AMR Compass: Community Based Geospatial Model for AMR Surveillance

AMR Compass is a geospatial model that utilizes genomic sequencing of pooled community waste samples to map the transmission of AMR. It also identifies novel and emerging patterns of drug-resistant infections. Our community-based One Health approach involves community engagement, collecting, testing and comparing waste samples from households, communities, and environment.

Dr. Patrick Orikiriza, Head of Microbiology Department, Principal Investigator

AMR poses a global health threat, and comprehensive surveillance is essential to combat it effectively. However, existing surveillance systems often fall short in capturing data from remote communities, leading to inequities and limitations. Specific problems we are trying to solve include: 

Community-Based Gap: Current surveillance primarily relies on clinical data reported by laboratories, but this approach overlooks patients in far-flung communities. These underserved populations lack access to clinical microbiology services, resulting in their exclusion from national and global AMR data. 

Uncharted Drivers of AMR: The specific factors driving AMR in these communities remain unknown. Rural areas in Rwanda face limited access to antibiotics and pharmacies compared to urban residents. 

Geospatial mapping: knowledge of hotspots for emerging and re-emerging resistance patterns is not known in Rwanda like in many similar settings. 

AMR Compass aims to bridge these gaps by establishing a comprehensive community-based AMR surveillance system. By understanding local contexts and addressing inequities, we can tailor interventions effectively and combat AMR more strategically. 

This solution targets communities in rural Rwanda, including (but not limited to) Butaro in the north border, Rwinkwavu in the east, and Kirehe in the South. Community members from churches, schools, health centers are an integral part of the solution. National government such as the National Reference Laboratory will also play a key role,   

 Remote underserved communities in Rwanda 

Our solution serves remote communities who are currently under-represented in national and global AMR surveillance data. The overwhelming majority of Rwandans live in rural settings (72%, NISR 2023) and have limited access to microbiology services. By engaging community members in implementation design, our solution will help raise the awareness of AMR among wide range of community members. 

Healthcare facilities, local and national policy makers 

We work closely with public health facilities and Rwanda Biomedical Center (RBC). Our solution will provide healthcare practitioners and policy makers with additional data and evidence that can be used for 1) future AMR surveillance strategies in remote communities; 2) making informed decisions on prevention and treatment measures based on the pattern of transmission and underlying drivers of AMR. 

We plan to publish our findings, insights, and learnings so that other low resource settings can learn from our experience. 

Leveraging environmental sampling from pit latrines is an attractive option as it is non-invasive and conveniently batches stool samples from many community members. Validating this approach by comparing it to individual clinical, animal, and livestock samples would offer a cost-effective solution for surveillance in similar communities. Furthermore, it provides an efficient means of identifying outbreaks and priority pathogens that may be found too infrequently to warrant routine widespread testing. 

 Genomic sequencing technologies offer powerful tools for monitoring AMR. As the cost of genomic sequencing continues to decrease, the future of surveillance will undoubtedly shift toward genomics rather than phenotypic methods. However, routine adoption of these technologies remains challenging, especially in low-income settings. Insights from this study offer valuable use cases for applying genomic sequencing technologies to community-based AMR surveillance in resource-constrained environments. 

The solution will generate significant impact for underserved populations, healthcare practitioners, local and national policy makers in following ways: 

Bridging the data gap in national AMR surveillance: By collecting, testing, and analyzing waste samples from clinical and non-clinical locations in remote communities where current AMR surveillance is limited or absent. 

Early detection and outbreak prevention: 

• Identifying emerging AMR threats and tracking their spread within and between communities, including carbapenemase-producing organisms. 
• Providing timely guidance for public health interventions, such as targeted antibiotic stewardship programs, vaccination campaigns, and infection control measures. 

Improving treatment strategies and outcomes: 

• Informing treatment guidelines and appropriate prescribing practices. 
• Enhancing national data to guide public health policies on AMR containment. 

Economic benefit: 

• Offering a cost-effective approach through batched/pooled testing from entire communities to identify low-prevalence, high-concern pathogens (e.g., ESBLs and carbapenemase-producing Enterobacteriaceae). 

• Facilitating resource allocation for prevention and control efforts, allowing policymakers to effectively address resistance drivers in specific settings. 

• Fostering public awareness campaigns: The community participatory approach to this study raises communities’ awareness about AMR and responsible antibiotic use.

Our scaling strategies are two-fold: one through the reach of our partner organization Inshuti mu Buzima (IMB),  one through engagement with National AMR Working Group led by the government. Although, not in the scope of this application, insights from this study will be shared with our parent organization, Partners In Health (PIH), for adaptation across PIH supported communities. 

