Millions of lives could be saved by a new rapid testing system set to be rolled out nationwide over the next two years.
World-first NHS genetic analysis can provide results in seven hours instead of three days.
It could see lifesaving treatment given sooner and help to reduce NHS backlogs rapidly. The technology, tested at Guy’s and St Thomas’ Trust in London, involves swabs and other samples from intensive care patients with respiratory conditions being speedily swept for all known diseases – including ones not under consideration.
It even identifies drugs to which patients may be resistant – with data sent to the UK Health Security Agency, improving the chance of early detection of new diseases or viruses such as Covid.
A two-year pilot will expand the genomic sequencing ability across 10 hospitals in England thanks to £2.08million from the Department of Science, Innovation and Technology plus £1.3million from NHS England. The tests may later be used on patients with a wide range of symptoms and, in as little as five years, even to check people within GP surgeries.
Prof Ian Abbs, chief executive of Guy’s and St Thomas’ NHS Foundation Trust, warned infection is a major problem in healthcare:
“The faster you can get to a diagnosis, the better the outcomes are for patients — and that time is measured in minutes, not in days.
“Hours saves lives. We need to take this new lifesaving technology to the patients in the NHS.”
One big hope is the trial will more quickly spot patients whose infections can lead to sepsis. Without prompt care, they risk organ failure and death. The UK Sepsis Trust says there are some 48,000 sepsis-related deaths annually.
Prof Abbs, inset right, said each hour that a sepsis patient is on the wrong treatment raises their chance of dying by 2% – and currently testing is taking days.
Serious respiratory conditions can be caused by bugs, bacteria, fungal infections or sepsis while lung diseases can include chronic obstructive pulmonary disease, emphysema, pulmonary hypertension and tuberculosis.
Prof Abbs went on: “We have got to get faster. What we are developing is a novel, disruptive technology that really takes over from technologies that were developed in the 19th century.”
Visiting the lab at St Thomas’s recently, Deputy Prime Minister Oliver Dowden said the project could be a huge advance in helping resilience against biological threats.
Typically scientists take patient samples and grow them over three days to see what is there. They test for likely bacteria or viruses – but may miss the unexpected.
The new technology, known as metagenomics, helps scientists to identify and sequence the genetic data from all bacterial, viral and fungal micro-organisms which might be causing the infection.
Unlike other tests, it will pick up everything present not just what is being checked. It analyses the genetic information of a sample by monitoring changes to an electrical current passed through tiny pores. Algorithms are used to decode the resulting signal and identify all known pathogens and microbes.
A three-year trust pilot with Oxford Nanopore Technologies staff led to a change in antibiotics given to almost half of the patients, with an typical seven-hour turnaround from sample to result. It is hoped the expanded project will prove economic benefits, such as shortening stays in hospital.
Prof Abbs said: “Historically, we used to try and fish with a rod and pick up one bug. We’re now fishing with a massive net and so we can pick up everything within the patient but use the combination of biology and data analysis, the combination of digital biology, now to take us to a much faster diagnosis.”
A statement on the Guy’s and St Thomas’ website said: “The study has trialled new technology which enables fast-track genetic testing for patients with suspected respiratory infectious diseases, enabling people to get faster and more accurate treatment. This new funding will enable multiple hospitals, and their patients, to benefit over the next two years.”
The pilot’s expansion, backed by the South East Genomic Medicine Service plus Central and South Genomics, will introduce metagenomics into intensive care units across England.
Waiting lists have dipped from last July’s record high but hundreds of thousands of patients still face long delays for treatment, with 7.61 million queuing for routine hospital care in England last November. Patients waiting more than a year totalled 355,412 – the lowest since May 2022 – while 65-week waits were 94,563, down from a 233,051 peak in June 2021.
The figures also showed 11,168 people waited more than 18 months for routine hospital care.
At least 151,295 people were kept waiting more than 12 hours at A&E last month – as the service was hit by flu, Covid and strikes. Prof Abbs, co-chairman of the South East Genomic Medicine Service, said: “It is vital that the sickest patients in our intensive care unit receive the right medication as quickly as possible. This new genetic test can make that happen and we are delighted that we now have funding to ensure other intensive care units, and their patients, can also benefit.”
Jonathan Edgeworth, consultant microbiologist at the trust’s department of infectious diseases, said that by finding the sequence of all organisms in a sample, scientists could tell “whether it’s a certain type or it’s novel, whether it’s rare, unexpected, an emerging bug”. Data can be stored digitally forever, offering “an accumulating insight into the evolution of pathogens”.
Dr Meera Chand, UKHSA deputy director, said: “We are working closely with the NHS and other partners to integrate metagenomic data into our surveillance and to maximise its potential for public health and biosecurity.”
Infections are usually diagnosed by taking blood samples from patients and sending them to a lab, where scientists grow cultures. They can then test for bacteria or viruses – but the process takes a few days.
This new low-cost technique analyses the genetic information of a sample within hours. It involves an array of tiny holes known as nanopores which are connected to electrodes.
DNA or RNA molecules that pass through the nanopores disrupt the electrical current, creating a distinct pattern which is analysed by an algorithm to identify the pathogens and microbes present.
DNA contains all the biological instructions to build and operate an organism. RNA is a messenger molecule that carries instructions from the DNA code to guide the synthesis of proteins.
Identifying the DNA and RNA in a sample can provide vital clues about a pathogen’s identity or how an organism evolved.
