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AFENET Projects

AFENET currently operates 13 projects, including:

African Programme for Advanced Research Epidemiology Training Fellowship (APARET)

 APARET is a European Union funded four-year program that is implemented by a consortium of institutions including AFENET, the Bernhard Nocht Institute for Tropical Medicine (Germany), the US Centers for Disease Control and public health training institutions in Africa, among others.

The program targets recent graduates of FELTP/FETPs with the aim of providing fellows with specialized training to support the development of independent research activities including writing and applying for a major research grant in order to catalyze the development of self-driven research activities. Each fellowship lasts two years, during which fellows conduct an epidemiologic research with their host institutes, where they are supervised and mentored.



One Health e-Surveillance Initiative (OHSI)






In 1998, the World Health Organization African Regional Office (WHO/AFRO) and its 46 Member States, adopted the Integrated Disease Surveillance and Response (IDSR), as a strategy for developing and implementing comprehensive public health surveillance and response systems in African countries. 


The IDSR framework defines the workforce and programmatic needs of public health surveillance and response at each level, and provides a roadmap for achieving compliance with the WHO International Health Regulations (IHR [2005]). Most surveillance systems in Africa are paper based however the ever-increasing power and accessibility to technology enables widespread implementation of electronic tools used for public health, especially in lower resource settings. This   vastly improves capacity and reduce burden for public health surveillance, leading to faster response.

What is OHSI?
The African One Health e-Surveillance Initiative (OHSI) is a pilot project to help African countries develop strategic plans for implementing sustainable electronic surveillance (e-Surveillance) within the IDSR framework while embracing the One Health concept and promoting use of public health informatics and Information Technology (IT) standards for interoperability. This project will also result in a toolkit that can be used by countries to conduct an e-Surveillance assessment. The project is implemented by the African Field Epidemiology Network (AFENET) in partnership with Public Health Practice PHP (LLC) and other stakeholders. 


The OHSI will provide countries with a tailored roadmap to develop and enhance their public health infrastructure and workforce through the integration of electronic tools. This strategic plan, through the promotion of informatics and IT standards, will enable countries to coordinate the development of electronic tools to form a robust e-Surveillance network that is capable of adapting to emerging needs. The objective of the OHSI is to develop and recommend country-specific strategic plans for implementing One Health e-Surveillance that abides by the IDSR and IHR (2005) strategies and guidelines by using regional and national country level workgroups (CLWGs).

OHSI Strategy

The CLWGs will be comprised of public health, medical, veterinary, laboratory, and IT experts who will develop strategic plans for e-Surveillance tailored to their country’s needs, resources, and infrastructure. These strategic plans will be built upon global best practices, including IT standards which allow for integration of electronic tools and sustainability of IT solutions, and employ a health systems capacity building conceptual framework endorsed by the World Health Organization for the IHR (2005).

The strategic plan for e-Surveillance is intended to augment and complement existing national strategic plans and policies and to establish multi-sectoral and multidisciplinary coordination among one health and e-Surveillance initiatives within the country.

As part of the process, country assessments for e-Surveillance will be conducted by CLWGs for their respective countries to develop a baseline for the strategic plan. Topical trainings on public health informatics and One Health will be provided to pilot participants to provide the needed technical background and develop domestic expertise in these areas.

The project will also provide evidence-based information to the World Health Organization’s African Regional Office (WHO-AFRO) to address its important mission of establishing e-Surveillance in the region.

This project is supported by funding from the US Defense Threat Reduction Agency and is in collaboration with the WHO-AFRO, US CDC, and  Public Health Pratice, LLC.

For more information, contact Dr Herbert Kazoora ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )



One Health e-Surveillance Initiative (OHSI) Information Sheet

One Health e-Surveillance Initiative (OHSI) - Country Level Working Group (CLWG) Orientation Presentation




Initiative commune de surveillance électronique de la Santé






En 1998, l'Organisation mondiale de la Santé, Bureau Afrique (OMS/AFRO) et ses 46 États membres, ont adopté la Surveillance Integrée de la maladie et de la Riposte (SIMR), comme une stratégie pour développer et mettre en œuvre la surveillance complète de la santé publique et des systèmes d’intervention dans les pays africains.


que et des systèmes d’intervention dans les pays africains. Le cadre SIMR définit les besoins programmatique et en personnel pour la surveillance de la santé publique et la riposte à chaque niveau et offre une feuille de route pour réaliser la conformité avec le Règlement Sanitaire International de la Santé de l’OMS (RSI [2005]). La plupart des systèmes de surveillance en Afrique sont basés sur papiers ; cependant, l'accessibilité et la puissance technologiques sans cesse croissant permettent la mise en œuvre répandue d'outils électroniques utilisés pour la santé publique, particulièrement les milieux ou zones defavorisés. Ceci améliore énormément la capacité et réduit le poids de la surveillance de santé publique, conduisant à des ripostes plus rapides.

Qu’est-ce que l’OHSI ?

L'Initiative commune africaine de Surveillance électronique de la Santé (OHSI) est un projet pilote pour aider les pays africains à développer des plans stratégiques pour mettre en œuvre la surveillance électronique durable (l'e-surveillance) dans le cadre de la SIMR par embrassant le concept de santé commune et la promotion de l’utilisation de l’informatique en santé publique et des technologies de l’information standard (TIC) pour l'interopérabilité. Ce projet aboutira aussi à un kit d’outils qui peut être utilisé par des pays pour conduire une évaluation de la surveillance électronique. Le projet est mis en œuvre par le Réseau africain de l'Épidémiologie de Terrain (AFENET) en partenariat avec le Public Health Pratice PHP (LLC) et d'autres partenaires.

