Partnership for a cross-disciplinary approach to the ecology of antimicrobial drug resistance in Kenya
Lead Research Organisation:
University of Liverpool
Department Name: Institute of Infection and Global Health
Abstract
Antibacterial resistance (ABR) is a significant threat to the future of effective healthcare and veterinary care. Globally, we are dependent on antibiotics for treating common as well as severe infections, but we abuse the value of these compounds by using them irrationally. In Kenya, as in many other countries, antibiotics are prescribed un-necessarily and without properly identifying the micro-organims being targeted, a fact that often leads to treatment failures. In agriculture, antibiotics are often used directly by farmers, as they are readily available on the market without prescription. Kenya is a country undergoing a demographic transition towards urbanisation, with over half the population expected to be in urban zones by the middle of this century. Many of these people are likely to live in low income settlements (eg 60% of residents of Nairobi, the capital, live in low income settlements = slums). Provision of high quality heath care is lacking in such sites. Further, with more people living in towns and cities, the pressure will be on farmers to produce more food more efficiently, and a key part of this - as has been the case in more developed economies - will be to use antibiotic drugs. These factors combine to produce a great deal of risk for highly drug resistant micro-organisms to emerge. Essential in preventing this will be to collect high quality data in hospitals and on farms, to understand what levels of resistance are present now, and how the organisms share their genes, a process that can result in rapid spread of resistant traits. A key aspects of this is also to understand how antibacterial drugs are used in practice, how they are procured and what drives individual and collective decision making about their use. Our programme will investigate these different aspects and work with partners in Kenya and internationally who make policy, in order to develop long term surveillance tools, plans to limit the spread of resistance and advice to the public to conserve these important drugs.
Technical Summary
In Kenya and elsewhere, the antibiotic landscape for healthcare and livestock production is shaped by poor regulation and irrational drug use. There is a need for related evidence-based policy and the implementation plans for such policy. We will conduct in depth research in clinical and community settings to understand patterns of resistance, transmission of bacteria and their resistance determinants and genome based studies of resistance evolution. This will be combined with social and economic approaches to quantify the burden of antibacterial infection, the behavioural aspects of drug prescribing and use and the risks of mixing of bacterial populations between clinical settings, the community and the food systems that link them. Our approach is to build a strong network of antibacterial surveillance to monitor microbial ecology, and identify hotspots of selective pressure.
Our objectives are:
1) Surveillance in health care settings. We will establish longitudinal and cross sectional surveillance in clinical settings and explore changes in the diversity of bacterial flora with differing care pathways and drug exposure.
2) Community based longitudinal monitoring of ABR in livestock producers. We will recruit commercial farmers in to a series of longitudinal cohorts and monitor their bacterial ecology over time.
3) Microbiological dynamics within the household. We will explore the longitudinal dynamics of bacterial populations in humans, their animals and the immediate farm environment, as well as the products leaving the farms for market.
4) Microbiology and sequencing. We will develop robust microbiological and sequence-based approaches to quantifying bacterial diversity and drug sensitivity
5) Human behaviour and decision-making. We will emphasise the study of the social and economic environment in which antibiotic use takes place, both in domestic animals and humans and develop policy frameworks to limit irrational use.
Our objectives are:
1) Surveillance in health care settings. We will establish longitudinal and cross sectional surveillance in clinical settings and explore changes in the diversity of bacterial flora with differing care pathways and drug exposure.
2) Community based longitudinal monitoring of ABR in livestock producers. We will recruit commercial farmers in to a series of longitudinal cohorts and monitor their bacterial ecology over time.
3) Microbiological dynamics within the household. We will explore the longitudinal dynamics of bacterial populations in humans, their animals and the immediate farm environment, as well as the products leaving the farms for market.
4) Microbiology and sequencing. We will develop robust microbiological and sequence-based approaches to quantifying bacterial diversity and drug sensitivity
5) Human behaviour and decision-making. We will emphasise the study of the social and economic environment in which antibiotic use takes place, both in domestic animals and humans and develop policy frameworks to limit irrational use.
