International Livestock Research Institute 
 
 
 
 
Training course report 
 
 
 
 
 
Epi on Safari 
 
 
 
 
 
 
 
 
 
 
 
 
June 2013 
 
 
 
 
        
 
i 
 
 
© 2013 International Livestock Research Institute (ILRI)  
 
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the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License. To view this license, visit 
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only under the same or similar license to this one. 
 
 
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Any of the above conditions can be waived if permission is obtained from the copyright holder. 
Nothing in this license impairs or restricts the author’s moral rights. 
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Compiled and formatted by Tezira Lore 
 
 
Citation 
ILRI (International Livestock Research Institute). 2013. Epi on Safari: A training course report. 
Nairobi, Kenya: ILRI. 
  
ii 
 
Contents 
 
Introduction ..................................................................................................................... 1 
Objectives ........................................................................................................................................................... 1 
Training summary ............................................................................................................. 2 
Allocation of priority research areas ................................................................................................................... 2 
Indicators used to determine A4NH budget allocated to scientists’ research programs .................................... 4 
Annex 1: Program ............................................................................................................. 5 
Annex 2: List of participants ............................................................................................. 6 
Annex 3: Training materials .............................................................................................. 7 
 
 
 
 
1 
 
Introduction 
The Epi on Safari training course was held from 24 April to 3 May 2013 at the Serena Mountain Lodge, Mount 
Kenya National Park, Nyeri. The course was designed for a small group of newly recruited postdoctoral fellows 
and graduate students attached to the Food Safety and Zoonoses program of the International Livestock 
Research Institute (ILRI). The course program is provided in Annex 1 and the list of participants in Annex 2. 
 
Objectives 
The main objectives of the course were to: 
 introduce the postdoctoral scientists to epidemiology research at ILRI;  
 identify areas for targeted capacity strengthening through discussion and practical; and  
 get input on epidemiological real world datasets we are working on. 
 
The main speaker was Prof Ian Dohoo, professor emeritus from the University of Prince Edward Island, 
Canada. In addition, Prof Brian Perry was present as an invited guest speaker. Prof Perry is an honorary 
professor of the University of Edinburgh; visiting professor at the University of Oxford and honorary professor 
of the University of Pretoria. 
 
 
 
  
2 
 
Training summary 
The training materials and presentations are provided in Annex 3. 
 
Allocation of priority research areas 
On the evening of Monday 29 April 2013, the team held a meeting to discuss the allocation of various research 
projects to the postdoctoral fellows. Table 1 below gives a summary of what was agreed upon. 
 
Table 1: Datasets for analysis and peer-reviewed publication 
Dataset Postdoc  
Avian influenza in Nigeria, Bangladesh and Egypt Cristobal 
GET Dairy  Johanna 
Uptake of Newcastle disease vaccine in Tanzania and Kenya Johanna 
Cysticercosis prevalence  Cristobal 
Cysticercosis risk factors Silvia 
Cost effectiveness analysis of participatory disease surveillance in Kenya  Cristobal 
Validation of participatory epidemiology  Pablo & Barbara 
Risk factors for bloody diarrhoea in children in Cambodia  Silvia 
Prevalence of pig diseases and zoonoses in Laos Silvia 
Leptospirosis in South Vietnam  Barbara 
Slaughterhouse in Vietnam   Barbara 
 
It was also agreed that the postdocs would take a major role in supporting various projects. These were 
allocated as shown in Table 2 below. 
 
