Culture-independent, sequence-based pathogen diagnostics: in the field and by the bedside

Aim: This work package aims to establish real-time metagenomics diagnosis, initially of a broad selection of trauma patients including those with presumed sepsis, wound infections, pyrexia of unknown origin and encephalitis. This will provide rapid clinical support for infectious agents that are not readily detectable by conventional clinical microbiology or targeted molecular tests.

Background: The study builds on previous SRMRC microbiology work to establish a routine, fast turnaround diagnostic metagenomics function, linking clinical samples with the high-throughput sequencing facility at the University of Birmingham. Previously the team have demonstrated success with culture-independent sequencing of chronic osteomyelitis, eye infections and faeces using conventional next-generation sequencing technologies. The team have also demonstrated the use of fieldable nanopore sequencing to sequence Ebola in Guinea (Quick et al., 2016) and Zika in Brazil.

Method: Sample preparation protocols will be established in order to produce sequencing libraries and data within an initial 48 hour turnaround. In phase one this will be done with Illumina sequencing to establish proof of concept. The team will initially attempt metagenomics diagnostics in 50 patient samples with well characterised microbiological diagnoses, in order to validate and assess the method’s sensitivity.  Then they will attempt metagenomics diagnostics in 50 trauma patient samples where a diagnosis in unclear. Where pathogens are detected they will then subject these samples to validation through targeted, gold standard assays. In phase 2 the system will be made portable and fieldable and could then form part of research projects that fit with future plans for military deployments, particularly in the developing world and places without a well-established laboratory infrastructure.

Lead researchers