Wildlife is considered a significant reservoir of emerging infectious diseases; 70% of emerging zoonoses have a wildlife origin. This element of the UrbanZoo project focusses on the role that synanthropic wildlife (species that live in close association with humans) play in the epidemiology of disease emergence. These animals are abundant in cities, with different species occupying a variety of ecological niches; mammals such as rodents have small home ranges and are thus restricted to localised areas such as households, whilst birds and bats may forage over considerable distances for food. Interfaces that bring humans and livestock into contact with wildlife are proposed to be at ‘high-risk’ of EID spill-over to humans. This component therefore aims to assess the importance that wildlife play in disease transmission at ‘interfaces’ across Nairobi, where contact between humans, livestock and wildlife may potentiate disease transmission (Table 1).

Documenting pathways of transmission between wildlife, domestic animals and people

In many developing cities livestock are kept within household premises, resulting in close contact with humans and creating a resource-rich environment for wildlife to exist in. The first part of wildlife sampling will focus on these informal livestock-keeping practices in Nairobi as a key interface across which EID’s might be transmitted. By comparing the genetic similarity of E. coli in samples collected from humans, livestock and wildlife within each household, we aim to assess the significance of this interface for disease transmission. Wildlife sampled will include birds, bats, rodents, meso-carnivores and non-human primates. The study will be conducted in 99 households, representing a range of informal livestock-keeping practices in different socioeconomic conditions throughout Nairobi.

Assessing the relative importance of wildlife species, and their role in the transmission of gastrointestinal bacteria, at proposed EID interfaces across the city of Nairobi

Interfaces that bring humans and livestock into contact with wildlife, which in doing so may facilitate EID spill-over from wildlife reservoirs, also exist on a wider scale across urban landscapes. Wildlife may be attracted to human activity that increases resource provision (i.e. rubbish dumps, sewage works and agricultural land) whilst human encroachment into natural habitats may directly increase contact with native wildlife (i.e. forest edges, national parks). This aspect of the project will focus on sampling wildlife at a selection of these interfaces. Here we are interested in using whole genome sequencing to develop phylogenies and network models to assess how E. coli genetics in wildlife varies according to the interface at which they exist, and thus less on the particular dynamics of transmission between wildlife, humans and livestock. In addition to collecting fecal samples for E. coli isolation from wildlife, we are also taking the opportunity to collect a range of other biological samples (oral swabs, whole blood, serum, urine etc.) for future pathogen work. In order to collect the appropriate samples, most animals will be caught live and sampled before being released, whilst a subset of rodents and bats will be anaesthetised for humane euthanasia and post mortem examination.

For the wildlife sampling aspect of the project we are working closely with the following collaborators: National Museums of Kenya and Kenya Wildlife Services

By Dr. James Hassell