Utilising nanopore metagenomic sequencing for rapid identification of infections
Judith Breuer is Professor of Virology at UCL and Clinical lead for Virology at Great Ormond Street Hospital for Children. Professor Breuer established a now UKAS accredited diagnostic metagenomics at GOSH for the detection of pathogens in suspected cases of encephalitis. She leads work on metagenomics of sterile sites within the Serious Presentation of Infection Genomic Network of Excellence and GEMS Blood Transfusion Research Units, identifying metagenomically adeno-associated virus 2 (AAV2) as the unexplained paediatric hepatitis occurring in children in 2022. Professor Breuer chairs and is a member of several national government and UKHSA committees on vaccines and infection.
Abstract
In this talk Judith Brueur discusses the experience of Great Ormond Street Hospital (GOSH) in implementing the respiratory metagenomics protocol at Guys and St Thomas Hospital (GSTT) using Oxford Nanopore technology and reviews the first 5-6 months of results. Judith examines the lessons learnt during the process of establishing the existing protocol within a busy diagnostic laboratory and the particular challenges of applying the pipeline to severely ill and often immunocompromised paediatric patients. In addition, Judith presents the measures taken to facilitate useful interpretation of polymicrobial upper respiratory tract specimens, which are more commonly taken from children. GOSH has also since 2014 delivered a metagenomics service (UKAS accredited in 2024) for detection (and exclusion) of pathogens in sterile sites and tissue, in cases where infection is suspected but conventional methods remain negative. The current sterile-site pipeline is slow, and Oxford Nanopore technology offers the potential for faster turnaround times, provided comparable sensitivity can be achieved. She presents the work in her lab to develop sufficient improvement in Oxford Nanopore sensitivity to potentially enable rapid (12-48 hour) detection and exclusion of pathogens in sterile sites.