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Oxford University co-lead: Prof Derrick Crook

UKHSA co-lead: Prof Deborah Williamson

We aim to determine how to analyse and compare the genetic code of millions of microbes causing infections from across the world. Our vision is to find better ways to manage and prevent threats from antimicrobial resistance and healthcare associated infections by detecting them faster, working out who needs protecting most and how we can do this.  We will develop automated software to read, interpret and report results from genetic code identifying the type of microbe, whether it is resistant to certain antimicrobials and whether there is an. We will also improve our workflow to obtain the pathogen DNA/RNA (and thus genetic code) directly from clinical samples and our understanding of how the genetic changes leads to antimicrobial resistance. 


Improved genomic surveillance of tuberculosis  

Substantial efforts are ongoing to improve genomic surveillance of tuberculosis. We are working to devise a semi-automated extraction system reducing labour intensive processing. 

This will introduce a whole genome amplification step, reducing failure rate and improve the depth of sequence. We will initially optimise the methods first for Illumina then long-read ONT (Nanopore) sequencing. We have refactored processing bioinformatics pipelines to be operated by a laboratory scientist, agnostic to long- and short-read sequencing platforms (initially Illumina), and that can be hosted on any commercial or on-premises cloud infrastructure. This mycobacterial service will include a mix of metagenomic and species-specific components, optimising the workflow for mycobacterial species identification, characterisation of subspecies, lineages of all mycobacteria while focussing principally on M. tuberculosis complex, resistance, outbreak detection and automated reporting.  


SARS-CoV-2 sequencing pipeline  

We developed a fast and high-throughput SARS-CoV-2 sequencing pipeline that was translated successfully to the routine laboratory at the Oxford University Hospitals Foundation NHS Trust. The sequencing results were integrated into the national system for SARS-CoV-2 surveillance, as well as being added to the Global Pathogen Analysis Service(GPAS), to aid the surveillance and tracking of SARS-CoV-2 globally. The lab team reported that using GPAS had cut processing times from days to minutes, and allowed wet lab members to get directly involved in analysis.