Update: 99 Households study: wildlife component

Update: 99 Households study: wildlife component

Wildlife 2As we approach the final quarter of the 99 household study, it is a pleasure to be asked to reflect on the wildlife sampling component of this study. The wildlife sampling team has come a long way since its inception in September 2015, when we were all relative novices in trapping Nairobi’s diverse array of wildlife species. We have had some long days and sleepless nights, but to their credit, the enthusiasm of those involved has never waivered.

A typical day for the wildlife team starts at 5am, when we embark on bird sampling. To ensure we follow best practice for all of our trapping we collaborate with experts at the National Museums of Kenya, and in the mornings Titus Imboma (an ornithologist from the museums) helps us set up an array of mist nets, aimed at trapping birds as they fly in proximity to the household and livestock-keeping areas of each compound. Once caught, each bird is placed in a paper bag to collect a faecal sample, before a number of other body measurements and biological samples are collected. Such opportunistic sampling is a common philosophy among wildlife Table 1-Taxadisease ecologists, and additional samples provide an important resource for future epidemiological work. We next check the rodent traps – we use live-capture Sherman traps which are set throughout the house, livestock-keeping facilities and the household compound. Any rodents that we catch are transported back to the lab at ILRI, where they are humanely euthanized and subjected to a post-mortem examination (PME). This procedure is used to permit the collection of fresh faeces and organ samples which are stored frozen and in formalin. The latter ensures that tissues from these animals are preserved for histopathological interpretation, should the need arise in the future. As dusk settles over Nairobi, the sampling team heads back to the house to trap bats.

The techniques used to trap bats are vey similar to those for birds; very fine mist nets are suspended between fly-ways where bats seek their food (either insects or fruit depending on the species of bat). Due to their propensity to bite, bats present a challenge to remove from the nets and restrain during sampling, but with the appropriate techniques and equipment (i.e. tough gloves!) they can be safely held to collect measurements and samples. We sacrifice a maximum of two bats each night, which are taken back to the lab at ILRI for PME. The rest are sampled live, and released Wildlife 4unharmed. When we encounter a bird or bat roost, we use tarpaulins spread underneath the roost in order to collect pooled faecal samples representative of the individual animals using the roost.

Something that has become evident as we move from house-to-house, navigating Nairobi’s  maze of leafy suburbs, high-rise apartments and river-side slums, is the shear diversity of wildlife habitat present in this city. This is reflected in the number of species (birds, rodents, bats, primates and carnivores) we have sampled to date (see table 1). All of these species inhabit different ecological niches which likely govern their levels of interaction with humans and livestock; as an example one would expect very different levels of interaction between house rats that scavenge on animal feed and sunbirds that rely on nectar. How this translates to the risk of disease transmission is something we hope to shed light on by studying the genetic diversity of E. coli in these wildlife, and comparing it to those from humans, livestock and the

James Hassell

Article By James Hassell


This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.

Update: 99 Household study update

Update: 99 Household study update

Well, time has flown since we sampled the first household in the 99 households study. On 7th June we visited our 66th household, meaning that after 8 months we are now two thirds of the way through. The project is taking us to all parts of Nairobi, as the maps illustrate. The field teams normally spend Monday to Wednesday collecting data, then use Thursdays and Fridays to recruit new households to the study, meet with local chiefs and county officials, give feedback to participants and keep on top of all the other jobs, such as vehicle maintenance, stock-keeping, accounting and paperwork. The wildlife team regularly go out on evenings and weekends to set and check traps for rodents and bats (who inconveniently refuse to venture out during normal working hours!) In some areas it has occasionally been necessary to conduct the study interviews in the evening, when participants return from work. Having to be flexible to fit around our human and animal participants’ needs, plus the perennial problem of Nairobi traffic, means early starts and long days.

The laboratory teams also come in for their share of hard work. Even with motorbike couriers, samples normally do not arrive at the labs until the afternoon, especially when large households are sampled. To process all these samples takes time. Each sample is first incubated in an enrichment broth, then undergoes two rounds of purification on a special type of agar which selects for E. coli, before being cultured on a more general agar prior to freezing the bacteria for storage. As you may imagine, this is several days’ work – each step takes at least 24 hours – and of course the bacteria don’t stop growing at weekends! Timing of steps is crucial, to ensure that pure colonies can be selected for storage. Later on, batches of isolates are revived and a number of biochemical tests are performed, to check that the bacteria we send to the UK for sequencing really are the E. coli that we are interested in. Once we are reasonably sure that what we have is an E. coli, they have to be regrown once more so that they can be sent to ILRI, where the DNA is extracted to send to the sequencing facility at Oxford.

