Update: 99 Households study: wildlife component

Jun 15, 2016 | Blog, Latest news, Research, Urban Zoo Project, Zoonotic Diseases

Update: 99 Households study: wildlife component

Wildlife 2 As 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-Taxa disease 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 4 unharmed. 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
environment.

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

Jun 15, 2016 | Blog, Emerging Diseases, Latest news, Research, Urban Zoo Project

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 66^th 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!

Article 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.

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Click to view enlarged maps

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

Jun 15, 2016 | Blog, Emerging Diseases, Latest news, PI&Co-PI letters, Research, Urban Zoo Project

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

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.

‘One Health for the Real World’ (or, ‘real livestock for real global wellbeing’)

Apr 7, 2016 | Blog, Latest news

‘One Health for the Real World’ (or, ‘real livestock for real global wellbeing’)

The four members of the organizing committee of the One Health for the Real World Symposium and key players in the Dynamic Drivers of Disease in Africa Consortium: (left to right), James Wood, University of Cambridge; Andrew Cunningham, Zoological Society of London; Ian Scoones, Institute of Development Studies; and Melissa Leach, Institute of Development Studies (this and all photos on this page except the ILRI photo directly below of Annie Cook are via Flickr/ Dynamic Drivers of Disease in Africa Consortium).

This post is written by Annie Cook, post-doctoral scientist, ILRI

Annie Cook

One Health can be defined as the collaborative effort of several disciplines
to attain optimal health for people, animals and our environment.

The 27 speakers at a recent One Health for the Real World Symposium: Zoonoses, Ecosystems and Wellbeingmake up a (very) respectable ‘who’s who’ in the world of One Health, which includes all those working to unite the knowledge, practices and approaches of medical, veterinary and environmental sciences for the healthy wellbeing of all three.

The symposium was held at the Zoological Society of London (ZSL) 17–18 Mar 2016 and organized by ZSL and a three-year project called the Dynamic Drivers of Disease in Africa Consortium (DDDAC). The symposium marked the culmination, and ending, of the consortium.

Twenty organizations, including the Africa-based International Livestock Research Institute (ILRI), made up the Dynamic Drivers consortium, which from 2012 to 2015 coordinated research exploring the relations among African ecosystems and zoonotic diseases—those transmitted between animals and people—that impinge on ecosystem, human and animal wellbeing.

The ‘real world’ in the symposium’s title reflected the ambition of the consortium members to share their three years of research results not only with each other but also with the policymakers and practitioners who could make a real difference in advancing the One Health agenda.

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Indeed, Melissa Leach, chair of the DDDAC and director of the Institute of Development Studies at the University of Sussex, stressed in her welcome address the importance of linking science and research to policy and practice. ‘Politics is key to moving forward on difficult One Health issues’, she said.

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Leach was followed by Wellcome Trust director Jeremy Farrar, whose keynote presentation raised the bar even higher: ‘If we make the right choices, make the right connections, we can change the course of history’, Farrar argued. He also stressed that tackling today’s growing global health threats called not only for strong leadership but also for exceptional trust in such sensitive areas as disease surveillance and response, governance and data sharing.

One of the ‘right choices’ and ‘right connections’ that Farrar mentioned must be greater public understanding of, investment in, and policy focus on the transmission to humans of diseases originating in wild and domesticated animals. A remarkable 61% of all human pathogens, and 75% of new human pathogens such as those causing bird flu and HIV/AIDS, originate in animals. This ‘zoonotic’ thread (and threat), while often overlooked and under-appreciated in similar fora, happily was apparent in each of the following five major themes raised in the symposium’s subsequent keynotes and discussions.