Pourquoi l’OHSI ?

L'OHSI offrira aux pays une feuille de route adaptée pour développer et améliorer leurs infrastructures de santé publique et le personnel par l'intégration d'outils électroniques. Ce plan strategique, a travers la la promotion de l'informatique et des technologies de l’information (TIC) standards, permettra aux pays de coordonner le développement d'outils électroniques afin d’ établir un réseau important de surveillance électronique capable d'adapter des besoins émergeants. L'objectif de l'OHSI est de développer et recommander des plans stratégiques spécifiques au pays pour la mise en œuvre de la surveillance électronique commune de la Santé qui prend en compte les stratégies et aux directives de la SIMR et de la RSI (2005) en utilisant des groupes de travail au niveau national et régional (CLWGs).

Stratégie de l’OHSI 

Les Groupes de travail seront constitués d’ experts en santé publique, médecins, de vétérinaires, de laborantins et d’informaticiens qui développeront des plans stratégiques pour la surveillance électronique adaptée aux besoins, aux ressources et aux infrastructures de leurs pays. Ces plans stratégiques seront établis sur les bases de bonnes pratiques, y compris les normes de la technologie de l’information qui permettront l'intégration des outils électroniques et la durabilité des solutions par les technologies de l’information, et utilisent un cadre conceptuel de renforcement des capacités de systèmes de santé approuvé par l'OMS pour la RSI (2005).

Le plan stratégique de la surveillance électronique vise à renforcer et compléter les plans stratégiques et politiques nationaux existants et d’établir une coordination multisectorielle et pluridisciplinaire au sein de l’ initiatives de la santé commune et e-surveillancedans le pays.

Dans le cadre du processus, des évaluations des pays de l’e surveillance seront faites par les groupes de travail pour leurs pays respectifs afin de developper une base pour le plan stratégique. Des formations en Informatique de santé public et santé commune seront dispensées aux participants afin de fournir des competences techniques et developer l'expertise locale dans ces domaines.

Le projet fournira aussi des informations basées sur l’evidence à l’OMS/AFRO pour l’accomplissement de sa mission d’etablissement de e-surveilance dans la région.

Ce projet est financé par US Defense Threat Reduction Agency, en collaboration avec l’OMS-AFRO, le US CDC et Public Health Pratice, LLC.

 Pour plus d'informations, contactez le Dr Herbert Kazoora( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )


One Health e-Surveillance Initiative (OHSI) Information Sheet

One Health e-Surveillance Initiative (OHSI) - Country Level Working Group (CLWG) Orientation Presentation





The AFENET-LAB project seeks to assist Ministries of Health to build and strengthen public health laboratory capacity in Africa by creating a laboratory network to aid communicable disease control and inform public health policy. AFENET-L is funded through the U.S. President’s Emergency Plan for AIDS Relief (PEPFAR).

To better enable data capture, use and sharing, AFENET-L is pioneering the implementation of the Basic Laboratory Information Systems software in partnership with the U.S. Centers for Disease Control and Prevention (CDC), Georgia Institute of Technology, and Uganda’s Ministry of Health.


To achieve its Objectives AFENET-L also trains equipment technicians in selected countries, and supports their laboratories through equipment calibration aimed at fast tracking laboratory accreditation.


  • Developed and distributed laboratory outbreak kits to countries in the Network
  • Supported response efforts to cholera outbreak in Zimbabwe (2008-09) by providing laboratory testing reagents
  • Participated in the harmonization of laboratory training materials in Uganda
  • Developed AFENET Field Laboratory Training Manual
  • Launched HIV Quality Assurance Proficiency Testing Program

AFENET Lab projects include:  

  • HIV External Quality Assurance (EQA)
  • Strengthening Laboratory Management Towards Accreditation (SLMTA)
  • African Society for Laboratory Medicine (ASLM)
  • African Center for Laboratory Equipment Maintenance (ACLEM)
  • Biosafety and Equipment maintenance
  • Prevention of Mother to Child Transmission (PMTCT)
    • PIMA evaluations in Tanzania, Cameroon
    • HIV Drug resistance study in Uganda

AFENET/CDC/EPT one Health Fellowship

The One Health Fellowship proposes to enhance knowledge and skills of field epidemiology graduates from Kenya, Uganda and Tanzania through a one year fellowship. Specifically, the fellowship seeks to strengthen the Integrated Disease Surveillance and Response core functions:


Identification of cases and events, reporting, health data analysis and interpretation, investigation and confirmation, response, evaluation and improvement of multi-disease surveillance for animal and human health sectors.

The goal of the One Health Fellowship is to strengthen public health system and workforce capacity in One Health to improve surveillance, rapid detection, investigation, and timely response to emerging pandemic threats in the Congo Basin region.

The program has three components namely: short courses, field attachment, and mentorship.

On completion of the fellowship, the fellows are expected to provide technical expertise to their respective sectors in disease surveillance, outbreak investigation, and response, as well as control and prevention of zoonoses .


One Health Fellows

Dr. Arthur Bagonza is a veterinarian with a master’s degree in Public Health from Makerere University. As a public health practitioner, he has worked with both government systems and non-governmental organizations to offer agricultural advisory services to farmers, and in prevention and control of zoonotic diseases.

During the One Health Fellowship, Arthur was attached to the Ministry of Health where he participated in several disease outbreak investigations including the anthrax in Sheema district, where he was the principal investigator.

