Reduction of antibiotics use in farming practices in East Africa with a technology transfer and pilot project in Kenya

PROBLEM DEFINITION – STARTING POINT FOR PROJECT PREPARATION

Smallholder farmers’ vulnerability:

Agriculture is vital to Kenya’s economic growth, national food security, and poverty reduction. Smallholder farmers account for about 75% of agricultural output in Kenya. They are the primary producers of food for the country, and their livelihoods are important for food security. Smallholder farmers farm in land sizes between 1-5 acres (less than 2Ha). Many are poor and food insecure and have limited access to markets and services. Their choices are constrained, but they farm their land and produce food for a substantial proportion of the Kenyan population.

Factors of poverty and food security for smallholders can be grouped in 4 main categories. This includes (i) affordability barriers when it comes to acquiring goods and services needed in their activity, (ii) Farmers are not able to increase their productivity unless the problems of plant diseases, reducing soil fertility, and increasing soil acidity are overcome, (iii) Climate change significantly impacts smallholder farmers by causing decreased crop yields due to extreme weather events like droughts, floods, and heat waves, (iv) Land fragmentation is one of the key reasons for low productivity

Food insecurity in numbers:

According to FAO, approximately 1.7 million people were severely food insecure in Kenya in December 2024. Furthermore, Kenya is facing the challenge of having to feed a growing population (100 million by 2050) in the context of increasing climate shocks (drought and floods mainly) and declining soil health, moisture and fertility. In Kenya, declining soil health is a major issue primarily caused by poor agricultural practices like overcropping, excessive chemical fertilizer and pesticides use, and inadequate soil management, leading to soil acidification, erosion, low fertility, and ultimately impacting crop yields and food security across the country; this problem is particularly prevalent in arid and semi-arid regions due to the harsh climate.

Unsustainable smallholder farming practices:

Unsustainable farming practices such as deforestation, overgrazing, and the use of chemical fertilizers and pesticides, have led to soil degradation, reduced crop yields, and environmental degradation.
The misuse and overuse of antibiotics in Kenyan agriculture, particularly in vegetable farming, has reached critical levels, posing significant risks to public health, environmental sustainability, and agricultural productivity. Key statistics and evidence highlight the urgency of intervention:

• Environmental Impact: Water and Soil Quality Degradation
  • Water Contamination: Antibiotics leach into surface and groundwater through agricultural runoff. Studies have shown that antibiotic residues in water sources contribute to the spread of antimicrobial resistance (AMR). Globally, livestock is responsible for nearly two-thirds of antibiotic usage, with developing regions like Kenya seeing rising trends due to unregulated use Source: CAbiagBio
  • Soil Microbial Imbalance: Excessive antibiotics disrupt beneficial soil microbes, leading to reduced fertility, lower crop yields, and long-term degradation of agricultural land. The loss of microbial diversity hampers soil’s natural nutrient cycling capacity. Source: Nature.
• Economic and Social Impact on Rural Communities
  • Livelihood Risks: Women, who comprise between 42% and 65% of Kenya’s agricultural labour force, are disproportionately impacted by the misuse of antibiotics in farming. Antibiotic misuse directly affects their productivity by degrading soil and water resources while increasing the cost of inputs. Sources: CAbiagBio, USAID
  • Gender Inequities: Women in rural farming communities face disproportionate challenges due to limited access to sustainable farming practices and technologies, compounding economic vulnerability. Sources: MDPI, CAbiagBio
• Health Risks from Antibiotic Residues and Resistance
  • Human Exposure: Residues of antibiotics found in vegetables and other agricultural products contribute to the proliferation of antibiotic-resistant bacteria. Prolonged exposure to low levels of antibiotics in food increases resistance risks, with Sub-Saharan Africa, including Kenya, accounting for 22% of the global AMR burden. Sources: CAbiagBio, APS Journals MDPI
  • Resistance Hotspots: Kenya has been identified as an AMR hotspot, with resistant bacteria frequently found in both livestock and agricultural outputs. This poses a dual risk of untreatable infections in humans and declining livestock productivity. Source: 
• Lack of Awareness and Regulatory Enforcement
  • Despite Kenya’s proactive measures, such as the National Policy for the Prevention and Containment of Antimicrobial Resistance (2017), enforcement remains weak. Farmers often purchase antibiotics without prescriptions, and up to 44% of antibiotics sold in Kenya are substandard or counterfeit, exacerbating resistance problems. Sources: FAO, CAbiagBio
  • Training Deficit: Structured education programs are essential to disseminate best practices, reduce reliance on harmful inputs, and promote innovative solutions.
• Quantifiable Costs and Global Comparisons
  • Global projections estimate a 67% rise in antibiotic consumption in agriculture by 2030, primarily driven by developing region. Source: PNAS
  • Economic losses due to AMR in livestock could result in an 11% decline in output by 2050, with low-income countries bearing the highest burden. Source: WorldBank.