View Farrar’s slide presentation: The real world: One Health—Zoonoses, ecosystems and wellbeing

1 Anthropogenic drivers of disease, including changes in land-use and human behaviour

bernardbett_onehaelthfortherealworld_cropped

Bernard Bett, a veterinary epidemiologist at ILRI, presented a case study of the DDDAC program that investigated the effects of irrigation on levels of the virus causing Rift Valley fever in human blood serum. Rift Valley fever is an acute, fever-causing viral disease of domesticated animals, such as cattle, buffalo, sheep, goats, and camels, with ability to infect and cause illness, sometimes fatal, in humans. Bett’s study found that those living in irrigated areas had higher levels of antibodies to the pathogen than those in pastoralist areas. Preliminary results indicate sheep and goats from irrigated and riverine areas had higher rates of exposure to the Rift Valley fever virus than those from pastoral areas. But because the results were statistically not significant, further research is required to determine the role of irrigation in acute human and animal infections with Rift Valley fever.

View Bett’s slide presentations: Irrigation and the risk of Rift Valley fever transmission—A case study from Kenyaand A mathematical model for Rift Valley fever transmission dynamics

View Bett’s media interview: The hidden dangers of irrigation, SciDevNet, 22 Mar 2016

View Bett’s impact case stories: One Health working brings widespread Rift Valley fever out of the shadows andProtecting livestock and securing livelihoods during threats of epidemic

2 The need for an interdisciplinary approach to One Health research

Zinsstag

Jakob Zinsstag, of the Swiss Tropical and Public Health Institute, emphasized the added value of integrating human and animal health approaches rather than allowing them to work in isolation. The knock-on effects of considering One Health problems in isolation was also stressed by David Waltner-Toews, of Veterinarians without Borders-Canada, who stated that ‘emerging infectious diseases are symptoms of related wicked problems embedded in complex social-ecological feedbacks’. A novel approach to considering One Health was raised by Jan Slingenbergh, a consulting animal health specialist formerly with the United Nations Food and Agriculture Organization, who proposed a ‘global risk analysis framework’ similar to that developed to address global warming.

View Zinsstag’s slide presentation: Understanding zoonotic impacts: the added value from One Health approaches

3 The relationship between One Health and poverty

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The keynote address for this theme was given by ILRI veterinary epidemiologist and food safety specialist Delia Grace, who presented an in-depth review of the relationships among ecosystems, poverty and zoonoses. ‘Human sickness is a major cause of falling into and remaining in poverty and much of this is related to agriculture’, she said. This was further emphasized by Jo Sharp, of the University of Glasgow, in her presentation highlighting the catastrophic effects of ill health. Grace reported that misdiagnosis and underreporting were two big challenges in tackling emerging infectious diseases. She warned that ‘hurried responses to zoonoses are often anti-poor, causing more harm’. And she underlined how effective control can be: ‘Every dollar invested in brucellosis control returns six dollars in reduced burden’.

View Grace’s slide presentation: The economics of One Health

4 Should One Health research focus on emerging or endemic diseases?

Peter Daszak

Peter Daszak, president of the EcoHealth Alliance, highlighted drivers of emerging disease, such as land conversion, intensification of livestock production and wildlife trade, and the costs of controlling pandemic threats. He noted a false dichotomy between neglected tropical diseases and emerging diseases: ‘Emerging diseases become endemic diseases’, he said. Sarah Cleaveland, of the University of Glasgow, stressed the complementarities and gains ‘from adopting shared approaches to emerging and endemic diseases’. Endemic zoonoses and emerging zoonoses often have similar drivers, she said, but emerging zoonoses get more publicity. ‘Effective health systems for neglected endemic zoonoses will also help control emerging diseases.’

View Daszak’s slide presentation: Pre-empting the emergence of zoonoses by understanding their socio-ecology

5 The need to incorporate different perspectives into One Health research

Bassirou Bonfoh

Bassirou Bonfoh, director general of the Centre Suisse de Recherches Scientifiques en Côte d’Ivoire, stressed the need to incorporate ‘different viewpoints, knowledge and expertise’ when designing health systems. Several presentations reiterated the need to incorporate the voices of different people; a commonly repeated phrase at the symposium was ‘whose knowledge counts?’ Hayley Macgregor, of the Institute of Development Studies, highlighted a danger in research: ‘People’s cultural logics or social practices are readily cast in negative terms’.

