An inquiry into an outbreak of a lethal "superbug" that infected 300 patients and caused 12 deaths at Stoke Mandeville Hospital in Buckinghamshire has been delayed because the infection is still spreading.

The independent inquiry into the outbreak of Clostridium difficile, which causes severe diarrhoea, was ordered by the Health Secretary, Patricia Hewitt, eight days after it was revealed by The Independent on 6 June. The Healthcare Commission, the Government's NHS watchdog, announced on 14 June that it would conduct the inquiry.

More than five weeks on, the commission said it was not yet ready to go into the hospital. "The investigation will begin when it is clear the outbreak of C. difficile at Stoke Mandeville Hospital is under control," it said on Thursday.

The number of infections with C. difficile have soared in hospitals across the NHS from about 1,200 in 1990 to more than 43,000 in 2004. Latest figures show there were 934 deaths in 2003, a 38 per cent rise in two years.

Stoke Mandeville was infected with a new strain of the bug, C. difficile 027, which is more virulent and harder to eradicate than existing strains, in late 2003. The number of infections peaked between January and March 2004, fell back in the summer and then peaked again last winter.

A spokesman for the hospital said yesterday: "We have now had a prolonged period of declining levels of infection. New cases are running at around eight to ten a month, which is about where they were before the outbreak began."

Marcia Fry, head of operations at the Healthcare Commission, said it was for the Health Protection Agency to declare when the outbreak was under control. "The thinking is that it would not be helpful for us to be in there while the infection control people and the Health Protection Agency are in there getting it under control.

"The evidence from Canada is that this has a seasonal pattern and can flare up again. If that were to happen we could find ourselves going in and then having to come out again."

The aim of the investigation was to learn the wider lessons of the outbreak for the NHS, she said. "We expect them to accept us into the hospital in the early autumn. The investigation should take four to six months."

Under terms of reference, the commission will examine all cases of infection with C. difficile from 1 November 2003 and the action taken to control and arrest the spread of the bug, as well as the role of local agencies and national policy.

A second outbreak of C. difficile struck the Royal Devon and Exeter Hospital, where 265 patients were infected in the first five months of the year and 23 died. The bug has also been identified in patients at 13 other hospitals across the nation.

Ms Fry said the commission would consider how the other hospitals were affected and how they had responded, but there were no plans to send investigators into them at this stage. "We want to take account of them and how they handled it and put all that in the pot."