AMR SeWatch - watching phenotypic/genotypic AMR in sewage

In West Africa, limited facilities and resources hinder effective AMR surveillance. Our proposal presents an innovative, tailored method for monitoring phenotypic and genotypic AMR in the region. This method will be used to identify AMR hot-spots and conduct rapid assessment of interventions designed to curb the rise of AMR. 

Anna Roca, Principal Investigator and Deputy Theme Leader, MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine

In 2019, AMR caused 1.3 million deaths globally and contributed to 5 million deaths. AMR poses a significant challenge in Africa, especially in West Africa, where limited infrastructure, high infection rates and widespread antibiotic misuse exacerbate its impact. This is highlighted by the fact that more resistance genes have been recorded there than elsewhere in Africa.

Effective AMR management requires comprehensive surveillance, incorporating both phenotypic and genotypic analysis to map resistance patterns accurately. Phenotypic surveillance assesses a bacteria’s capability to survive antibiotic exposure, crucial for patient treatment decisions, while genotypic surveillance provides early detection of resistance mutations, aiding in the tracking of resistance genes across populations.

In West Africa, the AMR monitoring is hindered by inadequate laboratory capabilities, resulting in data that are both insufficient and biased towards urban populations. In addition, the region has limited visibility in the international tracking of resistance genes. This hampers the development of effective antibiotic guidelines, timely identification of AMR outbreaks and control the AMR spread.

Our solution is to implement a tailored AMR surveillance approach in the region. Once established, the surveillance system will be used to evaluate AMR trends, rapidly identify AMR hot-spots, and target and evaluate interventions to reduce AMR.

The proposed solution targets national/international stakeholders to boost national capacity to respond to AMR, potentially leading to improved health outcomes and reduced healthcare costs through a more efficient allocation of resources.

At an international level, the project will contribute data to the global fight against AMR. The data generated would benefit not only to the academic community, including environmental scientists, epidemiologists, and geneticists engaged in the AMR battle but also to international public health agencies. Organizations like the World Health Organization (WHO) will gain evidence-based data crucial for targeted assistance on developing global policies.

For the success and sustainability of this initiative, engaging national stakeholders from the outset is crucial. This includes the selection of sampling sites and implementing necessary interventions upon identifying AMR hot-spots. Project planning will be conducted in collaboration with the national Ministries of Health and local communities.

The WHO will be involved during the planning phase to ensure comprehensive support. Stakeholders from the academic sector will be engaged at a later stage through presentations at international conferences and peer-reviewed publications. This approach ensures a broad-based commitment to and participation in enhancing AMR surveillance, leveraging both local insight and global expertise for a unified fight against AMR.

Sub-Saharan Africa faces the risk of increasing AMR due to factors such as inadequate infrastructures and regulations, high incidence of infections and limited AMR-awareness. Limited resources available exacerbate the public health threat posed by the spread of resistant pathogens. Thus, timely access to high-quality surveillance data is vital for implementing preventive measures to mitigate the significant human and economic impacts of resistant infections.

We will make our data readily accessible through the SeWatch dashboard, with the anticipation that it will be used by health professionals, policymakers, and researchers within West Africa and beyond.

In particular, we envisage that these data will empower health professionals and laboratory personnel by providing essential data to inform treatment decisions and the prompt identification of AMR outbreaks - data that, under current circumstances, would remain unavailable. Furthermore, these data will support the implementation and monitoring of interventions for infection control measures.

While large AMR networks exist in high-income countries, we plan to expand our solution to other West African countries, creating a regional network of AMR data. This initiative seeks to bridge the gap in AMR surveillance and response capabilities, enhancing public health outcomes in the region. 

For sustainable development, addressing the needs of target populations requires robust collaboration with the government, health officials and community leaders before implementation. This collaborative approach is particularly necessary when working with vulnerable populations and forms a core part of our strategy.

We expect that the project will increase the knowledge of AMR at all community levels. The potential impact of the SeWatch surveillance can be categorized into three areas: community, health care workers/laboratory professionals, and local government. From the community’s perspective, SeWatch has the potential to lower AMR and related infections. This reduction would improve health outcomes and decrease the costs associated with bacterial infections, leading to a decrease in health inequalities both within/between populations. Moreover, the SeWatch aims to empower government officials and health/laboratory professionals by providing them with comprehensive data and enhancing their capabilities through capacity building in genomics, microbiology and big-data analysis. In addition, for government authorities, the SeWatch provides valuable data that can be used to optimize resources through implementation of measures targeted to specific settings. In conclusion, the SeWatch surveillance system represents a holistic approach to combating AMR, with the potential to bring about significant improvements in public health, economic savings, and overall societal wellbeing. 

