Untargeted metagenomics protocol for the diagnosis of infection from CSF and tissue from sterile sites

Laura Atkinson; Jack Cd Lee; Alexander Lennon; Divya Shah; Nathaniel Storey; Sofia Morfopoulou; Kathryn A Harris; Judy Breuer; Julianne R Brown

doi:10.1016/j.heliyon.2023.e19854

Untargeted metagenomics protocol for the diagnosis of infection from CSF and tissue from sterile sites

Heliyon. 2023 Sep 9;9(9):e19854. doi: 10.1016/j.heliyon.2023.e19854. eCollection 2023 Sep.

Authors

Affiliations

¹ Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Microbiology, Virology and Infection Control, London, UK.
² Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK.
³ Royal London Hospital, Barts Health NHS Trust, Department of Virology, London, UK.

Abstract

Metagenomic next-generation sequencing (mNGS) is an untargeted technique capable of detecting all microbial nucleic acid within a sample. This protocol outlines our wet laboratory method for mNGS of cerebrospinal fluid (CSF) specimens and tissues from sterile sites. We use this method routinely in our clinical service, processing 178 specimens over the past 2.5 years in a laboratory that adheres to ISO:15189 standards. We have successfully used this protocol to diagnose multiple cases of encephalitis and hepatitis.