SaferDrops: Empowering researchers and communities against AMR

Data integration on bacterial diversity and resistance profile in drinking water sources for enhanced understanding and improved public health in Brazil and Mozambique. Through an affordable and simplified sequence-based workflow this solution will provide essential knowledge to scientists and promote actions to improve the quality of life of local communities.

Professor Päivi Tammela, Faculty of Pharmacy, University of Helsinki

Antimicrobial resistance (AMR) affects all countries, but the burden is disproportionately higher in low and middle-income countries (LMICs). In Mozambique in 2019, there were 7,800 deaths attributable to AMR and 31,100 deaths associated with AMR, being amongst the highest 10 countries in mortality rate per 100,000 population associated with AMR. Moreover, AMR surveillance data is practically non-existing: in 2014 the WHO retrieved only three reports from African countries. In Brazil in 2019 there were 33,200 deaths attributable to AMR and 137,900 deaths associated with AMR.

Aquatic environments (AE) play a key role in the spread of ARB (Antibiotic Resistant Bacteria) by acting as reservoirs, and consequently source of infection. Drinking water consumed by communities in LMICs is frequently extracted directly from wells and rivers without any treatment. For example, more than 60% of Quilombolas community (descendants of Afro-Brazilian slaves who escaped from plantations), do not have access to treated water. In Mozambique information regarding waterborne infections is scarce, but high mortality rates particularly among children (10%) confirm its impact. AE-related infections are primarily attributed to pathogenic Escherichia coli and Vibrio cholerae. The latter continues to pose a substantial public health burden with recurrent annual outbreaks driven by ARB.

Our solution entails a simplified data-gathering workflow to increase information availability on ARB for scientists and health authorities in Brazil and Mozambique, from AE locations utilised by the population as drinking water source. The solution will deliver and implement an accessible system for continuous surveillance plan, which will have direct impact on ARB mitigation and public health. All partners have had prior cooperation which this project builds on. Prof Lilian and Teobaldo jointly participated in a project at Fiocruz (Brazil). In 2023, Prof Lilian and her team visited Prof Tammela’s group for several months.

We will promote workshops with vulnerable communities in Brazil and Mozambique to advise on good hygiene practices, use and disposal of unused medications, and AMR environmental impact. Residents will receive ceramics filters to improve water quality. Rural population have no access to treated water, proper sanitation and live in poor hygiene conditions. In Brazil we will work with three Quilombola communities and in Mozambique in four provinces severely affected by cyclones and suffering from land mining and deforestation. Both partners have a strong presence and well-established connections within local communities through other projects. Prof Lilian has an on-going water-based surveillance program in Goiás.

Public health and capacity building: Promote and implement an affordable, inclusive, and easy-to-use data collection system for ARB surveillance. International mobilities foster collaboration, knowledge exchange and capacity building between participant countries.

Community well-being: The data acquired on ARB will help on initial responses toward educating communities about associated health risks. Scientists and health authorities from participant countries will actively engage with residents, emphasizing the critical importance of maintaining good hygiene practices and preserving the environment. It also includes the distribution of ceramic filters to every household within the community. Residents will receive guidance on the proper usage and maintenance of these filters, ensuring the access to safe drinking water quality. By empowering communities with the tools and understanding to safeguard their health we will promote well-being.

Open science: Scientists and health authorities involved in the project are committed to publishing the results in the form of open access articles and social media channels. This dissemination strategy will provide visibility, potentially inspiring similar actions worldwide. By sharing our findings openly, we aim to contribute to the global knowledge on water quality, ARB, and public health, fostering collaborative efforts to address these pressing issues across regions.

Simple pipeline on ARB bioprospecting: By promoting accessibility and ensuring faster response times with on-site analysis, our solution addresses the challenges faced by communities that lack access to centralized laboratories and support better-informed decisions related to the burden of ARB and public health.

Cost-effectiveness and resource optimization: The implementation of nanopore technology aims to reduce costs associated with sequencing platforms, making the process more affordable. By lowering costs our solution will provide a more accessible tool to researchers and public health authorities with limited financial resources.

Community engagement: Workshops on antibiotic use, AMR awareness, and good hygiene practices are tailored to the specific needs of communities in Brazil and Mozambique. By directly engaging with communities, our solution empowers individuals with knowledge and skills that contribute to better health practices.

Water quality improvement: By providing affordable and locally available ceramic filters, our solution addresses waterborne diseases, contributing to improved community health.

Research capacity building: International mobilities and research guidance support the development of research capabilities in Brazil and Mozambique. Building local research capacity ensures sustainable solutions tailored to the specific needs of these regions. It fosters scientific independence and long-term impact.

