Epidemiology, Ecology and Socio-Economics of Disease Emergence in Nairobi

There is a global trend towards increasing urbanization. Already, half the world?s population lives in urban areas, and that proportion is rising. It is widely accepted that urbanization, especially when associated with poverty and poor living conditions, increases the risk of disease. Moreover, a number of influential reports have postulated that increased urbanization increases the risk of the emergence of novel pathogens. Though this idea sounds reasonable there is very little hard evidence to back it up: does urbanization really pose a risk of emerging disease and, if so, how? Without this information it is very difficult for policy makers to do anything practical to mitigate any risks that urbanization poses.
We propose a study involving experts in a wide range of relevant subjects to investigate this issue in the specific context of urban livestock keeping in Nairobi, Kenya. We will ask whether there is an association between livestock keeping and diarrhoeal disease in children, but also tackle the broader question of how the presence of livestock affects the microbial ecology of the city: how are the microbial floras of humans, livestock, other animals (such as rodents and birds) and the wider environment related? We will do this by collecting isolates of a ubiquitous bacterium ? Escherichia coli ? from all these environments and undertaking genetic analysis to show how the bacteria are related. This will allow us to determine the ?microbial footprint? of urban livestock and whether this footprint extends to the human population. We propose that novel pathogens are most likely to emerge via the same routes by which humans become exposed to known microbes.

At the same time, we will undertake a series of social and economic studies ? centred on the concept of the ?value chain? (which places supply chains in their socio-economic context) - which will examine the drivers of urban livestock keeping, relate these to other sources of livestock products, and explore how practices are related to supply and demand. This will tell us how the risks are likely to change in the future as urban livestock keeping becomes more widespread and food security more challenging, not just in Nairobi but worldwide. Finally, we will relate the results to policy development: legislation regarding livestock keeping in Nairobi is changing and this study will provide supporting evidence for the potential effectiveness of new regulations, balancing public health risks with the need for food security and income.

Our overall objective is to understand the mechanisms leading to the introduction of pathogens into urban populations, and their subsequent spread. We focus on livestock as sources of these pathogens: 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. It is often claimed that urbanization makes pathogen emergence more likely, but the underlying mechanisms are poorly understood. What is it, exactly, about urban environments that might predispose to an emergence event, and what is the contribution of livestock keeping to this process? We will investigate two key aspects of this. Firstly, 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? Secondly, we will investigate exposure to livestock products traded for food or other purposes. Do supply chains for these products bring people into contact with microbial diversity over and above what they would otherwise experience? Why do people source food from particular places, and what influences the microbial flora to which people are exposed through food? 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? We have created an interdisciplinary team of epidemiologists, microbiologists, urban planners, demographers, social scientists, geographers, public health specialists, ecologists and economists to address these questions, examining in detail the city of Nairobi, Kenya. We will focus on Escherichia coli, an exemplar of many potential emerging pathogens, which exists in a diversity of hosts, in the environment, on food, in waste. We will take a landscape genetics approach to understanding E. coli distribution and spread and how this is affected by environmental and socio-economic factors. Our approach, which builds on state-of-the-art methodologies across a range of disciplines, is likely to become a benchmark for future studies, and will be applicable to a wide range of situations where animals, people and the environment interact. 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.