He also took part in a Yellow Fever risk assessment in Kabale district, conducted investigations into a brucellosis outbreak in Mubende district, and lightning strikes in many parts of Uganda. These experiences and others during the Fellowship broadened Arthur’s knowledge and expertise in field epidemiology and public health research.


Arthur is proud to have been an AFENET/CDC/EPT One Health Fellow and is confident that with his newly acquired competencies, he can effectively conduct an outbreak investigation in any part of the world. For Arthur, learning to design and use monitoring and evaluation techniques in an organizational setting were among his most interesting and memorable lessons.

His highlight during the One Health Fellowship was being able to bring importance to diseases like anthrax which have become endemic in Uganda and yet receive little attention from the government. Additionally, surveillance for mass gatherings was also an exciting learning and information sharing opportunity. Arthur is proud to have contributed to disease outbreak prevention and control in Uganda, and for this he has AFENET, CDC, EPT, the Ministries of Health, as well as Agriculture, Animal Industry, and Fisheries to thank.

Dr. Ben Nsajju is a public health practitioner, born in Uganda in 1967. He has a Bachelor of Medicine and Surgery from and a Master of Public Health (MPH) from Makerere University, as well as a Diploma in Education from Kyambogo University in Uganda. After his undergraduate degree, Ben became a physician at Mbale Regional Referral Hospital. He then joined the Uganda Peoples’ Defence Forces (UPDF) as an army doctor where he works currently.

During his MPH, Ben focused his studies on epidemiology- a subject he is very passionate about. He enjoys carrying out disease surveillance, outbreak investigations, as well as data collection and analysis.

He believes that the ACE One Health fellowship was a wonderful opportunity for him to enhance his knowledge, skills, and passion for epidemiology. His best moment during the Fellowship was meeting researchers from the American navy who attended the 4th AFENET Scientific Conference in Dar es Salaam, Tanzania in 2011, where he presented findings of mass gathering surveillance on Martyrs’ Day at Namugongo in Uganda.

Ben hopes to one day set up a post-deployment surveillance system for the armed forces in Uganda.

Ben is married and has one daughter.

Dr. Benard Ngago is a One Health epidemiologist with a Bachelor of Veterinary Medicine and a Master of Public Health (MPH) degree from Makerere University, Uganda. His professional interests include: research, surveillance, and investigation of public health events and his research areas of interest are emerging and re-emerging zoonotic diseases, plus One Health.

Before enrolling for the Fellowship, Bernard was a senior veterinary officer with the local government in Uganda. Bernard is very passionate about disease surveillance and control and has done a lot of work in the field. He has previously worked as a district coordinator of a project called Pan African Control of Epizootics (PACE), which focused on monitoring, reporting, and controlling diseases in animals.

The One Health Fellowship therefore enriched his skills in the area of zoonoses.

What Bernard enjoyed most during the Fellowship was working with multidisciplinary teams to achieve a common goal- preventing and controlling zoonoses through active investigation and timely response. He participated in investigation and response to several outbreaks including: anthrax, Ebola, lightning strikes, and food poisoning among others. Bernard was among the pioneer group of epidemiologists who designed and implemented the novel surveillance system for a mass gathering in Uganda. He was also the principal investigator for a pilot project on brucellosis control in Mubende district and also led assessment of the environmental, water, and food safety at a mass gathering in Uganda. This experience sharpened his leadership skills and through the Fellowship, he also got better at his project management and proposal writing.

Since graduating from the One Health Fellowship, Bernard’s mind has been opened to the immense potential he has to create a difference in public health in Uganda and in the world. He now aspires to be one of the epidemiologists who will popularize, sensitize, train, and carry out research in the area of One Health in Uganda to help improve public health outcomes in the country.

Dr. Eric Mogaka Osoro is a medical doctor with over seven years’ experience in post graduate training in applied epidemiology through the Field Epidemiology and Laboratory Training Programme (FELTP). He is the Provincial Disease Prevention and Control Officer at the Ministry of Public Health and Sanitation, Kenya, and is responsible for supervising and coordinating in planning, implementation, and evaluation of disease control activities including surveillance in Western Province.

During his one-year One Health fellowship at AFENET, Eric teamed up with another fellow- Dr. Kelly Nelima to carry out an evaluation of abattoir surveillance system and investigated an anthrax outbreak in Western Kenya. Results from the evaluation have improved collaboration between the animal and human health sectors in the province through surveillance information sharing in joint dissemination meetings.

Eric is interested in research on zoonotic diseases-diseases which affect both humans and animals- and is confident that the knowledge and skills learnt through the One Health fellowship will greatly enhance his understanding of the One Health concept and implementation of the same.

Dr. Kelly Auma Nelima has a Bachelors degree in Veterinary Medicine from the University of Nairobi and is the first veterinarian in Kenya to graduate with a Master of Science in Applied Epidemiology.

She has served in the Ministry of Livestock in various capacities; first as the veterinary officer in charge of hygiene, and thereafter rising through the ranks to provincial veterinary officer in charge of hygiene- a position she currently holds.

As a One Health Fellow, she has gained vast experience and knowledge in zoonotic diseases outbreak investigation and response, using One Health concept, leadership and management skills, participatory epidemiology, and monitoring and evaluation. Kelly enhanced and learnt most of these skills through well-planned short didactic courses facilitated by qualified persons from reputable institutions like the Eastern African Management Institute (ESAMI), mentorship, and through field placement.

During the fellowship, Kelly was able to evaluate the abattoir surveillance system in Kenya’s Western province, from which she hopes to design a standardized surveillance tool, which featured up as a major gap. Kelly has shared her findings from the evaluation at various fora including the International Kenya Veterinary Scientific Conference in April 2012. She has also participated in anthrax outbreak surveillance, investigation, and response in Kakamega, East Western province, free mass vaccination of dogs, and sensitization in schools in Matungu district Western province- where dog bites are rampant.

