Co PI’s Letter: Planning and Policy Thread

Co PI’s Letter: Planning and Policy Thread

Prof. Julio D. Davila

Prof. Julio D. Davila

Our projects policy team aims to examine the links between social-environmental and spatial conditions and the microbial diversity that people are exposed to in urban and peri-urban areas. It also seeks to outline the institutional and planning context in which zoonotic diseases develop in Nairobi, and how this is shaped by spatial fragmentation.

In cooperation with Slums Dweller International-Kenya and APHRC, the Team previously collected data through a variety of means, including co-producing knowledge with local communities. In partnership with IIED, we have produced working papers, conference papers and policy briefs to showcase the results, with some currently being submitted to journals. Under the guidance of Prof. Muki Haklay and Dr. Sohel Ahmed, UCL post-graduate student Maayan Ashkenazi wrote a fascinating MRes dissertation on the different livestock keeping strategies by women in the low-income settlement of Mathare. She found that these not only vary according to the women’s economic abilities but along multi-scalar social and social characteristics arising from living in different villages within Mathare.

In 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.

To that effect, earlier this year Dr. Sohel Ahmed conducted a series of interviews with research scholars, planners and policy makers in Nairobi. The results suggest that urban and peri-urban agriculture, including livestock keeping, are still not considered a legitimate urban land use neither in the Nairobi Master Plan and land-use maps, nor in the daily practice of local government officials. As a result of antagonistic views towards pro-poor informal farming from planners and other powerful actors, we argue that urban agriculture, particularly livestock keeping in Nairobi and its periphery, is unlikely to survive the effects of the rapid increases in land prices seen in Nairobi in recent years. This is partly the result of a lack of reliable investment alternatives, but also the result of inadequate or non-existent land-value capture mechanisms and an effective regulatory framework that guides growth and allows price increases to be re-invested in much needed infrastructure that benefits the city as a whole. Rapid urbanisation is accompanied by continued land speculation, rapid appearance of multi-storey buildings and conversion of large tracks of agricultural land to urban uses. As tracts of land become sub-divided into smaller plots, there is an observable shift to zero-grazing forms of livestock keeping (e.g. poultry). Hence, livestock and their material flows (i.e. meat, dairy and poultry) are continuously moving further away from central Nairobi.

Despite the 2010 constitutional reform allowing Nairobi County to prepare its own plan and control development under an ‘integrated development planning’ framework, in reality the County has little say over where new infra-structure, particularly electricity and roads, should be located. Water, roads and electricity are controlled by para-statals, thus taking away from the County government the power to decide on crucial components of its current and future growth. The County’s chronic institutional and resource deficiencies mean that the city will continue to allocate resources in such a way that mostly benefits a minority of residents, thus entrenching an east-west socio-economic divide. The inadequate and unsafe provision of water, sanitation and solid waste management has severe public health consequences for residents of poorer areas. Poor infrastructure places some people and their livestock at increasing risk of communicable diseases, and helps reproduce the conditions leading to chronic expo-sure to higher microbial diversity.

Julio D Dávila is Professor of Urban Policy and International Development, and Director of the Development Planning Unit, University College London.

Letter from the Co-PI: Public health and demography and economic threads

Letter from the Co-PI: Public health and demography and economic threads

Prof. Kangethe Eratus

Prof. Kang’ethe Eratus

Epidemiology Ecology and Social-Economics of Disease emergence in Nairobi (ESEI) is a project that has been implemented in Nairobi city for the last five years. In this newsletter I would like to review the public health and demography and economic threads of the research Project. At the outset, I wish to state that this is not sharing of the results obtained, as this is an on-going activity. The project uses E. coli as an exemplar to understand the processes and the pathways of pathogen introduction in the population through animal source foods.