In Year 1 all participants will buy the MinION device and accessories for the portable laboratory implementation. In Finland, initial testing with spiked samples will be conducted to optimize workflow steps. Our mobile laboratory will be validated using samples from a river in Helsinki, allowing for the optimization of our pipeline. Later during Year 1, we will utilize the system in Cavalcanti (Goiás, Brazil) and Vila de Gondola (Manica, Mozambique), with knowledge transfer through international mobilities. Local community engagement begins with interviews to understand their needs and by integrating household water filters with sanitation and hygiene promotion. 

In Year 2 we will expand testings to other municipalities: Silvania and Aparecida de Goiânia (Goiás) and Beira and Mocuba (Sofala and Zambézia provinces) actively involving communities and health authorities. Sampling continues in Year 1 locations for dataset enrichment.

In Year 3 we will design a framework for long-term use and expand into different regions. In Mozambique we will work in the Northern region, in the municipalities of Lichinga and Cuamba (Niassa) and Nampula and Pemba (Cabo Delgado) where local NIH branch members will also help. Community integration persists throughout Years 2 and 3, fostering sustainable practices.

We will measure our success by assessing both the technical effectiveness of our pipeline and the impact on public health.

Technical performance

• Sequencing accuracy and turnaround time: Measure the accuracy of bacterial identification and resistance gene detection compared to standard methods and time for completion. This will be tracked through the percentage of correct identification in spiked samples during the initial testing phase in Year 1.

Research capacity building

• International mobilities: Measure the participation of trainees and mentors and the knowledge exchanged through reports.
• Open science: Track the numbers of publications and presentations

Public health and community engagement

• Strengthen knowledge and surveillance: Correlate findings with antibiotic use, disposal practices, and environmental conditions. Communicate findings to health authorities, local communities and other organizations that might contribute to this project.
• AMR awareness: Conduct pre- and post-workshop surveys to measure the increase in in knowledge in the targeted communities.
• Hygiene practices improvement: Track the adoption of hygiene practices through interviews and observation of community members.
• Ceramic filter distribution: Monitor the distribution and utilization of ceramic filters in the communities. Assess the impact on drinking water quality and reduction in waterborne diseases through interviews and health assessment.

Finance: Implementing a portable nanopore sequencing-based workflow is financially demanding for LMICs. Participants of the projects are constantly seeking funding from governmental agencies, international organizations, and private foundations that support research in public health. In Mozambique we will align the project with existing priorities. In Finland and Brazil grant proposals on AMR have been submitted and is upon appraisal. Outcomes are expected to be announced this year.

Capability: Limited technical expertise or access to specialized equipment in some partner countries may hinder successful implementation. We aim to collaborate with local institutions and universities to build capacity through training programs and utilize their resources as needed.

Legal and regulatory: Data collection from the communities requires approval from ethical committees in Brazil and Mozambique. This is known to be a lengthy and bureaucratic process. Communication with national regulatory bodies and collaboration with legal experts will take place in advance. Prof Lilian has already initiated this process in Brazil.

Cultural: Differences in cultural practices and beliefs may affect community engagement and the effectiveness of educational workshops. We will conduct systematic cultural assessments in each target location and collaborate with local community leaders and influencers.

Our aim extends beyond technological advancement, encompassing community-based learning initiatives, fostering collaboration and knowledge exchange, aligned with the Trinity Challenge's pillars of inclusivity, collaboration, and innovation. 

Our innovative solution harnesses the power of cost-effective metagenomics to gather evidence on ARB from aquatic environment in LMICs. It is centred around implementing a portable, user-friendly, fast, and affordable workflow for bacterial identification and the detection of resistant genes in AE samples. With the support from Trinity Challenge we will build a portable laboratory system in remote locations and implement sampling collections stations in at least six local communities in Brazil and in Mozambique. In time a data-driven evaluation on ARB in drinking water sources will warn scientists, health authorities and the population of potential hazards.

We are aware of the need to create better solutions to improve health in vulnerable communities in Brazil and Mozambique. The Trinity Challenge partnership can make our solution a reality and promote a lasting impact for the public good.

We have identified potential partners that could help us with the implementation and dissemination of our project:

• Institute for Health Metrics and Evaluation can help us to communicate our findings and to transform our data into real practices for improved public health.
• Fiocruz functions as the National Institute of Health in Brazil. They directly work with science health-related research training of public health and health workers providing information and communications related to health, science, and technology.
• Clinton Health Access Initiative has trusted relationships with governments and healthcare professionals. They can help us to drive change across the health system.

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