Data Standards and Harmonisation

Aims

1. The working group meetings have focused on the challenges of diverse AMR surveillance systems, and particularly focused on the difficulties that all these systems experience during the process of recording, managing and sharing data that can be used to inform policy activities. The group concluded that an Open Source Laboratory Information Management System (LIMS) designed with the needs of diagnostic microbiology laboratories in mind would fill a key gap in laboratory data management.

Timeline

• 1 October 2019 First working group meeting held in London
• 2 October 2019 – present A subgroup leads the development of the LIMS work

Scope of work

SEDRIC invited a wide range of relevant stakeholders to a round table event at Wellcome in 2019 to discuss AMR surveillance, including the Fleming Fund, US-CDC, European-CDC, Africa-CDC, representatives of Indian and Nigerian national AMR surveillance networks, plus research groups that are carrying out AMR surveillance in Africa and Asia.

Outputs

This working group is therefore focused on creating a freely available LIMS that provides specimen management, bench workflow, result reporting, automated and manual analysis of AMR data and to interface with local hospital systems, WHONet and GLASS. A system has been created and is currently being piloted in Cambodia.

Who and how can participate

Applications to participate in this working group are not open

Members

• Nick Feasey Co-lead
• Paul Turner Co-lead
• Ben Amos Co-lead
• Susie Dunachie Co-lead

Blood Culture Sampling Working Group

Aims

1. Identify the barriers and facilitators clinicians face in the adoption of blood culture sampling recommendations in South East Asia.

Timeline

• 1 October 2019 Commence work
• 2 April 20222 Report published

Scope of work

– Conduct in-depth interviews and surveys (mixed method) to explore generalizability of review among medical doctors in Thailand, Viet Nam and Indonesia – Develop electronic questionnaire based on Part 1 – Translate to local languages – In-depth interviews with 5-10 physicians in each country – Translate scripts back to English, and analyze – Revise the questionnaire

Outputs

Results of the study will also be disseminated in a report and made available on the SEDRIC website.

Who and how can participate

Applications to participate in the working group are not open

Members

• Direk Limmarotsakul (group lead) Lead
• Pornpan Suntornsu
• Vu Thi Lan Huong
• Ralalicia Limato
• Rogier van Doorn
• Raph Hamers
• Fabriana Lorencatto
• Lou Atkins

Genomic surveillance Working Group

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.

Aims

1. To undertake a comprehensive overview of the potential for genomics to provide actionable information through improved surveillance

2. To make recommendations to relevant stakeholders (including health agencies, other international organisations, funders, and researchers) on (a) 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 (b) future directions for research and development to support this

Timeline

• 1 January 2022 Work commences
• 2 July 2022 Report published

Scope of work

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.

Outputs

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.

Harnessing genomics for AMR surveillance

Who and how can participate

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.   Working Group participants: 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

Members

• Professor Kate Baker (Co-lead) (group lead)
• Dr Elita Jauneikaite (Co-lead) (group lead)
• Professor Sharon Peacock
• Professor Nicholas Feasey
• 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 Hendriksen
• Professor Sabiha Essack
• Dr Beverly Egyir
• Dr Duncan MacCannell
• Dr Padmini Srikanthia
• Dr Alison Laufer Halpin
• Dr David Aanensen
• Dr Simon Harris

Policy & Knowledge Mobilisation Working Group

To accelerate learning and facilitate knowledge mobilisation to inform policy implementation trajectories in countries and regions.

Aims

1. Conduct analysis of policy journeys of positive and negative outlier example countries.

2. Understand the relevance to AMR, of success in other public health and global health challenges

3. Identify generalisable mechanisms which lead to change.

4. Share this learning with specialists in AMR as well as wider stakeholders in public health and global health policy development and implementation and evaluation.

Timeline

• 1 September 2020 First working group meeting held
• 2 September 2020 – present Ongoing work

Scope of work

Outputs

The outputs of this working group will be coordinated with emerging evidence from the other SEDRIC Working Groups to help keep policy recommendations relevant and will further inform the role of SEDRIC in terms of policy development, implementation and evaluation.

Who and how can participate

To be confirmed

Members

• Raheelah Ahmad (group lead) City, University of London
• Mirfin Mpundu Head of Antibiotic Resistance (ReAct) Africa
• Jyoti Joshi ICARS
• Rifat Atun Harvard University
• Sian Williams Wellcome Trust
• Jamie Nunn Wellcome Trust