Letter from the PI: Introducing the ZooLink Suite of Projects

Letter from the PI: Introducing the ZooLink Suite of Projects

Prof. Eric Fèvre

Prof. Eric Fèvre

It’s a real pleasure to write the first “Letter from the PI” for the Zoonoses in Livestock in Kenya (ZooLinK) project, part of the Zoonoses in Emerging Livestock Systems programme, funded by the UK Research Councils (led by the BBSRC), UK DFID and UK DSTL.

Our project has been underway since 2015, engaged in planning and staffing, followed by refurbishing of our field lab and the commencement of field activities in Kenya.  It’s satisfying, a year and a half in, to now be able to start reporting on how we are doing and what we are up to. While we have been and will continue to share updates through social media on a regular basis, our project newsletters serve to provide slightly more indepth ongoing reporting of our work.  Newsletter articles will also appear on our project website as blog articles – we are active on social media both on the web at www.zoonotic-diseases.org and through twitter @ZoonoticDisease, with #zels #zoolink.

Dr. Laura Falzon has been appointed as our postdoctoral epidemiologist, leading activity in our field sites.  Laura is co-ordinating scientific activity at our primary laboratory, based in the town of Busia, on Kenya’s border with Uganda. The lab houses BSL-2 standard biosecurity and is fully spec’ed for basic parasitological diagnostic work, serological assays, PCR and molecular diagnostics and microbiological assays.  Later this year, we’ll have some exciting DNA sequencing capacity there too. Samples are flowing through this laboratory where a number of our project scientists are working, and two Masters theses have already resulted from this ongoing work (projects undertaken by Isaac Ngere and Maurice Omondi on arboviruses and Fasciola spp– see our blog). Dr. hristine Mosoti is our ZooLinK project manager, and is the primary point of contact for any external queries on the project.

While the ZELS programme does not directly fund PhD students, we’ve successfully attracted a real diversity of academic interests to our programme with some innovative co-funding mechanisms.  Ten PhD students are currently active in the programme, some nearing the end of their first year, others just beginning their studies, on topics as wide ranging as within household economics to genetic diversity of parasites – we’ll ensure that the students’ work is highlighted regularly in the student’s section of this newsletter – see Jessica Floyd’s entry in this edition.

We’ve been engaging very successfully with the national veterinary system too, with two seconded members of County Veterinary Staff attached to our project and so far two cohorts of Animal Health Diploma holders coming through on 3 month “One Health” graduate internships.  Elsewhere in Kenya, we’re investing, with our national partners, in the surveillance of several other zoonotic disease issues: we put significant effort into surveillance for Rift Valley Fever during the rainy season early this year and in to understanding the epidemiology of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in camelids and humans.  We’ve also been working on enumerating and vaccinating dogs for rabies in central Kenya.  Much work, and many challenges lie ahead, but our excellent team is already proving that it can face these challenges successfully, and I am very proud of the excellent interdisciplinary work that we are doing.

Dr. John Kiiru: My experience as a Post Doc

Dr. John Kiiru: My experience as a Post Doc

I joined the Urban Zoo Project in June 2014 as a laboratory coordinator. The Urban Zoo study is a collaborative project bringing together experts from various institutions in the UK (University of Liverpool, The Royal Veterinary College, University of Edinburgh etc.),  and at least three institutions in Kenya (The University of Nairobi (UoN), International Livestock Research Institute (ILRI) and the Kenya Medical Research Institute (KEMRI). The Team in ILRI handles the fieldwork while the teams at KEMRI and UoN handle the lab work. My main responsibility has been to develop standard protocols for use in the two labs and to ensure that the data generated is not only robust, but accurate. The two labs have approximately 10 technicians, numerous students on attachments and a number of interns from Kenya and the UK.

esei-meeting

With Lord Alexander Trees in London during an ESEI meeting

In order to appreciate the uniqueness of zoonoses, it is important to realize that there are approximately 600 pathogens which are known to infect humans and 61% of these cause zoonotic diseases. Zoonotic bacteria originating from food animals can reach people through direct faecal oral route, contaminated animal food products, improper food handling, and inadequate cooking.  These diseases have a negative im-pact on travel, commerce, and economies worldwide. It has been my view that the unique dynamic interaction between the humans, animals, and pathogens, sharing the same environment should be considered within the “One Health” approach, which dates back to ancient times of Hippocrates. The Urban Zoo project combines mapping, sampling from humans, animals and their environment, determination of antimicrobial resistance profiles and whole genome sequencing of isolates obtained from human and environmental sources. Joining this study therefore gave me that unique opportunity to gain a lot of insights in this subject.

The very fact that this study brings so many experts with unique expertise together makes Urban Zoo project unique. Work-ing with different labs requires substantial managerial skills and the need to consult and reach consensus on all major issues that impact on the quality of the data generated. Through my engagement in the study, I have not only gained considerable organization/leadership skills, but also better communication skills. My participation in this study has also impacted positively on my career and I have been invited as an expert in antimicrobial resistance as a trainer in international workshops by the WHO, the Welcome Trust Advanced Courses and for the drafting on a situation paper by the FAO on application of whole genome sequencing of foodborne pathogens in developing countries.

This article has been written by  John Kiiru (Post Doc under the 99HH Study, based jointly between the KEMRI 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.

journal-club-presentation

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 www.zoonotic-diseases.org 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.

team-building-session

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.

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