Table 2: Research for a postdoc to take a major role in supporting 
Project Postdoc  
Rapid integrated assessment Silvia and others 
Rift Valley fever projects  Cristobal 
Mycotoxins in the feed-dairy chain in Kenya (MyDairy) Johanna 
EcoZD outputs  Silvia/Barbara 
Safe Food, Fair Food project – Tanzania and Ethiopia  Barbara/Cristobal (economics)/Silvia/Pablo  
(Hung, Kohei, Delia, Eric, Johanna) 
PigRisk Barbara/Cristobal/ Pablo  
(Hung, Kohei, Delia, Eric, Johanna) 
Multiple pathogen survey in dairy cattle in Tanzania  Barbara & Silvia 
Disease, poverty and the environment: Costs and benefits 
of One Health  
Johanna/Cristobal 
3 
 
Specific postdocs were assigned to be the contact points for country value chains. These are indicated in Table 
3 below. 
 
Table 3: Country value chains for a postdoc to be the contact point 
Country value chain Contact point 
Ethiopia Barbara 
Tanzania Barbara 
Uganda Kristina 
Senegal Sylvia 
India Johanna 
Vietnam Cristobal 
Nicaragua Cristobal 
 
 
 
  
4 
 
Indicators used to determine A4NH budget allocated to 
scientists’ research programs 
 
Indicator 
Author or co-author of a peer reviewed paper / book chapter (ISI or other recognized journal) 
Author or co-author of an oral presentation/poster at a scientific conference, symposium or major workshop 
Author or co-author of guide/manual/training course/methodology/set of tools or instruments which can be 
used by external people 
Be a member of editorial or other board 
Organize or co-organize a big meeting or major event  
(e.g. workshop with 30-70 external participants; symposium at ISVEE) 
Document involvement in development, testing or release of tools/decision-support/diagnostic which can be 
used by external people 
Run or maintain a platform or database 
Maintain a website/blog/network 
Write an article/brief/technical paper/blog post 
Supervise graduate students at ILRI 
Lead a training course 
Have a high level policy engagement (national, regional or global level) 
Write a successful proposal 
Be a project principal investigator or coordinator 
Number of outputs 
All time on A4NH (%) 
Time funded by A4NH; A4NH should fund no more than 50% of any scientist’s time  
Time project funded 
 
Only outputs in Mahider, websites, reported to A4NH or in the Markets, Gender & Livelihoods Theme 
publication list included. 
The number of outputs produced will influence the amount of A4NH budget you receive for your science 
agenda. 
Food Safety and Zoonoses should put all planned and achieved outputs in work plans, key result areas and 
performance evaluations 
 
Other outputs valued but not included in this metric include:  
 be a reviewer for a journal;  
 give a training module or session in a course led by others;  
 lower level policy engagement (municipal, provincial etc.);  
 organize a small meeting;  
 write an unsuccessful proposal;  
 submit a peer-reviewed paper;  
 be a member of a project team;  
 support interns;  
 present at a meeting; and  
 be a trainer on a course organized by someone else. 
  
5 
 
Annex 1: Program 
 
 0900 to 1300 hours 1400 to 1700 hours 1830 to 1930 hours 
Thurs 25 Apr Participatory epidemiology   
Fri 26 Apr Survey planning Bias Presentations: Research 
background and interests 
Postdoctoral fellows 
Sat 27 Apr ILRI administrative procedures   
Sun 28 Apr FREE DAY 
Mon 29 Apr Missing data 
Ian Dohoo 
Causal diagrams Project allocation 
Tue 30 Apr Presentations: Research 
background and interests 
Postdoctoral fellows 
Publications: Writing a 
thesis chapter or journal 
article 
Ian Dohoo 
Livestock & Fish  
Tom Randolph 
Research Methods Group 
Jane Poole 
Wed 1 May Model validation/multinomial 
models 
Ian Dohoo 
Guest presentation  
Brian Perry 
Grand explorations  
Thurs 2 May Flexible   Bush walk Systematic literature review 
1700 to 1800 hours: ‘Cow Killer’ 
Fri 3 May Impact assessment 
Ian Dohoo 
Leave after lunch  
 