THEORY OF CHANGE

Statement: Organic solutions can lead to higher crop yields, healthy environment and contribute to lift beneficiary groups beyond poverty threshold .

Agroecology stands at the forefront of sustainable agricultural transformation in East Africa, providing integrated solutions that intertwine ecology with well-being of communities. In this context, the East African Legislative Assembly (EALA), in partnership with the Food and Agriculture Organization of the United Nations (FAO) and the Centre for Food and Adequate Living Rights (CEFROHT), has adopted a resolution that addresses the urgent challenges related to environmental degradation and food security, which includes the overuse of antibiotics in farming.

The resolution officially acknowledges agroecology as a strategic priority and commits to development of regional legal frameworks, continuous advocacy and policy recommendations to adhere to sustainable practices across the region.

The Food and Agriculture Organization of the United Nations (FAO) plays an important role in the adopted resolution by providing technical expertise and policy guidance in formulating and recommending appropriate agroecological policies, assisting in capacity building by equipping Member States with relevant insights and practical tools, and fostering awareness through advocacy amongst stakeholders. FAOs role in the resolution could benefit our project in the execution and post-completion phase (3-5 years) as follows:

1. Implementation phase: assistance in adaptation of bacteriophage technology to local conditions, supporting training programmes for farmers and local biotech partners; assistance in ensuring compliance with local/regional policies, facilitating the development of guidelines for bacteriophage use in agriculture; assistance in developing monitoring and evaluation process to assess the project’s impact on antibiotic reduction, soil health, water quality, yield improvement and the well-being of communities.
2. Post completion phase: Continued support for capacity building to ensure long-term sustainability; ongoing advocacy for supportive policies relating to sustainable agricultural technologies, helping to embed our project results into national/regional agricultural strategies; utilization of FAOs network for support in scaling the project to other regions, documenting and sharing best practices to encourage wider adoption; long term impact assessment to evaluate environmental benefits, economic improvements and progress with respect to gender equality.

The resolution’s call for developing regional legal frameworks to promote agroecology creates a conducive environment for the introduction of innovative solutions, which could streamline regulatory approvals and facilitate a seamless mesh of the technology transfer process. Furthermore, the resolution supports our project’s aim to reduce antibiotic reliance in agriculture, leading to improved food security and environmental health.

Emphasis on sustainable agriculture practices in the resolution is directly aligned with the aspect of our project related to the prevention of soil damage, improving water quality and encouraging soil microbial balance via the use of bacteriophages.

The resolution’s commitment to leaving no one behind resonates with our project’s goal of empowering local communities and actively supporting gender equality and women as a factor of development in agriculture. Awareness raising and advocacy as an important focus of the resolutions enhances support for educational activities, which is a critical component of our project that emphasizes training of local farmers and other relevant stakeholders in advanced technologies, such as bacteriophages.

The resolution aligns with our project in:

• shared objectives (transformation of agrifood systems in a sustainable fashion by reduction of harmful practices),
• integrated approaches (addressing issues of water quality, soil health, as also community empowerment and gender equality),
• fostering supportive policies that promote innovation and adoption of sustainable technologies, which is essential for successful introduction and implementation of bacteriophage solutions by Jafral.

SUSTAINABLE DEVELOPMENT GOALS:

SDG 1: No Poverty: empowers rural farmers by increasing agricultural yields and income through sustainable practices. Reduces economic vulnerability by providing knowledge and resources to adopt advanced technologies.

