Do livestock have a role in the emergence of disease in urban cities?

One of the primary objectives of the Urban Zoo project is to quantify and understand microbial diversity in an urban setting and to try and link that to urban livestock keeping. In so doing we aim to elucidate the possible role of livestock as a risk factor in the emergence of disease in cities.

To give us a handle on microbial diversity we have chosen commensal Escherichia coli as an indicator species, which we have isolated from samples taken from a diversity of sources across the city of Nairobi. These comprise people and their living spaces, including the food they eat; their immediate environments, including water sources, waste and wildlife; and the livestock that they keep either for their own consumption or for sale. From these samples we isolate and culture E. coli, extract their DNA, and perform whole genome sequencing, enabling us to compare isolates from different compartments and to determine how closely related they are, and thus how microorganisms might pass from one to another.

The collection of these samples has been guided by a highly structured sampling frame, which I described in Urban Zoo newsletter number 7. Essentially, we have selected 33 sub-locations in Nairobi representing a range of social strata and, within each, have chosen 3 households to sample: one with no livestock; one with only monogastric species (pigs or chickens); and one with ruminant livestock (sheep, goats or cattle); You can view the spatial maps at our earlier post by clicking here .

The collection of such comprehensive data from these 99 households was an enormous undertaking and has been a considerable logistical feat of coordination between the field and the laboratory. The good news is that the sampling is now complete, thanks to the heroic efforts of the field team, led by Judy Bettridge and James Akoko, and of our colleagues in the laboratories.

Overall, 2,351 samples have been collected and we managed to culture E. coli from 80% of these (1,850). Once the last few have been done this will give us 1,809 whole genome sequences to analyse. 327 of these are from people; 58 from the places where they prepare food; 64 from animal source foods (milk meat and eggs); 644 from 12 different species of livestock; 239 from the environment around the home-stead including water sources; and 477 from a wide diversity of wildlife in the vicinity of the household.

But it is not over yet. We will very soon have finalised the sequencing and now comes the equally challenging task of deciphering all of this genetic data to unveil the pattern of microbial diversity across Nairobi. Over to you Melissa!

On that note, I would like once again to congratulate the field and laboratory teams, and to wish everyone a great year ahead, 2017.

This article was authored by Dr. Timothy Robinson who is a co-principal investigator in the Urban Zoo project and also a principal scientist with ILRI’s Livestock Systems and Environment research group.

Endemic infectious diseases: the next 15 years

I have recently returned from the International AIDS Conference in Durban, South Africa. It was, as many have noted, a landmark event: a chance to celebrate the remarkable success of the HIV response over the past 15 years.

But it was also a stark wake-up call. Despite the tangible results – which include millions of lives saved – it is increasingly clear that to achieve the goal of ending the AIDS epidemic as a public health threat by 2030, the world needs to take the fight several steps further.

Accelerating progress across all infectious diseases

Dr Ren Minghui, Assistant Director-General for HIV/AIDS, Tuberculosis, Malaria and Neglected Tropical Diseases WHO

Dr Ren Minghui, Assistant Director-General for HIV/AIDS, Tuberculosis, Malaria and Neglected Tropical Diseases

The Sustainable Development Goals (SDGs), agreed last September at the United Nations in New York, offer an ample opportunity to accelerate progress across all infectious diseases. The focus on equity, health systems strengthening, universal health coverage, and multi-sectoral action will transform the way we tackle these diseases.

The SDGs build on the momentum generated during the Millennium Development Goals era, and on lessons learned during the first 15 years of this century. And they recognize that while the global response has significantly reduced the infectious disease burden and saved over 50 million lives, much more needs to be done.

In 2000, who would have thought that by 2015 the world could get 17 million people in low- and middle-income countries on antiretroviral treatment, reduce malaria mortality rates by 60% and cut tuberculosis (TB) deaths by 47%? Who would have predicted that, within the space of 15 years, it could bring down the number of guinea worm infections from over 75 000 to just 22? But it did.

What we have to do now is maintain our resolve and further intensify our efforts.

“More than anything, the next 5 years should be about creating solid foundations for ending the infectious disease epidemics everywhere. This is not a moment to lift our foot off the accelerator. These diseases are known for returning with a vengeance, if we ever slow down.”

Dr Ren Minghui, WHO Assistant Director-General for HIV/AIDS, Tuberculosis, Malaria and Neglected Tropical Diseases

Infectious diseases continue to have far-reaching impacts on people’s lives. In some of the poorest countries of the world, they continue to devastate economies and cripple health systems. Progress remains uneven and millions are not being reached with prevention measures and treatment.

