Image credit: David Mutua, Photographer & Multimedia Producer

Project Overview

With a significant award from the Medical Research Council (UK)-coordinated programme on the Environmental and Social Ecology of Human Infectious Diseases, itself funded through the UK Government’s Living With Environmental Change Initiative, we are undertaking a research programme on the “Epidemiology, ecology and socio-economics of disease emergence in Nairobi.”

The research is focused around the important question of pathogen emergence, and the role of urbanization in the emergence of zoonotic pathogens.  The project is organised around 12 partner institutions in the UK and Kenya (see section on collaborators). A combination of growth and migration is resulting in massive increases in the population of urban and peri-urban (UPU) zones in Africa.  The United Nations has estimated that city populations in Africa will rise from 35% of the total population in 2007 to 51% by 2030. The impacts of this on human welfare, healthcare, sanitation, and other policy-orientated fields has received vast attention, but there has not been a substantive effort to integrate across disciplines, particularly with regard to the impacts of these diverse issues on disease transmission.

The overall objective is to understand the mechanisms leading to the introduction of pathogens into urban populations through livestock commodity value chains, and their subsequent spread. The focus is on livestock as sources of these pathogens, because emerging diseases are likely to be zoonotic in origin, and livestock pathogens, through the close interactions between livestock, their products and people, are at high of risk crossing the species barrier.

The focus in this project is on Escherichia coli, as an exemplar of many potential emerging pathogens, which exists in a diversity of hosts, in the environment, on food, in waste, etc.  The geographical focus is the city of Nairobi, Kenya, and its hinterlands.  In the microbiology components, the project takes a landscape genetics approach to understanding E. colidistribution and spread, with a view to understanding how this is affected by environmental and socio-economic factors.  The project includes a public health component investigating the etiology of diarrhoea in children in low income settlements, centred on the Korogocho and Viwandani slums, part of the Nairobi Urban Health Demographic Surveillance System.


Research Questions

Our broad set of questions include:

  • Does urban livestock keeping pre-dispose people to acquiring new or more diverse microbial flora?
  • Is the risk compounded by poverty status or other social factors?
  • How is the microbial flora influenced by the keeping of livestock in these areas?
  • Do supply chains for livestock and livestock products bring people into contact with microbial diversity over and above what they would otherwise experience?
  • Why do people source food from particular places? What social and economic factors define food sourcing in a complex city?
  • What influences the microbial flora to which people are exposed through food?
  • How does the design of complex urban environments influence exposure to microbial flora?
  • How has the city of Nairobi grown, how does it continue to grow, and how does urbanization in the region affect exposure to microbial diversity in the human and animal population?
  • What is the role of per-domestic wildlife in transmission of zoonotic pathogens and the transport of microbial flora?
  • Why do supply chains exist in the way that they do, and how might they change as demand for products changes with urban growth, or as a consequence of legislation?

The findings will inform development of policy on urban livestock keeping by improving knowledge of the public health risks and by putting those risks in a wider socio-economic context, including the risks associated with alternative sources of livestock products.

PI and co PI's

Prof. Eric FevreEric Fèvre is a Professor of Veterinary Infectious Diseases, Institute of Infection and Global Health, University of Liverpool with expertise in epidemiology of zoonoses at the livestock human interface. View his profile



Jonathan Rushton is an agricultural economist who specialises in the economics of animal health and livestock production and food systems. He is currently involved in global research on One Health and food systems, and has 25 years of international experience of livestock production and the control of animal diseases in South America, Africa and Asia. View his profile


Dr. Cecilia TakoliCecilia Tacoli is a sociologist with interest in urban-rural linkages, food security, migration and gender. She is the Co-Head, Human Settle-ments Group; Team Leader, Rural-urban Development at IIED. View profile


Dr. Catherine Kyobutungi

Catherine Kyobutungi is a clinician and an epidemiologist. She leads the Health Systems and Challenges Research Program at the APHRC. View profile



Prof. Kangethe

Erastus Kangethe is a Professor of Veterinary Public Health at the University of Nairobi. He is a veterinarian with interests in veterinary public health, meat hygiene, urban livestock and zoon-oses and urban development policy in Kenya. View profile