SDG 2: Zero Hunger: the project will enhance agricultural productivity and food security by increasing access to safe and affordable pest and disease control technologies for smallholder farmers (often not able to afford expensive antibiotics to treat bacterial plant diseases). By promoting sustainable practices, the project will help increase crop yields, production and diet diversity, while ensuring safer food for communities.

SDG 3: Good Health and Well-being: mitigates public health risks by reducing antibiotic-resistant bacteria in food and the environment. Enhances food safety and the overall well-being of rural populations.

SDG 5: Gender Equality: Women undertake 70-80% of the agricultural productive activities in horticulture farming in Kenya. Therefore, the introduction and adaptation of bacteriophage technology in horticulture crops, will largely support women’s role in agriculture including through (but not limited to) training and decision-making processes. Improves economic opportunities for women, addressing systemic disparities in land access and income.

SDG 6: Clean Water and Sanitation: prevents contamination of water sources and aquifers by curbing antibiotic runoff. Safeguards water quality for drinking and irrigation, improving community health.

SDG 8: Decent Work and Economic Growth: the project fosters economic growth in rural areas by improving agricultural output, creating job opportunities, and supporting local economies with better farming practices.

SDG 12: Responsible Consumption and Production: by shifting from antibiotic-dependent farming to sustainable and biotechnological solutions like bacteriophages, the project promotes responsible farming methods that reduce environmental impact and ensure the overall health of the ecosystem.

SDG 15: Life on Land: restores soil health by reducing antibiotic-induced microbial imbalances. Promotes sustainable farming that preserves biodiversity and combats land degradation.

SPECIFIC PROJECT OBJECTIVES

• Development of a bacteriophage cocktail suitable for treating bacterial infections in tomatoes in Kenya
• Transfer of methods for finding and isolating bacteriophages in nature to the team at University of Nairobi
• Implementation of agroecological practices in alignment with EALA-FAO resolution by introduction of Jafral’s bacteriophage technology in Kenya,
• Reduce Antibiotic Use in Farming,
• Protection of antibiotics runoff into underground water and water systems,
• Offering a safe, natural alternative to use of antibiotics, addressing AMR development and related issues,
• Enhancement of soil and water quality,
• Protection of local biodiversity,
• Transfer of biotechnological knowledge, technology and expertise to local partners in Kenya,
• Promotion of women within the project (women specialists, biotech
• nologists, farm owners),
• Empowerment of rural Communities, specifically those where Women play a critical role in farming,
• Build Regulatory and Technical Capacity in Kenya,Demonstrate Efficacy Through Field Trials,
• Promote Education and Awareness relating to overuse of antibiotics and natural alternatives,
• Finding a local biotechnology partner for Jafral to check the possibility of Kenya-wide after project bacteriophage product availability, project sustainability and continuous development, development of applications for other bacteriophage uses in farming (potatoes, animal husbandry, etc). This would assist in wider bacteriophage transfer of knowledge, acceptance and availability of products for small farmers in Kenya and East Africa and achieve a broader positive impact.

After project completion the developed and tested bacteriophage cocktail will be given to University of Nairobi for further research and for commercial use, should they decide to do so. University of Nairobi will be free to distribute the bacteriophage product to local farmers when University develops them to commercial use.

ALIGNMENT OF THE SPECIFIC OBJECTIVE OF THE PROJECT WITH THE NEEDS OF THE PARTNER COUNTRY

Implementation of agroecological practices in line with EALA-FAO resolution: The resolution calls for actionable collaboration between international technology providers and local stakeholders to drive sustainable agricultural transformation in the region, by highlighting the necessity of innovative solutions that address critical issues.

Reducing Antibiotic Overuse: Kenya faces critical issues with the overuse and misuse of antibiotics in agriculture, contributing to antimicrobial resistance (AMR), environmental degradation, and food safety risks. This project aligns with the Kenyan National Policy for the Prevention and Containment of AMR (2017) by introducing bacteriophage-based alternatives, reducing reliance on antibiotics, and safeguarding public health.