Nairobi consumers obtain animal source foods from a varied number of pathways. It is imperative to understand these pathways by studying product value chains. These value chains are key to linking consumers to livestock and therefore the risk of transmission of microflora between them. Value chain analysis includes describing, mapping (directional).

understanding the governance and upgrading of the value chain. Red meat, poultry and milk value chains were targeted for this analysis. Sampling will be done at particular nodes of the value chains to isolate, phenotypically and genotypically characterize E. coli. Additionally, antimicrobial resistance profiles and genes associated with the resistance will be determined. To understand the mobility of the isolates between different animal and human populations is being undertaken by whole genome sequencing.

The project has also undertaken to understand the spatial distribution of E. coli among the different cross-sections of population in Nairobi. We are seeking to understand whether socio-economic stratus influence the spatial distribution or how keeping livestock  or contact with livestock may influence this distribution. Nairobi was divided into 7 economic zones based on income and a total of 99 households from 33 sub-locations are being sampled. Of the three households one has large livestock, one no livestock and one small livestock. The 99 households residents are interviewed, clinical examination, and food consumption and economic data collected as well as fecal samples from the livestock and humans, food, environmental and water samples from surface pools collected for E. coli isolation and characterization.

Sample analysis takes place in two laboratories at the University of Nairobi that analyses all the livestock and environmental samples and Kenya Medical Research Institute analyses human samples. Synthesis of the data will help answer the questions set out under these two threads.


This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.

Letter from the PI: Emergence of pathogens in the human and animal population

Letter from the PI: Emergence of pathogens in the human and animal population

It’s a real pleasure to have the opportunity to write for the UrbanZoo newsletter in this first quarter of 2016.  This is a job of the co-PIs on this large project do in turn, and as I wrote for the first newsletter, this must make this issue the 10th so far.

The 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.

The last 18 months have been pivotal for this project.  We’ve been working extremely hard on the “99 household study,” which is described in this newsletter and in other newsletters in this series, and which focuses on mapping bacterial genetic relationships in isolates in a diversity of ecological niches at the household level.  The sample frame is stratified both by type of livestock kept and by socio-economic status.  Material gets selected in the field, at the point of collection, for forwarding for whole genome sequencing (WGS) with our partners in the UK.  It won’t be long now before we have our first WGS-derived phylogenetic tree of E. coli isolated from this part of the project, a major milestone.

The productivity in data gathering in the early years of the project is starting to pay off.  At the last count, there are 15 manuscripts in preparation, with a long string of others awaiting data to come back from collaborators so we can get down to analysis and paper writing.  We’re in negotiations with journals to have special issues bringing some of our key papers together, and have our eye on some very high impact journals to report our key results.  We have been, and continue to be, grateful not only to the ESEI programme for funding this far reaching work, but also to the other funders who have contributed to specific elements, including the CGIAR Research Programme on Agriculture, Nutrition and Health, the Leverhulme Centre for Integrative Research on Agriculture and Health and the funders of several of our PhD students.

With now just over a year to go on this project, we are working hard to understand the mechanisms that may lead to the introduction of pathogens into urban environments, and the emergence of those pathogens in the human population.

Eric 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

Co PI’s Letter: Microbiology Thread

Co PI’s Letter: Microbiology Thread

On a dark and cold November afternoon, Edinburgh feels very far from Nairobi and the UrbanZoo project. But I like to think that we still have a useful contribution to make, not least by helping to put together different pieces of research together to reveal the “big picture”. It is going to be a very unusual picture though; we want to construct a kind of map of Nairobi from the point of view of a ubiquitous bacterium, Escherichia coli. We want to find out where different strains of E. coli live and how they move through the different compartments that make up Nairobi: healthy people  in the community, sick children in clinics, wildlife, food, water and waste and especially the livestock species that live in the city.

Those urban livestock are central to UrbanZoo: we want to know how they fit into the ecology of E. coli in Nairobi and, in doing so, we hope to illuminate a general theme of the entire ESEI programme (of which UrbanZoo is one of 3 funded projects). We will be testing the idea that urban livestock are a risk factor for outbreaks of emerging diseases (not just E. coli-related disease) in cities everywhere.

