Three hospitals in Kent were so decrepit, overcrowded, understaffed and badly managed that when a lethal bacterial infection took hold it spread unchecked, causing death and disease on an unprecedented scale.

An investigation found that more than 1,100 patients were infected with the Clostridium difficile bacterium at the hospitals between April 2004 and September 2006 which directly caused the deaths of 90 of them. In all it contributed to the deaths of 345 people.

It is the worst outbreak of the bacterium recorded by the Healthcare Commission, the Government's NHS watchdog, whose report on the hospitals run by the Maidstone and Tunbridge Wells NHS Trust is published today. The affected hospitals were the Maidstone Hospital with 738 cases, Kent and Sussex Hospital (353 cases) and Pembury Hospital (85 cases).

Mainly affecting elderly patients, C. difficile causes diarrhoea, dehydration, inflammation of the gut and death. It is highly contagious and can be spread on hands, bedclothes and furniture. Yet infected patients who begged for commodes were told by overstretched nurses to "go in the bed", because it was less time-consuming than helping them to the lavatory. The report criticised lack of hygiene involving lavatories, commodes and walking frames.

C. difficile bacterium first came to national attention through an outbreak at Stoke Mandeville hospital in Buckinghamshire – revealed by The Independent in June 2005 – where 334 patients were infected and 33 had died over the previous two years.

An investigation by the Healthcare Commission, published in June 2006, blamed "serious failings" by senior managers who gave priority to government targets and control of their finances and ignored warnings from infection control specialists.

That report came too late to prevent the same errors being made at Maidstone and Tunbridge Wells. Today's report from the commission identifies many of the same failings among senior managers whose "main focus" was on finance rather than on the safety of patients. Anna Walker, chief executive of the Healthcare Commission, said: "What happened to the patients at this trust was a tragedy. This report fully exposes the reasons so that the same mistakes are never made again.

"I urge all trusts to heed the lessons of this report so that they can look patients in the eye and say that everything possible is being done to protect people from infection.

The report includes photographs showing a filthy commode, with faecal stains clearly visible, a dirty shower and sink and beds crammed so close together they resemble wards in a Third World hospital. One ward had 23 beds when it should have had 13. The lapses occurred after the commission had begun its investigation.

Bed occupancy exceeded 100 per cent on some medical wards, where the trust had to open up "escalation" areas to accommodate extra patients, but nurse staffing levels were 10 to 20 per cent below average. Patients were moved around, spreading the infection as they went, in some cases to meet government targets on waiting times in A&E wards. The high turnover of patients and the proximity of the beds made efficient cleaning impossible. The scandal brought the resignation of the trust's chief executive, Rose Gibb, last week.

Glenn Douglas, acting chief executive, said he would review management, as recommended by the commission, and refused to rule out further resignations. He said that C. difficile infection rates at the trust had halved in the past year and were now below the average for England.

The trust had claimed that no patients had died as a result of the C. difficile outbreak and, in a press release issued in June last year, implied that patients were to blame for bringing the bacterium into the hospitals. However, the report found 90 per cent of the cases were acquired by patients after admission.

Malcolm Stewart, medical director of the trust since January 2006 said: "This trust was simply not equipped to deal with an outbreak of this size. We have put in a raft of measures to deal with hygiene and change clinical behaviour. The organisation could have handled press statements better – some of the terminology was sloppy and did give rise to an unfortunate and erroneous impression."

'An undignified and very distressing death'

Mary Hirst was aged 83 when she fell and broke her hip in April 2006. She recovered well from the operation and a consultant at The Maidstone Hospital told her daughter, Jackie Stewart, that she should be home the following week. Ms Stewart, 54, said: "We went to see her on the Thursday and she told us she had diarrhoea. From then on she got progressively worse. Knowing what I know now, I wish I had moved her earlier."

During the following seven weeks, Mrs Hirst battled against the infection, identified later as Clostridium difficile. Later her surgical wound became infected with MRSA. She died on 24 May 2006. Mrs Stewart said: "The care she received was abysmal. My mother died an untimely, undignified and very distressing death and she shouldn't have done. I blame the hospital for it."