Planned Impact
In our Pathways to Impact document we have outlined partnerships we have enrolled with the ABR policy community in Kenya. Reviewing the recently published National Action Plan on Prevention and Containment of Antimicrobial Resistance, 2017-2022 (Government of Kenya, May 2017), developed in partnership with the Fleming Fund, it is clear that our proposed scientific research is in demand. Quoted below, the Plan's aims include:
- Increasing knowledge and understanding of antimicrobial resistance and antimicrobial use, especially in the healthcare, food, and livestock production sectors;
- Understanding the state of AMR emergence and prevalence, and use of antimicrobials (including surveillance and monitoring), and to assess the risk of emergence;
- Enhancing proper infection prevention and control;
- Ensuring antimicrobial stewardship (AMS) in order to reduce antimicrobial-resistant organisms;
- Accelerating research on the mechanism of AMR emergence and transmission, and its impact on social economy.
Our scientific outputs will be in demand by this policy community to take action in Kenya within the lifespan of the Consortium award, and our programme will be geared towards providing the best quality evidence available.
We will also have impact in training a cohort of future leaders in this field. All the co-Is are committed to training and capacity building, and all manage undergraduate, Masters and PhD level students with diverse funding sources. Aside from registered students, in Kenya, Fèvre's team manages annual cohorts of Kenya Field Epidemiology and Laboratory Training (FELTP) residents, young medical and veterinary clinicians who will benefit from our Consortium phase through specific training on the epidemiology and management of ABR. Already in the Development phase award we will engage 3 such individuals. Birungi, through the BecA Africa Bioscience Challenge Fund (ABCF) hosts emerging scientists from a range of national research institutions, providing mentorship, skills and access to top class facilities. Revathi hosts trainee microbiologists at Aga Khan; our Consortium phase would provide specific training in diagnosis and management of ABR for such trainees. Bukachi is currently engaged with UK-Kenya training in social anthropology. Kariuki is deeply engaged in training cohorts of young Kenyan microbiologists and laboratory technicians. Our activities in Kenya will also provide a template for trainees from across the Horn of Africa funded by our recent RCUK Capability and Capacity Strengthening Award (involving Universities of Liverpool, Nairobi, KEMRI and BecA). The programme will also enhance partnerships between the Kenya-based institutions, providing opportunities for further collaborative activity.
- Increasing knowledge and understanding of antimicrobial resistance and antimicrobial use, especially in the healthcare, food, and livestock production sectors;
- Understanding the state of AMR emergence and prevalence, and use of antimicrobials (including surveillance and monitoring), and to assess the risk of emergence;
- Enhancing proper infection prevention and control;
- Ensuring antimicrobial stewardship (AMS) in order to reduce antimicrobial-resistant organisms;
- Accelerating research on the mechanism of AMR emergence and transmission, and its impact on social economy.
Our scientific outputs will be in demand by this policy community to take action in Kenya within the lifespan of the Consortium award, and our programme will be geared towards providing the best quality evidence available.
We will also have impact in training a cohort of future leaders in this field. All the co-Is are committed to training and capacity building, and all manage undergraduate, Masters and PhD level students with diverse funding sources. Aside from registered students, in Kenya, Fèvre's team manages annual cohorts of Kenya Field Epidemiology and Laboratory Training (FELTP) residents, young medical and veterinary clinicians who will benefit from our Consortium phase through specific training on the epidemiology and management of ABR. Already in the Development phase award we will engage 3 such individuals. Birungi, through the BecA Africa Bioscience Challenge Fund (ABCF) hosts emerging scientists from a range of national research institutions, providing mentorship, skills and access to top class facilities. Revathi hosts trainee microbiologists at Aga Khan; our Consortium phase would provide specific training in diagnosis and management of ABR for such trainees. Bukachi is currently engaged with UK-Kenya training in social anthropology. Kariuki is deeply engaged in training cohorts of young Kenyan microbiologists and laboratory technicians. Our activities in Kenya will also provide a template for trainees from across the Horn of Africa funded by our recent RCUK Capability and Capacity Strengthening Award (involving Universities of Liverpool, Nairobi, KEMRI and BecA). The programme will also enhance partnerships between the Kenya-based institutions, providing opportunities for further collaborative activity.