  
6 
 
Annex 2: List of participants 
No.  Name Designation  Sex 
(M/F) 
1 Prof Ian Dohoo 
(Main Speaker)  
Professor emeritus (epidemiology), Department of Health 
Management, Atlantic Veterinary College, University of Prince Edward 
Island, Charlottetown, Canada  
M  
2 Prof Brian Perry 
(invited guest 
speaker) 
Honorary Professor, College of Medicine and Veterinary Medicine,   
University of Edinburgh, UK; Visiting Professor of Tropical Veterinary 
Medicine, Nuffield Department of Clinical Medicine, University of 
Oxford, UK; and Honorary Professor, Department of Veterinary 
Tropical Diseases, University of Pretoria, South Africa 
M 
3 Bernard Bett  Veterinary epidemiologist, Food Safety and Zoonoses Team, ILRI 
Kenya 
M*  
4 Delia Grace  Program Leader, Food Safety and Zoonoses and Theme Leader, 
Agriculture Associated Diseases, A4NH, ILRI Kenya 
F  
5 Fred Unger  Poultry Health Specialist / Epidemiologist, ILRI Thailand  M  
6 Hung Nguyen  Joint scientist of Swiss TPH (Basel, Switzerland) and ILRI (Nairobi, 
Kenya)  
M*  
7 Jane Poole  Statistician and head of the Research Methods Group, ILRI Kenya  F  
8 Jeffrey Gilbert  Project coordinator, Ecosystem approaches to the better management 
of zoonotic emerging infectious diseases in the Southeast Asia region 
(EcoZd project), ILRI Laos  
M  
9 Tom Randolph  Director, CGIAR Research Program on Livestock and Fish, ILRI Kenya  M  
10 Barbara Szonyi Postdoctoral fellow F 
11 Cristobal 
Verdugo  
Postdoctoral fellow, ILRI Kenya  M*  
12 Johanna Lindahl  Postdoctoral fellow, ILRI Kenya  F  
13 Natalie Carter  PhD candidate (Epidemiology), University of Guelph; graduate fellow, 
ILRI Uganda  
F  
14 Pablo Alarcon  Postdoctoral research fellow, Veterinary Epidemiology, Economics and 
Public Health group, Royal Veterinary College. Visiting scientist, ILRI  
M  
15 Sylvia Alonso  Postdoctoral fellow, ILRI Kenya  F  
16 Rosekellen Njiru  Senior administrative assistant, Food Safety and Zoonoses program, 
ILRI Kenya  
F*  
*Developing country 
 
  
	






	

 
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Education and research background 
 D. V. M. Cornell University, USA, 2005 
 Ph.D. Cornell University, USA, 2010 
 National Institutes of Health/ Fogarty 
International Clinical Research Scholar 
(NIH/FICRS), 2008, F. Oswaldo Cruz, Brazil 
 Diagnostic epidemiologist at Texas Veterinary 
Medical Diagnostic Laboratory 2010-2011 
 Post-doc at Texas A&M University, 2010-now 
Dissertation 
 
 Geographic distribution and zoonotic potential of 
Cryptosporidium in dairy cattle 
◦ Cross-sectional study 
 Szonyi B, Seasonal variation in the prevalence and molecular epidemiology of 
Cryptosporidium infection in dairy cattle in the New York City Watershed. 
Parasitology Research (2010), 107(2): 317-25. 
◦ Case-control study and risk factor modeling 
 Evaluation of factors associated with the risk of infection with Cryptosporidium 
parvum in dairy calves. American Journal of Veterinary Research (2012), 73(1): 76-85.   
◦ Spatial analysis and Bayesian statistics 
 Szonyi B. Temporal and spatial dynamics of Cryptosporidium parvum infection on 
dairy farms in the New York City Watershed:  a cluster analysis based on crude and 
Bayesian risk estimates. The International Journal of Health Geographics (2010), 9:31.  
◦ Molecular typing of samples from Kenya 
 Szonyi et al. First report of Cryptosporidium deer-like genotype in Kenyan cattle. 
Veterinary Parasitology (2008), 153(1-2): 172-175 
 
