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Genomic surveillance ‘must be applied to antimicrobial resistance’, says group co-led by University of Cambridge

Genomic surveillance must be put to use to help us win the ‘arms race’ against antimicrobial resistance, says an international group of researchers.

Co-led from Cambridge, the group of nearly 100 experts has set out how the technique that was so crucial in tracking the Covid-19 pandemic can be adopted widely to tackle a potentially even greater global health challenge.

Prof Sharon Peacock Picture: Churchill College
Prof Sharon Peacock Picture: Churchill College

AMR was responsible for an estimated 1.27 million deaths in 2019. But some estimates suggest that could rise to 10 million annually by 2050.

Prof Sharon Peacock, from the University of Cambridge – who led the UK’s pioneering Covid-19 Genomics UK Consortium (COG-UK) – said: “Over the past century, antibiotics have transformed our ability to treat infection and illness and reduce mortality. But bacteria are becoming increasingly resistant, and with a limited pipeline of new antibiotics, we risk effectively returning to the pre-antibiotic era where we can no longer treat infections.

“When the world was hit by the Covid-19 pandemic, we showed how powerful a tool genomic surveillance could be in helping us fight back. This work grew out of its increasing application to real-world problems such as detecting outbreaks in hospitals and in the community – including food borne outbreaks. We now need to take what we learned from the pandemic including its bold and large-scale use and reapply it to the complex problem of AMR.”

Just as reading the genome of SARS-CoV-2 enabled scientists to identify the sources of infection and spot variants of concern, so reading the genome of AMR pathogens can help us detect and track outbreaks. It can also helps predict effective treatments, reveal the mechanism leading to resistance, such as mutations, and explain the movement of resistance mechanisms between bacteria.

The technique is already used by some researchers, such as those at the Wellcome Sanger Institute, but the practice is not routine globally.

Barriers include a lack of resources and political will. Many countries also have a weak epidemiological surveillance and microbiology infrastructure, poor supply chains and pricing structures, and issues around effective cooperation.

A working group, writing in The Lancet Microbe, has explained how genomic surveillance could be applied to AMR more widely by building capacity, training existing and new workforces, particularly in bioinformatics, standardising the way that surveillance is done to detect AMR and agreeing equitable data sharing and governance.

Funded by Wellcome and initiated by Prof Peacock in conjunction with Wellcome SEDRIC (Surveillance and Epidemiology of Drug Resistance Infection Consortium), the team was co-led by Prof Kate Baker at the University of Cambridge and Dr Elita Jauneikaite, of Imperial College London.

They are publishing five papers in the same edition of the journal on the subject.

Prof Baker said: “We are on the cusp of realising the full potential for genomics in tackling AMR, but there is still a lot of work that needs to be done. We need the scientific, public health and political communities to work together to make this happen. AMR is an urgent problem. It is not something that will happen in years to come – it is happening now.”

Dr Jauneikaite added: “We are going to be locked in an ongoing arms race with bacterial pathogens indefinitely. Genomic surveillance offers real promise to help us fight back, providing invaluable information to limit the spread and impact of AMR.”

Prof Peacock concluded: “It was clear from the pandemic that sequencing was a vital tool that was needed in every country worldwide. AMR is a global problem and once again we need to make sure countries worldwide are in a position both to contribute to, and benefit from genomic surveillance data.”

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