The project will start in The Gambia by identifying specific locations for sewage collection, targeting both community and health facility levels. These locations will be determined following community engagement activities and securing agreements with various stakeholders, including community members, health facility and government health officials. Over the initial 6-12 months of the project, we plan to expand the initial number of collection sites to better represent the diverse regions within The Gambia, thereby scaling the project’s impact. This expansion will enhance our ability to identify AMR hot-spots, enabling a wider and more targeted implementation of measures to control spread of AMR. The impact of the project will escalate as these interventions take place, from month 6 to year 3. During the phase of expansion to other West African countries (during year 3), the impact of the project will expand to the region as a similar process of identifying sampling sites and responding to the hot-spots will be implemented throughout the participating sites.

To measure success, we will evaluate progress against pre-defined goals:

• AMR knowledge: Level of understanding regarding AMR prevention/control among individuals from health facilities and communities involved in the study, before and after the implementation of the project.
• Capacity building: Number of individuals trained in microbiology/genomics/big-data analysis will be quantified.
• SeWatch dashboard: Several indicators pre-set here. (i) The creation of the dashboard within the first six months of the study. (ii) Its utilization in subsequent months by different stakeholders such as scientists, health/laboratory professionals and government officials by tracking entries made by these stakeholders. (iii) Assess the utilization of the dashboard data in shaping national guidelines. (iv) Conduct satisfaction questionnaires among stakeholders with visual access to the dashboard.
• AMR Outbreak Detection and Control Measures: We will record the number of AMR outbreaks identified throughout the study and document measures implemented in response.
• AMR prevalence: Impact of infection control measures on the AMR trend, to understand the effectiveness of quick implementation measures resulting with timely generation of data.
• Global AMR database: Number of sequences submitted to the global genomic AMR database will be tracked.
• Publications: The number of publications because of the project.

The main barriers are categorized as technological, economical, logistical and cultural.

For project implementation, we confront cultural barriers, primarily due to the limited awareness about the threat posed by AMR. Engagement activities coupled with capacity building are crucial to overcome these barriers.

A laboratory logistical challenge is the restricted regional infrastructure, which hampers access to essential consumables. Reliable electricity supply for the proper storage of reagents presents a challenge for some laboratories in the area. Our strategy involves leveraging West African institutions within our network that already have the infrastructure to serve as sentinel sites to coordinate activities. In areas lacking stable electricity-supply, we will provide stand-alone solar-power systems capable of powering a refrigerator and a freezer for 10 hours, ensuring the safe storage of temperature-sensitive reagents. This solution incurs significant economic costs.

In terms of application implementation, we face a limited number of developers our unit can afford. To address this, we plan to recruit a developer to assist our team in creating the dashboards and integrating the necessary systems. Poor and unstable internet my restrict access to the dashboard by some relevant stakeholders. We intend to employ technologies like “WebAssembly” in the mobile apps to enhance accessibility.

AMR represents a global health crisis with implications for human health and the economy. We emphasize the importance of harnessing data generation and analytics as essential evidence-based tools for crafting interventions and responding to this global threat. A pro-active approach, incorporating new technologies and data-driven strategies, is critical for an effective response to AMR. This aligns with the objectives of the Trinity Challenge, making it an ideal platform for addressing the challenge.

In today’s interconnected world, microbes have the potential to spread globally with ease, exacerbating the AMR challenge. To redress this problem, we are applying to the AMR challenge to create a technological solution specifically designed to meet local needs. Our aim is to develop a sustainable approach that enhances capacity and improves the utilization of locally generated data for timely response to AMR.  

 West Africa has not met the demand for AMR response largely due to inadequate infrastructure and limited laboratory capacity for data generation in the region. This lack of local data in the region hampers both global surveillance efforts and the region’s ability to respond effectively to outbreaks.

We propose to leverage collective and multi-disciplinary expertise and resources to enhance global health resilience against AMR. 

We would benefit by collaborating with institutions with experience in worldwide AMR genomics surveillance or that could be interested in supporting us in expanding the SeWatch dashboard beyond West Africa.