Respiratory metagenomics in clinical service


A prospective clinical pilot study was conducted in ICU patients with respiratory failure, using a unified respiratory metagenomic (RMg) workflow encompassing DNA and RNA sequencing. The study aimed to compare RMg to standard microbiology assays and assess its clinical impact. One hundred and thirteen respiratory samples were processed from 73 patients and for 104/113 with same-day results (92%). RMg demonstrated high sensitivity and specificity for bacteria and fungi. However, RMg did not detect three viruses with high cycle thresholds (greater than 28 CT) but showed 100% specificity. When a detected virus had more than 10 reads, the median genome coverage was 85% (range 67–100) at 5x depth. RMg offers rapid turnaround time and facilitates the detection of unexpected microorganisms, enabling targeted antibiotic selection and deescalating antimicrobial use.


Dr. Gaia Nebbia, MBBSeq, MRCP, FRCPath, PhD, trained in virology and infectious diseases in London and completed her PhD in virology in 2008. Subsequently, she pursued further research in the field of viral immunology as an NIHR clinical lecturer. In 2015, Gaia joined Guy’s & St Thomas’ Hospital as a consultant virologist and in 2019, she was awarded the MRC Clinical Academic Research Partnerships grant to spearhead the development of real-time nanopore influenza sequencing and to conduct studies on influenza vaccine efficacy. Additionally, Gaia played a key role in implementing a whole-genome sequencing service for SARS-CoV-2 and respiratory metagenomics.

Authors: Dr. Gaia Nebbia