In a recent article published in The Lancet Microbe, researchers described the discussions of an expert working group convened by the Surveillance and Epidemiology of Drug-resistant Infections Consortium (SEDRIC) to assess the utility of genomics for antimicrobial resistance (AMR) surveillance. They reviewed the benefits and challenges of the approach and provided recommendations for its effective implementation.
Study: Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group Image Credit: Sergei Drozd / Shutterstock
AMR is a global health challenge, affecting millions of people and causing significant mortality and morbidity. WHO's Global Action Plan on AMR was framed in 2015 to enhance awareness, reduce incidence, and promote research and surveillance. The emergence of the coronavirus disease 2019 (COVID-19) pandemic has highlighted the significance of genomic surveillance, gathering pace for its integration into routine surveillance programs. Therefore, SEDRIC formed a working group to review the evidence and offer recommendations for genomics-based AMR surveillance.
About the working group
The SEDRIC working group, comprising about 100 international experts, conducted four workshops and an online survey to assess the utility of genomics in AMR surveillance. Identifying members through diverse means, the workshops focused on bacterial AMR surveillance, producing landscape analyses and stakeholder recommendations. A final workshop explored innovations like metagenomics, gene tracking, and machine learning. The outcomes informed a consolidated position expanded to the community via a survey, thereby generating expert views and recommendations.
Findings and recommendations
The nine recommendations from the group are summarized below:
- The objectives, methods, and results of genomic AMR surveillance data should be clearly defined at all levels.
- The cost-effectiveness of genomics varies based on throughput and geographical location. Overcoming these challenges is possible by implementing regional hub-and-spoke models that consolidate training, supply chains, and infrastructure.
- New and existing health scientists need to be trained to develop competencies in genetic epidemiology.
- The surveillance needs to be standardized by developing and agreeing upon a common list of bug-drug combinations, clinical standards, evidence-based guidelines, single-access user portals, and sampling frameworks.
- To maximize the benefits of the approach, open, equitable, and immediate sharing of data, accompanied by robust governance, is crucial.
- It is essential to foster better communication, trust, and partnerships among stakeholders, including policymakers, health deliverers, and researchers.
- Funding models are required for research and capacity-building programs, surveillance implementation, and further improvement. Real-time cost-effectiveness needs to be evaluated.
- While genomic surveillance innovations, including clinical and environmental metagenomics, machine learning, and gene or plasmid tracking, are advantageous, there is a need for research to establish their associations with health outcomes.
- The environmental reservoir of AMR genes needs to be explored further. Especially in agriculture, the impact of surveillance and interventions has been characterized and needs to be built on.
The use of genomics allows the fine tracking of individual strains of pathogens resistant to antimicrobials. Additionally, the digital analysis of post-sequencing data aids in better data handling and quality assurance. The genomic surveillance of drug-resistant bacteria is particularly advantageous as:
- Genotypes associated with resistance against multiple drugs can be assayed simultaneously.
- The emergence of AMR in new and existing lineages can be effectively tracked.
- The genetic basis of resistance can be identified to support links to outbreaks and predict the spread of AMR.
Developing and continuously improving an infrastructure for genomic AMR surveillance, in terms of facilities and workforce, can effectively contribute to pandemic-preparedness efforts.
The applications of genomic surveillance of AMR can be categorized in three different settings:
- Hospital settings:
- Detecting outbreaks
- Providing actionable information to teams for infection prevention and control
- Supporting clinical decision-making at the patient level
- Public health level:
- Detecting emerging threats
- Designing and assessing interventions
- Supporting treatment recommendations
- Shaping vaccine formulations
- One Health interfaces:
- Operating effectively for food-borne diseases
- Transmission risk assessment frameworks
- Exploiting environmental monitoring
The challenges highlighted by the group can be categorized as follows:
- Common challenges:
- Scarcity of resources and lack of political will
- Emphasis on clear use cases and advocacy alongside robust cost-effectiveness studies
- Need for additional training, particularly in bioinformatics
- Hospital and infection prevention and control:
- Lack of effective epidemiological surveillance infrastructure
- Poor supply chain and pricing structure
- Challenges in effective cooperation within a hub and spoke model
- Public health and international sphere:
- Requirement to improve cooperation among stakeholders
- Working towards harmonized surveillance with strong data governance
- One Health interfaces:
- Complex relationships to define common goals
- Cooperation challenges across ministries and sectors
- Need for predefining the use of surveillance information
In summary, the high-resolution actionable data on AMR surveillance provided by genomics can offer valuable insights to prevent the spread of AMR. These interconnected recommendations provided by the expert group are essential to achieve optimal outcomes from genomic surveillance of AMR, serving as a guide to discussions among all the stakeholders for improved public health outcomes.