Same-Day Test Helps Doctors Detect Hidden Infections in Critically Ill Children

A pioneering same-day test has been used to detect hidden and drug-resistant infections among children in intensive care.

Respiratory samples from more than 100 critically ill young patients at London's Great Ormond Street Hospital (GOSH) were sent for metagenomic testing. The test can identify bacteria, viruses and fungi from a single sample. In many cases, the results influence what doctors prescribe.

Metagenomics can detect infections that standard tests miss. This can lead to better outcomes for some critically ill patients.

A life-saving result

In March, 10-year-old Willow Crowther became dangerously ill with pneumonia. It triggered a seizure and multiple cardiac arrests.

Willow, from Kent, was admitted to intensive care at GOSH. Her mother, Stacey Moore, was told she had 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.”

The team at GOSH used metagenomics. This diagnostic test sequences all genetic material present in a sample. Conventional methods, by contrast, require clinicians to decide in advance what they are looking for.

The test identified a drug-resistant bacterial infection. Willow needed a different antibiotic from the one she had been prescribed.

“The fact that they had a test there available to her was paramount. It saved her life,” said Stacey.

“It's a miracle she's here and we're extremely grateful for that,” added Willow's father, Russ.

With the right treatment, Willow was able to recover from her infection. She needed several months in hospital.

Wider use at the hospital

Willow is one of many patients at the children's hospital to benefit from the new testing.

During a study in 2024-5, metagenomic testing was used on 122 critically ill children in the paediatric intensive care unit (ICU) at GOSH. The results have now been published in the journal Lancet Microbe.

The most common method of identifying bacteria involves trying to culture them in Petri dishes. This technology has been used since Victorian times. Another test, PCR, can identify viruses and some bacteria, but doctors must specify what they are trying to detect.

Metagenomic testing at GOSH identified around nine in 10 bacteria and viruses, and all fungi, in samples. In a quarter of cases, the results influenced prescribing decisions, including starting, stopping or changing an antibiotic.

Dr Sam Ray, consultant in paediatric intensive care medicine at GOSH and co-author of the study, said traditional testing required clinicians to make an educated guess about which infection they were looking for.

“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.”

Early warning potential

Metagenomic testing at GOSH also detected 50 organisms that routine diagnostics did not identify. This means it could play an early warning role against new infections.

Dr Julianne Brown, head of the GOSH Metagenomics Service and co-senior author of the study, said the new testing is being gradually rolled out to around 30 intensive care units across the UK. These units treat both adults and children.

“It could be a powerful tool for identifying new infections that pose a pandemic threat,” she said.

“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 project at GOSH builds on trials at Guy's and St Thomas' NHS Trust. Those trials first used metagenomics to test for respiratory infections in adult patients.