Cleaning dirty hospitals should be the top priority for the NHS and is much more important than giving patients a choice of where they are treated, a poll of patients conducted for the doctors' organisation, the British Medical Association (BMA) found.

The YouGov poll of 2,000 people, published on the eve of the association's annual conference in Manchester, shows the threat from superbugs outranks conventional worries about the NHS of long waits for treatment and poor standards in accident and emergency departments.

The findings come in the wake of growing concern about a new strain of the bug Clostridium difficile, which is spreading in NHS hospitals. As revealed by The Independent, three hospitals are known to have been stricken by the Type 027 strain, which is more virulent and more difficult to eradicate than the ordinary strain.

More than 500 patients have been infected in outbreaks of C.difficile at Stoke Mandevillle, Royal Devon and Exeter and Oldchurch hospitals with more than 30 deaths. Public health specialists expect further hospitals to be infected by the new strain.

Last week, a report from the Commons Public Accounts Committee criticised the NHS's inertia and complacency over hospital infections and said the issue was lost in a "fog of ignorance". The Government countered with figures suggesting that MRSA rates may have peaked with a 6.1 per cent fall in bloodstream infections to 7,212 cases in 2004-05 compared with the previous year.

But in a blow to ministers, the BMA poll showed the Government's strategy of giving all patients a choice of where to have an operation was ranked bottom on a list of priorities for the NHS.

Ministers have pledged that all patients needing operations will have a choice of four or five hospitals, including at least one private, by December. The measure is a key plank of the reforms aimed at creating a patient-centred NHS and introducing market competition between hospitals.

James Johnson, chairman of the BMA, said the findings showed what mattered to the public. "Patients are obviously extremely worried about hospital-acquired infections and quite rightly patients want their hospitals to be clean," he said. "It seems what is not so important to them is the choice of where to have their operation.

"The BMA has been saying for a long time that patients are not so interested in a choice of five hospitals but they want a good service in a clean, local hospital."

"To have five hospitals to choose from is a good soundbite but it is meaningless outside the metropolitan areas where patients will be lucky to get a choice of two or three. What is important for patients is to have a say in how their illness is managed."

The BMA conference is due to debate motions today claiming that high bed occupancy and contracting out of hospital cleaning services has contributed to high rates of hospital infection.

In a separate development, 300 NHS consultants from trusts across the UK have signed an open letter to the Prime Minister attacking the Government's plans to increase market competition in the NHS.

The letter, co-ordinated by the lobbying organisation the NHS Support Federation, says plans to make hospitals compete will result in greater unfairness and waste of public funds. It says the government should focus on improving local services rather than increasing patient choice and attacks increasing private sector involvement for undermining the NHS. It calls for an end to short-term targets for cutting waiting times and says it is crucial to build up NHS capacity.

Harry Keen, president of the NHS Federation, said: "Senior doctors working in frontline services are sending a clear message of their concern.

"The NHS is at a crossroads. These major changes should await the verdict of wider public debate or the NHS as a collaborative network will be lost, unlikely ever to return."