Innovations in genomic antimicrobial resistance surveillance

Nicole E Wheeler; Vivien Price; Edward Cunningham-Oakes; Kara K Tsang; Jamie G Nunn; Janet T Midega; Muna F Anjum; Michael J Wade; Nicholas A Feasey; Sharon J Peacock; Elita Jauneikaite; Kate S Baker; SEDRIC Genomics Surveillance Working Group

doi:10.1016/s2666-5247(23)00285-9

Innovations in genomic antimicrobial resistance surveillance

Nicole E Wheeler, Vivien Price, Edward Cunningham-Oakes, Kara K Tsang, Jamie G Nunn, Janet T Midega, Muna F Anjum, Michael J Wade, Nicholas A Feasey, Sharon J Peacock, Elita Jauneikaite, Kate S Baker^*, SEDRIC Genomics Surveillance Working Group

^*Corresponding author for this work

Microbiology and Infection

Research output: Contribution to journal › Article › peer-review

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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.

Original language	English
Pages (from-to)	e1063-e1070
Number of pages	8
Journal	The Lancet Microbe
Volume	4
Issue number	12
Early online date	14 Nov 2023
DOIs	https://doi.org/10.1016/s2666-5247(23)00285-9
Publication status	Published - Dec 2023

Bibliographical note

Acknowledgments:
This research was funded by the Wellcome Trust. The funding source had no role in study or workshop design, data collection, analysis, interpretation, writing of the Series paper, or the decision to submit the Series paper for publication. Developmental editing support for this work was provided by Germinate Science Consulting. KSB is affiliated with the NIHR Health Protection Research Unit (HPRU) in gastrointestinal infections at the University of Liverpool in partnership with the UKHSA, in collaboration with the University of Warwick. EJ is an Imperial College Research Fellow, funded by Rosetrees Trust and the Stoneygate Trust; and is affiliated with the NIHR HPRU in health care-associated infections and antimicrobial resistance at Imperial College London in partnership with the UKHSA, in collaboration with Imperial Healthcare Partners, the University of Cambridge, and the University of Warwick. The views expressed are those of the authors and not necessarily those of the National Health Service, the NIHR, the Department of Health and Social Care, or the UKHSA. Members of the SEDRIC Genomics Surveillance Working Group are listed in the appendix of the first paper in this Series.17

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Cite this

Wheeler, N. E., Price, V., Cunningham-Oakes, E., Tsang, K. K., Nunn, J. G., Midega, J. T., Anjum, M. F., Wade, M. J., Feasey, N. A., Peacock, S. J., Jauneikaite, E., Baker, K. S., & SEDRIC Genomics Surveillance Working Group (2023). Innovations in genomic antimicrobial resistance surveillance. The Lancet Microbe, 4(12), e1063-e1070. https://doi.org/10.1016/s2666-5247(23)00285-9

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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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Innovations in genomic antimicrobial resistance surveillance

Abstract

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