Genomics for public health and international surveillance of antimicrobial resistance

Kate S Baker¹, Elita Jauneikaite², Katie L Hopkins³, Stephanie W Lo⁴, Leonor Sánchez-Busó⁵, Maria Getino⁶, Benjamin P Howden⁷, Kathryn E Holt⁸, Lillian A Musila⁹, Rene S Hendriksen¹⁰, Daniel G Amoako¹¹, David M Aanensen¹², Iruka N Okeke¹³, Beverly Egyir¹⁴, Jamie G Nunn¹⁵, Janet T Midega¹⁶, Nicholas A Feasey¹⁷, Sharon J Peacock¹⁸; SEDRIC Genomics Surveillance Working Group

Affiliations

¹ Department for Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK. Electronic address: kb827@cam.ac.uk.
² 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.
³ HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK.
⁴ Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
⁵ Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain; CIBERESP, ISCIII, Madrid, Spain.
⁶ NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK.
⁷ The Centre for Pathogen Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.
⁸ Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
⁹ Department of Emerging Infectious Diseases, United States Army Medical Research Directorate - Africa, Nairobi, Kenya; Kenya Medical Research Institute, Nairobi, Kenya.
¹⁰ National Food Institute, Technical University of Denmark, Lyngby, Denmark.
¹¹ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa; School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Pathobiology, University of Guelph, Guelph, ON, Canada.
¹² Centre for Genomic Pathogen Surveillance, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Oxford, UK.
¹³ Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria.
¹⁴ Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana, West Africa.
¹⁵ Infectious Disease Challenge Area, Wellcome Trust, London, UK.
¹⁶ Drug Resistant Infections, Wellcome Trust, London, UK.
¹⁷ Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Malawi.
¹⁸ Department of Medicine, University of Cambridge, Cambridge, UK.

PMID: 37977162
DOI: 10.1016/S2666-5247(23)00283-5

Free article

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Genomics for public health and international surveillance of antimicrobial resistance

Kate S Baker et al. Lancet Microbe. 2023 Dec.

Free article

. 2023 Dec;4(12):e1047-e1055.

doi: 10.1016/S2666-5247(23)00283-5. Epub 2023 Nov 14.

Authors

Affiliations

¹ Department for Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK. Electronic address: kb827@cam.ac.uk.
² 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.
³ HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK.
⁴ Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
⁵ Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain; CIBERESP, ISCIII, Madrid, Spain.
⁶ NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK.
⁷ The Centre for Pathogen Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.
⁸ Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
⁹ Department of Emerging Infectious Diseases, United States Army Medical Research Directorate - Africa, Nairobi, Kenya; Kenya Medical Research Institute, Nairobi, Kenya.
¹⁰ National Food Institute, Technical University of Denmark, Lyngby, Denmark.
¹¹ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa; School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Pathobiology, University of Guelph, Guelph, ON, Canada.
¹² Centre for Genomic Pathogen Surveillance, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Oxford, UK.
¹³ Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria.
¹⁴ Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana, West Africa.
¹⁵ Infectious Disease Challenge Area, Wellcome Trust, London, UK.
¹⁶ Drug Resistant Infections, Wellcome Trust, London, UK.
¹⁷ Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Malawi.
¹⁸ Department of Medicine, University of Cambridge, Cambridge, UK.

PMID: 37977162
DOI: 10.1016/S2666-5247(23)00283-5

Abstract

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.

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Conflict of interest statement

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.

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Genomics for public health and international surveillance of antimicrobial resistance

Affiliations

Genomics for public health and international surveillance of antimicrobial resistance

Authors

Affiliations

Abstract

Conflict of interest statement

Publication types

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Grants and funding

LinkOut - more resources

Full Text Sources

Medical