The lethal bug, a resistant strain of E.coli - which occurs naturally in the gut - was unknown before 2000 and only started spreading rapidly in 2003. It causes blood poisoning in vulnerable people and cannot be treated with conventional antibiotics.
Outbreaks have been recorded in Shrewsbury, which had 300 cases of infection in 18 months, and Southampton, where more than 1,000 people have succumbed since 2003, a report by the Health Protection Agency (HPA) said.
In Southampton, 357 people, half of those infected, were taken to hospital with the superbug in 2004 and 29 died. Attempts to control the outbreak have failed.
The organism has spread nationwide and is infecting people in the community as well as in hospitals. More than 1,000 cases have been confirmed from samples sent in by more than half of the clinical laboratories in the country.
The total number of cases was "far higher" as "not all producer isolates [specimens] are referred," the HPA said.
Today's report, the first of its kind, aims to alert GPs and hospital staff to improve laboratory reporting and to increase surveillance. Difficulties in containing the spread of the infection have been compounded by laboratories using methods inadequate to identify the bug.
Professor Peter Borriello, the director of the centre for infections at the HPA, said: "This is a bigger issue [than a hospital infection] because it was in the community. These things can go from bubbling under to boiling over very quickly. We need enhanced surveillance."
The surge in infections caused by resistant strains of E.coli was first mentioned in the annual report of the Government's Chief Medical Officer, Sir Liam Donaldson, in July. The resistant strains of the new superbug - called extended-spectrum beta-lactamase (ESBL)-producing E.coli - mostly cause urinary tract infections in elderly or chronically ill patients. Most of those infected had been taking antibiotics or had been recently admitted to hospital. In the Southampton outbreak, almost nine out of 10 cases were urinary infections. Treatment options are limited - only two oral antibiotics are effective.
Georgia Duckworth of the HPA, who compiled the report, said:"The findings show evidence of people carrying these bacteria in their guts. If this is found to be commonplace in the general population, this may point towards the food chain being a potential source."
Professor Pat Troop, the chief executive of the HPA, said: "The use of antibiotics by the medical and veterinary professions is one contributor. It is important that antibiotics are only used when necessary."
MRSA: Infections have risen steeply for a decade. Although cleanliness is a factor, they are a product of overuse of antibiotics.
Clostridium difficile: Hit the headlines three months ago after an outbreak at Stoke Mandeville hospital in Buckinghamshire. Although not resistant to antibiotics, the new strain is more difficult to treat.
Escherichia coli: A common cause of bloodstream infections, the emergence of multidrug-resistant strains since 2000 is what has led to the latest warning from the Health Protection Agency.