Genomics for public health and international surveillance of antimicrobial resistance

SEDRIC Genomics Surveillance Working Group; Kate S Baker; Elita Jauneikaite; Katie L Hopkins; Stephanie W Lo; Leonor Sánchez-Busó; Maria Getino; Benjamin P Howden; Kathryn E Holt; Lillian A Musila; Rene S Hendriksen; Daniel G Amoako; David M Aanensen; Iruka N Okeke; Beverly Egyir; Jamie G Nunn; Janet T Midega; Nicholas A Feasey; Sharon J Peacock

doi:10.1016/S2666-5247(23)00283-5

Genomics for public health and international surveillance of antimicrobial resistance

SEDRIC Genomics Surveillance Working Group, Kate S Baker^* (Member of author collaboration), Elita Jauneikaite (Member of author collaboration), Katie L Hopkins (Member of author collaboration), Stephanie W Lo (Member of author collaboration), Leonor Sánchez-Busó (Member of author collaboration), Maria Getino (Member of author collaboration), Benjamin P Howden (Member of author collaboration), Kathryn E Holt (Member of author collaboration), Lillian A Musila (Member of author collaboration), Rene S Hendriksen (Member of author collaboration), Daniel G Amoako (Member of author collaboration), David M Aanensen (Member of author collaboration), Iruka N Okeke (Member of author collaboration), Beverly Egyir (Member of author collaboration), Jamie G Nunn (Member of author collaboration), Janet T Midega (Member of author collaboration), Nicholas A Feasey (Member of author collaboration), Sharon J Peacock (Member of author collaboration)

^*Corresponding author for this work

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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.

Original language	English
Journal	The Lancet Microbe
Volume	4
Issue number	12
Pages (from-to)	e1047-e1055
Number of pages	9
ISSN	2666-5247
DOIs	https://doi.org/10.1016/S2666-5247(23)00283-5
Publication status	Published - 2023

Bibliographical note

Harnessing Genomics for Antimicrobial Resistance Surveillance 3 - This is the third in a Series of five papers about harnessing genomics for antimicrobial resistance surveillance. All papers in the Series are available at www.thelancet.com/microbe.

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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SEDRIC Genomics Surveillance Working Group, Baker, K. S., Jauneikaite, E., Hopkins, K. L., Lo, S. W., Sánchez-Busó, L., Getino, M., Howden, B. P., Holt, K. E., Musila, L. A., Hendriksen, R. S., Amoako, D. G., Aanensen, D. M., Okeke, I. N., Egyir, B., Nunn, J. G., Midega, J. T., Feasey, N. A., & Peacock, S. J. (2023). Genomics for public health and international surveillance of antimicrobial resistance. The Lancet Microbe, 4(12), e1047-e1055. https://doi.org/10.1016/S2666-5247(23)00283-5

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SEDRIC Genomics Surveillance Working Group, 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 2023, 'Genomics for public health and international surveillance of antimicrobial resistance', The Lancet Microbe, vol. 4, no. 12, pp. e1047-e1055. https://doi.org/10.1016/S2666-5247(23)00283-5

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A2 - Sánchez-Busó, Leonor

A2 - Getino, Maria

A2 - Howden, Benjamin P

A2 - Holt, Kathryn E

A2 - Musila, Lillian A

A2 - Hendriksen, Rene S

A2 - Amoako, Daniel G

A2 - Aanensen, David M

A2 - Okeke, Iruka N

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A2 - Feasey, Nicholas A

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N2 - 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.

AB - 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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DO - 10.1016/S2666-5247(23)00283-5

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SN - 2666-5247

VL - 4

SP - e1047-e1055

JO - The Lancet Microbe

JF - The Lancet Microbe

IS - 12

ER -

Genomics for public health and international surveillance of antimicrobial resistance

Abstract

Bibliographical note

UN SDGs

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