Healthcare Commission chief executive.Anna Walker spoke to HSJ before launching the new annual healthcheck for 2007-08 at the annual NHS Confederation conference.
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 earlier this week of trusts' self-assessments, which showed a drop in the number of trusts meeting standards on patient safety.
Ms Walker said: 'There was a concern expressed in the consultation that we were worrying too much about safety. I make no apologies for that.
'Patients and the public resoundedly said safety is a real concern.
'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 diff underground.'
The Healthcare Commission is working with the Health Protection Agency on ways to improve the way C diff is measured.
This could lead to the introduction of a universal measure, on top of local targets.
They will also assess the new local targets and carry out a 'significant' bout of spot checks starting this month.
Ms Walker also 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 policies.
As the consultation showed strong support for improving assessment for mental health and ambulance trusts, separate types of criteria for assessment will be published, specific to each type of trust.
Overlaps with the NHS Litigation Authority are being eliminated due to concerns that the burden on regulation needed to be reduced.