Britain's health system could slip back by 200 years unless the "catastrophic threat" of antibiotic resistance is successfully tackled, the Government's Chief Medical Officer warns today.

In her first annual report, Dame Sally Davies says the problem of microbes becoming increasingly resistant to the most powerful drugs should be ranked alongside terrorism and climate change on the list of critical risks to the nation.

The growing ineffectiveness of many antibiotics against infection is being compounded by a "discovery void", as few new compounds are being developed to take their place. Dame Sally calls for a string of actions to tackle the threat, which is likely to include tighter restrictions on how GPs prescribe antibiotics for their patients.

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Declaring that in 20 years' time even minor surgery may lead to death through untreatable infection, she warns: "This is a growing problem, and if we don't get it right, we will find ourselves in a health system not dissimilar from the early 19th century."

Although the problem of antibiotic or antimicrobial resistance has long been recognised, Dame Sally has chosen to give it new prominence, urging that the level of threat it represents to the nation as a whole needs to be sharply re-evaluated. "I knew about antimicrobial resistance as a doctor, but I hadn't realised how bad it was or how fast it is growing," she said.

In her report, published today, she says: "There is a need for politicians in the UK to prioritise antimicrobial resistance as a major area of concern, including on the national risk register and pushing for action internationally as well as in local healthcare services.

"Antimicrobial resistance is a ticking time-bomb not only for the UK but also for the world. We need to work with everyone to ensure the apocalyptic scenario of widespread antimicrobial resistance does not become a reality. This threat is arguably as important as climate change."

The Government's Chief Pharmaceutical Officer, Keith Ridge, said although the control mechanism for prescribing antibiotics had been strengthened in hospitals, there would need to be tighter and more thoughtful control of antibiotic prescriptions in GPs' surgeries.

In Britain, although hospital infections from bugs such as MRSA and C. difficile have been greatly reduced from the levels of 10 years ago – falling by 80 per cent – they are being replaced by other bacteria such as E. coli and klebsiella, which are now the most frequent agents of hospital-acquired infection.

About 5,000 patients a year in the UK are dying from bloodstream infections, half of them caused by drug-resistant organisms.

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Yet while antibiotic use is rising – not least in agriculture for farmed animals and fish – resistance is steadily growing and the "pipeline is drying up" of new drugs which can replace those becoming useless. No new classes of antibiotics have been developed since 1987, and none are in the pipeline across the world, although a small number of new individual drugs are being developed, including by major British pharmaceutical companies such as GSK and AstraZeneca. The reason, Dame Sally says, is market failure – for Big Pharma, there is little money in expensively developing new compounds which will only be taken in short courses, compared to a drug for blood pressure, say, which may have lifelong use for patients. Addressing the "discovery void" is now the key problem, she says, which may have to be tackled internationally, and may involve governments intervening in the hitherto private sector of drug development.

"We may have to work with the pharmaceutical companies in public-private partnerships, and we may have to do some development of antibiotics on a public basis," she said.

She gave the example of the Innovative Medicines Initiative, a joint undertaking between the European Union and the pharmaceutical industry which supports collaborative research to boost pharmaceutical innovation in Europe. The other key action would be to improve stewardship of antibiotics, making sure they were only prescribed when absolutely necessary, to reduce the challenges of resistance developing.

"We are going to have to up our education, so that the doctors and nurses and vets who prescribe antibiotics do it knowing the risks and advantages, and think about that balance, and also spend time with patients explaining why they're not prescribing them," she said. In two weeks' time the Department of Health will publish the UK Antimicrobial Resistance Strategy, setting out how the Government intends to respond to the challenges outlined by Dame Sally.

"Professor Dame Sally Davies rightly flags the issue of antimicrobial resistance to be of national and international concern," said Professor Nigel Brown, president of the Society for General Microbiology. "Urgent action is required by microbiologists and other scientists to identify and produce new antibiotics, and to tackle the problem of antibiotic resistance and its transmission."

Professor Christopher Thomas, professor of molecular genetics at the University of Birmingham, added: "We need new ways to kill resistant bacteria or reduce their carriage of resistance genes. Novel approaches that might have appeared unrealistic a few years ago need to be explored."