The rise in Clostridium difficile infections in recent years is due to genetic changes rather than dirty hospitals, say UK researchers.
Comparison of an historic strain and a strain from the outbreak at Stoke Mandeville hospital in 2003 found it had evolved to be more virulent.
It can spread more easily and cause more severe symptoms, the team reports in Genome Biology journal.
NHS trusts have a target to cut C. difficile infections by 30% by 2010/11.
The bacteria are present in the gut of as many as 3% of healthy adults and 66% of infants.
It rarely causes problems in healthy people but can lead to illness when the normal balance of bacteria in the gut is disrupted, for example with use of certain antibiotics, and it is the leading cause of hospital-acquired diarrhoea.
In the past five years, a new group of highly virulent C. difficile strains has emerged - PCR-ribotype 027 - which cause more severe diarrhoea and a higher rate of deaths.
Analysis of the full genome of the "hyper-virulent" strains and an older strain showed the bacteria have acquired genes which enable them to survive better in the environment, spread more easily and make patients more severely ill.
In all, five different genetic regions appear to have accumulated in the bacteria in past couple of decades, the team reported in Genome Biology.
The number of cases of C. difficile has risen dramatically since the 1990s, although latest figures show cases are now consistently falling.
Stoke Mandeville Hospital saw two major outbreaks of C. difficile between 2003 and 2006 that caused 35 deaths.
Study leader Professor Brendan Wren, from the London School of Hygiene and Tropical Medicine, said the study would help scientists understand how C. difficile became so aggressive.
"These strains came from nowhere and the sudden rise in C. difficile was due to their spread.
"The bugs are fighting back and the one clear thing that comes out of this study is it is not down to cleaning but that the strain has evolved with new chunks of DNA.
"The deep clean programme was never going to work against this organism in the long term."
Hygiene measures are still needed to keep the infection under control, he added.
A spokeswoman for the Health Protection Agency said it closely monitored the evolution of C. difficile strains.
"All strains of C. difficile require intervention and control - the intervention involved when dealing with the 027 strain is no different than how any other strain is treated.
"All C. difficile requires treatment and vigilant infection control procedures in order to reduce rates of infection."