Peri-domestic wildlife in urban Nairobi: ecology and epidemiological role in zoonotic pathogen emergence

By 22nd June 2012, interested individuals who meet the eligibility criteria
should send a pdf file - one document - including CV ( 2
pages including the email and name of two academic referees) and a one page
statement of research interests directly to [Email Address Removed], clearly
marking "ESEI PhD Project 2" in the subject line.

We are seeking a biologist/ecologist, preferably with a relevant Masters
level degree, with quantitative skills, and an interest in the epidemiology
of pathogen transmission. To be registered at the University of Edinburgh,
and part of collaborators research groups at the University of Nairobi, the
International Livestock Research Institute and the University of Liverpool.
This studentship would involve extensive periods of time in the field in
Kenya.

Urbanized environments in Africa are melting pots of activity and
interaction: the wealthy live alongside the poor; livestock live alongside
people; human and livestock waste is poorly disposed of near food production
areas; formal and informal trading take place in
internal and externally connected networks. This degree of mixing and
contact creates ecological niches with opportunities for pathogen
transmission.

Approximately 60% of human pathogens are zoonotic, and approximately 80% of
novel pathogens have zoonotic origins. Additionally, urbanization is likely
to make pathogen emergence more likely, but the actual mechanisms for this
happening are poorly understood.

This project would address a set of questions as part of a wider research
programme on disease emergence in urban environments. The focus would be on
the ecology and role of peri-domestic wildlife species (eg rodents,
scavenging birds) on transmission of pathogens between livestock, humans and
the environment in a study site in the city of Nairobi, Kenya. Questions to
be addressed are: 1) What is the diversity and community assemblage of both
micro-organisms and macro-parasites in the peri-domestic species? 2) What
is the nature of the peri-domestic wildlife interaction with domestic
livestock and humans in an urban setting? 3) How does microbial and
parasitic diversity in peri-domestic wildlife reflect the diversity in local
human and domestic animal populations, and the wider environment? 4) Lastly,
could the parasite community assemblage influence the probability of cross
species transfer of zoonotic transmission?

Urban settings maintain diverse peri-domestic rodent and bird species, 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, but
they are important scavengers on waste products (refuse, abattoir waste,
etc). Thus they may play an important role as liaison hosts to humans or
livestock.

This student will work closely with biologists working on natural
host-parasite communities, co-infection and disease emergence. The project
will involve the mastery, development and application of several research
tools. There will be a field element, trapping peri-domestic wildlife
species (in Nairobi, and elsewhere), the use of various ecological sampling
techniques, and 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.