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.

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 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.

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.

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.

“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.”

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.

Dr Julianne Brown, Head of the GOSH Metagenomics Service, co-senior author of the study - "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. "

Dr Robbie Forrest-Hammond, lead author of the study and Clinical Research Fellow at GOSH "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."

Dr Samiran Ray, Consultant in Paediatric Intensive Care Medicine at GOSH and co-author of the study said: "Respiratory infection is one of the commonest reasons children require intensive care, particularly during the winter months. Traditional testing requires clinicians to make an educated guess about which infection they are looking for. Metagenomics changes that approach completely. Rather than searching for one or two pathogens, we can look broadly across bacteria, viruses and fungi at the same time, helping us identify unexpected infections and make faster treatment decisions.

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

Professor Ian Abbs, Chief Medical Officer, Guy’s and St Thomas’ NHS Foundation Trust said: “In developing the respiratory metagenomics pathway and leading its deployment across the national NHS metagenomics network, Guy's and St Thomas' NHS Foundation Trust and our partner Trusts have sought to demonstrate that rapid metagenomics can be delivered effectively across different NHS settings. This early collaboration with GOSH, as the first children’s hospitals to adopt the pathway, has provided important evidence to help make this test available to children across the UK, including at the Evelina London Children’s Hospital and in paediatric units across our network of more than 20 hospital sites."

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