This opportunity is no longer open for applications.  Thanks for your interest.Project title: Peri-domestic wildlife in urban Nairobi: ecology and epidemiological role in zoonotic pathogen emergence

(This position was originally advertised, and not filled, in 2012.  Now being re-advertised in 2013).

A PhD opportunity is available for a wildlife disease ecologist, preferably with a relevant Masters level degree, with quantitative skills and with an interest in the epidemiology of pathogen transmission/emergence in natural populations.  The position is based in the Department of Epidemiology and Population Health at the Institute of Infection & Global Health, University of Liverpool (where this research group will soon be based). The studentship will be supervised by Prof Eric Fèvre and colleagues, and will involve working closely with partners in other institutions in the UK and Kenya.  This studentship will involve extensive periods of time in the field in Kenya.

The student will be part of the large, multi-centre “Epidemiology, ecology and socio-economics of disease emergence in Nairobi” (Urban-Zoo) project funded by the UK Research Council Environmental and Social Ecology of Human Infectious Diseases (ESEI) initiative.  Urban-Zoo is an interdisciplinary project aiming to understand the mechanisms leading to the emergence of pathogens into urban populations, and their subsequent spread. The PhD will be co-supervised by members of the project consortium, and will involve working closely not only with the specific expertise relevant to the project, but also with economists, public health and veterinary public health practitioners, social scientists, epidemiologists and urban planners. The project will involve interacting with policy makers and a formal policy advice process in both the UK and Kenya.

The focus of the PhD project will be on the ecology of peri-domestic wildlife species (eg rodents, scavenging birds) in the city of Nairobi, Kenya, and their role in microbial movement through different ecological niches within the city.

Questions to be addressed are:
1) What is the nature of the peri-domestic wildlife interaction with domestic livestock, food products and humans in an urban setting?
2) What is the diversity and community assemblage of both micro-organisms and macro-parasites in the peri-domestic species?
3) How does microbial and parasitic diversity in peri-domestic wildlife change along gradients of human and domestic animal population densities, and other markers of urbanization?
4) Is there evidence of parasite co-infection dynamics in urban peridomestic species?
5) Lastly, could the parasite community assemblage influence the probability of cross species transfer/zoonotic transmission?

Urbanized environments in Africa are melting pots of activity and interaction: the wealthy live alongside the poor; livestock live alongside people; peridomestic species have intimate contact with humans and their waste; human and animal movements take place in internal and externally connected networks. This degree of mixing and contact creates ecological niches with opportunities for pathogen transmission across species.  Urban settings maintain diverse species of peri-domestic rodents and birds (Castillo et al., 2003), and a number of them are likely to be important in the microbial landscape in a city like Nairobi as they not only live in close proximity to humans (Mohr et al., 2007) (Pomeroy, 1975), but they are important scavengers on waste products (refuse, abattoir waste, etc). Thus they may play an important role as liaison hosts (Ashford, 2003) to humans or livestock. This project addresses a set of questions as part of a wider research programme on disease emergence in urban settings.

This successful candidate will work in an interdisciplinary field and laboratory team, and would be expected to master the application of several research tools: there will be a field element, trapping peri-domestic wildlife species (in Nairobi, and elsewhere) using various ecological sampling techniques, habitat mapping, biological sample collection for bacterial culture and macroparasite identification and quantification, followed by microbial typing as well as complete genome sequencing and analysis of SNP data from isolated organisms.

Note: Due to restrictions imposed by the funding body, this opportunities is only open to either a) UK residents (resident in the UK for 3+ years) or b) European Economic Area residents (resident in the EEA for 3+ years).  See the Medical Research Council eligibility criteria for PhD funding for details.  The PhD position is remunerated at the normal MRC rate.

How to apply: By 30 June 2013, interested individuals who meet the eligibility criteria should complete the Preliminary Application Form 2013 and email to Laura Hand ( along with your CV and covering letter stating why you want to study for a PhD, why you believe that you are suitable and why you have chosen the project/s in no more than 400 words.  Please include the name of two academic referees.


Ashford, R.W. (2003). When is a reservoir not a reservoir? Emerging Infectious Diseases, 9, pp. 1495- 1496.
Castillo, E., et al (2003). Commensal and wild rodents in an urban area of Argentina. International Biodeterioration and Biodegradation, 52, pp. 135-141.
Knobler, S., et al (2006). The Impact of Globalization on Infectious Disease Emergence and Control: Exploring the Consequences and Opportunities. Washington: National Academies Press.
Mohr, K., et al (2007). Monitoring rodents movements with a biomarker around introduction and feeding foci in an urban environment in Tanzania. African Zoology, 42, pp. 294-298.
Pomeroy, D.E. (1975). Birds as scavengers of refuse in Uganda. Ibis, 117, pp. 69-81.
Smolinski, M.S., et al (2003). Microbial Threats to Health: Emergence, Detection, and Response. Washington: National Academies Press.
Woolhouse, M.E.J. & Gowtage-Sequeria, S. (2005). Host range and emerging and reemerging pathogens. Emerging Infectious Diseases, 11, pp. 1842-1847.

Image credits:
Dump site with maribou storks: Joel Kanunga
Nairobi landuse map: Nairobi GIS Maps, Center for Sustainable Urban Development

You will be responsible for a range of tasks, including, but not limited to:

  •  Developing the study protocol ensuring compliance with all ethical and governance requirements
  • Drafting applications to the Human Research Ethics Review Board and Institutional Animal Care and Use Committee
  • Establishing and maintaining links with all relevant professionals required to deliver the research project on time and on budget
  • Working closely with project partners in Nairobi’s local authorities to assist with recruitment of individuals to participate in the project, while being guided by the project sample frame.
  • Managing the electronic data gathering system used by the project (Open Data Kit, ODK)
  • Regularly ensuring data integrity and developing and implementing data quality control procedures
  • Taking part in project related research meetings and project management activities
  • Creating a fluid working interface between the field activities and the laboratory activities in the project
  • Take a leading role in determining and conducting appropriate quantitative analyses of the field and laboratory data, and ensuring suitable interpretation of the data.
  • Take a leading role in the drafting of scientific publications; this will involve cross-disciplinary working with other epidemiologists, economists, microbiologists, geneticists, urban planners, social scientists, veterinarians and public health specialists.
  • Producing reports, statistics and charts using the research databases and spreadsheets for relevant audiences
  • Assisting the Project Manager with preparing updates for project partners on a regular basis, including proof-reading content of public dissemination activities (eg project newsletter) and managing the public face of the project through various electronic media.
  • Ensuring Professor Fèvre is regularly informed of study progress
  • Organising, attending and presenting findings at study meetings and/or meetings with the External Advisory Group as appropriate
  • Representing the project with policy and implementation partners in Kenya
  • Representing the project with the funders where appropriate
  • Working closely with the Project Manager to ensure successful delivery of the “99 household study” on time and on budget
  • Participate in the wider academic life of the study team
  • Contributing to appropriate interim and final reports for the funding body
  • Producing peer-reviewed publications
  • Presenting findings at national and international conferences and to other appropriate audiences
  • Developing research ideas and contributing to writing bids for further research grant funding

The Zoonotic and Emerging Disease group studies a range of epidemiological issues revolving around the domestic livestock, wildlife and human interface

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