The chairman of the crisis-hit Maidstone and Tunbridge Wells NHS Trust, James Lee, has resigned.
James Lee resigned just days after the report into the fatal outbreak
The announcement was made by Health Secretary Alan Johnson, who also apologised on behalf of the government.
He said the Healthcare Commission report into the clostridium difficile outbreak, which caused 90 deaths, was "a truly shocking document".
In a statement, Mr Lee said he was "deeply saddened by these terrible events" and apologised unreservedly.
He also said he took full responsibility for his part in the events as Chairman of the Board for the past five years.
Speaking in the Commons Mr Johnson said he hoped MPs would recognise that "the awful failures" were entirely unrepresentative of the standards of care expected and delivered in hospitals across the country.
He said sorry to those affected by the outbreak.
In response, shadow health secretary Andrew Lansley said the outbreak was not an "isolated" occurrence.
"We have had other cases and the common link between them is that managers in the NHS have been more focused on the government's targets and the government's imperatives, than they have on patient safety."
Earlier, Kent County Council (KCC) offered NHS bosses a £5m loan to help restore public confidence in hospitals where the outbreak occurred.
The offer was made to managers of Maidstone and Tunbridge Wells NHS Trust at a crisis meeting on Monday.
Kent Air Ambulance said it had now resumed flights to Maidstone Hospital after personal assurances it was safe.
The Healthcare Commission said in its report that a "litany" of errors in infection control was the main cause of death for 90 patients at Maidstone, the Kent and Sussex and Pembury hospitals.
It was definitely a contributing factor in the deaths of a further 124, and a probable factor in another 55.
Interim chief executive of the NHS trust, Glenn Douglas, attended the meeting at County Hall with Steve Phoenix, chief executive of the West Kent Primary Care Trust, which was also criticised.
Ninety deaths were put down to poor handling of clostridium difficile
Leader of KCC, Paul Carter, told them: "I genuinely believe the National Health Service, to a degree, has lost its dignity and humanity."
He said the £5m loan would be available to the health trust over the next two to three years.
He also offered KCC managers to the NHS on secondment and county councillors to sit on a new board of directors.
The council also wants to set up an independent hot line for patients to contact with complaints.
The two health managers apologised for poor patient care at the trust and welcomed offers of help from KCC.
Mr Phoenix said there had been significant improvements in the last 12 months.
Mr Douglas promised "zero tolerance" of C.difficile in the future.
He admitted in an interview with BBC South East Today that Maidstone and Tunbridge Wells NHS Trust still had vacancies for cleaners.
Ahead of the meeting, Mr Carter had called for the resignations of the chair and entire board of Maidstone and Tunbridge Wells NHS Trust.
Kent Air Ambulance Trust boycotted Maidstone Hospital on the day of the Health Commission report, saying it was "deeply concerned".
On Monday it said it had received a personal assurance from Candy Morris, chief executive of South East Coast Strategic Health Authority, that it was safe to take patients to Maidstone.
Four MPs from West Kent are due to meet Mr Johnson on Wednesday.