Genomic surveillance of AMR Working Group
09 March, 2022
The transformational nature of genomics for microbiological surveillance has been indisputably evidenced during the COVID-19 pandemic. Antimicrobial resistance is a slower pandemic of greater significance and improved surveillance is a strategic objective of the World Health Organisation’s Global Action Plan on Antimicrobial Resistance. Our new working group will review the current evidence base, and the potential, for genomics to generate actionable AMR surveillance data, and develop recommendations for how to build on that base and further unlock potential.
The working group exists to develop:
- a comprehensive overview of the potential for genomics to provide actionable information through improved surveillance
- make recommendations to relevant stakeholders (including health agencies, other international organisations, funders, and researchers) on:
- where genomics for AMR surveillance would be of the most benefit across both high income and lower-to-middle income settings and how this can be implemented
- future directions for research and development to support this
An early ‘review of reviews’ by the group on the use of genomics for AMR surveillance highlighted the need to work across surveillance domains (e.g. human, animal, environmental). Hence, distinct from much previous work, the group has an intentionally broad scope and will consider the use of genomics for AMR surveillance within and across human, animal, and environmental health, taking a broad One Health approach, and consider how to capitalise on innovations for AMR surveillance offered by genomics. This breadth will result in a consolidated view on the potential benefits of genomics for AMR surveillance and offer the opportunity to identify common barriers and facilitators to genomics implementation across domains including integrated and unified ways to collect and analyse AMR data.
The anticipated outputs are synthesised scientific format output(s) of the review of the field and from the working group and community consultation, as well as a report with recommendations for future actions. These will be made available on the SEDRIC website and disseminated to stakeholders.
The work of the group commenced in January 2022 and will be in its final stages in July 2022.
Opportunities for participation
Working group members and workshop participants are being asked to participate by invitation based on expertise across the scope of the work as well as in policy development. The group will also seek broader community views through a survey, which will be posted here and disseminated through professional networks and social media. If you would like to be sent the community survey directly, please email SEDRIC@wellcome.org.
Alongside a formal survey of existing academic and grey literature, the working group will conduct a series of workshops, a community survey, and a stakeholder consultation workshop.
The first three workshops will use a common framework to define the potential benefits and challenges of implementing genomics to provide actionable information for AMR surveillance within and across different domains of scale.
The three domains on which the working group will focus are:
- Hospital-based use including for culture dependent clinical microbiology and infection prevention and control
- Population-based use for national and international public health networks
- Integrated One Health surveillance including humans, animals, and environmental sources (e.g. crops, food, water, soil, and air)
An additional workshop will consider innovations and potential futures for genomics and AMR surveillance. This workshop will cover promising methods and approaches that are specific to genomic surveillance, and either are not based on single isolate sequencing or are new methods that might offer benefit (e.g. bedside diagnostics, gene/plasmid based surveillance, new models, machine learning with aggregate data). If you wish to suggest a disruptive technology/methodology for consideration in the innovations workshop, please email SEDRIC@wellcome.org.
Stakeholder consultation workshop
During the final phases of the working group a stakeholder consultation workshop will be held to present and discuss the group’s findings ahead of finalising outputs. Our stakeholders include public and global health organisations, research funders, and scientific community initiatives, and professional networks. Please send an expression of interest to SEDRIC@wellcome.org if you would be interested in attending the workshop and/or be notified of the outcomes of the working group.
Working Group Leads
Professor Kate Baker (co-lead) University of Liverpool (firstname.lastname@example.org)
Dr Elita Jauneikaite (co-lead) Imperial College London (email@example.com)
Professor Sharon Peacock (oversight member, founding chair of SEDRIC) University of Cambridge
Professor Nicholas Feasey (oversight member, SEDRIC chair) Liverpool School of Tropical Medicine
Jamie Nunn, SEDRIC Lead, Wellcome (J.Nunn@wellcome.org)
Janet Midega, Senior Research Manager, Drug Resistant Infections, Wellcome
Working group members
- Professor Rifat Atun
- Dr Kamani Walia
- Professor Ben Howden
- Dr Heather Tate
- Professor Iruka Okeke
- Professor Alessandra Caratolli
- Associate Professor Li Yang Hsu
- Dr Katie Hopkins
- Dr Dishon Muloi
- Dr Nicole Wheeler
- Professor Kat Holt
- Professor Rene Hendriksson
- Professor Sabiha Essack
- Dr Beverley Eygir
- Dr Duncan MacCannell
- Dr Padmini Srikanthia
- Dr Alison Laufer Halpin
- Professor David Aanensen
- Dr Simon Harris
Dr. Randall Hayden, Prof. Rogier Van Doorn, Dr. James Price, Dr. Rowlinson Marie Claire, Prof. Vitali Sinchenko, Dr. James Hatcher, Dr Daniela Maria Cirillo, Dr. Uduak Okomo, Mirfin Mpundu, Dr Silvia Agrimon, Dr Josefina Campos, Dr Matt Holden, Dr Margaret Ip, Dr Catrin Moore, Prof. Dorothy Yeboah – Manu, Dr. Sam Kariuki, Dr. Claire Jenkins, Dr Daniel Amoako, Dr Alejandro Petroni, Dr. Lillian Musila, Dr Stephanie Lo, Dr Maria Getino, Dr Mark Holmes, Dr Martin Antonio, Dr Johan Bengstsson-Palme, Dr Sam Kariuki, Dr Joshua Mbanga, Dr Luther King Abia Akebe, Dr Alison Mather, Dr Felipe Colon Gonzalez, Dr Elena Baez, Dr Luria Leslie Founou, Dr Muna Anjum, Dr. Muhammad Farooq Tahir, Dr David Singleton, Dr Nicola Williams, Professor Stuart Reid, Dr William Gaze, Dr Stefan Schwarz, Dr Dorcas Fatoba, Dr Ruth Zadoks, Dr Carlos Bezuidenhout, Dr Lawrence Mugisha, Dr Adrian Cookson, Dr Deb Williamson, Dr Josephine Bryant, Dr Gregorio Iraola, Dr Emmanuel BenYeogor, Dr Niranjan Nagarajan, Dr Edward Cunningham-Oakes, Dr Lindsay Hall, Dr Soren Wacker, Dr Frank Moeller Aestraup, Dr Oon Tek Ng, Dr Niti B Jadeja, Dr Nicole Stoesser, Dr Steve Paterson, Dr Matthew Wade, Dr Vivien Price, Dr Xavier Didelot, Dr Bilal Mateen, Dr Gwen. Knight, Dr Leonid Chindelevitch, Dr John Lees, Dr Stephanie Lo, Dr Bruno Gonzalez-Zorn, Dr Tong Zhang, Dr Muna Anjum, Dr Sally Partirige, Dr Andreas Kellar, Dr John Nash, Dr Kara Tsang