Zoonoses in Livestock in Kenya – The Beginnings of Surveillance

By Steven Kemp, PhD student, University of Liverpool

After a period of intense lab work at both KEMRI and the UK, investigating the patterns of antimicrobial resistance in faecal bacteria isolated from slaughterhouse workers in Busia County and the surrounding areas, I have returned to Kenya to begin the next phase of my PhD project.

ZooLinK is a cyclical programme which aims to set up surveillance systems of both human and animal health sectors over a long period of time. Surveillance of disease is particularly important, as the more information we have, the better we can treat diseases in both human and animal sectors. Recent research by colleagues indicates that the incidence of several zoonotic diseases, including E. coli, Salmonella sp. and others are vastly underestimated.

In recent times, we often hear about how we should now look to conform to the ‘One Health’ approach; this is where, in order to combat issues surrounding antimicrobial resistance and associated issues effectively, intersectoral approaches which share the cost and responsibility evenly between environmental, human & veterinary health professionals is required. In theory, this would be a perfect way to help educate and better promote antimicrobial stewardship.

Currently, I have large amounts of data on access to, use of, and perceptions of antimicrobials from a variety of parties, including animal healthcare workers, district veterinary offices, farmers and agrovet shops. Over the last three months, I have added to this repository by investigating the amounts of antibiotic resistance found in E. coli, which have been isolated from the faeces of workers in 142 slaughterhouses which were selected in western Kenya. These included slaughterhouses in Busia County and the surrounding Kakamega and Bungoma counties.

For the next portion of this study, I am attempting to collect four different sets of samples – to complete the ‘picture’. I will attempt to collect both human and animal faecal samples, from farmers and farm animals, water samples (to determine if there are patterns of resistance in animals which share common grazing grounds) and environmental samples (from the inside of homesteads, where animals are allowed to roam). By covering all of these bases, we will be able to eventually determine not only if there is transfer of antimicrobial resistance between animals and humans and the environment, but also which direction it is going in.

Typical small-holder farm in Funyula, Busia. Most farmers manage between 5-25 cattle.

Example of environment which may also be a good idea to sample in the future. If antimicrobial resistance can be found in the envi-ronment, then why not in wild animals such as these Zebra?

Do livestock have a role in the emergence of disease in urban cities?

One of the primary objectives of the Urban Zoo project is to quantify and understand microbial diversity in an urban setting and to try and link that to urban livestock keeping. In so doing we aim to elucidate the possible role of livestock as a risk factor in the emergence of disease in cities.

To give us a handle on microbial diversity we have chosen commensal Escherichia coli as an indicator species, which we have isolated from samples taken from a diversity of sources across the city of Nairobi. These comprise people and their living spaces, including the food they eat; their immediate environments, including water sources, waste and wildlife; and the livestock that they keep either for their own consumption or for sale. From these samples we isolate and culture E. coli, extract their DNA, and perform whole genome sequencing, enabling us to compare isolates from different compartments and to determine how closely related they are, and thus how microorganisms might pass from one to another.

The collection of these samples has been guided by a highly structured sampling frame, which I described in Urban Zoo newsletter number 7. Essentially, we have selected 33 sub-locations in Nairobi representing a range of social strata and, within each, have chosen 3 households to sample: one with no livestock; one with only monogastric species (pigs or chickens); and one with ruminant livestock (sheep, goats or cattle); You can view the spatial maps at our earlier post by clicking here .

The collection of such comprehensive data from these 99 households was an enormous undertaking and has been a considerable logistical feat of coordination between the field and the laboratory. The good news is that the sampling is now complete, thanks to the heroic efforts of the field team, led by Judy Bettridge and James Akoko, and of our colleagues in the laboratories.

Overall, 2,351 samples have been collected and we managed to culture E. coli from 80% of these (1,850). Once the last few have been done this will give us 1,809 whole genome sequences to analyse. 327 of these are from people; 58 from the places where they prepare food; 64 from animal source foods (milk meat and eggs); 644 from 12 different species of livestock; 239 from the environment around the home-stead including water sources; and 477 from a wide diversity of wildlife in the vicinity of the household.

But it is not over yet. We will very soon have finalised the sequencing and now comes the equally challenging task of deciphering all of this genetic data to unveil the pattern of microbial diversity across Nairobi. Over to you Melissa!

On that note, I would like once again to congratulate the field and laboratory teams, and to wish everyone a great year ahead, 2017.

This article was authored by Dr. Timothy Robinson who is a co-principal investigator in the Urban Zoo project and also a principal scientist with ILRI’s Livestock Systems and Environment research group.

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.

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