So as you might imagine, it is extremely gratifying to finally start to see some of the results of all this hard work. Dr. Melissa Ward recently visited the teams in Nairobi and brought with her some of the first outputs of the sequencing to show us. In return, we took her along to see the sampling in action, in one of the slum sites. Melissa said, “It really brings the project to life, to see exactly how all the data and the samples are collected. Now, when I sit at my computer, I can really understand where it’s all coming from.” For us, it was equally exciting to get some tantalising glimpses of what the final dataset might look like and what kind of patterns we may be able to identify from the phylogenetic structure and genomic data. We’re not giving anything away at this stage – but we can tell you that we definitely have E. coli – and lots of it!

Judy_BettridgeArticle by Judy Bettridge

This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.

Click to view enlarged maps

Map ruminants
Map poultry
Map monogastrics

Letter from the Co-PI: Public health and demography and economic threads

Letter from the Co-PI: Public health and demography and economic threads

Prof. Kangethe Eratus

Prof. Kang’ethe Eratus

Epidemiology Ecology and Social-Economics of Disease emergence in Nairobi (ESEI) is a project that has been implemented in Nairobi city for the last five years. In this newsletter I would like to review the public health and demography and economic threads of the research Project. At the outset, I wish to state that this is not sharing of the results obtained, as this is an on-going activity. The project uses E. coli as an exemplar to understand the processes and the pathways of pathogen introduction in the population through animal source foods.

Nairobi consumers obtain animal source foods from a varied number of pathways. It is imperative to understand these pathways by studying product value chains. These value chains are key to linking consumers to livestock and therefore the risk of transmission of microflora between them. Value chain analysis includes describing, mapping (directional).

understanding the governance and upgrading of the value chain. Red meat, poultry and milk value chains were targeted for this analysis. Sampling will be done at particular nodes of the value chains to isolate, phenotypically and genotypically characterize E. coli. Additionally, antimicrobial resistance profiles and genes associated with the resistance will be determined. To understand the mobility of the isolates between different animal and human populations is being undertaken by whole genome sequencing.

The project has also undertaken to understand the spatial distribution of E. coli among the different cross-sections of population in Nairobi. We are seeking to understand whether socio-economic stratus influence the spatial distribution or how keeping livestock  or contact with livestock may influence this distribution. Nairobi was divided into 7 economic zones based on income and a total of 99 households from 33 sub-locations are being sampled. Of the three households one has large livestock, one no livestock and one small livestock. The 99 households residents are interviewed, clinical examination, and food consumption and economic data collected as well as fecal samples from the livestock and humans, food, environmental and water samples from surface pools collected for E. coli isolation and characterization.

Sample analysis takes place in two laboratories at the University of Nairobi that analyses all the livestock and environmental samples and Kenya Medical Research Institute analyses human samples. Synthesis of the data will help answer the questions set out under these two threads.


This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.

Kenya Field Epidemiology and Laboratory training (FELTP)

Kenya Field Epidemiology and Laboratory training (FELTP)

NL10-FELTP community outreach

Cohort 12 residents participating in a class group activity to assess community knowledge, attitude and practices towards cholera, Machakos County, November 2015

The Kenya program is the first FELTP to be started in Africa in 2004, and its objective is to strengthen in-country public health systems and infrastructure.  It is anchored within the Department of Promotive and Preventive Health in the Ministry of Health (MOH) and trains field epidemiologist for the Ministry of Health and Ministry of Agriculture, Livestock and Fisheries (MALF).

It’s an experiential based training with 30% classwork and 70% hands on field experience and service provision culminating into a Master of Science Degree in Field Epidemiology from Moi University. The program embraces the One Health approach by  bringing together physicians, veterinarians, laboratory scientists, Nurses and environmental health professionals who are trained together and given the skills to effectively address the ever-growing threats of zoonotic diseases, Non communicable Diseases (NCD’s) and other emerging and re-emerging infections.