View Bonfoh’s slide presentation: Motivation, culture and health in a socio-ecological system in Africa

Charlotte Watts

In the final keynote, Charlotte Watts, chief scientific advisor at the UK’s Department for International Development (DFID), argued that One Health approaches can be very effective for decision-makers facing a crisis. As an example, she listed the diverse options available for controlling the ongoing Zika outbreak using ecosystem, medical and veterinary scientific knowledge and technologies.

The final panel discussion, with representatives from the World Health Organisation (WHO) and the United Nations Food and Agriculture Organization (FAO), summarized the themes of the symposium’s discussions and introduced further relevant issues concerning biodiversity, conservation and animal welfare.

A highlight of the symposium were lively one-minute ‘flash talks’ by poster presenters. The 28 posters presented covered diverse topics, including many with a livestock focus, such as the following.
Kathryn Berger, of the University of Cambridge, presented a ‘Global atlas of animal influenza’ that can be used for surveillance and control programs.
Birungi Doreen, of Makerere University, pointed out that research on possible Ebola virus disease in pigs in Uganda had some negative impacts on the pork value chain in that country and required sensitizing stakeholders to reduce any harm such research could cause.
Natascha Meunier, of the Royal Veterinary College, showed that diseases transmitted from wildlife to cattle most likely occurred via indirect routes, particularly vector-borne disease transmissions.
Robin Wiess, of the University College London, reminded us that zoonosis is a two-ways street: Humans can be a source of infectious disease in animals. ‘Don’t forget the “anthroponoses!”’.

Kevin Bardosh

The symposium also included the launch of a book, One Health—Science, Politics and Zoonotic Disease in Africa, edited by Kevin Bardosh, which offers ‘a much-needed political economy analysis of zoonoses research and policy’.

The closing statement Melissa Leach stressed that One Health is not always comfortable integration. ‘As a social scientist, I see that One Health is about solving puzzles, dispelling bullshit, learning new things and making the future different’. Indeed, a recurring theme throughout the symposium was the need for a new generation of ‘multidisciplinary professionals’.

Ian Scoones

And there was a final plea from Ian Scoones, of the STEPS Centre and the Future Agricultures Consortium: ‘Let’s not make a new One Health discipline—yet another silo!’

The symposium was organized by the Dynamic Drivers of Disease in Africa Consortium (DDDAC) and the Zoological Society of London (ZSL) with support from the Royal Society. The DDDAC is multidisciplinary research consortium funded by the UK’s Ecosystem Services for Poverty Alleviation (ESPA) program, which works to ensure that developing-country ecosystems are sustainably managed to alleviate poverty alleviation as well as to support inclusive and sustainable growth.

Go here to find out more about ILRI research on zoonotic diseases and here for past ILRI news stories on One Health.

About the Dynamic Drivers of Disease in Africa Consortium
The Dynamic Drivers of Disease in Africa Consortium was an international, multidisciplinary research programme. From 2012 to 2016 it explored the relationships between ecosystems, zoonoses, health and wellbeing, focusing on four emerging or re-emerging zoonotic diseases in four diverse African ecosystems: henipavirus infection in Ghana, Rift Valley fever in Kenya, Lassa fever in Sierra Leone, and trypanosomiasis in Zambia and Zimbabwe. Its innovative, holistic approach married the natural and social sciences to build an evidence base which is now informing global and national policy seeking effective, integrated One Health approaches to control and check disease outbreaks.

This post originally appeared on the ILRI website on 7th April, 2016 authored by Annie Cook. Available at: http://news.ilri.org/2016/04/07/one-health-for-the-real-world-or-real-livestock-for-real-global-wellbeing/

Kenya Field Epidemiology and Laboratory training (FELTP)

Mar 12, 2016 | Blog, Epidemiology, Latest news, Research, Urban Zoo Project

Kenya Field Epidemiology and Laboratory training (FELTP)

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.