The deaths of 90 hospital patients from clostridium difficile are "scandalous", Health Secretary Alan Johnson has said.
The commission found countless examples of dirt
Kent police have launched an investigation into whether the Maidstone and Tunbridge Wells NHS Trust should be prosecuted for the deaths.
The Healthcare Commission said a "litany" of errors in infection control had caused the "avoidable tragedy".
The trust said it had not been prepared for "an outbreak of that size and complexity" but had learned lessons.
The commission's report said nurses at the trust were too rushed to wash hands and left patients to lie in their own excrement.
Mr Johnson said he was shocked by the findings, but denied accusations the problems were caused by staff being put under pressures to meet government A and E targets.
He said copies of the report would now be sent to all trusts so lessons could be learnt.
A Kent Police spokesman said the force was "in the process of reviewing the contents" of the report.
"The purpose of the review is to see if any criminal acts have taken place," he said.
Heather Wood, the report's lead author, told BBC Radio Five Live many lives could have been saved.
"I think it's certainly a call to arms for the National Health Service.
"I would think the lessons, not just about cleanliness, hygiene and infection control, but the care provided to patients who contract C.difficile is something that has wider lessons for the NHS.
"For many of these patients there may well have been a good chance that they would have recovered if all steps had been taken."
The commission began its investigations amid a string of complaints about cleanliness, and was particularly alarmed after the trust claimed no-one had died from the condition despite admitting there had been hundreds of cases.
This seemed highly improbable given that the average death rate is between 6% and 7%.
Nigel Ellis, head of investigations at the Healthcare Commission, told BBC One's Breakfast: "The hospital trust didn't even pick up the first of the two outbreaks... wasn't aware that it was an outbreak at the time.
NURSES DID NOT ALWAYS
Help patients go to toilet
"And when the second outbreak came about, they were still not quick enough to act to take the steps that we would consider to be reasonable."
He said the commission concluded that "presumably their priorities were elsewhere".
He added: "There is no reason that the safety of patients in this way can be considered to be a secondary consideration."
The watchdog examined a sample of 50 patients out of a total of 345 to whom various causes of death had been attributed, but who were also known to have had C.difficile, between April 2004 and September 2006.
It concluded that C.difficile - a bacterial infection of the gut which mainly affects the elderly - was definitely or probably the main cause of death for 90 patients.
It was definitely a contributing factor in the deaths of a further 124, and a probable factor in another 55.
The trust's chief executive, Rose Gibb, resigned last week.
But the Healthcare Commission said despite her departure, nothing short of a full review of the trust's leadership would be appropriate in the circumstances.
Commodes were not properly cleaned after use
The commission described the trust as one which had been facing some "serious challenges", not least those brought on by a recent merger.
But it suggested that the board's fixation with meeting financial targets got in the way of making sure safety was a priority, and it accused members of not addressing problems consistently raised by patients and staff.
These included the shortage of nurses, which in turn led to poor care for patients.
For instance, nurses did not have time to wash their hands properly, and left patients to lie in their own excrement because they had not been able to assist them to a commode.
The report found that shortages were so dire that nurses told patients to "go in their beds".
Patients with C.difficile were also moved between wards, increasing the risk of infection.
In some instances this was due to concerns about meeting the government's targets for waiting times for treatment in A&E wards, the report said.
Isolation wards were few and far between, and sometimes the infected were simply kept in the middle of the ward.
The commission noted there were "worrying similarities" with the last serious C.difficile outbreak it had investigated at Stoke Mandeville hospital, in which 30 patients died.
Both involved old hospitals, both had recently undergone mergers, and at both the boards were "preoccupied with finance".
The commission is urging trusts to treat C.difficile as a condition in its own right, rather than a complicating factor.
In addition, antibiotics should be used with utmost care in treating the condition, as they can easily make it worse by killing the so-called "friendly" bacteria in the gut which help the body fight it.
MAIDSTONE AND TUNBRIDGE WELLS TRUST
Kent and Sussex Hospital
Maidstone and Tunbridge Wells Trust welcomed the recommendations.
Medical director Dr Malcolm Stewart said the trust had not been prepared for an outbreak of that size or complexity but said although it was a steep learning curve "lessons were learnt".
He added that managers of trusts were "trying to juggle with many balls".
His own trust was changing the way it offered services internally and externally, opening an independent sector treatment centre, managing a financial deficit as well as applying for foundation trust status.
"This is a hugely ambitious programme to manage at one point in time.
"That doesn't excuse what happened of course because your first priority must be always the safety and the quality of patient care."
The government has pledged £140m to tackle C.difficile as part of the Comprehensive Spending Review.