Controlling hospital infections such as salmonella and E.coli must be a priority, say experts.
While there has been a drop in rates of the superbug MRSA and C. difficile, other infections like E. coli appear to have taken their place, they say.
Health Protection Agency data gives a snapshot of infection rates and antibiotic use by NHS hospitals in England in the autumn of 2011.
It shows, overall, that infection rates are down but new bacteria are emerging.
The total prevalence of healthcare-associated infections (HCAIs) decreased from 8.2% in 2006 to 6.4% in 2011.
But much of this decrease was due to lower rates of MRSA and C. difficile - infections that the government has repeatedly targeted with policies.
At the same time, rates of other infections, like E.coli, appear to be rising.
In the 103 hospital trusts surveyed, covering more than 52,000 patients, a total of 3,360 patients (6.4%) had been diagnosed with a healthcare-associated infection.
In a third of cases, bacteria such as salmonella and E.coli - collectively known as coliforms - were the cause.
And 12% of these were resistant to the antibiotics normally used to treat these infections - cephalosporins.
Experts are concerned that coliforms infections are becoming more prevalent and harder to treat.
Surveillance figures gathered by the HPA suggest rates of infection are creeping up.
Over the last five years, there has been a 35% increase in reports of E. coli blood infections.
Report author Dr Susan Hopkins said: "When you get rid of one bacteria another one will sneak into its place. We are seeing a slow but steady rise in E. coli.
"It is clear that we need to find ways to control and prevent transmission of these bacteria, and this is an important priority."
Most HCAIs developed during the patients' stays in the hospital.
But a fifth of HCAIs were present on admission to hospital.
Unlike MRSA, which can be screened for, everyone possess coliform bacteria. In most people they exists harmlessly in the gut. But in some people - typically the elderly, very sick or very young - they can cause serious and even life-threatening infections.
Dr Hopkins said: "Everyone has it, so we can't screen and get rid of it. We need to look at better hygiene to prevent infections."
The report reveals that MRSA and C. difficile infections have gone down by more than 70% over the last five years. There was an 18-fold decline in overall MRSA infections (1.3% to 0.1%) and a five-fold decline in C. difficile infections (2.0% to 0.4%) between the 2006 and 2011 surveys.