Organisations
- University of Liverpool (Lead Research Organisation)
- Department of Health and Social Care (Co-funder)
- Veterinary Services Department (Collaboration)
- Ministry of Health (Collaboration)
- INTERNATIONAL FOOD POLICY RESEARCH INSTITUTE (IFPRI) (Collaboration)
- JOMO KENYATTA UNIVERSITY OF AGRICULTURE AND TECHNOLOGY (JKUAT) (Collaboration)
- Farmer's Choice Ltd (Collaboration)
- Aga Khan Hospital (Collaboration)
Publications
Obanda BA
(2022)
Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya.
in Antibiotics (Basel, Switzerland)
Muloi D
(2018)
Are Food Animals Responsible for Transfer of Antimicrobial-Resistant Escherichia coli or Their Resistance Determinants to Human Populations? A Systematic Review
in Foodborne Pathogens and Disease
Hassell JM
(2021)
Socio-ecological drivers of vertebrate biodiversity and human-animal interfaces across an urban landscape.
in Global change biology
Muloi D
(2019)
Epidemiology of antimicrobial-resistant Escherichia coli carriage in sympatric humans and livestock in a rapidly urbanizing city.
in International journal of antimicrobial agents
Muloi D
(2019)
A cross-sectional survey of practices and knowledge among antibiotic retailers in Nairobi, Kenya.
in Journal of global health
Muloi D
(2020)
One Health genomic epidemiology of antimicrobial resistant Escherichia coli carriage in sympatric humans and livestock in Nairobi, Kenya
in Journal of Infection and Public Health
Njoroge SM
(2022)
Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin.
in Microbiology resource announcements
Hassell JM
(2019)
Deterministic processes structure bacterial genetic communities across an urban landscape.
in Nature communications
Muloi DM
(2022)
Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape.
in Nature microbiology
Obanda BA
(2022)
Characteristics of Staphylococcus aureus Isolated from Patients in Busia County Referral Hospital, Kenya.
in Pathogens (Basel, Switzerland)
Worsley-Tonks KEL
(2022)
Strengthening global health security by improving disease surveillance in remote rural areas of low-income and middle-income countries.
in The Lancet. Global health
Hassell JM
(2019)
Clinically relevant antimicrobial resistance at the wildlife-livestock-human interface in Nairobi: an epidemiological study.
in The Lancet. Planetary health
Waage J
(2022)
Changing food systems and infectious disease risks in low-income and middle-income countries.
in The Lancet. Planetary health
Hassell JM
(2017)
Urbanization and Disease Emergence: Dynamics at the Wildlife-Livestock-Human Interface.
