A new publication by the WHO provides an overview of whole genome sequencing (WGS) to track antimicrobial resistance (AMR), by sharing information about how to implement the technique. This will help improve the global monitoring of antimicrobial resistance by enabling countries to track its spread in more detail.
The Technical Note, Whole-genome sequencing for surveillance of antimicrobial resistance, outlines the benefits and limitations of WGS for surveillance, and discusses what is needed to apply it more widely in the fight against AMR.
One of the authors, Professor David Aanensen from the Centre for Genomic Pathogen Surveillance (CGPS) at the Big Data Institute, University of Oxford, said: “AMR is a serious problem, and we desperately need better weapons to fight it. WGS has the potential to help us track, predict and ultimately prevent AMR infections around the world. Our aim with this Technical Note is to support this technology in countries that want to use it.”
Many bacteria and other pathogens are becoming resistant to antibiotics: infections like MRSA, tuberculosis and gonorrhea are increasingly hard to treat. This poses a major threat to public health. According to the World Bank, within a decade, AMR infections that result in increased morbidity, disability, premature deaths and reduced effective labour will become a significant threat to the global economy unless we take action.
Part of the response to this threat is the WHO Global Action Plan on AMR, which highlights the importance of surveillance. The WHO’s Global Antimicrobial Resistance and Use Surveillance System (GLASS) was set up to manage this surveillance. GLASS monitors several ‘priority pathogens’ using the results of laboratory testing. This involves taking samples from infected patients, growing and identifying the pathogens, and testing them to see if they are resistant to antibiotics.
This approach is effective, but it doesn’t provide much detail. WGS can be used to supplement the laboratory data and provide more information about the pathogens. In AMR surveillance, WGS gives the complete DNA sequence of the pathogen. This can be compared to a database of AMR genes and mutations to understand things like how virulent the pathogen is or what antimicrobials it is resistant to.
WGS gives researchers the information they need to identify exactly what type of pathogen has been identified and to track the spread and evolution of AMR. This means we get early signals of emerging threats, helping policymakers develop effective controls. It also helps researchers develop better, faster diagnostic tools.
However, there are limitations to the use of WGS in AMR surveillance. WGS is expensive to set up; this has been a barrier in low and middle income countries. But the costs associated with WGS are decreasing rapidly, and this may enable broader, affordable access around the world.
The Technical Note features case studies at the local, national and international levels to show the reality of using WGS for AMR surveillance globally. Professor David Aanensen said:
“A lot of the input into this publication has come directly from researchers in low and middle income countries – it’s a collation of experiences that highlights the barriers that need to be overcome to get the most out of implementing this game-changing technology for public health. WGS is undoubtedly going to help us in the fight against AMR, and it’s been great to have been involved in developing this Technical Note to help establish it in our global surveillance efforts.”
The Technical Note outlines steps that should be taken to support the use of WGS in AMR surveillance. For example, international standards should be set to ensure that results from different laboratories can be compared. Researchers should also have access to well curated public databases of genetic sequences. The authors note that as WGS methods continue to develop, this technology will become even more useful in the future.