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

Elita Jauneikaite¹, Kate S Baker², Jamie G Nunn³, Janet T Midega⁴, Li Yang Hsu⁵, Shweta R Singh⁶, Alison L Halpin⁷, Katie L Hopkins⁸, James R Price⁹, Padmini Srikantiah¹⁰, Beverly Egyir¹¹, Iruka N Okeke¹², Kathryn E Holt¹³, Sharon J Peacock¹⁴, Nicholas A Feasey¹⁵; SEDRIC Genomics Surveillance Working Group

Affiliations

¹ Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK.
² Department of Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK. Electronic address: kb827@cam.ac.uk.
³ Infectious Disease Challenge Area, Wellcome Trust, London, UK.
⁴ Drug Resistant Infections, Wellcome Trust, London, UK.
⁵ Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
⁶ Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
⁷ Division of Healthcare Quality Promotion, US Centers for Disease Control And Prevention, Atlanta, GA, USA.
⁸ HCAI, Fungal, AMR, AMU, and Sepsis Division and Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK.
⁹ Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, UK.
¹⁰ Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA, USA.
¹¹ Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana.
¹² Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria.
¹³ Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
¹⁴ Department of Medicine, University of Cambridge, Cambridge, UK.
¹⁵ Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Chichiri, Blantyre, Malawi.

PMID: 37977161
DOI: 10.1016/S2666-5247(23)00282-3

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

Elita Jauneikaite et al. Lancet Microbe. 2023 Dec.

Free article

. 2023 Dec;4(12):e1040-e1046.

doi: 10.1016/S2666-5247(23)00282-3. Epub 2023 Nov 14.

Authors

Affiliations

¹ Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK.
² Department of Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK. Electronic address: kb827@cam.ac.uk.
³ Infectious Disease Challenge Area, Wellcome Trust, London, UK.
⁴ Drug Resistant Infections, Wellcome Trust, London, UK.
⁵ Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
⁶ Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
⁷ Division of Healthcare Quality Promotion, US Centers for Disease Control And Prevention, Atlanta, GA, USA.
⁸ HCAI, Fungal, AMR, AMU, and Sepsis Division and Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK.
⁹ Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, UK.
¹⁰ Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA, USA.
¹¹ Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana.
¹² Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria.
¹³ Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
¹⁴ Department of Medicine, University of Cambridge, Cambridge, UK.
¹⁵ Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Chichiri, Blantyre, Malawi.

PMID: 37977161
DOI: 10.1016/S2666-5247(23)00282-3

Abstract

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.

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Conflict of interest statement

Declaration of interests EJ had partial salary cover from Wellcome Trust over the course of this work. KSB reports funding from the Biotechnology and Biological Sciences Council and Medical Research Council and partial salary cover from Wellcome Trust and the UK Health Security Agency over the course of this work. LYH reports funding from Pfizer and honoraria from BioMerieux for lectures in 2022. BE and INO report receiving funding from the UK Department of Health and Social Care: with a grant managed by the Fleming Fund and work performed under the auspices of the SEQAFRICA project. INO reports funding from the Bill & Melinda Gates Foundation, Joint Programming Initiative on Antimicrobial Resistance, Wellcome Trust, Grand Challenges Africa Award, and UK Medical Research Council, 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, and 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 European Congress of Clinical Microbiology and Infectious Diseases conference. NAF reports funding from the Bill & Melinda Gates Foundation, UK Research and Innovation, and National Institute for Health and Care Research. All other authors declare no competing interests.

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

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

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Conflict of interest statement

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