Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study
Severe respiratory infections in patients in intensive care units are often difficult to diagnose quickly because current clinical tests rely on slow culture methods, delaying effective treatment plans. Here, researchers investigated the use of metagenomics to detect pathogens from research samples without the need for culturing. Using Oxford Nanopore sequencing, they identified bacteria, fungi, and viruses from respiratory samples in a single assay, delivering results within 24 hours. This approach detected pathogens that were missed by standard methods and demonstrates the future potential of metagenomic nanopore sequencing to guide antimicrobial therapy and enhance public health surveillance.
‘Metagenomics showed substantial clinical impact through identification of pathogens where routine testing yielded negative results, such as after antibiotic treatment or where pathogens were not targeted by routine testing’
Alcolea-Medina and Snell et al. Lancet Microbe (2025)
Sample type: bronchoalveolar lavage
