Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group

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Baker, Kate 
Jauneikaite, Elita 
Nunn, Jamie G 
Midega, Janet T 
Atun, Rifat 

Nearly a century after the beginning of the antibiotic era, which has been associated with unparalleled improvements in human health and reductions in mortality associated with infection, the dwindling pipeline for new antibiotic classes coupled with the inevitable spread of antimicrobial resistance (AMR) poses a major global challenge. Historically, surveillance of AMR bacteria typically relied on phenotypic analysis of isolates taken from infected individuals, which provides only a low-resolution view of the epidemiology behind an individual infection or wider outbreak. Recent years have seen increasing adoption of powerful new genomic technologies with the potential to revolutionise AMR surveillance by providing a high-resolution picture of the AMR profile of the bacteria causing infections and provide real-time actionable information for treating and preventing infection. However, many barriers remain to be overcome before genomic technologies can be adopted as a standard part of routine AMR surveillance around the world. Accordingly, the Surveillance and Epidemiology of Drug-resistant Infections Consortium (SEDRIC; www.sedric.org.uk) convened an expert working group on Genomics Surveillance for AMR to assess the benefits and challenges of using genomics for AMR surveillance. This overview, and the associated four workshop summaries detail these discussions and provide a series of recommendations from the working group that can help to realise the massive potential benefits for genomics in surveillance of AMR.

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The Lancet Microbe
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KSB reports funding from the BBSRC and MRC and partial salary cover from Wellcome Trust and UKHSA over the course of this work. EJ had partial salary cover from Wellcome Trust over the course of this work. RAA reports funding unrelated to this study from Novo Nordisk, Roche, Novartis and UICC, and honoraria (unrelated to this study) from Merck&Co, Novartis, F. Hoffmann-La Roche Ltd. BE and INO report receiving funding from the UK Department of Health and Social Care: grant managed by the Fleming Fund and work performed under the auspices of the SEQAFRICA project. INO reports funding from the Bill and Melinda Gates Foundation, JPIAMR, Wellcome Trust, Grand Challenges Africa Award, UK MCR, royalties for Genetics: Genes, Genomes and Evolution (Oxford University Press), Divining Without Seeds and for Antimicrobial Resistance in Developing Countries (Springer), consulting fees from Wellcome Trust, honoraria for Harvard University seminars and Peter Wildy Lecture Award 2023. LYH reports funding from Pfizer Inc and honoraria from BioMerieux for lecture in 2022. DMM reports funding from BSAC. NEW reports funding from Nuclear Threat Initiative, MRC, Open Philantropy and Shionogi as well as consulting fees from Nuclear Threat Initiative. DMA reports funding from the NIHR. NAF reports funding from the BMGF, UKRI and NIHR. SJP is a member of the Scientific Advisory Board of Next Gen Diagnostics and was supported by Illumina to attend the ECCMID conference. All other authors declare no conflicts of interest.

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