Multi-Institutional Collaboration at its best

Multi-Institutional Collaboration at its best

The Epidemiology Ecology and Social-Economics of Disease emergence in Nairobi (ESEI) project has hosted a variety of studies each with different study designs since its conception. MSc students, Mercy Gichuyia, James Macharia and I had the opportunity to work within an aspect of this wider project which involved a cross-sectional study among livestock keeping house-holds in Korogocho and Viwandani informal settlements of Nairobi. We sampled blood and faeces from humans and different livestock species kept in the area and from the faecal samples, identified the prevalence and antimicrobial susceptibility patterns of Salmonella, Campylobacter and E.coli. This article will focus on the interaction with the different team members and partners during our field sample collection. The science we undertook is currently being prepared for publication.


MSc Students, James Macharia Mercy Gichuyia and Maurine Chepkwony

I had the opportunity to work with a large and robust multi-institutional team that was well coordinated and that gave me the best introduction anyone could hope for in how a collaborative project functions. Our typical field day began at 6am where we would be picked from the University of Nairobi, College of Agriculture and Veterinary Sciences by Fredrick Amanya, Lorren Alumasa or James Akoko (all from ILRI).  Our voyage would get us to the heart of the informal settlements where we would meet with a team from the African Population and Health Research Centre (APHRC): Sophie and Jacky, as well as three residents from each area who acted as our security guides and who are known to the chief, elders and the APHRC. These two groups of people were crucial in creating rapport with the households as well as locating the randomly selected households and also acted as guides while navigating the otherwise complex neighbour-hoods.

Lorren and Amanya (both Clinical officers based at ILRI) would give clinical feedback to household members whose laboratory findings required some form of clinical feedback. This acted as community feedback, one of the many community benefits from the project. After a morning of questionnaire administration, collecting human feacal samples (with the help of Fredrick and Lorren) and livestock sampling with the help of Akoko (project field coordinator), we (Mercy, Macharia and I) would then head to the University of Nairobi (UoN) for laboratory isolation and analysis of the livestock samples  while the human samples were transported to the KEMRI-CMR laboratory.

The fatigue from the morning physical work notwithstanding, laboratory work was very exciting owing to the very dedicated and motivating University of Nairobi Laboratory team led by Mr. Nduhiu Gitahi and comprising of Mr. Masinde, Mrs. Mungai, Ms. Wandia, Mrs. Gateri, Mr. Wambaru among others who offered us a lot of guidance and encouragement. The KEMRI –CMR laboratory team was also a huge part of our work and from my standing, a great resource to my work. I learnt several skills from this team particularly antimicrobial susceptibility testing using the agar dilution method from Mr. Ngetich and how to run a PCR as well as analysing of sequence data from Mr. Samuel Njoroge. The two institutional laboratories have very distinct tasks in the project, but the linkages of these activities and support from the Labora-tory coordinator, Dr. John Kiiru, gave me an excellent opportunity to accomplish different aspects of my project as a student since I was able to work in both laboratories with a lot of ease. The contribution of Dr. John Kiiru from KEMRI cannot be overstated especially in the facilitation of this inter-laboratory collaboration ob-served.

Now I understand that it takes a village to make a successful project. Even with the above mentioned activities, a lot went on in the background. The whole urban zoo team was very efficient in the coordinating of activities including field work, and laboratory equipment and reagent acquisitions.  Dr. Victoria Kyallo and Mr. James Akoko were very effective, including Maurice Karani and Patrick Muinde (research technicians based at ILRI) were also instrumental in the project implementation. We were lucky to have supervisors: Prof. Kang’ethe (UoN) and Prof. Fevre (University of Liverpool/ILRI) who were always available and ready to support and guide us whenever we needed assistance in solving problems. I also interacted with Dr. Gemma Wattret from the University of Liverpool who was of great assistance in my Campylobacter research and especially so, in the molecular analysis and Laura Made of University of Liverpool in the study design. I cannot forget Dr. Annie Cook who taught us the ropes of rodent trapping and handling.

Although  this article reports on a successful multi institutional interaction during my experience in the urban zoo project, it is actually an acknowledgement from Mercy, Macharia and myself to the project and, institutions and all the individuals mentioned and not mentioned in this article that were involved in making our Master of Science research projects a success. Working with the urban zoo team was without a doubt a very exciting experience as well as an opportunity for growth both personally and profession-ally. We are very grateful for all your input.

This article has been written by  Maurine  Chepkwony (An MSc student under the Urban Zoo Project, based jointly between University of Nairobi  and International Livestock Research Institute (ILRI) in Kenya). 


Urban Zoo Team-Breaking the barriers

Urban Zoo Team-Breaking the barriers

Managing a large multidisciplinary research team is a challenging task, especially when the teams are based in different organisations that are far apart from each other. This is the situation that Urban Zoonoses project is currently in. The 99 Household Study involves sampling 99 different households in different parts of Nairobi. Primary data and samples are collected by both veterinarians and medics based at ILRI, after which samples are sent to University of Nairobi, ILRI and the Kenya Medical Research Institute laboratories. Isolates from these laboratories are then sent  to Universities of Edinburgh, Oxford, Liverpool for further analysis and full genomic sequencing.


