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Innovations in genomic antimicrobial resistance surveillance.

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Wheeler, Nicole E 
Price, Vivien 
Cunningham-Oakes, Edward 
Tsang, Kara K 
Nunn, Jamie G 


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.



Humans, Anti-Bacterial Agents, Drug Resistance, Bacterial, Genomics, Genome, Whole Genome Sequencing

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Lancet Microbe

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Elsevier BV
NEW reports funding from Nuclear Threat Initiative, MRC, Open Philantropy and Shionogi as well as consulting fees from Nuclear Threat Initiative. VP reports funding from the Welldome Trust and NIHR. NAF reports funding from the BMGF, UKRI and NIHR. SJP is a member of the Scientific Advisory Board of Next Gen Diagnostics and was supported by Illumina to attend the ECCMID conference. EJ had partial salary cover from Wellcome Trust over the course of this work. KSB reports funding from the BBSRC and MRC and partial salary cover from Wellcome Trust and UKHSA over the course of this work. All other authors declare no conflicts of interest.