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.

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

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

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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

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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

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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)

Kenya Field Epidemiology and Laboratory training (FELTP)

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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!

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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.

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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.

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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

Urban Zoo Annual Meeting

Urban Zoo Annual Meeting

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Post meeting group photo

The multidisciplinary Epidemiology, ecology and socio-economics of disease emergence in Nairobi Project (Urban Zoo project) held its third annual meeting in London on January 19th and 20th, 2016. The meeting was attended by representatives from ILRI, APHRC, KEMRI, University of Nairobi, RVC, University of Liverpool, SOAS and the University of Edinburgh, UCL, IIED.   PIs, PhD students, post docs and other researchers involved in the project, as well as members of the External Panel, our group of ‘friendly critics’ who keep the project on track,  gathered to discuss this year’s progress.

The Urban Zoo project investigates the role of urbanization in the emergence of zoonotic pathogens. It fosters numerous PhD and MSc projects, thus achieving its capacity-building objectives. Jointly, these studies, which cover diversified fields such as peri-urban wildlife, livestock value chains and the social and spatial components of livestock rearing, will allow for a detailed understanding of Nairobi’s human-livestock-wildlife interfaces.

The “99 Households” (99HH) component of the project uses a landscape genetics approach to understanding E. coli distribution across Nairobi. Major progress in this component was reported. Not only have the sampling plan and laboratory protocols been finalised since the last meeting, but sampling across Nairobi is well underway. Thirty households have already been sampled in 10 sub-locations before December 2015. As planned, samples from humans, livestock, the environment and wildlife are being collected in each household. Quality assurance processes such as duplicate sampling and testing between both University of Nairobi and KEMRI laboratories have been put in place.

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Meeting participants taking a break

The pipeline for full genome sequencing of the selected 99HH samples has been finalised and tested on a first batch of samples at the University of Edinburgh. A high level of diversity and MLST was noted.

The group discussed next steps in terms of addressing the value chain component of the Urban Zoo project. It was agreed that sampling of the beef and pork value chains will start in a near future, the poultry value chain sampling being already covered by one of the PhD projects.

A proposal was made to initiate a demand survey in order to determine animal source foods consumption in Nairobi. Ongoing discussions about the scope and feasibility of this study are still ongoing. The PIs reported multiple initiatives in terms of public health trainings and promotions materials and the study team received very positive comments from the external panel. The next and final Urban Zoo meeting is planned to take place in Kenya next year.

Maud CarronAuthored by Dr. Maud Carron

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