Implementing rapid pan-microbial metagenomics in paediatric intensive care
Lower respiratory tract infections cause an estimated 502,000 deaths in children under five globally, but current routine testing is time-consuming and suffers from culture bias. Replicating the method used by Alcolea-Medina and Snell et al.1, researchers successfully adapted the method for research samples from paediatric patients. Within 24 hours, causative pathogens were identified with a high specificity of >99%, alongside an additional 50 pathogens previously missed by standard methods. This study demonstrates that this metagenomic Oxford Nanopore sequencing is replicable and has the potential to provide faster and more comprehensive results than current methods. Furthermore, it has the potential to positively impact patient outcomes and improve antimicrobial stewardship.
‘This had led to potential clinical impact (~30%) comparable to previous reports for this protocol, with the largest impact being on antimicrobial prescribing, suggesting a possible role for metagenomics in anti-microbial stewardship’
Hammond and Kopec et al. medRxiv (2025)
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Sample type: bronchoalveolar lavage, endotracheal secretions, sputum, nasopharyngeal aspirate, and pleural fluid