Kelly attributes all these achievements to AFENET, CDC, and the Emerging Pandemic threats Program which gave her a chance to be a One Health fellow.

Ms. Stella Immaculate Akech is an epidemiologist with a Bachelors degree in Environmental Health Science and a Master of Public Health degree from Makerere University. During her graduate studies, Stella was a public health officer attached to the Ministry of Health in Uganda, where she participated in disease outbreak investigations including pandemic influenza A (H1N1) and cholera among others. She has worked with civil society organizations and local government systems in developing public health interventions for prevention and control of communicable diseases.

Stella describes her One Health Fellowship experience as “unforgettable” because she had the enviable opportunity to enhance her knowledge and skills in epidemiology and research; she feels confident to investigate any outbreak in the world. Stella participated in outbreak investigations on anthrax and lightning strikes in Uganda. She was the team leader in the latter investigation. Stella believes her research skills got better through the Fellowship. Stella also appreciated the importance of team work which helped her to accomplish tasks easily.

The highlight for Stella was being part of the team that designed and implemented a novel mass gathering surveillance system for Uganda Martyr’s Day in June 2011.

Stella also enjoyed making presentations of investigations she did, at international and national conferences as well as her placement at the ministries of health and agriculture. At the ministries, she supported disease surveillance, generated weekly epidemiological reports, participated in risk assessments, and trained district health staff in epidemic preparedness, response, and surveillance.

To AFENET and CDC, Stella is extremely grateful for the opportunity and is eager to use her new knowledge and skills to improve people’s lives.


Abstracts of Cohort 1: AFENET CDC EPT One Health Fellowship

Multi-Species Outbreak of Pulmonary and Cutaneous Anthrax, Sheema District, Uganda, 2011

Arthur Bagonza1, Monday Busuulwa2, Stella Immaculate Akech1, Bernard Ngago1, Ben Nsajju1, Chima Ohuabunwo2, Sheba Nakacubo Gitta2, Olivia Namusisi2, Peter Wasswa2, Joseph Wamala3, Rose Okurut Ademun5 and David Mukanga2

  • 1AFENET CDC EPT One Health Fellowship, African Field Epidemiology Network
  • 2African Field Epidemiology Network (AFENET)
  • 3Ministry of Health, Uganda
  • 4Ministry of Agriculture, Animal Industry, and Fisheries, Uganda

Background: Anthrax is a highly fatal but vaccine preventable zoonotic disease caused by Bacillus anthracis. It manifests in three forms namely; cutaneous, gastrointestinal and pulmonary. In November 2011, following the death of nine livestock and two persons in a single outbreak in Sheema district of western Uganda, a multi- disciplinary “One Health” investigation team was constituted to determine the magnitude, source, cause and financial loss of the outbreak. We also assessed the district response capacity.

Methods: We interviewed the district health and veterinary officers to obtain baseline information about the outbreak using a pre-designed form. We reviewed medical and veterinary reports using a case- patient form to capture demographic, vaccination and clinical data. Four key informant interviews were purposively conducted with livestock farmers and family members of the affected persons during active community case search. The team inspected the farms, collected samples from cattle, goats and their carcasses. Laboratory tests were carried out on samples sent to the National Animal Disease Diagnostic and Epidemiology Centre in Entebbe. Outbreak data was analyzed and described by person, place and time using SPSS version 17.0

Results: Among the three farms affected, 8/295 cows, 1/90 goats and 2/5 persons died of anthrax, giving a case fatality rate of 2.7%, 1.11% and 40% respectively. Of the five human cases, two died of pulmonary complications. None of the animals had been vaccinated against anthrax. Laboratory samples were positive for B. Anthracis. A total financial loss estimated at 2.2billion Uganda Shillings ($885,000) was incurred by the district from low livestock sales in the month following the outbreak. The district had only one ill-equipped veterinarian instead of the three required and 2/5 (40%) of the required outbreak response team.

Conclusion: An outbreak due to B.anthracis with pulmonary complications, significant fatality and high financial loss occurred in a poorly resourced district of western Uganda. The source of this outbreak was an infected cow from a neighbouring district mingling with unvaccinated cattle followed by improper handling of carcasses by farm workers. Government should ensure an integrated country wide anthrax vaccination to prevent the disease amongst the animals and reduce human exposures. Adequate tracking of infected animals across the district boundaries should be encouraged. The ministry of agriculture should educate farmers and enforce proper handling of animal carcasses.

Keywords: Anthrax, Outbreak, Vaccination, Cattle, One Health, Zoonoses, Uganda

Public Health Surveillance for Mass gatherings: A case of Martyrs’ Day celebration, Uganda, 2011

Ben Nsajju1, Monday Busuulwa2, Stella Immaculate Aketch1, Bernard Ngago1, Arthur Bagonza1, Endie Waziri3, Chima Ohuabunwo2,&4, Peter Wasswa2, Sheba Nakacubo Gitta2, Monica Musenero2 and David Mukanga2

  • 1AFENET CDC EPT One Health Fellowship, African Field Epidemiology Network
  • 2African Field Epidemiology Network (AFENET)
  • 3Nigeria Field Epidemiology and Laboratory Training Program (NFELTP)
  • 4Morehouse School of Medicine, USA

Background: Mass gatherings present high risk environments for public health hazards. There is no surveillance system for mass gatherings in Uganda. Uganda Martyrs’ Day is an annual religious celebration with an estimated attendance of up to two million people in an area of less than a square kilometer. In 2011, the day coincided with an Ebola outbreak in the country. We set out to pilot a syndromic surveillance system for mass gatherings to facilitate rapid detection of and response to public health events.