Though often stated, that hypothesis has rarely been tested. It might not even be true: we shall see. It all starts with the highly structured collection of samples by the field teams, who are systematically working their way around Nairobi as they conduct the 99 Household survey. The microbiology teams will then give us a first glimpse of the big picture by carefully typing the E. coli isolated from those samples.

That work is vital, but although standard typing methods can tell us whether two samples share similar kinds of E. coli, they often cannot tell us the direction of movement. For example, if samples from a child and a pig in the same household contain very similar E. coli, does it mean that the pig infected the child, the child infected the pig, or they were both infected from some other source? The state-of-the-art tool for answering those questions is kind of statistical analysis called phylodynamics. Our phylodynamic analyses will use two kinds of information: whole genome sequences of UrbanZoo E. coli; and the metadata – place, time and host
species in particular – that go with those sequences.

That is why everyone is working so hard to obtain the best possible set of isolates for sequencing and all the field and typing data that go with them, why we are spending so much money on whole genome sequencing, and why Melissa Ward is devoting so
much of her time to doing the phylodynamics analyses.

Over the next 12 months or so we hope to build up a collection of E. coli sequences that is by far the best of its kind in the world and that gives us completely new insights into the ecology of the bacterium within the extremely complex ecosystem that is Nairobi. We hope to reveal a picture that no one else has ever seen before. I can’t wait.

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

Co PI’s Letter: Planning and Policy Team

Co PI’s Letter: Planning and Policy Team

Dr. TacoliThe Planning and Policy Team’s work focuses on the socioeconomic and environmental conditions that contribute to the diversity of microbial exposure of urban residents. It is estimated that 60 percent of Nairobi’s residents live in informal settlements, where inadequate housing, insufficient basic infrastructure and services and widespread livestock keeping translate into severe environmental hazards. Understanding how this affects local residents’ exposure to microbial diversity is key in formulating and implementing appropriate policies.

Much has happened since the last letter from the Team in April. We have continued to support the work of the Kenyan Federation of the Urban Poor, Muungano wa Wanavijiji, thanks also to additional funding from the UK Department for International Development. Building on the piloting of innovative participatory methodologies, researchers decided to focus more on food street vendors, for several reasons. The first is the central role of food vendors in providing cheap food to residents of informal settlements who often do not have space to cook and store food, nor time to prepare meals at the end of long working days. Street vendors also play an important role in the social life of the settlements, by congregating along the main roads until late at night and in this way increasing security for those residents, especially women, returning home after dark. Because of its flexible working hours and minimal need for starting capital, selling food, either raw or cooked, is also one of the main sources of income for women, especially those responsible for young children and sick relatives.

But while they may not be harassed by the authorities like their colleagues working in the ‘formal’ part of the city, street vendors within informal settlements face several challenges which can also generate health risks to their customers. These include food contamination due to proximity to solid waste dumps, open air sewers and roaming
livestock; limited access to water – in many cases only available at high prices from private vendors –to wash food, hands and utensils thoroughly; inadequate public lighting and high levels of insecurity that can prevent sellers, especially women, from selling after dark. Such issues require holistic interventions that address both socio-economic and environmental conditions. Documenting the challenges and setting up vendors’ associations that can establish a dialogue with local authorities to develop appropriate interventions are key steps, as described in a new working paper: Cooking up a storm: Community-led mapping and advocacy with food vendors in Nairobi’s informal settlements .

Another step has been the joint organisation with our Urban Zoo partners APHRC and ILRI of a series of ‘training of trainers’ on food safety and handling for street vendors and Muungano members, the first of which took place in July. Collaboration between grassroots organisations and scientists in the project enriches our understanding, and helps
identify ways in which research can inform and stimulate action.

Dr. Cecilia Tacoli is a Principal researcher, Human Settlements Group and a team leader, rural-urban development at IIED.

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