 
 
Dissertation 
◦ Experience might be relevant for:   
◦ Relation between poverty, pig-keeping and 
epilepsy in western Kenya.  
◦ Comparing traditional knowledge of farmers to 
laboratory analysis for animal disease and 
community knowledge of disease prevalence to 
conventional surveys in Kenya.  
◦ Prevalence of pig diseases and zoonoses in Laos. 
◦ Multiple pathogen survey in dairy cattle in 
Tanzania – small project -design 
◦ Testing food safety interventions –SFFF 
 
NIH/FICRS 
 Molecular epidemiology of leptospirosis 
in Latin America 
◦ Szonyi et al. An outbreak of severe 
leptospirosis in capuchin (Cebus) monkeys. 
The Veterinary Journal (2011), 188: 237-239. 
 Experience might be relevant for:   
◦ Leptospirosis in south Vietnam 
  
TVMDL/TAMU 
 Enhance collaboration between DL and Veterinary 
College in epidemiology 
◦ Evaluate accuracy of new diagnostic tools 
 Schroeder et al. Development and performance evaluation of calf diarrhea 
pathogen nucleic acid purification and detection workflow. Journal of Veterinary 
Diagnostic Investigation (2012), 24(5): 945-953. 
◦ Use diagnostic lab data to understand disease status 
of animal populations in TX 
 Szonyi et al. Spatio-temporal epidemiology of Tritrichomonas foetus infection in Texas 
bulls based on state-wide diagnostic laboratory data. Veterinary Parasitology (2012), 
186(3-4): 450-455. 
 Gautam et al.  Identifying high risk areas of Coccidioidomycosis in Texas using 
serology data from dogs. Zoonoses and Public Health. In Press.  
 Szonyi et al. Emergence of Corynebacterium pseudotuberculosis in Texas horses. 
 Szonyi et al. Epizootic hemorrhagic disease in captive white-tailed deer in Texas.  
◦ Understand Lyme disease distribution in TX - grant  
 Szonyi et al. Exploratory spatial data analysis of human Lyme disease cases in Texas. 
 
TVMDL/TAMU 
 Experience might be relevant for:  
◦ Sensitivity and specificity of PDS for detection 
bird flu in Egypt.  
◦ Comparing traditional knowledge of farmers 
to laboratory analysis for animal disease and 
community knowledge of disease prevalence 
to conventional surveys in Kenya.  
◦ Multiple pathogen survey in dairy cattle in 
Tanzania – small project -design 
◦ Prevalence of pig diseases and zoonoses in 
Laos. 
 
Research background and interests 
 
 
 
 
 
 
Pablo Alarcon 
Post-doctoral research fellow in food system 
 
Epi on Safari meeting – ILRI - 2013 
 
 
Education and Experience 
• Veterinary Medicine (University of Cordoba, Spain) – 2005 
 
• Meat Inspector in Abattoir (UK) - 2006 
 
• MSc in Veterinary Epidemiology (RVC/LHSTM) - 2007 
 
• Research assistant in veterinary epidemiology (RVC) – 2009 
 
• PhD in veterinary epidemiology (RVC) – 2009 
 
• Post-doctoral research fellow in food systems (RVC and ILRI) – 
since 2012 
 
 
 PMWS 
  (Post-weaning  Multi-systemic Wasting Syndrome) 
Porcine Circovirus type 2 
 
 
Multi-factorial disease ! 
(The virus itself is not enough 
to trigger clinical signs) 
 
 
Disease impact 
 
Animal welfare 
High cost to the farmer 
 
 
 
Subclinical pigs 
   
Aims and Objectives 
• Identify the most effective, profitable and social acceptable 
options to control PMWS at the farm level 
 
Understand severity of disease on farms 
 
Risk factors associated with severity of the disease 
 
Economic impact of the disease 
 
Identify the most cost-effective control measure 
 
Investigate best way of communication the results 
 
 
 