Enhancing Soil and Water Quality: Antibiotics disrupt microbial balance, reducing soil fertility and contaminating water sources in Kenya. This project addresses these needs by introducing eco-friendly bacteriophage solutions, improving soil productivity and water security, both of which are vital to rural farming communities. Source: Springer nature

Empowering Rural Communities: Women (30-80%), who form a significant portion of Kenya’s agricultural labour force, face economic and social vulnerabilities due to unsustainable farming practices. By prioritizing gender equality, training programs, and sustainable practices, the project aligns with Kenya’s goals for inclusive rural development and women’s empowerment.

Boosting Agricultural Productivity: Vegetable farming is a critical component of Kenya’s food security and economy 30 per cent of the Gross Domestic Product (GDP). The project will support higher crop yields, sustainable practices, and safer food production, directly addressing Kenya’s need to enhance agricultural output and rural incomes.

Building Local Capacity: Through partnerships with Kenyan biotech companies, research organizations (e.g., University of Nairobi), and local farms, the project aligns with the country’s need for knowledge transfer, capacity building, and the promotion of homegrown innovations in sustainable agriculture.

TARGET GROUPS

• Smallholder Farmers and Rural Communities: Primary beneficiaries, including vegetable farmers in Kenya, particularly those in rural areas who rely on agriculture for their livelihoods. Women farmers, who represent a significant portion of Kenya’s agricultural workforce, will be prioritized for capacity-building and empowerment.
• Kenyan Agricultural Organizations: Collaborators such as the University of Nairobi and local biotech companies will benefit through knowledge transfer, technology adoption, and participation in sustainable farming initiatives aligning them with the new framework The Country Programming Framework (CPF) 2022–2026.
• Policy and Regulatory Bodies: Kenyan regulatory authorities involved in agriculture, environmental conservation, and antimicrobial resistance management will gain valuable insights to improve policies and regulations. ICPE’s efforts will be supported by FAO Nairobi office for outreach and advocacy of the project.
• Consumers and Communities: Indirect beneficiaries include consumers who will have access to safer, antibiotic-free agricultural products, improving public health and food security. Communities in agricultural regions will benefit from improved water and soil quality, which are critical for sustainable living and farming.
• Educational and Research Institutions: institutions engaged in agriculture, environmental science, and biotechnology will gain new opportunities for research, training, and collaboration.

PLANNED RESULTS OF THE PROJECT:

• Isolation of local Kenyan bacteriophages, development of bacteriophage cocktails which will be used for laboratory and field trials and later commercial applications,
• Transferred protocols to University of Nairobi on the process of isolation of bacteria, bacteriophage sampling, designing and controlling field studies with bacteriophages
• Education of University of Nairobi team on development, testing and implementation of phages
• Donation and transfer of the developed bacteriophage cocktail to treat bacterial infections in tomatoes to University of Nairobi for their free future use for research applications, further donations, government or international organisation programmes or commercial applications
• Trained team on a local farm on application of bacteriophage products
• Establishment of a pilot project where technology and use of bacteriophages is showcased to local stakeholders as an example of good sustainable agriculture practices
• Completion of laboratory trials, controlled trials and farm trials to show and measure efficacy of bacteriophages and their potential to replace or supplement antibiotics,
• Empowerment of women in rural environments by presenting a safer alternative to antibiotics, increasing their resilience, revenue, independence,
• Identified local Kenya based technology transfer partner for Jafral,
• Transfer of technology to Kenya biotechnology laboratory which could serve as a local partner for collecting samples, isolation of bacteria and phages, phage development and phage testing
• Identified after project partner for scaling up bacteriophage solutions
• Building of awareness in target groups (farmers, government, regulatory experts, biotechnology experts, United nations) of a safe alternative to use of antibiotics,
• Capacity building among local biotechnology and farming experts.

ACTIVITIES AND IMPLEMENTATION PERIOD

Pre project start: organisation of a meeting for all stakeholders where project and project partners are presented, timelines, responsibilities and deliverables are confirmed. Partners are trained on bacteriophages and its applications, usability and development processes (ICPE, Jafral).

The project activities and timeline are presented in the table below.
For more detailed information on the activities and deliverables within each work package, please read the description below.