While in training, the residents are attached to various divisions, programs and units within MOH and MALF and other partner organizations in order to achieve the desired competencies/skills which include analysis of data from a surveillance system/evaluation of a surveillance system, scientific communication, and investigations of acute public health events and planned public health epidemiologic study. The residents have contributed significantly to investigation of major outbreaks in the country including polio, measles, aflatoxicosis, Ebola preparedness and screening at the port of entry. They have also participated in disease outbreak investigations across Africa, for instance Rift Valley Fever outbreak in Swaziland, Cholera outbreak in Zimbabwe and Cameroon, and Ebola and Marburg outbreaks in Uganda, Sierra Leone, Liberia and Guinea.

In recognition of the need to increase capacity in epidemiology among all cadres of public health workers, FELTP started 2-3 months training in basic level epidemiology for county medical and veterinary health care workers. The basic epidemiology trainings take place in selected venues on specified dates in various Counties. Since its inception over 300 participants from over 20 counties have been trained.

FELTP started a partnership with the ZED Group in ILRI where some of the FELTP residents at advance level training are  attached at ZED group/ILRI for their field placement. Currently, there are six residents attached at the ZED Group/ILRI. The ZED group has been hosting FELTP residents from cohort 11 onwards.

URBAN ZOO PROJECT: The interesting mix of the 99 household study an interesting and exciting diversity!

URBAN ZOO PROJECT: The interesting mix of the 99 household study an interesting and exciting diversity!

NL10-99HH poultry sampling

99 Household; Poultry sampling

Studying zoonoses of livestock and wildlife in an urban setting presents us with a very interesting study site. We collect samples from the slums (the very low income area), middle income areas and the very high income areas of Nairobi, with varied levels of environmental contamination, ranging from areas that are littered with garbage and permeated with open sewerage systems, (often complemented with the infamous ‘flying toilets’) to the very clean areas with high levels of infrastructure and garbage collection systems. We are eagerly anticipating what these radically different, yet often closely neighbouring environments will yield in terms of microbial diversity!

Another exciting variation is on the human, livestock and wildlife interface; there are sub-locations where livestock keeping is illegal, limiting the human-livestock interaction; whereas free ranging animals like goats and pigs are common in other areas, scavenging on rubbish, or grazing public spaces such as playing fields and road verges. Yet other sub-locations are endowed with lots of wild animals as they are neighbouring forests, or generally consist of large, well-established plots with many mature trees and well-tended vegetable gardens.

NL10-99HH low income area

99 Household; Low income area in Nairobi

In any of the randomly selected households, the project team collect a variety of sample types, including human stools, environmental samples, and  animal-source foods, such as meat, eggs or milk; as well as faeces from birds, rodents, and livestock. E. coli can be found in all of these places, but how are the different strains distributed between each of these different ecological niches that are in such close physical proximity? How much sharing of genetic material goes on between these bacterial communities, especially of those genes that give us cause for concern; ones that confer antibiotic resistance or ability to cause serious disease. In every sub-location, we sample one non-livestock keeping household and two households keeping livestock of diverse types. How these different combinations of people and animals in a similar urban environment influence the diversity of pathogens within a household- is another fascinating aspect of bacterial ecology that we hope this project will uncover.

NL10-99HH high income area

99 Household: High income area in Nairobi

The crowded and dusty streets in the low income areas in Nairobi are always full of food vendors selling both raw and cooked foodstuffs, unlike the high-income areas where majority of the residents buy food from supermarkets and high class butcheries. A difference in the food safety risk is anticipated between different types of suppliers of animal source foods, but the degree of this variation and the pathogens involved is something that remains largely unexplored. The 99 Households component of the Urban Zoo project is contributing to this, by starting to map E.coli and Campylobacter at the level of the consumer. We are beginning the next stage; to survey and collect samples along the length of the value chains that deliver meat to the tables of Nairobi citizens. Maud Carron, a PhD student, has this week begun sampling the chicken meat value chains in two contrasting areas of Nairobi, focusing mainly on Campylobacter; one of the leading causes of food-borne diarrhoeal illness in countries with a modern, intensive chicken production system. In the next few months, sampling will be expanded to the ruminant and pig meat value chains – watch this space for news of the next exciting phase of Urban Zoo!

James AkokoAuthored by James Akoko

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