Methods: We based on the WHO and National Integrated Disease Surveillance guidelines to develop surveillance form to collect demographic and clinical data from emergency medical posts within the venue. We conducted a pre and post event record review on patient load and drug consumption pattern in surrounding health units and pharmacies. Data was analysed in SPSS to identify common symptoms, syndromes and potential health hazards.

Results: We developed and implemented a surveillance system tracking patients presenting with symptoms and emergency syndromes. Nearby clinics and pharmacies indicated low patient turn-up on Martyrs’ day compared to the days before and after the event. Seven Ebola alert cases were identified and investigated. The commonest complaints among the 390 patients captured by the surveillance system were headache (187) fever (99) and abdominal pain (89). Of the estimated two million attendees of the event, there were three syncopal attacks and no death. Notable challenges to implementation of the system were overcrowding, limiting access to medical posts, poor human resource planning, lack of zoning and track ways as well as difficulty in estimating the population.

Conclusion: A useful surveillance system for mass gathering was developed which helped to rapidly detect and investigate potential infectious illnesses and hazards. The system should be used at future mass gatherings with adequate pre event resource planning.

Key words: Mass gathering, Syndromic-surveillance, Public Health hazard, Religious celebration, Integrated disease surveillance

Environment, Water and Food Safety Surveillance during a Religious Pilgrimage Mass Gathering, Namugongo, Uganda, 2011

Benard Ngago1, Monday Busuulwa2, Arthur Bagonza1, Stella Immaculate Aketch1, Ben Nsajju1, Endie Waziri3, Chima Ohuanubwo2&4 Peter Wasswa2, Olivia Namusisi2, Sheba Nakacubo Gitta2, Monica Musenero2 and David Mukanga2

  • 1AFENET CDC EPT One Health Fellowship, African Field Epidemiology Network (AFENET)
  • 2African Field Epidemiology Network (AFENET)
  • 3Nigeria Field Epidemiology and Laboratory Training Program (NFELTP)
  • 4Morehouse School of Medicine, Atlanta, USA

Background: In situations where large numbers of people are gathered in a single place, exposure to environmental hazards is inevitable. Such hazards include inadequate and /or poor sanitary conditions, contaminated water and food. Every 3rd of June, an estimated 2-3 million people gather in a restricted area of a peri-urban town in Uganda for annual religious pilgrimage. Because of the overwhelmingly large number of people, water and sanitary facilities may not be adequate. Furthermore, safe food handling procedures including animal slaughtering and meat inspection may not be followed. This study sought to assess environmental conditions, the safety of water and food consumed and to determine the potential risk of zoonoses transmission during the 2011 event.

Methods: A cross-sectional study was undertaken at Namugongo pilgrimage site, Uganda, where a pre-tested semi-structured questionnaire was administered to 297 consenting pilgrims to collect data on sources and quality of drinking water, usage and types of sanitary facilities, and solid waste disposal. Four key informant interviews were conducted to obtain data on availability of drinking water, sanitary facilities and the safety of meat. Checklists were used to assess the physical state of sanitary facilities, water quality, food vendors’ history of medical certification, and food handling procedures. Water and food samples were sent to laboratory for safety analysis. For potential zoonotic disease transmission exposure, data was obtained by observation of the practices of meat handlers and pilgrims during the preparation and consumption of meat. Qualitative data was analyzed manually using a master sheet where frequencies of responses were tallied according to themes. Univariate analysis of quantitative data was done using SPSS version 17.0. Triangulation was performed to validate findings.

Results: Available sanitary facilities for the estimated 2-3 million people were 22 stances of pit latrines and 29 stances of water closets, giving access rate of 2-3 toilet stances per 100,000 persons (51 /2 M). Of the 297 pilgrims interviewed, 11.2% practiced open defecation at the bush around the pond, 31% drank pond water and 24% bottled water. The pond water had a coliform (Escherichia coli) count of 20 c.f.u per 100ml and 26% of the respondents perceived it safe for consumption. On solid waste disposal 43.4% of the respondents disposed solid waste indiscriminately in the compound. Of the 37 food vendors 97.2% had not been medically certified to handle food. However, the food was not contaminated. Meat which was being sold to consumers had not been inspected. Meat handlers were indiscriminately mixing uncooked and cooked meat at the point of sale. In addition, 11/20 (55%) of the meat vendors visited sold undercooked meat to pilgrims for consumption.

Conclusion: The grossly insufficient sanitary facilities and consumption of contaminated pond water exposed the pilgrims to potential water borne diseases. Also there was high exposure to the possibility of zoonotic disease transmission through uninspected and improperly cooked meat.

Adequate mobile toilets should be provided at similar mass gatherings. Open defecation should be prohibited and the pond water preserved as holy but be purified. Government should ensure proper inspection of meat, certification of food handlers and adequate health education at such mass gatherings.

