Genomics for public health and international surveillance of antimicrobial resistance.

Historically, epidemiological investigation and surveillance for bacterial antimicrobial resistance (AMR) has relied on 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 revolutionise how public health surveillance networks monitor and tackle bacterial AMR. 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 to drive the adoption of genomics in public health AMR surveillance. These recommendations 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.

Informations de copyright

Copyright © 2023 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests KSB reports funding from the Biotechnology and Biological Sciences Research Council and Medical Research Council (MRC) and partial salary cover from Wellcome Trust and the UK Health Security Agency (UKHSA) over the course of this work. EJ had partial salary cover from Wellcome Trust over the course of this work. SWL has received the Robert Austrian Research Award sponsored by Pfizer in 2022. DGA reports funding from the NIHR. INO reports funding from the Bill & Melinda Gates Foundation, Joint Programming Intiative on Antimicrobial Resistance, Wellcome Trust, Grand Challenges Africa Award, and UK MRC; royalties for Genetics: Genes, Genomes and Evolution (Oxford University Press), and Divining Without Seeds and for Antimicrobial Resistance in Developing Countries (Springer); consulting fees from Wellcome Trust; honoraria for Harvard University seminars; and the Peter Wildy Lecture Award 2023. DGA, BE, RSH, and INO report receiving funding from the UK Department of Health and Social Care in the form of a grant managed by the Fleming Fund and work performed under the auspices of the SEQAFRICA project. LS-B reports funding by Conselleria de Sanitat Universal i Salut Pública, Generalitat Valenciana, Valencia (Spain), under Plan GenT (reference number CDEI-06/20-B). NAF reports funding from the Gates Foundation, UK Research and Innovation, and NIHR. SJP is a member of the Scientific Advisory Board of Next Gen Diagnostics and was supported by Illumina to attend the European Congress of Clinical Microbiology and Infectious Disease conference. All other authors declare no competing interests.