Farm recruitment 
April 2008 to April 2009 
147 farrow-to-finishing farms 
 
 Complete data for 141 farms  
      (17% England sow population) 
 
Researchers: 
• 2 qualified veterinarians 
• 2 days pig free before each visit 
 
Data collection: 
 
• PMWS 
• Production performance 
• Possible risk factors (management,  
    environment, etc.) 
Definition of PMWS severity 
Principal component 
analysis 
 
 
 
 
PMWS severity score 
            (0-10) 
Alarcon, P., et al., Assessment and quantification of post-weaning multi-systemic 
wasting syndrome severity at farm level. Pre. Vet. Med. 98 (2011), 19-28 
Alarcon, P., et al., Farm level risk factors associated with severity of Post-weaning multi-systemic 
wasting syndrome. Prev. Vet. Med. (2011) 101, pp.182-191 
Risk factors: 
Environment interaction 
Farm Biosecurity 
Co-infections 
PMWS – Disease economic model 
Industry cost : 
 -£53 million /year (-72 to -34) 
-200
0
200
400
600
800
0 1 2 3 4 5 6 7 8 9 10
£ 
/ s
ow
 / 
ye
ar
 
PMWS severity 
Total PMWS + PCV2SI PMWS-D + PMWS-R
Sub-D + Sub-S Total profits
Alarcon, P., et al., Cost of PMWS and porcine circovirus type-2 subclinical infection in England 
– an economic disease model. Pre. Vet. Med. (2013) In press. 
Alarcon, P., et al., Economic efficiency analysis of different strategies for the control of PMWS 
and porcine circovirus type 2 subclinical infection. Pre. Vet. Med. (2013) In press. 
Most cost-effective measure: Vaccination and Bio-security measures 
 
Development of a tool for decision-making process 
Investigation farmers decision process for 
disease control 
 
• Qualitative study (20 farmers) 
 
• Use of Socio-psychological framework 
 
• Provide recommendations to improve 
communication of research outputs 
Interests 
• Investigation of the epidemiology of zoonotic 
diseases in value chain context 
• Including link with human behaviour 
 
• Development of decision support tools: 
• Economic models 
• Risk analysis 
• Food system modelling 
 
• Multidisciplinary research  
 
THANK YOU 
 
palarcon@rvc.ac.uk 
Presentation Mt Kenya workshop 
2013 
Research background and interests 
Johanna Lindahl 
Quick-who am I 
• From Uppsala Sweden 
• DVM and PhD degree from Swedish University 
of Agricultural Sciences 
• Background as a clinician and county 
veterinarian 
Pojken (the boy) 
Pixel 
Thesis work 
Japanese Encephalitis Virus in pigs and vectors 
in the Mekong Delta- with special reference to 
urban farming 
• Publications 
– Reproductive performance in sows in relation to Japanese Encephalitis 
Virus seropositivity in an endemic area (Trop anim health and prod) 
– Occurrence of Japanese Encephalitis Virus Mosquito Vectors in 
Relation to Urban Pig Holdings (Am j trop med hyg)  
– Circulation of Japanese Encephalitis Virus in Pigs and Mosquito Vectors 
within Can Tho City, Vietnam (PLOS negl trop dis)  
 
What did I do? 
 
Teaching 
• Reproduction 
– Obstetrics 
– Gynaecology 
– Andrology 
 
• Master students 
– Presence of Japanese Encephalitis virus vectors in Can Tho City 
– Seroprevalence of Japanese Encephalitis Virus in pigs and dogs in the 
Mekong Delta 
– The quality of SLC selected semen 
 
 
Other projects 
• Stallion spermatozoa selected by single layer centrifugation 
are capable of fertilization after storage for up to 96 h at 6 C 
prior to artificial insemination (Acta Veterinaria Scandinavica) 
• Uganda cow reproduction study 
• Pan-flavivirus PCR 
Research interests 
 
