URBAN ZOO PROJECT: The interesting mix of the 99 household study an interesting and exciting diversity!

NL10-99HH poultry sampling

99 Household; Poultry sampling

Studying zoonoses of livestock and wildlife in an urban setting presents us with a very interesting study site. We collect samples from the slums (the very low income area), middle income areas and the very high income areas of Nairobi, with varied levels of environmental contamination, ranging from areas that are littered with garbage and permeated with open sewerage systems, (often complemented with the infamous ‘flying toilets’) to the very clean areas with high levels of infrastructure and garbage collection systems. We are eagerly anticipating what these radically different, yet often closely neighbouring environments will yield in terms of microbial diversity!

Another exciting variation is on the human, livestock and wildlife interface; there are sub-locations where livestock keeping is illegal, limiting the human-livestock interaction; whereas free ranging animals like goats and pigs are common in other areas, scavenging on rubbish, or grazing public spaces such as playing fields and road verges. Yet other sub-locations are endowed with lots of wild animals as they are neighbouring forests, or generally consist of large, well-established plots with many mature trees and well-tended vegetable gardens.

NL10-99HH low income area

99 Household; Low income area in Nairobi

In any of the randomly selected households, the project team collect a variety of sample types, including human stools, environmental samples, and  animal-source foods, such as meat, eggs or milk; as well as faeces from birds, rodents, and livestock. E. coli can be found in all of these places, but how are the different strains distributed between each of these different ecological niches that are in such close physical proximity? How much sharing of genetic material goes on between these bacterial communities, especially of those genes that give us cause for concern; ones that confer antibiotic resistance or ability to cause serious disease. In every sub-location, we sample one non-livestock keeping household and two households keeping livestock of diverse types. How these different combinations of people and animals in a similar urban environment influence the diversity of pathogens within a household- is another fascinating aspect of bacterial ecology that we hope this project will uncover.

NL10-99HH high income area

99 Household: High income area in Nairobi

The crowded and dusty streets in the low income areas in Nairobi are always full of food vendors selling both raw and cooked foodstuffs, unlike the high-income areas where majority of the residents buy food from supermarkets and high class butcheries. A difference in the food safety risk is anticipated between different types of suppliers of animal source foods, but the degree of this variation and the pathogens involved is something that remains largely unexplored. The 99 Households component of the Urban Zoo project is contributing to this, by starting to map E.coli and Campylobacter at the level of the consumer. We are beginning the next stage; to survey and collect samples along the length of the value chains that deliver meat to the tables of Nairobi citizens. Maud Carron, a PhD student, has this week begun sampling the chicken meat value chains in two contrasting areas of Nairobi, focusing mainly on Campylobacter; one of the leading causes of food-borne diarrhoeal illness in countries with a modern, intensive chicken production system. In the next few months, sampling will be expanded to the ruminant and pig meat value chains – watch this space for news of the next exciting phase of Urban Zoo!

James AkokoAuthored by James Akoko

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

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