Government targets to cut NHS hospital waiting times are putting patients at increased risk of infection with the superbug MRSA, an official report has revealed.

An internal policy review conducted by the Department of Health, leaked to The Independent, has for the first time shown that there is a direct link between the number of patients in hospital - measured by bed occupancy - and MRSA rates. Ministers have denied there is a link.

The most crowded hospitals, with occupancy rates over 90 per cent, have MRSA rates that are over 42 per cent higher than average, according to the report. Those with occupancy rates above 85 per cent have MRSA rates 16 per cent above average.

The findings of the review are considered so sensitive that two attempts by The Independent to obtain the report under the Freedom of Information Act were rejected. Reducing bed occupancy in all NHS trusts to a maximum of 85 per cent would save 1,000 cases of MRSA a year, it says.

The latest figures for 2004-05 show that 88 NHS trusts in England, one fifth of the total, had occupancy rates over 90 per cent and almost half (45 per cent) had occupancy rates over 85 per cent.

The disclosure comes as a report of an inquiry into an outbreak of a second hospital bug, Clostridium difficile, to be published today, is expected to blame pressure to hit waiting list targets as a factor in the deaths of at least 12 patients and the illness of more than 300 others at Stoke Mandeville hospital in Buckinghamshire.

The inquiry by the Healthcare Commission, the NHS watchdog, was ordered by Patricia Hewitt, the Secretary of State for Health, six days after the outbreak at Stoke Mandeville was revealed by The Independent in June last year.

Ministers have insisted that there is no link between hospital infection rates and pressure to cut waiting lists. Cases of MRSA infection rose from just over 1,000 in 1996 to more than 7,500 in 2004, coinciding with a government drive to cut hospital waiting lists to a maximum of six months, achieved last year. The new target is a maximum 18 week wait by 2008.

A report by the Public Accounts Committee in June 2005 accused the NHS of complacency in dealing with hospital infections and blamed "conflicts with other key targets and priorities". Jane Kennedy, a former health minister, said in response: "That is an excuse frankly. Some of the busiest trusts in the country have done best. It hasn't affected their ability to reduce their infection rates. I hear what they say, but I have little sympathy for it."

That view is challenged by the health department's own internal review, Hospital Organisation, Specialty Mix and MRSA, conducted last year by Professor Barry McCormick, the department's economics adviser, and Ian Stone of the Corporate Analytical Team.

It found that the level of crowding rose from 2001-02 to 2002-03 with more than half of hospitals operating above 85 per cent occupancy. "These increases ... are sufficient to explain the observed growth in MRSA between those two years," it says.

The cleanest hospitals had the lowest MRSA rates but those heavily dependent on temporary nurses performed worse. There was no link with the amount of money spent on cleaning or whether cleaning was contracted out, but a 10 per cent improvement in the average cleanliness score reduced MRSA rates by 7 per cent.

The higher use of temporary nurses in the capital "can explain a large fraction of the differential between MRSA rates in London and elsewhere."

The authors say their review is "the first attempt to ... identify the organisational factors that may drive MRSA". The exact human and financial cost of the infection is unknown, they say, but it is thought to "contribute to or directly cause many hundreds of deaths each year and costs the NHS many tens of millions of pounds". Today's report from the Healthcare Commission on Stoke Mandeville will be accompanied by the latest national figures on hospital infection rates, to be published by the Health Protection Agency.

Deaths linked to MRSA rose by 22 per cent between 2003 and 2004 to 1,168, according to official figures published last February, despite ministers' claims to have cut infections from hospital superbugs.

Rise of hospital infections

* MRSA, methicillin resistant Staphylococcus aureus, is a blood infection that can cause fever, septicaemia and organ failure. Some strains are resistant to almost all known antibiotics. It lurks in the noses of one-third of the population where it is harmless. But if the skin is broken, through cuts or the insertion of needles, it can invade. There were 7, 212 bloodstream infections with MRSA in England in 2004-05 and 1,168 deaths.

* Clostridium difficile is the most common cause of diarrhoea in hospitals and can lead, in severe cases, to inflammation and death, mainly in the elderly. It is present naturally in the guts of healthy people but can overwhelm vulnerable patients being treated with antibiotics. It produces spores which are resistant to normal methods of cleaning. Cases have doubled since 2001 to 43,000 in 2004, while deaths have risen from 975 in 1999 to 2,247 in 2004.

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