Hung Nguyen-Viet 
 - EPH, SwissTPH 
 - FSZ, ILRI 
 - CENPHER, Hanoi School of Public Health 
Epi on Safari expectations 
 
Nairobi, 27 April 2013 
1. Mai 2013 Präsentationstitel 2 
Hung Nguyen-Viet, 36 
 
2005 PhD in Life and Environmental Sciences: Besançon, FR 
2001 MSc in Environment, Health, Society: Besançon, FR  
1999 BSc in Biology: Hanoi, VN 
 
2009-now: Center for Public Health and Ecosystem Research, HSPH 
2011-Now: joint appointee ILRI - Swiss TPH  
2006-2009: Postdoc, Swiss TPH, Sandec/Eawag (Thailand, Vietnam, 
Côte d’Ivoire) 
 
2011-now: lecturer HSPH environmental health  
2011-now: Adjunct Faculty of AIT, Bangkok 
2004 - 2006: Lecturer, Besançon, France 
Center for Public Health and Ecosystem Research 
(from 6.2013) 
Mission & activities 
CENPHER studies the health and well-being impacts of development 
factors (environmental, ecological, cultural, socio-economic, and 
demographic) using the integrative approaches of Ecohealth/One 
Health (Transdisciplinarity), with special focus on South East Asia as 
well as links to analogous issues in Africa. 
 
 We focus on the link between health and agriculture, infectious and 
zoonotic diseases, chemical pollution, and food safety and nutrition, at 
all levels from the lab to the field. 
 
Main themes of research and training: 
1. Ecosystem Health / One Health 
2. Food Safety 
3. Health Impact Assessment 
Team in Hanoi 
Ongoing projects: 
1. Environmental sanitation and health: balancing between health risk, livelihood 
opportunities and environmental impacts 
 
2. Ecohealth Field Building Leadership Initiative (FBLI): Advancing Ecohealth in 
Southeast Asia / Agricultural intensification and Health  
 
3. Human-Animal-Environment transmission and risk factors of Leptospirosis 
1. Ecosystem Health / One Health 
• Human health is determined by inter-linkages of human, animal 
and environmental health in a socio-ecological context using an 
integrated approach such as Ecohealth or One health. 
• Health impact of environmental pollution, agricultural 
intensification, urbanization, and environmental sanitation. The 
main health issues are tropical neglected diseases, zoonoses + 
environment, socio-economics. 
 
Main research themes Main research themes 
Ongoing projects: 
1. PigRISK “Reducing disease risks and improving food safety in smallholder pig 
value chains in Vietnam” 
2. FOOD-RISK “Strengthening Risk Assessment Capacities in Food Safety” 
3. Risk assessment task force for food safety 
4. Dioxin and food 
5. Chemical contamination of drinking water 
6. QMRA Asia 
2. Food Safety 
 • High food demand  an intensification of agricultural 
production   many benefits but also causes negative 
environmental and health effects 
• Main issues: microbial contamination, pesticide use, 
antibiotic residues, growth promoter, and toxins and how 
to use a risk-based approach to food safety management in 
the developing world. 
 
Prospective projects: 
1. Air pollution and health (risk assessment) 
2. Building up capacity and expertise on HIA for the region 
Main research themes 
3. Health Impact Assessment 
 • SEA – hotspot for infrastructure development projects 
(dam construction, mining industry) 
• Urbanisation, climate change, agriculture, waste 
management 
• Clear need for Health Impact Assessment in the region 
 
Expectation/interest 
- Design Quantitative Microbial Risk Assessment 
- Design Quantitative Chemical Risk Assessment 
- Design Lepto research – Thanh Hoa Vietnam  
- Testing food safety interventions – PigRISK- 
design (EcoZD) 
- Statistical modeling 
- Model validation 
- Analysis of EcoZD SH-Vietnam 
1. Mai 2013 Präsentationstitel 8