Dr. Delia GraceDelia Grace is a veterinary epidemiologist and food safety specialist at ILRI. She brings exper-tise in applied veterinary public health, food safety and food chain risk assessments and participatory epidemiology. View profile


Prof. Sam Kariuki

Sam Kariuki is currently the Chief Research Scientist and Head of Department, Centre for Microbiology Research at KEMRI in Nairobi. View profile



Prof. Mark Woolhouse

Mark Woolhouse is a Professor of Infectious Disease Epidemiology at the University of Edinburgh in Scotland. View profile



Prof. Julio Davila

Julio Davila is Professor of Urban Policy & International Development, & Director of the Development Planning Unit, University College London (UCL). View profile



Dr. Tim Robinson

Tim Robinson is a Senior Spatial Analyst at ILRI. He maintains the only comprehensive global resource on sub-national livestock statisitcs. View profile



To learn more about our opportunities, please visit our opportunities page.



PI & CO-PI Letters

April 15, 2015The economics thread of the Urban Zoo project began work just over two and half years ago with a visit to Nairobi by Barbara Haesler and Joshua Onono. They returned to London with infor-mation around the complexity of the livestock and meat markets and the different types of animal slaughter. [...]
April 15, 2015The Ebola epidemic currently raging on in West Africa highlights the importance of our urban zoonoses project on the emergence or introduction of zoonotic diseases in urban areas. [...]
April 15, 2015The Planning and Policy Team primarily aims to con-tribute to the Urban Zoo project by tackling the following questions: Are there links be-tween social-environmental and spatial conditions and the micro-bial diversity that people are exposed to in urban and peri-urban areas? What is the planning, economic development and institu-tional context in which zoonotic diseases develop in Nairobi? How is this shaped by social and spatial fragmentation? [...]
April 15, 2015Ongoing work mainly involves the Public Health and Demography thread. In collaboration with APHRC and KEMRI, we are involved in the case control study, in which we are analyzing environmental and food samples. [...]
April 15, 2015Emergence in Nairobi’ project (or ‘Urban Zoo’ for short). We are now almost 2 years in to this interdisciplinary undertaking, and it has been, at once an exciting, frustrating, energizing and stimulating journey so far.I have been hugely impressed with the efforts of our many staff, students, interns and consultants in getting this project off […] [...]
June 15, 2015Two key objectives of the Urban Zoo project are to explore the genetic diver-sity of Escherichia coli within Nairobi city and to explore the links between microbial diversity and urban livestock. This is at the core of the “99 household” study. Choosing 99 house-holds, within 33 sub-locations in Nairobi, has been challenging. It has also been the subject of heated debate during our Urban Zoo annual meetings. [...]
March 12, 2016The Urban Zoo project is certainly an exciting and challenging ‘beast.’ Funded by the UK Research Council Environmental and Social Ecology of Human Infectious Diseases (ESEI) initiative, we’ve certainly been deeply engaged in building an evidence base that is allowing us to understand the human, natural, wildlife and social environment of the complex and fascinating city of Nairobi. Our teams, each led by specific expertise in different leading academic institutions in Kenya and the UK, have lifted the lid on the complex worlds of livestock production, food supply, human nutrition, diarrhoeal disease, wildlife-human-livestock interfaces, microbial genetics, low income settlement patterns and urban planning. The efforts and energy of the field teams and lab teams in delivering the samples and the data on this project are quite astounding. [...]
October 31, 2016In our work we have also sought to build on the decade-long efforts of APHRC in gathering a rich array of primary information on health in informal settlements. We also found that not much attention has been paid in the literature to the planning, policy and structural issues that would appear to play a significant role in reproducing and entrenching endemic pathogenic environmental conditions, conditions that make disease (including zoonoses) prevalent in these settlements. Part of our work has involved outlining the institutions, actors, norms, practices, interactions, their (in) adequacy and complexities around the provision of infrastructure (water, sanitation and solid waste management) that promotes and perpetuates such pathogenic conditions in many parts of Nairobi. We have also sought to examine how legal, policy and institutional realities have influenced urban and peri-urban land use in Nairobi, and how such practices and interventions help shape livestock keeping and farming activities. [...]

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