Genomics for public health and international surveillance of antimicrobial resistance

Historically, epidemiological investigation and surveillance for antimicrobial resistant (AMR) bacteria has relied on relatively low-resolution isolate-based phenotypic analyses undertaken at local and national reference laboratories. Genomic sequencing has the potential to provide a far more high-resolution picture of AMR evolution and transmission and is already beginning to revolutionize how public health surveillance networks monitor and tackle AMR bacteria. However, the routine integration of genomics in surveillance pipelines still has considerable barriers to overcome. In 2022, a workshop series and online consultation brought together international experts in AMR and pathogen genomics to assess the status of genomic applications for AMR surveillance in a range of settings. Here we focus on discussions around the use of genomics for public health and international AMR surveillance, noting the potential advantages of, and barriers to, implementation and proposing recommendations from the working group to help drive the adoption of genomics in public health AMR surveillance. These include the need to build capacity for genome sequencing and analysis, harmonising, and standardising surveillance systems, developing equitable data sharing and governance frameworks and strengthening interactions and relationships among stakeholders at multiple levels.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. SWL has received Receive Robert Austrian Research Award sponsored by Pfizer in 2022. DGA reports funding from the NIHR. 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. DGA, BE, RSH, 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. LSB reports funding by Conselleria de Sanitat Universal i Salut Pública, Generalitat Valenciana, Valencia (Spain), under Plan GenT (Ref. CDEI-06/20-B). 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