Letter from the PI: Emergence of pathogens in the human and animal population

It’s a real pleasure to have the opportunity to write for the UrbanZoo newsletter in this first quarter of 2016.  This is a job of the co-PIs on this large project do in turn, and as I wrote for the first newsletter, this must make this issue the 10th so far.

The Urban Zoo project is certainly an exciting and challenging ‘beast.’  Funded by the UK Research Council Environmental and Social Ecology of Human Infectious Diseases (ESEI) initiative, we’ve certainly been deeply engaged in building an evidence base that is allowing us to understand the human, natural, wildlife and social environment of the complex and fascinating city of Nairobi.  Our teams, each led by specific expertise in different leading academic institutions in Kenya and the UK, have lifted the lid on the complex worlds of livestock production, food supply, human nutrition, diarrhoeal disease, wildlife-human-livestock interfaces, microbial genetics, low income settlement patterns and urban planning.  The efforts and energy of the field teams and lab teams in delivering the samples and the data on this project are quite astounding.

The last 18 months have been pivotal for this project.  We’ve been working extremely hard on the “99 household study,” which is described in this newsletter and in other newsletters in this series, and which focuses on mapping bacterial genetic relationships in isolates in a diversity of ecological niches at the household level.  The sample frame is stratified both by type of livestock kept and by socio-economic status.  Material gets selected in the field, at the point of collection, for forwarding for whole genome sequencing (WGS) with our partners in the UK.  It won’t be long now before we have our first WGS-derived phylogenetic tree of E. coli isolated from this part of the project, a major milestone.

The productivity in data gathering in the early years of the project is starting to pay off.  At the last count, there are 15 manuscripts in preparation, with a long string of others awaiting data to come back from collaborators so we can get down to analysis and paper writing.  We’re in negotiations with journals to have special issues bringing some of our key papers together, and have our eye on some very high impact journals to report our key results.  We have been, and continue to be, grateful not only to the ESEI programme for funding this far reaching work, but also to the other funders who have contributed to specific elements, including the CGIAR Research Programme on Agriculture, Nutrition and Health, the Leverhulme Centre for Integrative Research on Agriculture and Health and the funders of several of our PhD students.

With now just over a year to go on this project, we are working hard to understand the mechanisms that may lead to the introduction of pathogens into urban environments, and the emergence of those pathogens in the human population.