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

Heliyon (Sep 2023)

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

Affiliations

Laura Atkinson: Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Microbiology, Virology and Infection Control, London, UK; Corresponding author.
Jack CD. Lee: Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Microbiology, Virology and Infection Control, London, UK
Alexander Lennon: Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Microbiology, Virology and Infection Control, London, UK
Divya Shah: Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Microbiology, Virology and Infection Control, London, UK
Nathaniel Storey: Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Microbiology, Virology and Infection Control, London, UK
Sofia Morfopoulou: Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Microbiology, Virology and Infection Control, London, UK; Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
Kathryn A. Harris: Royal London Hospital, Barts Health NHS Trust, Department of Virology, London, UK
Judy Breuer: Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Microbiology, Virology and Infection Control, London, UK; Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
Julianne R. Brown: Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Microbiology, Virology and Infection Control, London, UK

Journal volume & issue: Vol. 9, no. 9
p. e19854

Abstract

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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.

Published in Heliyon

ISSN: 2405-8440 (Online)
Publisher: Elsevier
Country of publisher: United Kingdom
LCC subjects: Science: Science (General); Social Sciences: Social sciences (General)
Website: https://www.cell.com/heliyon/home

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