How could we incorporate metagenomics into routine diagnostic microbiology? | LC 25

Biography

Judith Breuer is Professor of Virology at UCL and Clinical lead for Virology at Great Ormond Street Hospital for Children. Judith established a 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 Infectious Disease (SPID) Genomic Network of Excellence (GNoE) and the Genomics to Enhance Microbial Screening (GEMS) Blood Transfusion

Abstract

In this talk I will discuss the clinical need for routine metagenomics and the solutions that are currently being proposed for detection of pathogens in sterile sites such as the brain and blood versus respiratory samples. I will describe briefly the UKAS accredited pipeline for the former at Great Ormond Street Hospital (GOSH). In addition, I will outline our experience in implementing the respiratory metagenomics protocol developed by Guys and St Thomas Hospital (GSTT) in collaboration with Oxford Nanopore Technologies and review the first 5–6 months of our results.

I will examine the lessons learnt during the process of running both pipelines within a busy laboratory setting and review what would be needed to develop a single-platform pipeline that could address both needs. The current sterile-site pipeline is slow and Oxford Nanopore technology offers the potential for faster turnaround times, provided comparable sensitivity can be achieved.

I will present the work in our laboratory to develop sufficient improvement in Oxford Nanopore sensitivity to potentially enable rapid (12–48 hour) detection and exclusion of pathogens in sterile sites.