Key words: Mass gathering, Environmental hazard, Food safety, Zoonoses, Pilgrims, Sanitary facilities; Uganda

Outbreak Investigation, Response, and Community Awareness of Anthrax in Kakamega, Kenya, 2011

Eric Osoro1&3, Kelly Nelima2&3, Monday Busuulwa4, Jared Mulala2, Qiudo Ahindukha1, Chima Ohuabunwo4&5

  • 1Ministry of Public Health and Sanitation, Kenya
  • 2Ministry of Livestock Development, Kenya
  • 3One Health Fellowship Program, African Field Epidemiology Network (AFENET), Kampala, Uganda
  • 4African Field Epidemiology Network, Kampala, Uganda
  • 5 Morehouse School of Medicine, Atlanta, USA

Background: Anthrax remains common in Asia and Africa with cutaneous anthrax the most common form (about 90%) in humans. In late November 2011, an anthrax outbreak was reported in Kakamega East District, Kenya. We carried out a study to describe the outbreak, assess the outbreak response and determine community knowledge, attitudes and practices on anthrax using the One Health approach.

Methods: A cross sectional study was conducted to describe the outbreak. Key informant interviews were used to assess the outbreak response while participatory rural appraisal (PRA) approaches were applied to determine community knowledge, attitudes and practices on anthrax. The study population was all persons who handled/consumed meat of the carcass of the infected animal. A suspected case was any person with a typical skin lesion after exposure to infected animal in Kakamega East District. An interviewer-administered questionnaire was used to collect data for the cross sectional study. Interviewer guides were used for key informant interviews and for PRA.

Results: Of 40 respondents, 65% were female. Median age was 32 years (range: 2 years to 88 years) and were from one sub- location. Sixteen (40%) were suspected case-patients while 24 (60%) were asymptomatic. The outbreak response was coordinated by the District Health Management Team and did not include the District Veterinary Office. The response of the outbreak did not include rapid dissemination of advice to clinicians on detection and treatment. All the laboratory specimens were collected after administration of antibiotics. While anthrax was recognized as an important zoonotic disease by the community, there was low awareness about its presentation.

Conclusion: There was lack of collaboration between the animal and human health professionals in the anthrax outbreak response. Community awareness on anthrax was low. There is need for community health education on anthrax and other zoonoses and systematic collaboration between human and animal health sectors during anthrax response.

Key Words: Kakamega, Anthrax, Outbreak response, Participatory rural appraisal, One Health

Evaluation of Abattoir Surveillance System for Zoonoses in Western Province, Kenya

Kelly Nelima1&3, Eric Osoro2&3, David Mutonga2, Jared Omolo2, Monday Busuulwa4, Mulala Jared1, Muriithi Mbaabu2, Musenero Monica4, Peter Wasswa4, Sheba Nakacubo Gitta4, Chima Ohuabunwo4& 5 and David Mukanga4

  • 1Ministry of Livestock Development, Kenya
  • 2Ministry of Public Health and Sanitation, Kenya
  • 3AFENET CDC EPT One Health Fellowship, African Field Epidemiology Network (AFENET)
  • 4African Field Epidemiology Network, Plot 4B Mabua Road, Kampala, Uganda
  • 5Morehouse School of Medicine, Atlanta, USA

Background: Surveillance for zoonoses in abattoirs is essential in public health because it facilitates early detection, monitoring and control of diseases at human- animal interface. Systematic inspection of animals at pre and post slaughter can provide critical data for animal diseases of public health and food safety importance. The abattoir surveillance system is part of the general disease surveillance system of the Department of Veterinary Services and includes private and public slaughter houses. Since the adoption of the 1975 meat control act, zoonoses surveillance in abattoirs has remained rudimentary in Kenya. We carried out an evaluation to describe the Western province abattoir surveillance system, assess the system’s attributes, determine if it is meeting set objectives and design a standard surveillance system for zoonoses in abattoirs.

Methods: We interviewed key stakeholders including meat inspectors, provincial and district veterinary officers using an interview guide. Surveillance documents at the veterinary office and data collection processes at representative abattoirs were assessed with an observational checklist. Surveillance dataset for 2010 was reviewed and analyzed by person, place and time. Qualitative and quantitative system attributes were assessed using CDC updated guidelines for public health surveillance system evaluation. A simple data collection tool, data flow algorithm and data analysis plan was designed.

Results: There were no standard reporting tools and case definitions. Data collection, storage and transmission were manual. Standard operating procedures on meat inspection and data management were not available. Routine information sharing with public health authorities was not done. Laboratory services to support the surveillance system were lacking in the province. Of the 27 districts, the annual completeness of reports was 100% but only one district reported on time. The duration of delay in monthly report submission ranged between 18.7- 37.3 days with a mean of 28.7 days . All reports had essential data required but 20% were unduely repetitive.

Cattle constituted 66% of animals slaughtered while 5% were pigs. Female animals constituted 48% of slaughtered animals; 17% of the females were reported pregnant. Three- quarters of whole carcass condemnations were cattle; dropsy contributed 55% while cadaver was 36%. Two thirds of organs condemned were liver; mostly due to liver flukes (76%) and hydatid cysts (16%).

Conclusion: The abattoir surveillance system in Western province is not up to standard. Though it is simple and representative, timeliness, data quality and information sharing are unsatisfactory thereby limiting its usefulness. Laboratory diagnosis to compliment the surveillance system is lacking.
Provision of standardized surveillance tools and resources combined with laboratory support and animal-human health authorities information sharing will enhance the usefulness of the system.

