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.

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.

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!

Authored by James Akoko