The urban zoo team during a journal club presentation

Proper planning and efficient communication has been the key to ensuring that everything is well coordinated. Team leaders (management or PI’s) from all the collaborating institutions hold fort-nightly teleconferences to update, consult and agree on a unified way of moving forward. It is a common practice for staff to communicate through emails, phone calls, skype and one on one talks with each other. The group has a “WhatsApp group chat” that is used to share updates/progress including photos of both the labs and fieldwork. It is also the easiest and simplest way of sharing information with the entire group. Our active website and the quarterly newsletters, publications and scientific conference presentations are some of the effective means used to ensure that the public is informed of the projects progress and findings.

Staff development and mentoring of young talents, is an area where the project has excelled with several Kenyan staff having either completed or ongoing with their Masters studies in the different collaborating Universities; University of Edinburgh, University of Liverpool, Royal Veterinary College at the University of London. In addition, five MSc students from the University of Nairobi, and six from Moi University through the Field Epidemiology Training program have been supported to undertake their research projects. The project has also attracted a number of European, American and Asian graduate fellows who joined to either gain experience or undertake research projects.


The urban zoo field team on a team building session

Team building sessions, write-shops, journal clubs and support to present scientific findings in both National and International Conferences coupled with inspiration and guidance from our dedicated Project Investigators, post-doctoral fellows and management are some of the ways that have helped in forming a united and dedicated team. Looking back, we all feel like one family, really privileged to be part of this big success!

Article written by  James Akoko and Victoria Kyallo  (Field Coordinator and Project Manager, respectively)

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.

Sampling Kibera chickens-a look at urban farming in its most innovative form

Sampling Kibera chickens-a look at urban farming in its most innovative form

IMG_20160525_122708896Under the Urban Zoo umbrella, we have been sampling chicken farms as well as chicken    meat retailers in Kibera, Nairobi, in order to investigate the prevalence of a food-borne pathogen, Campylobacter. Kibera, said to be the largest urban slum in Africa, is a surprising, challenging and rewarding environment to work in. The constantly evolving environment illustrates urban farming in its most inventive form. Densely populated and very low-income, the urban landscape goes from shiny newly-built roads, public toilets and other community spaces, often sponsored by donors, to muddy alleyways with open sewers and precarious living spaces.

Livestock is part of everyday life. Goats roam everywhere – some even took a nap under our car – as well as chickens, ducks, and sometimes even camels. People are keen to discuss their farming arrangements and projects, or laugh at our interest for the local chickens (kienyeji kukus), which seem so uneventful to them. As sampling is ongoing, results for Campylobacter presence are not yet available. This bacteria, common in chickens, yet not harmful to them, can lead to severe diarrhoea in humans, especially children. Poultry in Kibera often sleep in houses; kids and chickens run alike in courtyards; we have found chicken-raising pens on a shelf, behind doors, above some roofs and in other unexpected places. With such a diverse interface between humans and chickens, it will be valuable to determine the presence of Campylobacter and better understand related public health risks.

Maud Carron

Article by Maud Carron


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

Human, Food and Environmental data collection

Human, Food and Environmental data collection

WhatsApp-Image-20160607Human, food and environmental data are among the wide range of data collected within the 99 households. The data are often collected by Clinical Officers. Human sampling involves among others, individual consenting to participate, questionnaire interviews administration, general physical examination and anthropometric measurements, biological data collection and offering feedback and health education on the outcome of the laboratory based investigations. Two sets of structured questionnaires are administered; a general household and individual participant questionnaires. Biological data that is collected includes fecal samples and nasal swabs. Fecal samples are assessed for E. coli and campylobacter bacteria while nasal swabs are assessed for antimicrobial resistance. Collection and transportation of human samples from the field to laboratories involves sterile techniques.

Like human sampling, sterile steps are also observed during food and environmental data collection. Only livestock sourced foods are collected in the study. A sample of meat, milk and a wipe of egg shells if available, are collected. Sterile wipes of kitchen working surfaces such as chopping boards as well as kitchen door knobs are also collected. Environmental samples are collected using sterile boot socks. Normal saline-wet boot socks are worn and environmental samples collected by walking around the area surrounding the household as well as surfaces within livestock pens if available. Whirl pack bags are used in transportation of environmental samples. Water samples from water puddles, boreholes or storage water tanks are also collected as environmental samples. Subsamples of food and environmental samples are marked with a red dot to identify those going for whole genome sequencing and a blue dot on those being analyzed for campylobacter. All collected data are de-identified using barcode numbers to enhance participant and sample anonymity.

On completion of data collection, participants in the household are either given Albendazole or Mebendazole anthelminthic depending on age. Anyone found to be clinically ill is offered a prescription. If they are seriously ill a written referral letter to the nearest and most preferred health facility for further management is offered. Laboratory outcomes are communicated back to individual participants within two to three weeks of data collection. This is accompanied by health education with emphasis on how to maintain proper hygiene as well as interaction with livestock. Like many other community studies, our study is not devoid of challenges. Some of the challenges encountered involve heavy traffic. As investigators, we have to sometimes anticipate early morning starts. Participants which means rescheduling the day to collect data. Others include withdrawal from participation and inability to access household heads especially in high income settings.

Laureen AlumasaFredrick Amanya

 Article by Lorren Alumasa & Amanya Fredrick

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

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