Some clinics are over-crowded and patients are facing “unacceptably” long waits to be seen, according to the Care Quality Commission.
The Commission identified problems with out-patients in its report of findings from new-style inspections of some 18 NHS Trusts.
But it said that in all hospitals it found examples of compassionate care among front-line staff.
The inspectors said that most services could not demonstrate whether they are giving “effective care” – with the exception of maternity services and critical care units, which was described as the best service.
And they confirm the pressure on accident & emergency services – reporting they are under greater strain than other services.
Two hospitals were named as “requiring improvement” – the Heart of England NHS Foundation Trust in the West Midlands and the Dartford and Gravesham NHS Trust in Kent.
Hospital chief inspector Professor Sir Mike Richards said: “This review shows that inspections with larger, more expert teams work. Our experience so far shows we are moving in the right direction and we have had positive feedback from the hospitals and others.
“However, we will not rest on our laurels and are continuously improving our approach.”
The Enterobacteriaceae bacteria can cause lethal infections when they get into the blood stream although they are carried in the guts of all humans and animals.
They have also developed an ability to destroy the most powerful antibiotics, carbapenems, Public Health England warned.
There were more than 600 incidents of people carrying the drug-resistant strains last year, it revealed. In 2006 just five cases were reported.
In Manchester, two trusts have had 100 cases in five years.
The incidents include patients infected with the bacteria and others who have simply been found to carry them in the gut.
It also called for good hand hygiene.
Yesterday Public Health England set out how hospitals can prevent the infection spreading, calling for samples to be taken as soon as possible if the drug-resistant bacteria are thought to be present.
It calls for improved infection prevention procedures, together with a review of the use of medical devices to ensure they are not contaminated or likely to cause injury.
Chief medical officer Professor Dame Sally Davies said: "Antibiotic resistance poses a real threat to our ability to treat diseases. Although there has been an increase in this strain of bacteria, the new toolkit will ensure that hospitals are well placed to detect, manage and control any cases.
"Systems of monitoring for resistant bacteria are essential in safeguarding the effect of our antibiotics.”
The organisation's medical director Dr Paul Cosford said: "These infections are already causing national concern due to the observed increasing trends in the number of infections, outbreaks and clusters across England.
"We now have a window of opportunity, if we act quickly and decisively, to address this very real public health treat and prevent widespread problems by minimising the negative impact of these organisms."
The Health and Social Care Information Centre is in charge of the care.data project, which has been shelved for six months amid controversy over the security of patient information.
Its troubles were made worse after it emerged that its predecessor, the NHS Information Centre, had supplied hospital data to a number of commercial organisations.
Yesterday it promised a full report, to be released on April 2nd, setting out all data it has released to external organisations and the reasons why.
It will then issue quarterly up-dates.
In a second measure, organisations which receive data from the centre are to be reminded of their "responsibilities" under their agreements with the centre.
The actions of the former NHS Information Centre are to be subject to an audit by former Terence Higgins Trust chief executive Sir Nick Partridge, who sits on the centre board.
And the number of non-executive directors on the centre's board is to be increased from two to five.
Centre chair Kingsley Manning said: "The HSCIC is absolutely committed to improving its own transparency and engagement with the public. In both reviewing the actions of the old NHS Information Centre and publishing our own decisions, we are encouraging public scrutiny.
"The clear benefits to patients of research and analysis of medical outcomes must drive our lawful release of data."
Sir Nick said: "We must be open and honest about all our decisions and processes. I want to challenge the organisation in order to understand why and when decisions were taken, to ensure that patients and the public can have confidence in the organisation's work in the future."
The Dundee University scientists say their research gives the most detailed picture yet of how genes work in cancer cells as they divide.
It comes from a study of more than 6,000 genes found in cancer cells.
By taking a series of dozens of measurements of cell activity, the researchers say they have created the equivalent of a video of genes at work.
They say their work is like "jumping from still photography to video."
The researchers have reported their "detailed analysis" of protein activity in the journal eLIFE.
Researcher Professor Angus Lamond said: "What we have been able to produce is a detailed analysis of protein activity in human cancer cells that exceeds what was previously possible.
"It is essential to study how gene activity varies over time if we are to understand the complex processes in cancer cells, as the dynamic is changing all the time."
He added: “Previously it has been possible to capture a time-averaged snapshot of this activity, but what we can now do is give a much fuller picture.”
eLIFE 6 March 2014