One in sixteen patients in hospital last year had an infection contracted as a result of their medical care that made them sicker rather than better.

A snapshot survey carried out  in England last October and November shows what unhealthy places hospitals are.  Some 6.4 per cent of patients in hospital at any one time during 2011 were found to have an infection such as MRSA or C Difficile which they caught while in hospital.

The figure is an improvement: the infection rate has fallen 22 per cent since the previous survey in 2006. But the Health Protection Agency (HPA), which did the research, said that while MRSA and C.diff rates had fallen, rates for other infections, such as salmonella and E.coli had risen.

Professor Anthony Kessel, medical director of the HPA said: "There are new challenges to meet."

Healthcare-associated infections (HAIs) claim thousands of lives and cost the NHS an estimated £1bn a year. In 2006, MRSA and C.diff caused 5,000 deaths but infections caused by these bugs have since been reduced by nearly 95 per cent for MSRA and by 80 per cent for C.diff.

Enterobacteriaceae, including salmonella and E.coli, now account for a third of all HAIs.

The HPA surveyed more than 50,000 NHS and 1,600 private patients in 103 hospitals. The results showed 6.4 per cent of patients had an HAI, down from 8.2 per cent in 2006. The most common were infections of the respiratory tract such as pneumonia, the urinary tract and surgical sites.

Susan Hopkins, a healthcare epidemiologist and author of the report, said: "Enterobacteriaceae have increased – they have been slowly and surely rising over the last 10 years and now account for a third of all infections. It is clear that we need to find ways to control and prevent transmission of these bacteria and this is an important priority."