Key words: Surveillance system, Abattoir, Zoonoses, Evaluation, Kenya

Epidemiological Study of Lightning Strikes in Uganda, June-July, 2011

Stella Immaculate Akech1, Monday Busuulwa2, Bernard Ngago1, Arthur Bagonza1, Chima Ohuabunwo2&4, Peter Wasswa2, Sheba Nakacubo Gitta2, Monica Musenero2 and David Mukanga2

  • 1AFENET CDC EPT One Health Fellowship, African Field Epidemiology Network (AFENET)
  • 2African Field Epidemiology Network (AFENET)
  • 3Nigeria Field Epidemiology and Laboratory Training Program (NFELTP)
  • 4Morehouse School of Medicine, Atlanta, USA

Between 19 June and 3 July 2011, a total of 45 deaths and 155 injuries due to lightning strikes were reported in Ugandan media. The pattern of injuries and deaths was not clear but the distribution was countrywide. Information on the peculiarities of the geographical areas, communities and persons affected was scanty. We therefore investigated and conducted a community assessment to characterize the distribution and magnitude of the lightning strikes; identify associated risk factors, beliefs and practices, as well as to assess the impact of lightning strikes on affected communities. This provided evidence to inform public health action and interventions.

Methods: A lightning-strike case was a person admitting a history of exposure to lightning strike with or without visible injury or a person said to have died following exposure to lightning strikes in the selected Ugandan districts during June and July 2011. Eight districts were purposively selected based on number of reported lightning-strike injuries or deaths. We reviewed line-lists and records, interviewed key informants at district/community health units, administration units, schools, and traditional healing homes and conducted active community case-search. Structured questionnaire was administered to case-patients to obtain data on demographics, known risk factors, knowledge, beliefs and practices related to lightning strikes, outcomes and impact of lightning strikes. For the minors, unconscious and the deceased, their caretakers were interviewed. Focus group discussions, direct observations with observational checklist, and environment assessment were conducted to obtain in-depth information and lightning-related environmental data. The study population were the communities affected by lightning strikes. Quantitative data was entered into Epi-Info version 3.3.2 soft ware and then exported into SPSS Version 18 for univariate analysis. Qualitative data was analysed using manifest content analysis technique. Triangulation was performed to further validate data and information on lightning-strike.

Results: Most (80%) of the places that experienced severe lightning strikes were at a relatively higher altitude than the surrounding places and had little or no tree cover. Almost all these places (39/40) did not have lighting arresters or electricity. Risk factors included rainwater harvesting and sheltering under trees during thunderstorms. The majority of casualties (67%) were bare-footed and 78% of the affected were primary school pupils. These lightning episodes caused 32 deaths in nine districts, various physical injuries and induced anxiety in the population, with a resultant decrease in attendance at school and other social events. The affected communities suffered economically through destruction of property, death of live stock, hospital and burial expenditure. Peculiar cultural traditional practices included smearing the victims with human faeces as treatment and taking all property from the affected households.

Conclusion: Lightning strikes were widely distributed in the country, affecting areas where there were no lightning arresters. Incidence of lightning strikes in the community was high with associated high case fatality rate. Individual risk factors included bare footedness, sheltering under trees and rain water harvesting. The knowledge about lightning is generally poor and there are high risk practices. The socio economic and public health impacts of these strikes were paramount. Ministries of Education, Health and Works should promote community awareness on the risks associated with lightning and enforce installation of lightning arresters in all buildings. School uniforms should include shoes with rubber soles as part of policy. Children should stay indoors during rainstorms.

Key Words: Lightning strikes, Epidemiological Study, Community Assessment, Lightning Risks, Uganda


AFENET/USAID/CDC Trainee Grants Program

The The Trainee Grants Program offers trainees the opportunity to develop novel and effective strategies and interventions that will help improve public health practice in their countries. Current trainees of Applied or Field Epidemiology Training Programs in Africa working with an Academic Supervisor are eligible for funding. Trainees working collaboratively with District or Provincial Health Authorities or the Ministry of Health are preferred.


This program will create a unique opportunity for field epidemiologists in training to focus their research projects on improving public health practice. It will go beyond the goals of a traditional research grant program by requiring recipients to share their results with local and national level policy makers and advocate for broader adoption of their proven intervention or strategy through changes in health policy and programming.

Click this link to download the call for proposals-2011


African Cholera Surveillance Network (AFRICHOL)

AFRICHOL is intended to strengthen surveillance systems in Africa and reinforce outbreak investigation and provide accurate data that would inform vaccine decision making for Africa.


AFRICHOL is implemented in eight African countries by a group of project partners .

The overall goal of the project is to obtain improved information about cholera in Africa and the burden of the disease by establishing an enhanced regional surveillance network that can routinely track and confirm cholera cases, and provide support to reinforce outbreak investigation .

AFRICHOL project goals

  • Establish a consortium of organizations that will plan and oversee the development and implementation of a cholera surveillance network in eight African countries
  • Enhance regional cholera surveillance by establishing a network of sites that can generate high quality data and routinely confirm cases by laboratory testing
  • Reinforce capacity to investigate cholera outbreaks
  • Strengthen laboratory capacity to support cholera surveillance and outbreak investigation.
  • Design activities to be compatible with existing plans and policies, and develop strategies for sustainability

For more information about AFRICHOL visit the project website http://africhol.org/


African Programme for Advanced Research Epidemiology Training Fellowship (APARET)

APARET is a European Union funded four-year program that is implemented by a consortium of institutions including AFENET, the Bernhard Nocht Institute for Tropical Medicine (Germany), the US Centers for Disease Control and public health training institutions in Africa, among others.


The program targets recent graduates of FELTP/FETPs with the aim of providing fellows with specialized training to support the development of independent research activities including writing and applying for a major research grant in order to catalyze the development of self-driven research activities. Each fellowship lasts two years, during which fellows conduct an epidemiologic research with their host institutes, where they are supervised and mentored.

