Policy Webinar 2.

AMR Surveillance: Past, Present and Future


Dr Pascal Ondoa, African Society of Laboratory Medicine (ASLM), introduced Dr John Stelling, Co-director of the WHO Collaborating Center for Surveillance of AMR, based at the Brigham and Women’s Hospital in Boston. The focus of Dr Stelling’s work has been to support public health infrastructure for laboratory services, including enhancing routine surveillance. He provided a history of the use of computer science/IT in data collection for surveillance, including the development of the WHONET software: currently used to support over 120 countries, and 2,300 hospitals, public health, food and veterinarian laboratories.

Dr Stelling described how resistance surveillance had started largely as an academic exercise among researchers and microbiologists, without the connections needed for full policy on antimicrobial use on hygiene, and also on awareness, to get the broader perspectives. Major improvements have taken place over time:

“One of the good things in the last 20 years is the growing recognition and involvement of national health authorities in data collection and in data analysis and in data use…. there’s a much more holistic sense of bringing together all of the different sectors on the data collection side, but also on the data use side: the media, educators, researchers, industry, patient advocacy groups.”

Dr Stelling emphasised the importance of a local approach: where there are the infected patients, and the hygiene issues and policy issues, and the necessity to treat these patients locally; and where there must be value to local data generators – the laboratories and the institutions that generate the data – if data is to be used for national and global surveillance. He also highlighted regional approaches to develop national structures: translating global messages/recommendations, customising them to the needs and the priorities of the region – with ownership by the region – and working with countries to enable experiences to be shared with others in their region through national or regional networks, to enable best practices to be learned and implemented.

“We need to take those data and translate them into action: action for capacity building and continuous quality improvement, so the quality of the data and the knowledge and the interventions are improving and translating data into action.”

The key areas to identify for the future can be summarised as:

  • What actions are needed and what data are needed to support those actions?

  • What data exists, what are their strengths and their weaknesses?

  • What are the information gaps, where we need to dedicate some new resources?

  • What partners and skill sets are needed?

  • What are the costs of action? What are the costs of inaction?

Dr Ondoa introduced the second speaker, Dr David Aanensen of Big Data Institute at University of Oxford. Dr Aanensen is the Director of the Centre for Genomic Pathogen Surveillance.

Dr Aanensen’s described his work on data flow and use of genome sequencing for surveillance of microbial pathogens. The approach is to translate the use of genome sequencing and the rapid and large-scale analysis of data into information that can be used for public health decision-making at a local, national, international level. Currently BDI are partnering in AMR strategies in the Philippines, Columbia, Nigeria, and India to implement genomic surveillance.

“I think our major focus should be on enabling local data generators to have access to the tools and own those tools and interpretation to be able to then leverage feeding into these bigger broader initiatives. It has to be bottom-up and top-down.”

In the Philippines, the project integrated genome sequencing within the routine phenotypic surveillance system: to allow the information to come off the sequence and be interpreted locally to identify the strain, and how similar the genomes are to each other; and to identify the genomic mechanism for AMR and whether that is a particular mutation or whether it’s a mobile genetic element that is coming into the country. They are able to identify particular clones and have been able to identify ongoing transmissions at local hospitals that have led to infection control procedures being put in place to stop the spread of particular pathogens. This is part of a broader project to work out the key components that would need to integrate genomics into routine national AMR surveillance, including technical support packages around what are the key pieces that need to be implemented around laboratories.

Dr Aanensen highlighted crucial elements of capacity building: “Communities of practice, sharing of previous information, sharing of previous expertise and successes is an incredibly important way to upskill….Community of practice around digital epidemiology, data engineering, data science and also software engineering: there’s a huge pool of talent across the world that can be brought to bear. We need to actually encourage locally.”

Dr Ondoa summarised the presentations, describing how the field is evolving positively, from a topic among scientists to a public health and global health topic with a multi-sectoral collaboration; and with initiatives in data generation at local and global levels. However, many countries – in Africa for example – face challenges due to Internet and electricity access issues. The next generation sequencing – whole genome sequencing – is an opportunity to move to the next level and understand better what AMR is all about. It is an important tool for public health interventions.

Low- and middle-income countries face choices, depending on their capacity, their finances, and their health priorities, which emphasise the need to have their own data, know their epidemiology make their decisions. Although international organizations provide support, there has to be a transition whereby countries make the decisions independently.