WP1: Collection of bacterial strains (M1 – M3) – Jafral

T1.1 Preparation, development and transfer of protocol
documentation for isolation of bacteria strains to
University of Nairobi (Jafral)
T1.2 Training of the team at University of Nairobi (Jafral)
T1.3 Bacterial strains isolation (University of Nairobi)
T1.4 Delivery to Slovenia (University of Nairobi)

Deliverables
D 1.1 Document outlining the protocol for
isolation of bacterial strains
D 1.2 Bacteria strains delivered to Jafral in Slovenia

WP2: Phage hunt (M4 – M6) - Jafral

T2.1 Preparation, development and transfer of phage hunt
protocol documentation to University of Nairobi (Jafral)
T2.2 Training and education of University of Nairobi team (Jafral)
T2.3 Collection of samples from Kenyan environment (soil, water, etc)
(University of Nairobi)
T2.4 Delivery of samples to Slovenia (University of Nairobi)
T2.5 Isolation of phages at Jafral laboratories (Jafral)

Deliverables
D 2.1 Document with a protocol for collection of materials
containing phages
D 2.2 List of phages collected

WP3: Phage production (M7 – M8) - Jafral

T3.1 Production of phages isolated in WP2 (Jafral)
T3.2 Preparation of phage cocktail targeting a specific
Kenyan bacteria (Jafral)

Deliverables
D 3.1 Internal Jafral report on the manufacturing process

WP4: Phage testing (M9 – M10) - Jafral

T4.1 Preparation of phage testing protocols, testing best practices
and instructions, transfer to University of Nairobi (Jafral)
T4.2 Training and education of University of Nairobi team
in testing protocols (Jafral)
T4.3 Delivery and transfer of phage cocktails to University of Nairobi
(Jafral)
T4.4 Testing of phage cocktail efficacy (Jafral + University of Nairobi)
T4.5. Comparison of results (Jafral)

Deliverables
D 4.1 Document outlining testing protocols and instructions for tests
D 4.2 Test results of Jafral testing
D 4.3 Test results of Kenya partner testing

WP5: Documentation preparation
(M11 – M12) - Jafral

T5.1 Preparation of documentation for field trials permit
(Jafral)
T5.2 Documentation filing with appropriate Kenyan authorities
(University of Nairobi)

Deliverables
D 5.1 Documents for field trial approval application

WP6: Controlled field trials (M13 – M17) - Local partner

T6.1 Phage manufacturing (Jafral)
T6.2 Delivery of a larger quantities required for field trials
of phages to Kenya (Jafral)
T6.3 Preparation of protocol and transfer of protocols for testing
to University of Nairobi (Jafral)
T6.4 Field trials in controlled environment in Kenya
(University of Nairobi)

Deliverables
D 6.1 Manufactured batch of phage cocktail
D 6.2 Document describing a protocol for testing

WP7: Analysis of results (M18 – M18) - Jafral

T7.1 Data collection (Jafral and University of Nairobi)
T7.2 Analysis of results (Jafral)
T7.3 Preparation of a test report (Jafral)

Deliverables
D 7.1 A report describing test results

WP8: Extensive field trials study in Kenya (M19 – M23) -
University of Nairobi

T8.1 Selecting a farm suitable for the field study
(FAO + University of Nairobi, Jafral)
T8.2 Preparation of field trials on a local farm
(Jafral +University of Nairobi)
T8.3 Training of local farmers at the location on use of bacteriophages
T8.4 Testing execution (local partner + University of Nairobi + FAO)
T8.5. Regular sampling and sending of samples to Jafral
(University of Nairobi)
T8.6 Promotion of sustainable agriculture and of this pilot
project to local stakeholders (FAO, University of Nairobi)

Deliverables
D8.1 Field trials protocol
D8.2 Foto and video materials of field trials

WP9: Analysis of field trial results
(M24 – M24) - Jafral

T9.1 Data collection (University of Nairobi + Jafral)
T9.2 Analysis of data (Jafral)
T9.3 Final report preparation
(Jafral and University of Nairobi)

Deliverables
D9.1 Final field trial analysis document

WP10: Project management and promotion (M1 – M24) - ICPE

T10.1 Partner coordination, monitoring of budgets and timelines
(ICPE)
T10.2 Local project advocacy, promotion and guidance
(FAO UN)

Deliverables
D10. 1 A report on delivered activities after project completion

IMPACT OF THE PROJECT ON FOOD SECURITY

According to research, improving soil health can lead to an estimated yield benefit of between 5% and 30% depending on the crop, location, and specific soil management practices implemented, with some studies showing even higher increases in certain cases; healthy soils can improve water retention, nutrient availability, and root development, leading to increased crop yields.

