Ikhawu: community shield

A first-of-its-kind high throughput BioFoundry and data integration concept that will empower citizen scientists to monitor, advise, test, and predict AMR infections in South Africa's poultry industry and the associated workers, their communities, and ameliorate the socioeconomic and medical burdens caused by AMR infections. 

Stefan Kühn, Ph.D in biochemistry from Stellenbosch University and Vrije Universiteit Amsterdam.

The One Health burden of anti-microbial resistant pathogens remains unexplored in South Africa and the greater Southern African Development Community (SADC). Further, the COVID pandemic highlighted two key shortcomings in South African community healthcare that remain understudied: zoonotic transfer and the spread of diseases from workers that move in and out of communities daily.  

Considering these factors, the overall burden of AMR organisms on the health of our communities, the stability of our food chains, and the hygiene of our environments in South Africa (and the broader SADC community) is unknown. While South Africa already has pre-existing, sophisticated data gathering mechanisms – the challenge lies in directing these to gather the data required to discern the impact of AMR on communities.   

However, data collection is only one piece of the puzzle as ultimately, data needs to be translated into action. This project will therefore sit at the intersection of data collection, development, and regulatory recommendations. Our communities deserve more than “just” data collection – they deserve to have their lives and livelihoods shielded from AMR and the socio- and medico-economics effects of AMR infections. 

Rapid, early, and precise identification of pathogenic strains, AMR, and their spread would serve these stakeholders:   

Poultry farmers: Rapid, early identification would prevent outbreaks or mitigate their reach. Precise screening would reduce the amount and variety of antibiotics used, allowing farmers to tailor their interventions to the prevalent or most concerning strain. This would reduce culling, antibiotic use, and unnecessary expenditure.   

Farm workers: reducing the zoonotic transfer of pathogens and AMR organisms – secures their health, their family’s health, and their employment.   

Farming communities: as with COVID, the main vector for disease outbreaks in communities are the movements of essential workers in and out of them. Reducing the incidences of zoonotic transfer or knowing which strain has been transferred into a community will lead to rapid implementation of public health measures as well as medical interventions by community clinics. Shielding communities from these diseases means lower mortality, fewer lost educational and employment opportunities, and a reduction in the environmental burden due to overmedication and waste-water contamination.  

General Public: protecting the cheapest source of animal protein from repeated price and supply disruptions builds a more secure and resilient public. A lower environmental antibiotic burden will lead to improved public health outcomes. 

While there hasn’t been a widespread outbreak of AMR-linked disease in South Africa, given global trends and increasing antibiotic use in agriculture, it is a matter of when, not if. Consequently, this project will provide several public goods to the citizenry of South Africa: 

• COVID demonstrated that a significant vector for communicable diseases are the people who move in and out of their communities daily. The monitoring pipeline developed herein will allow community health practitioners to more rapidly and precisely target interventions to stall outbreaks.
• The data generated from high-throughput screening technologies will be used to inform farmers, workers, and communities as to the appropriate type and quantities of antibiotics to use thereby reducing the overall burden of antibiotics in the environment and foodchain and forestalling the appearance of novel AMR strains. 
• The data gathering and visualisation mechanisms developed in this project will be publicly accessible; allowing everyone to track the incipience and spread of AMR pathogens in real time. 
• Informing the public of a potential outbreak of AMR in specific areas enables them to be part of the solution as citizen scientists, thereby empowering these communities with the tools to monitor and prevent AMR infections.  

Ikhawu will impact South Africa in several ways: 

Real-time monitoring of AMR infections within the poultry industry will shield not only the food supply, but also the workers and communities that directly rely on the poultry industry for employment. A more secure poultry industry means fewer supply and price shocks which leads to a more stable food supply. 

The BioFoundry and data analytic frameworks which underpin this project will lead to significant up- and re-skilling of people by providing training, further education, and employment opportunities.

The development of a pipeline to rapidly sample, identify, and track incipient outbreaks and develop low-cost screening tools will expedite and target interventions by community healthcare workers.

Reducing the use of antibiotics will lead to a lower burden of antibiotics in the food chain and wastewater which will feedback into a lowered incidence of AMR infections. Additionally, this will reduce the financial burden of regular antibiotic treatment, culling, lost employment opportunities and will likely lead to lowered input costs for farmers and stabilised prices for the consumer.

The project consists of three phases spread over three years. Each phase prepares the foundation for the following phase. The final phase, in year three, prepares the project for scaling into production as well as expansion into other One Health concerns:

Year 1: Track

• Secure collaboration and funding by stakeholders. 
• Source pre-existing data to guide future data and sample gathering strategies.
• Determine origins of historic outbreaks among poultry farms, farm workers, and communities. 

