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Xiu L, Kassegne K, Yin J. Editorial: One Health in clinical microbiology. Front Cell Infect Microbiol 2024; 14:1404276. [PMID: 38686095 PMCID: PMC11056643 DOI: 10.3389/fcimb.2024.1404276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Affiliation(s)
- Leshan Xiu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Kokouvi Kassegne
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Jianhai Yin
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China
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Baker KS, Jauneikaite E, Hopkins KL, Lo SW, Sánchez-Busó L, Getino M, Howden BP, Holt KE, Musila LA, Hendriksen RS, Amoako DG, Aanensen DM, Okeke IN, Egyir B, Nunn JG, Midega JT, Feasey NA, Peacock SJ. Genomics for public health and international surveillance of antimicrobial resistance. THE LANCET. MICROBE 2023; 4:e1047-e1055. [PMID: 37977162 DOI: 10.1016/s2666-5247(23)00283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
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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Affiliation(s)
- Kate S Baker
- Department for Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Elita Jauneikaite
- 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
| | - Katie L Hopkins
- 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
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Leonor Sánchez-Busó
- 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
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Benjamin P Howden
- The Centre for Pathogen Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Lillian A Musila
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate - Africa, Nairobi, Kenya; Kenya Medical Research Institute, Nairobi, Kenya
| | - Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Daniel G Amoako
- 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
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Oxford, UK
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana, West Africa
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Malawi
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Wheeler NE, Price V, Cunningham-Oakes E, Tsang KK, Nunn JG, Midega JT, Anjum MF, Wade MJ, Feasey NA, Peacock SJ, Jauneikaite E, Baker KS. Innovations in genomic antimicrobial resistance surveillance. THE LANCET. MICROBE 2023; 4:e1063-e1070. [PMID: 37977163 DOI: 10.1016/s2666-5247(23)00285-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
Whole-genome sequencing of antimicrobial-resistant pathogens is increasingly being used for antimicrobial resistance (AMR) surveillance, particularly in high-income countries. Innovations in genome sequencing and analysis technologies promise to revolutionise AMR surveillance and epidemiology; however, routine adoption of these technologies is challenging, particularly in low-income and middle-income countries. As part of a wider series of workshops and online consultations, a group of experts in AMR pathogen genomics and computational tool development conducted a situational analysis, identifying the following under-used innovations in genomic AMR surveillance: clinical metagenomics, environmental metagenomics, gene or plasmid tracking, and machine learning. The group recommended developing cost-effective use cases for each approach and mapping data outputs to clinical outcomes of interest to justify additional investment in capacity, training, and staff required to implement these technologies. Harmonisation and standardisation of methods, and the creation of equitable data sharing and governance frameworks, will facilitate successful implementation of these innovations.
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Affiliation(s)
- Nicole E Wheeler
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, Edgbaston, UK
| | - Vivien Price
- Department of Clinical Infection, Immunology and Microbiology, Liverpool Centre for Global Health Research, University of Liverpool, Liverpool, UK
| | - Edward Cunningham-Oakes
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kara K Tsang
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - Matthew J Wade
- Data Analytics and Surveillance Group, UK Health Security Agency, London, UK; School of Engineering, Newcastle University, Newcastle-upon-Tyne, UK
| | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Chichiri, Blantyre, Malawi
| | | | - Elita Jauneikaite
- 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
| | - Kate S Baker
- Centre for Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
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