal ward's nightmare. It has been reported in other hospitals across the country before as the country struggles to deal with overcrowding in public health facilities.