Year 2: Trace

• Determine the extent and reach of outbreaks. 
• Use commercial AMR screening panels together with biological samples on a high-throughput BioFoundry platform to determine incipient outbreaks, the burden of AMR, IC50 values for strains of interest.
• Develop AMR screening panels for unique and under-represented local AMR organisms of interest. 

Year 3: Test 

• Test the data gathering and analysis framework on other regional health concerns to ensure the translatability of the method.
• Trial the newly developed AMR screening panels with the commercial and community stakeholders their efficacy as an early warning system. 
• Develop LAMP-based test kits for rapid, low-cost identification of AMR infections. 
• Develop a mobile application which provides a real-time dashboard of which infections occur in which parts of the country.  

Progress will be measured along the following indicators:

Agroeconomic:

• The ZAR-value of economic damage that was averted.
• The amount of productive human hours that were saved.
• The percentage reduction in per-farm antibiotic use. 
• The percentage reduction in wastewater antibiotics.
• The reduction of pathogenic and AMR strains in wastewater.

Human & Social: 

• The amount of people that were re- or upskilled.
• The number of successful community health interventions
• The degree to which the project receives positive evaluations by the communities it serves. 

Reach & Collaboration: 

• The number of commercial, civic, research, and government organisations that have contributed expertise, data, or funding.
• The number of farming communities that are onboarded. 
• The reach generated by public outreach opportunities and social media messaging.

Research & Development:

• The amount of data integrated into a single topological map of South Africa.
• The number of pilot-ready commercial testing kits.
• The number of pathogenic and AMR strains that are screened for and identified.

The three main barriers to this project. 

Firstly, South Africa lacks a consistent electricity supply. Power outages may be scheduled for up to 12 hours a day. While the BioFoundry facility has backup battery and generation capacity, the same may not be true for the farms or communities we rely on for data or sampling. This risk will be mitigated threefold: designing data generation activities in a technology-independent manner, scheduling technology-dependent activities around the planned outages, and providing backup power supplies for mobile devices for unplanned outages. 

Secondly, the social fabric of South Africa remains precarious. Indigent, impoverished, and working-class communities may be reticent about cooperating with a project like this. Risk mitigation will include engaging community leaders, social workers, and government offices to build trust and secure “buy-in”. 

Thirdly, while South Africa has the most developed data-gathering mechanisms in the region, data on the spread of AMR organisms, zoonotic transfer, and the environmental burden of antibiotic treatment are scarce. Similarly, little infrastructure exists which centralises these data. Data gathering and centralisation will be accelerated with this project being a nexus for each stakeholder to access and deposit their data. Outsourcing of data collection will address the current data insufficiency.  

AMR disproportionately affects LMICs, by partnering with The Trinity Challenge, Ikhawu will develop the capacity needed to monitor and intervene in AMR infections with local expertise and infrastructure.  

The Trinity Challenge therefore provides Ikhawu with one crucial resource that is lacking in most LMICS: access. Specifically, access to the following: 

• The international community: The Trinity Challenge already presents as a case-study in international collaboration and diversity of applicants and management. The award would not only provide the financial resources to engage with international stakeholders, but also the legitimacy and opportunity to do so. Collaborations from LMICs and Africa in general are viewed as risky or with scepticism. The legitimacy and positive press offered by the award would minimise those barriers.
• Funding: the funding provided by the Challenge will not only secure the collaboration of local and international experts, collaborators, and stakeholders, but will also be used to train and upskill local persons in the form of employment, consulting, and post-graduate studies. Similarly, the funding will provide access to crucial technologies necessary for the implementation of Ikhawu’s year three such as web-hosting, LAMP kit development, qPCR capabilities, and contracting for next-generation sequencing.  

The scale and ambition of this project requires the expertise of various local and international organisations, including but not limited to: 

• SAVC: the SA Veterinary Council would be approached for their expertise in collecting biological samples from animals. 
• SAMRC: the SA Medical Research Council has access to databases, expertise, and funding mechanisms to investigate AMR and community health. 
• SAHSRC: expertise of the SA Human Sciences Research Council will be leveraged to enage with communities in an ethical, non-disruptive, and non-exploitative manner. 
• SAPA: the SA Poultry Association’s collaboration is central to gaining access to farmers, farms, and farm workers. 
• CERI: The team under Prof. Tulio de Oliveira has considerable experience with monitoring and modelling incipient pandemics as demonstrated by their leading role during the COVID pandemic. 
• Biotikum: founder, Dr. Deon Neveling, has considerable experience working with poultry and manufactures probiotic supplements that improve the health of poultry. His expertise in dealing with poultry and managing and monitoring their disease states will be invaluable. 
• LGC Biosearch Technologies (https://www.biosearchtech.com/sectors/molecular-diagnostics) partnership to develop and scale molecular diagnostics.

The nature of Ikhawu is such that collaborations can be developed rapidly should they fall within the strategic ambit of the project.