Healthcare Commission chief executive Anna Walker spoke to HSJ before launching the new annual healthcheck for 2007-08 at the confederation's conference last week.
She confirmed that trusts are to be assessed on Clostridium difficile rates, despite resistance from some trusts during a two-month consultation.
The news follows the publication of trusts' self-assessments, which showed a drop in the number of trusts meeting standards on patient safety.
Ms Walker said: 'There was concern expressed in the consultation that we were worrying too much about safety. I make no apologies for that.
'It isn't sufficient for trusts to be working hard on infection control, we need independent assurance that this is happening, otherwise it will push C difficile underground.'
The Healthcare Commission is working with the Health Protection Agency to improve the way rates of the infection are measured.
This could lead to the introduction of a universal measure in addition to local targets.
The commission will also assess the new local targets and carry out a 'significant' bout of spot checks starting this month.
Ms Walker revealed that trusts will no longer be required to declare their progress against developmental standards.
A small set of benchmark indicators will show trusts' position relative to similar trusts regarding safety, quality and public health.
Two service reviews will be carried out into urgent and emergency care and substance misuse. National studies will focus on modernisation, mental health and public health.
As the consultation showed strong support for improving assessment for mental health and ambulance trusts, separate types of criteria will be published for each type of trust.
Overlaps with the NHS Litigation Authority are being eliminated because of concerns that the burden on regulation needed to be reduced.