In the context where a minimum of 1.7 million people are severely food insecure in Kenya (the figure can increase manifold in time of drought), and factoring the need to feed a population that will (almost) double by 2050, it is anticipated that the project will contribute to restore crop productivity and therefore contribute to struggle or reduce severe food insecurity.

IMPACT OF THE PROJECT ON GENDER EQUALITY

Gender equality is not simply a matter of human rights, but is key to eliminating poverty and hunger. It is only by closing the gender gap that sustainable agriculture and rural development can reach their full potential. The project will focus on intentionally including women within the teams delivering it in Slovenia and Kenya, but a successful market entry of bacteriophage products into Kenya can have the most impact on women who are the driving force in Kenya’s vegetable farming:

• Reduced exposure of Women (who represent a 70-80% of workforce in horticultural crop production in Kenya) to antibiotics, directly impacting their health, making them more productive,
  Lower cost of bacteriophages can help women save money in their households and invest it in education or a small business,
• Crops grown with sustainable practices like bacteriophage treatment might meet higher export or premium market standards, increasing incomes. Women involved in farming benefit directly,
• Women trained in bacteriophage farming methods can become community leaders and educators, challenging traditional gender roles,
• Bacteriophage products could simplify farming processes, reducing the physical labour involved. This is significant for women, who often have dual roles in farming and household responsibilities,
• With improved agricultural outcomes, societal perceptions of women’s farming capabilities, might shift, fostering greater respect for their contributions.

IMPACT OF THE PROJECT ON ENVIRONMENTAL PROTECTION

Improved Water Security:
Safeguarding water quality by eliminating contaminants such as antibiotic residues ensure better access to clean water for rural communities and ecosystems. This is critical for sustainable agricultural practices and aligns with Kenya’s goals under the FAO agreement.

Prevention of Soil Degradation:
The project enhances soil health by reducing antibiotic-induced microbial imbalances, promoting biodiversity, and restoring natural nutrient cycling. This supports SDG 15 (Life on Land) by combating land degradation and preserving soil fertility.

Mitigation of Antimicrobial Resistance (AMR):
By reducing reliance on antibiotics, the project addresses AMR development in agricultural ecosystems. This prevents the proliferation of resistant bacteria in soil and water, contributing to improved ecosystem resilience and public health (SDG 3 – Good Health and Well-being).

Promotion of Sustainable Agricultural Practices:
Introducing bacteriophage solutions fosters eco-friendly farming, protecting local biodiversity and reducing the environmental footprint of agriculture. This directly supports SDG 12 (Responsible Consumption and Production) and SDG 2 (Zero Hunger) by enhancing sustainable production methods.

Climate Resilience:
By improving soil and water quality, the project indirectly contributes to climate change mitigation. Healthy soils act as carbon sinks, and reduced water contamination ensures ecosystem stability amidst climate pressures.

PROJECT PARTNERS:

• International Center for Promotion of Enterprises (ICPE)
• Jafral d.o.o.
• University of Nairobi, Department of Biology
• JTBD Ltd.
• Kenya farm (to be identified during the project)

PROJECT TEAM:

• Dr Franc Smrekar (CEO, Jafral)
• Dr Barbara Hubad (Jafral)
• Janja Kozjek (Jafral)
• Dr Alice Gichuhi (University of Nairobi)
• Dr Cecelia Ngugi (University of Nairobi)
• Dr Peter Wachira (University of Nairobi)
• Prof Catherine Lukhoba (University of Nairobi)
• Prof George Ongamo (University of Nairobi)
• Prof Maina Wagacha (University of Nairobi)
• Jure Tomc, MBA (ICPE)