The 31-year-old five-time Olympic gold medallist contracted the bugs after undergoing a series of surgeries on his shoulder at a hospital near his home in the Swiss town of Ronco sopra Ascona.
He has returned to Sydney and is receiving treatment at an intensive care ward.
Thorpe has received a number of visitors in hospital and is said to be in good spirits, despite the apparent seriousness of his illness.
"It's serious but it's not life-threatening," Thorpe's agent James Erskine told AAP.
"He's contracted two forms of bugs in hospital.
"He's undergone two or three operations over the last two months so ... I mean bad luck.
"He's quite sick but that's the situation."
Mr Erskine rubbished reports Thorpe could lose the use of his arm because of the infections but said Thorpe would never swim again competitively.
"From a competitive point of view - he will not be swimming competitively again I don't think," Mr Erskine added.
"The shoulder operation was a major operation, he's got as many plates as Barry Sheene (the now deceased world champion motorcycle rider)."
It's understood the infection contracted by Thorpe is similar in nature to the potentially deadly Methicillin-resistant Staphylococcus aureus (MRSA) superbug that has swept some hospitals in Europe.
It is the latest upset in Thorpe's life.
His father revealed in February that Thorpe was battling depression.
The popular swimmer sought help in early 2014 after being found disoriented near his parents' home in southern Sydney, having taken a combination of antidepressants and medication for a shoulder injury.
Thorpe was sent for medical assessment to Bankstown Hospital and then entered a rehabilitation program.
The swimmer made an ill-fated attempt to compete at the 2012 London Olympics.
