A same-day genetic sequencing test has identified hidden and drug-resistant infections in critically ill children at Great Ormond Street Hospital in London, with results now published in the Lancet Microbe.
Metagenomic testing analyzes all genetic material in a respiratory sample to detect bacteria, viruses and fungi simultaneously. Unlike conventional methods that require doctors to guess which pathogen to look for, or culture-based tests that take days, metagenomics identifies thousands of potential pathogens from a single sample.
A 2024-25 study at GOSH tested 122 critically ill children in the pediatric intensive care unit. The test identified around nine in 10 bacteria and viruses and all fungi present in samples. In a quarter of cases, results changed treatment decisions, including starting, stopping or changing antibiotics.
One case involved 10-year-old Willow Crowther, admitted to intensive care in March with pneumonia that triggered seizures and cardiac arrests. Her parents were told she had a 50% chance of survival. Metagenomic testing revealed she carried a drug-resistant bacterial infection requiring a different antibiotic than she had been prescribed. With the correct treatment identified by the test, Willow recovered after several months in hospital.
Dr Sam Ray, consultant in pediatric intensive care medicine at GOSH and study co-author, said traditional testing forced clinicians to "make an educated guess about which infection they were looking for." The new approach allowed doctors 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."
The test detected 50 organisms not identified by routine diagnostics, potentially serving as an early warning system for emerging infections. Dr Julianne Brown, head of the GOSH Metagenomics Service, noted it "could be a powerful tool for identifying new infections that pose a pandemic threat" and could enable rapid detection of novel pathogens.
Metagenomic testing is being gradually rolled out to around 30 intensive care units across the UK treating both adults and children, building on earlier trials at Guy's and St Thomas' NHS Trust.