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World-first same-day metagenomics for children can detect hidden infections in intensive care

World-first same-day metagenomics for children can detect hidden infections in intensive care

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World-first same-day metagenomics for children can detect hidden infections in intensive care

Great Ormond Street Hospital (GOSH) has successfully implemented a pioneering same-day respiratory metagenomics testing service for children in intensive care, helping clinicians identify infections more quickly and make better-informed treatment decisions. The findings, published today in The Lancet Microbe, mark the first implementation of a same-day pan-microbial metagenomics service for children.

October 16, 2026

The implementation at GOSH represents a significant milestone for the NHS Respiratory Metagenomics Network, which is funded by Department for Science, Innovation and Technology (DSIT) and is working to roll out rapid respiratory metagenomics across hospitals nationally. The work forms part of NHSE’s Genomic Network of Excellence with the metagenomics network led by South East and Central and South Genomic Medicine Services.

The service, developed from a pathway first established at Guy’s and St Thomas’ NHS Foundation Trust, was implemented at GOSH during the 2024-25 winter season. The team analysed 177 respiratory samples from 122 critically ill children and found that the technology could rapidly detect bacteria, viruses and fungi with high accuracy, while identifying infections that routine testing had missed.

Metagenomics works by sequencing all genetic material within a sample, enabling clinicians to search broadly for potential infectious causes rather than testing for a limited number of suspected pathogens. Unlike conventional diagnostic approaches, clinicians do not need to decide in advance what they are looking for.

The study found that metagenomics delivered results that altered clinical management in almost one-third (29%) of samples tested. In a quarter of cases (26%), the results influenced antimicrobial prescribing, including starting, stopping or changing antibiotics, or providing confidence that the current treatment was appropriate.

Importantly, the service detected 50 organisms that were not identified by routine diagnostic tests, all of which were subsequently confirmed by additional testing.

Willow’s story

Same-day metagenomics testing for Willow meant that the cause of her pneumonia could be traced to a bacteria that had become resistant to the antibiotic she was given. This bacteria (Mycoplasma pneumoniae) is impossible to grow in a lab through the standard processes and, if suspected, can only be confirmed through PCR. Even with PCR, care teams would not have been aware of the bacteria’s antibiotic resistance and Willow would not have had the right treatment.

Willow Crowther, age 10, has Kabuki Syndrome, a rare genetic disorder that affects multiple body systems and causes characteristic facial features, developmental delays, and growth abnormalities. She has epilepsy and in March 2026 experienced a prolonged seizure that required hospitalisation and led to her having two cardiac arrests – an extreme medical emergency where her heart had stopped beating.

Willow was intubated and transferred to GOSH, where she was still very poorly and continued to have cardiac arrests.

Willow was moved to the specialist cardiac intensive care unit while she was given life support called ECMO (Extracorporeal membrane oxygenation) in the hope that she could recover.

Willow in ICU bed ventilated

As the metagenomic testing was underway at GOSH, Willow’s blood was tested for unknown organisms and Mycoplasma pneumoniae was found. Crucially this cutting-edge testing was able to show that the bacteria was resistant to the antibiotic she had been prescribed – this would not have been possible through standard means.

With the right treatment now available to her, Willow was able to recover from her infection but still spent several months recuperating on various wards at GOSH.

Mum, Stacey, (40, a semi-permanent make-up specialist) said: “Willow has been a patient at GOSH since she was a little baby and, even though it was a terrible time, we were reassured that we were going there when we knew the hospital so well, and they knew us. She is a sassy 10 year-old who loves the trampoline and Harry Styles – it was heartbreaking to see her so ill.

“Taking part in this research didn’t distract us at that time – it was just part of what was happening to get Willow the care she needed. We only found out recently that she was lucky and this doesn’t happen everywhere.

Willow in ICU

“Doctors gave Willow a 50:50 chance of survival and this quick test meant she got the treatment she needed as fast as possible.

“To know that this could help more families and more children get the answers they need, as quickly as possible is amazing – surely this will save lives. She’s back to herself now, chatting all the time, busy and singing Christmas songs all year around.”

Willow in hospital, smiling at camera

The team believe the programme could play an important role not only in patient care and antimicrobial stewardship, but also in pandemic preparedness by helping clinicians identify unexpected or emerging infectious threats.

This study has helped us to spot infections we would have missed, get children on the right treatments and stop treatments when we know they aren’t going to work – Removing unnecessary treatment is incredibly important for the fight against growing antimicrobial resistance.

All research at GOSH is underpinned by support from our NIHR GOSH Biomedical Research Centre.

“We’ve shown that rapid respiratory metagenomics can be successfully transferred from the centre where it was developed and embedded into routine clinical care for children. That in itself is a big step forward for healthcare, but we have also demonstrated that a same-day metagenomics service can work at scale in paediatric intensive care, delivering results that have a real impact on patient care for some of the sickest children in our hospital.

This really shows the power of collaborative working to build on excellence and cutting edge techniques and get the impact to as many people as possible, as quickly as we safely can. “

“This technology has implications well beyond this study. Because metagenomics is not tailored to a specific ‘bug’, it could be a powerful tool for identifying unusual, rare or emerging infections. As the NHS expands this capability nationally, it has the potential to strengthen both routine patient care and the UK’s preparedness for future infectious disease threats, like the Covid-19 pandemic.”

“Respiratory metagenomics is a prime example of how the NHS Genomic Networks of Excellence are playing a critical role in fast-tracking innovation into frontline NHS practice.

Connecting healthcare, academia, and industry, the networks provide a framework for rapid evaluation, robust evidence generation and faster adoption at scale of new and emerging technologies, giving patients faster and more equitable access to life-changing benefits of genomic medicine.”

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