UKHSA launches metagenomic surveillance for health security

Earlier this year, the UK Health Security Agency (UKHSA)  launched mSCAPE – the metagenomics Surveillance Collaboration and Analysis Programme – a world-first initiative that is piloting the use of metagenomic data for public health surveillance and pathogen analysis.

The programme involves a consortium of NHS and academic partners including the University of Edinburgh, University of Birmingham and the NHS Clinical Respiratory Metagenomics Network led by Guy’s and St Thomas’ NHS Foundation Trust.  

Traditional genomic methodologies have required scientists to target sample sequencing towards pathogens that are already known to the scientific and medical community.  

However metagenomics allows the analysis of all nucleotide sequences in patient samples, potentially including novel pathogenic viruses and bacteria.UKHSA is now taking anonymous pathogen data from multiple labs that are using metagenomics for diagnosis, including those in the NHS, and analysing it at a national level to monitor trends, epidemiology and pathogen emergence.  

This approach will significantly improves detection of new disease outbreaks, as well as enabling the source of an outbreak to be better understood, and informing predictions about the effectiveness of potential treatments or interventions.

Researchers from the School of Biological Sciences at the University of Edinburgh – Rachel Colquhoun, Andrew Rambaut and Angela Sun – have been involved in designing several of the core analysis processes for the project.

The initial processing has been designed to allow data to be queried by pathogen content, with relevant reads extracted. This is fundamental to storing and accessing the data in order to answer different research questions such as the prevalence and characteristics of a particular pathogen over time.

Secondly, researchers have developed a method to provide additional insights into robustness of the new lab protocols and potential reagent contamination, which can be fed back to labs.

Finally, the team have been researching how to improve methods to select only the microbial part of the read data, in order to address future privacy concerns. This will one day enable metagenomic data to be shared more widely with academic researchers.

Rachel Colquhoun

Andrew Rambaut

School of Biological Sciences, University of Edinburgh

Institute of Microbiology and Infection, University of Birmingham

Metagenomics Surveillance Collaboration and Analysis Programme

Guy’s and St Thomas’ NHS Foundation Trust

UK Health Security Agency Pathogen Genomics Strategy

UKHSA