A pioneering same-day diagnostic test has enabled doctors at a major children's hospital to identify hidden and drug-resistant infections among young patients in intensive care, with results now published in a leading medical journal.
Respiratory samples from more than 100 critically ill children at London's Great Ormond Street Hospital (GOSH) underwent metagenomic testing, a technique that sequences all genetic material present in a sample to identify bacteria, viruses and fungi simultaneously. Unlike conventional diagnostic methods, which require clinicians to predict which pathogen they are seeking, metagenomics can detect thousands of different organisms from a single sample, often revealing infections that standard tests miss.
The approach has already transformed outcomes for some of the hospital's most vulnerable patients. In March, 10-year-old Willow Crowther from Kent developed severe pneumonia that triggered a seizure and multiple cardiac arrests, requiring admission to intensive care. Her mother, Stacey Moore, was told her daughter had only a 50% chance of survival.
"The consultant said... we should bring our family up to say goodbye to her. This is how critical and in how much danger she was of passing away."
Metagenomic analysis revealed that Willow had contracted a drug-resistant bacterial infection that required a different antibiotic from the one she had initially been prescribed. Once doctors switched to the correct treatment based on the test results, her condition improved, though she required several months of hospital care to fully recover.
"The fact that they had a test there available to her was paramount. It saved her life,"
said Stacey. Her father, Russ, added:
"It's a miracle she's here and we're extremely grateful for that."
How does metagenomic testing differ from traditional methods?
Metagenomic testing represents a fundamental shift in how infections are diagnosed. The most common conventional method involves attempting to culture bacteria in Petri dishes—a technology that has remained largely unchanged since the Victorian era. Another widely used test, PCR, can identify viruses and some bacteria, but only if clinicians specify in advance which pathogens they suspect.
Metagenomics, by contrast, sequences all genetic material in a sample without requiring prior assumptions about what infection might be present. At GOSH, the test successfully identified approximately nine in 10 bacteria and viruses, and all fungi present in samples.
What impact did the test have on patient treatment?
During a study conducted in 2024-25, metagenomic testing was applied to 122 critically ill children in the paediatric intensive care unit at GOSH. The results, now published in the Lancet Microbe, showed that in a quarter of all cases, the test findings directly influenced prescribing decisions—leading doctors to start, stop or change antibiotics based on confirmed pathogen identification.
Dr Sam Ray, consultant in paediatric intensive care medicine at GOSH and co-author of the study, explained the clinical significance:
"The study has helped us to spot infections we would have missed, get children on the right treatment and stop antibiotics when we know they aren't going to work. Removing unnecessary treatment is incredibly important for the fight against growing antimicrobial resistance."
Beyond identifying known pathogens, metagenomic testing at GOSH detected 50 organisms that routine diagnostic methods had failed to identify, demonstrating its potential as an early warning system for emerging infections.
What additional clinical benefits has the test provided?
Since the respiratory metagenomics service became operational, GOSH has documented several cases where the technology identified infections that would otherwise have gone undetected. According to the NHS Metagenomics Network, the service identified measles in a child with respiratory failure who presented without a rash or typical symptoms; the diagnosis prompted immediate infection-control measures. The same service also detected Group A Streptococcus in a child with sepsis, enabling correct treatment 24 hours before a PCR result would have been available, and identified influenza C—a virus that standard PCR panels would not have detected.
GOSH operates a separate metagenomics service for infections in sterile sites, such as brain tissue and cerebrospinal fluid, which was established before the respiratory service. According to the hospital, this service is typically deployed after conventional tests have failed to identify a suspected pathogen. In an earlier study of 60 children with unexplained neurological presentations, metagenomic testing detected a causative pathogen in 14 cases (23%) that standard diagnostic methods had not identified, according to research published in the Lancet Microbe.
How is metagenomic testing being expanded across the UK?
Dr Julianne Brown, head of the GOSH Metagenomics Service and co-senior author of the study, indicated that the technology is being gradually rolled out to approximately 30 intensive care units across the United Kingdom, treating both adult and paediatric patients. The project at GOSH builds on earlier trials at Guy's and St Thomas' NHS Trust, which first used metagenomics to test for respiratory infections in adult patients.
Looking ahead, GOSH and UCL teams are engaged in nationwide collaborations to explore the application of metagenomics in critical care settings and to understand immune responses to central nervous system infections.
What is the potential for pandemic preparedness?
Dr Brown highlighted the broader implications of metagenomic testing for public health:
"It could be a powerful tool for identifying new infections that pose a pandemic threat. In the future, if there was to be a new mystery pathogen that could be a cause of the next pandemic, we would detect that very quickly and put the right measures in place."
The ability to rapidly identify novel pathogens without prior knowledge of their characteristics positions metagenomic testing as a potentially transformative tool in infectious disease surveillance and pandemic preparedness.
Key Facts
- Metagenomic testing identified drug-resistant infections in 10-year-old Willow Crowther that standard tests had missed, enabling life-saving treatment changes.
- During a 2024-25 study of 122 critically ill children at GOSH, metagenomic testing influenced prescribing decisions in 25% of cases and detected 50 organisms missed by routine diagnostics.
- The technology is being rolled out to approximately 30 intensive care units across the UK and has already identified measles, Group A Streptococcus and influenza C in patients where conventional tests failed.
- Unlike culture-based methods or PCR testing, metagenomics sequences all genetic material in a sample without requiring advance assumptions about which pathogen is present.
- The approach has potential applications in pandemic preparedness, enabling rapid identification of novel pathogens that could pose future public health threats.