In year one, we will focus on Butaro communities, which have a population of over 38,000 and are located near UGHE. We aim to validate that pit latrine sampling is a highly sensitive method for pooling resistance testing across a broader community. In year two and three, we will identify the underlying causes of CPE presence found in Butaro Hospital data, and neighboring communities including schools, adapt and implement the project regionally, creating geospatial maps across rural and urban, community and healthcare facilities settings in Rwanda to further examine possible routes of transmission.  

Throughout the three years, we will engage the National AMR Working Group led by Rwandan government to ensure coordination with other organizations in the working group and sharing of the study with government for integration with the overall National AMR Action Plan.   

The project will establish a multidisciplinary team including an expert in monitoring and evaluation. This team, together with the technical team, will develop a consolidated tool to measure deliverables quarterly. The M & E person will conduct regular audits to ensure progress against timelines. A mid-term evaluation will be conducted in year 2, and an end-of-project evaluation will be conducted in year 3. Programmatic success will be evaluated using routinely collected data and feedback from stakeholders. We will partner with the Government and external evaluators to conduct process evaluations, identify best practices, and share lessons learned to guide improvements and scale-up efforts. 

Indicators examples: 

# of communities recruited into the project 

# and % of sample collectors trained 

# and % of lab technicians trained 

# of community engagement activities 

# and % of community personnel added to working groups 

# and Type of community actors engaged  

# and % of samples tested positive for CPE

Geospatial map established for the host spot locations. 

% of households aware of proper disposal of animal fecal matter and use of antibiotics in animals 

% of household samples found resistant strains that resemble human samples 

Changes in treatment plans at project participating hospitals  

We anticipate rural communities' buy-in could be a potential barrier due to lack of awareness from limited access to information, cultural and social norms. This barrier will be mitigated through a Community Advisory Group (CAG) set up by another study that evaluates current practices on antibiotic use, livestock interaction, sanitation, and migration. The CAG can guide us to develop a culturally informed plan, disseminate information, participants recruitment, and future community engagements.

There could be logistical challenges related to sample handling. We anticipate a constraint related to distance to a healthcare facility, and storage conditions of the stool samples. To overcome this barrier, we shall leverage on the already existing facilities that UGHE and IMB have in place. There is existing significant investment in laboratory infrastructure and storage facilities (-80 C freezers). The recently upgraded laboratories can facilitate the initial sample processing.

Geospatial Mapping of Hot Spots: Our team currently lacks the necessary experience and expertise in geospatial mapping. This deficiency could potentially hinder us from fully leveraging this promising technology. However, we remain confident that by recruiting a specialist and adopting a trial-and-learn approach, we can successfully apply geospatial mapping to its fullest potential. 

• Opportunity to further build evidence and use cases on innovations that has untapped potential for low resource settings. The challenge provides us the opportunity to build evidence and use community and pit latrine sampling approach, genomic sequencing technology, and geospatial technology for mapping hot spot.  

• Strengthen our capacity in innovations – We hope to leverage on your networks of experts to strengthen our project, specifically in areas of geospatial mapping and data analytics. Through such collaboration, we hope to strengthen our local staff’s capabilities in these areas.

• Strengthen our solutions - We would like to connect and learn from other applicants and alumni to strengthen our solutions. Some of cultural barriers mentioned earlier are not unique to our communities. We hope to learn from similar projects and best practices in solving barriers rooted in cultural and traditional beliefs. 
• Enhancing our current AMR work – UGHE is one of the implementing partners for an AMR project supported by BD and Pfizer. The project  emphasizes on health facility settings, specifically diagnostics, AMR stewardship, and IPC. The challenge’s commitment to a One Health approach and community involvement synergizes with the existing project, bolstering AMR surveillance and stewardship across the current AMR project sites. 

UGHE has a strong track record of partnerships, which we will leverage for this project. We will build on existing collaborations with Ministry of Health divisions such: National Reference Laboratory, Rwanda Biomedical Centre's One Health department, and technical working groups like the AMR working group. 

Our initial phase involves engaging community-based health workers and other influential figures in underserved communities in Rwanda. They will be integrated into the AMR working group, which will drive stewardship efforts. For expansion within Rwanda, we will partner with IMB and Government. 

Additionally, UGHE is in the process of partnering with Project ECHO, an organization at New Mexico University that utilizes virtual case discussions to train and empower frontline workers. This collaboration will help maintain cohesion among AMR groups and connect them to national and international communities. It is also a crucial component of our scaling up and sustainability plan for AMR initiatives. 

We hope to leverage MIT Solve’s network of experts, particularly in areas of geospatial mapping. Through the challenge, we hope to connect with colleagues around the world to learn from others’ innovations and share insights from our solution for future adaptation and scaling.