in Trends in ecology & evolution
Description | Key information about AMR in an East African context that has led to the design of the National Action Plan in Kenya, with Fleming Fund funding and co-implemented by our team |
Exploitation Route | Design of the National Action Plan for AMR |
Sectors | Agriculture Food and Drink Environment Healthcare |
Description | Public education on AMR through a training video endorsed by the Government of Kenya, and available here https://www.youtube.com/watch?v=T472S-zYZf0 Establishment of the National Action Plan on AMR, which our team are responsible for implementing in the agriculture sector in Kenya Significant new surveillance data for the national reporting systsm |
First Year Of Impact | 2020 |
Sector | Agriculture, Food and Drink,Healthcare |
Impact Types | Societal Policy & public services |
Description | Natioanl AMR Value Chain Survey |
Geographic Reach | Africa |
Policy Influence Type | Contribution to a national consultation/review |
Impact | Conducted a national agricultural value chain survey for antimicrobial drugs in Kenya |
Description | CGIAR AMR Hub |
Amount | $500,000 (USD) |
Funding ID | A4NH CGIAR AMR Hub |
Organisation | International Livestock Research Institute (ILRI) |
Sector | Charity/Non Profit |
Country | Kenya |
Start | 02/2019 |
End | 02/2022 |
Description | Fleming Fund Kenya Country Grant |
Amount | £6,000,000 (GBP) |
Funding ID | MML.574394-01681708-SUB |
Organisation | Fleming Fund |
Sector | Charity/Non Profit |
Start | 08/2019 |
End | 04/2021 |
Description | A4NH |
Organisation | International Food Policy Research Institute (IFPRI) |
Department | Agriculture for Nutrition and Health |
Country | United States |
Sector | Charity/Non Profit |
PI Contribution | Technical expertise |
Collaborator Contribution | Funding for sub-projects (eg on human nutrition in urban value chains), as well as technical staff support and some consumables |
Impact | Interdiciplinary. Outputs still in preparation |
Start Year | 2013 |
Description | Aga Khan |
Organisation | Aga Khan Hospital |
Country | Kenya |
Sector | Hospitals |
PI Contribution | Sharing of expertise and samples |
Collaborator Contribution | Sharing of expertise and samples |
Impact | Materials shared for whole genome sequencing |
Start Year | 2018 |
Description | DVS |
Organisation | Veterinary Services Department |
Country | Kenya |
Sector | Learned Society |
PI Contribution | Training for fresh veterinary graduates who are attached to our programme at no cost to us for 52 weeks |
Collaborator Contribution | Partners are administering contracts for newly qualified vets who are attached to our programme |
Impact | Wide ranging contributions to project outputs more generally |
Start Year | 2018 |
Description | Farmers Choice |
Organisation | Farmer's Choice Ltd |
Country | United Kingdom |
Sector | Private |
PI Contribution | Provision of data and the design of a data capture system for the farms |
Collaborator Contribution | Close collaborative relationship in understanding the pig industry in Kenya; provision of manpower and access to on farm resources. |
Impact | A handheld data collection system developed by a commercial partner |
Start Year | 2018 |
Description | Fleming Fund National Programme in Kenya |
Organisation | Government of Kenya |
Country | Kenya |
Sector | Public |
PI Contribution | We lead the National Fleming Fund partnership on behalf of the implementing funder for the Fleming Fund |
Collaborator Contribution | Funding and samples, personnel and expertise |
Impact | National database National sample collection |
Start Year | 2020 |
Description | Kenya FELTP |
Organisation | Jomo Kenyatta University of Agriculture and Technology (JKUAT) |
Department | Kenya Field Epidemiology and Laboratory Training Program |
Country | Kenya |
Sector | Academic/University |
PI Contribution | We train FELTP residents in our programme |
Collaborator Contribution | Provide 3x full time trainees every year (total of 6 trainees at any given time) at no cost to our programme. Effectively, we are given 6 free members of full time staff. |
Impact | MSc theses x3 so far Papers x 3 in preparation 6x theses expected over the next 2 years |
Start Year | 2015 |
Description | Kenya VMD |
Organisation | Government of Kenya |
Country | Kenya |
Sector | Public |
PI Contribution | We have partnered with the Kenya VMD to undertake a value chain analysis of antimicrobial drugs in Kenya. We provided an intern to undertake data entry, and we provided draft questionnaires and technical input to survey design. We will jointly write a paper. |
Collaborator Contribution | Partner has provided data collected through government funded work. |
Impact | No yet |
Start Year | 2017 |
Description | ZDU Kenya |
Organisation | Government of Kenya |
Department | Zoonotic Disease Unit |
Country | Kenya |
Sector | Public |
PI Contribution | ZDU is a policy partner to whom we have contributed policy advice for national level policy making |
Collaborator Contribution | Facilitation to work in Kenya |
Impact | Formal advice to policy fora. Involvment of the PI in two national task forces. |
Start Year | 2012 |
Description | World Antibiotic Awareness Week 2019 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Kenya Government and FAO Regional World Antibiotic Awareness Week Information event, Theme: Tackling AMR Together; 21-22 November 2019 |
Year(s) Of Engagement Activity | 2019 |