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Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities.

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Jauneikaite, Elita 
Baker, Kate S 
Nunn, Jamie G 
Midega, Janet T 
Hsu, Li Yang 


Integration of genomic technologies into routine antimicrobial resistance (AMR) surveillance in health-care facilities has the potential to generate rapid, actionable information for patient management and inform infection prevention and control measures in near real time. However, substantial challenges limit the implementation of genomics for AMR surveillance in clinical settings. Through a workshop series and online consultation, international experts from across the AMR and pathogen genomics fields convened to review the evidence base underpinning the use of genomics for AMR surveillance in a range of settings. Here, we summarise the identified challenges and potential benefits of genomic AMR surveillance in health-care settings, and outline the recommendations of the working group to realise this potential. These recommendations include the definition of viable and cost-effective use cases for genomic AMR surveillance, strengthening training competencies (particularly in bioinformatics), and building capacity at local, national, and regional levels using hub and spoke models.



Humans, Anti-Bacterial Agents, Drug Resistance, Bacterial, Genomics, Health Facilities, Computational Biology

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Lancet Microbe

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Elsevier BV
EJ had partial salary cover from Wellcome Trust over the course of this work. KSB reports funding from the BBSRC and MRC and partial salary cover from Wellcome Trust and UKHSA over the course of this work. LYH reports funding from Pfizer Inc and honoraria from BioMerieux for lecture in 2022. 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. SJP is a member of the Scientific Advisory Board of Next Gen Diagnostics and was supported by Illumina to attend the ECCMID conference. NAF reports funding from the BMGF, UKRI and NIHR. All other authors declare no conflicts of interest.