From the outset, the fight against infectious diseases has been dogged by social, legal and economic barriers, and funding gaps have been significant. These are a major reason why HIV, TB, malaria, viral hepatitis and neglected tropical diseases (NTDs) still kill more than 4 million people every year.

Globally, 480 000 people develop multi-drug resistant TB each year, and drug resistance is starting to complicate the fight against HIV and malaria, as well. A coordinated effort to tackle this challenge – under the umbrella of the WHO global action plan on antimicrobial resistance – will be critical to success.

Global strategies on infectious diseases

To help countries deliver on their pledge to ‘end the epidemics’ by 2030, the World Health Assembly has adopted global strategies on HIV, TB, and malaria. This year, it passed the world’s first-ever global hepatitis strategy and set the first global hepatitis targets. Since 2012, a WHO roadmap has been available to guide global efforts on NTDs which affect over a billion people.

The strategies are backed up by a set of evidence-based guidance documents to help countries design and implement their own plans. They emphasize opportunities to maximize the impact of prevention, treatment and care services, and to mitigate the impact of biological challenges, such as drug and insecticide resistance, and climate change.

At the same time, WHO is working to help countries move closer to universal health coverage, by ensuring that all people have access to the health services they need, without being thrown into poverty as a result.

As well as establishing robust health financing systems, this means building up a qualified workforce and investing in efforts to improve the quality of treatments, diagnostics and prevention tools. It means assuring adequate supplies of affordable, safe and effective health products and putting an end to stock-outs. And it means joining up the dots: a greater integration of services, as we are already seeing in many places.

More than anything, the next 5 years should be about creating solid foundations for ending the infectious disease epidemics everywhere. This is not a moment to lift our foot off the accelerator. These diseases are known for returning with a vengeance, if we ever slow down.

This post was authored by Dr. Ren Mingui (WHO Assistant Director-General for HIV/AIDS, Tuberculosis, Malaria and Neglected Tropical Diseases) originally appeared as a commentary on the World Health Organisation website on 17th August 2016. Available at:

Human, Food and Environmental data collection

WhatsApp-Image-20160607Human, food and environmental data are among the wide range of data collected within the 99 households. The data are often collected by Clinical Officers. Human sampling involves among others, individual consenting to participate, questionnaire interviews administration, general physical examination and anthropometric measurements, biological data collection and offering feedback and health education on the outcome of the laboratory based investigations. Two sets of structured questionnaires are administered; a general household and individual participant questionnaires. Biological data that is collected includes fecal samples and nasal swabs. Fecal samples are assessed for E. coli and campylobacter bacteria while nasal swabs are assessed for antimicrobial resistance. Collection and transportation of human samples from the field to laboratories involves sterile techniques.

Like human sampling, sterile steps are also observed during food and environmental data collection. Only livestock sourced foods are collected in the study. A sample of meat, milk and a wipe of egg shells if available, are collected. Sterile wipes of kitchen working surfaces such as chopping boards as well as kitchen door knobs are also collected. Environmental samples are collected using sterile boot socks. Normal saline-wet boot socks are worn and environmental samples collected by walking around the area surrounding the household as well as surfaces within livestock pens if available. Whirl pack bags are used in transportation of environmental samples. Water samples from water puddles, boreholes or storage water tanks are also collected as environmental samples. Subsamples of food and environmental samples are marked with a red dot to identify those going for whole genome sequencing and a blue dot on those being analyzed for campylobacter. All collected data are de-identified using barcode numbers to enhance participant and sample anonymity.

On completion of data collection, participants in the household are either given Albendazole or Mebendazole anthelminthic depending on age. Anyone found to be clinically ill is offered a prescription. If they are seriously ill a written referral letter to the nearest and most preferred health facility for further management is offered. Laboratory outcomes are communicated back to individual participants within two to three weeks of data collection. This is accompanied by health education with emphasis on how to maintain proper hygiene as well as interaction with livestock. Like many other community studies, our study is not devoid of challenges. Some of the challenges encountered involve heavy traffic. As investigators, we have to sometimes anticipate early morning starts. Participants which means rescheduling the day to collect data. Others include withdrawal from participation and inability to access household heads especially in high income settings.

Laureen AlumasaFredrick Amanya

 Article by Lorren Alumasa & Amanya Fredrick

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

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

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.

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