For more information about APARET visit the project website http://aparet.org/


Avian Influenza And Other Zoonotic Infections Project (AIZIP)

The Avian Influenza and Other Zoonotic Infections Project (AIZIP) was launched in March 2008 to strengthen capacity for Avian and Pandemic Influenza preparedness and response, following detection of the Avian Influenza (AI) virus in Africa.


Premised on the One World, One Health concept and with funding from USAID, AIZIP supports countries in the Network to establish structures within their human and animal health systems, to address surveillance, response, control, and prevention of zoonotic diseases.

To achieve its objectives ,is implementing AIZIP in several countries and plans to implement an All Africa Response Team which will provide technical support to any country in the Network in the event of a zoonosis outbreak.

  • Conducted successful Anthrax outbreak investigation in Bushenyi, Uganda in 2010
  • Supported response efforts to Influenza A (H1N1) in countries in Network in 2009
  • Successfully carried out plague prevention efforts in West Nile region, Uganda in 2009
  • Supported Kenya in fast tracking of International Health Regulations in 2009

Epidemiology of Burkhitt Lymphoma in East African Minors (EMBLEM)

EMBLEM is a case control study of 1,500 Burkhitt’s Lymphoma cases and 3,000 controls that is being conducted in East Africa to examine whether having one or more malaria-resistant single nucleotide proteins (SNPs) protects against Burkhitt’s Lymphoma.


Burkhitt’s Lymphoma is the most common childhood cancer in Equatorial Africa and malaria is the most widespread childhood exposure that is both treatable and preventable. Confirming the association between malaria and Burkhitt’s Lymphoma can suggest novel ways to prevent and possibly treat Burkhitt’s Lymphoma and offers a rare opportunity to gain insights in gene-environmental interactions that influence the geographic distribution of Burkhitt’s Lymphoma.

EMBLEM Objectives


  • Recruited and trained study staff in Lacor Hospital Established functional office and laboratory in Lacor Procured equipment and laboratory supplies Created awareness about the study in the community Developed study documents Conducted household census in three selected villages in three districts by Uganda Bureau of Statistics Screened 47 and enrolled 22 study subjects

For more information about EMBLEM visit the project website http://www.emblem.cancer.gov/collaboration/



Experience@AFENET gives public health trainees in Africa, the opportunity to enhance their knowledge and in-service practice of public health in Africa. It is a three-12 months fellowship program for Public Health graduates in the Network that offers fellows a unique learning experience during which they gain special skills for field epidemiology capacity development initiatives.


During this fellowship, AFENET fellows have the opportunity to work and be supervised by senior program staff across the AFENET Network. Fellows also have the opportunity to work with AFENET partners .

The fellowship provides international trainees with hands-on training in global health, and health systems in developing countries. Specifically, trainees are involved in outbreak investigation and response, teaching epidemiology to undergraduate and graduate trainees, data analysis, and manuscript writing, among others.


Health Diplomacy Program for Northern Nigeria

The Health Diplomacy Programfor Northern Nigeria aims at supporting the training and skill set development of frontline health workers in northern Nigeria, so as to increase access to, effectiveness, safety and quality of health services.


The programoffers two courses: the Basic Epidemiology Course for community healthcare workers and the Health Leadership and Management Course for health managers at State and Local Government Area (LGA) level. Each course runs for at least three months, and involves didactic, fieldwork and feedback sessions. Participants receive a certificate from Usmanu Danfodiyo University Sokoto, Nigeria upon completion of the course. So far, one of these courses, Basic Epidemiology has been delivered to 63 participants divided into two cohorts.


  • To establish training needs of potential participants within three months of the project
  • To design a curriculum and produce training materials based on findings of the needs assessment with the first three months of the project
  • To train 160 persons within 12 months
  • To develop and implement a mechanism for monitoring and evaluating project activities

Non-communicable Diseases (NCD) Project

AFENET is establishing a surveillance system for non-communicable diseases (NCDs) using data available from patients attending the institutions’ clinics , and periodically analyzing and publishing this data.


Currently, information gathered is managed manually. Through the NCD surveillance network, AFENET will help to improve data collection, analysis, and presentation related to the burden of non-communicable diseases in Uganda.

To achieve its objectives , AFENET also hopes to collaborate with the Uganda Heart Institute and Mbarara Referral Hospital to establish Centers of Excellence for training, surveillance, and research for NCDs to provide opportunities for young public health professionals in Africa to enhance their competencies.


  • Established surveillance system for diabetes and cardiovascular diseases at Mbarara and Mulago National Referral hospitals
  • Built databases to monitor patients with diabetes and cardiovascular diseases

Pan African Medical Journal (PAMJ)

PAMJ is a peer-reviewed, online, open-access medical journal, published with support from AFENET. A highly talented and qualified team of editorial staff with three managing editors and over 700 experienced reviewers from 20 countries manage manuscripts ranging from research papers to commentaries in manifold medical domains like epidemiology, maternal and child health, radiology, clinical medicine, health economy, and nutrition.



  • On 29 September 2010, PAMJ published its 100th article after only 2 years of existence
  • PAMJ is currently indexed on PubMed- the largest database for scientific journals in the world
  • PAMJ is also listed in the Directory of Open Access Journals (DOAJ), African Index Medicus (AIM), African Journals Online (AJOL), EBSCO,SciVerse, SCOPUS, Embase, Index Copernicus (IC), and is a member of the Open Access Scholarly Publishers Association (OASPA) and Health InterNetwork Access to Research Initiative (HINARI).
  • PAMJ has introduced and continues to operate an article-level metrics system to assess the impact of each article from the very day of publication.

Sustainable Management and Development Program (SMDP)

The program aims at strengthening health systems in Africa through improved public health leadership and management by engaging, developing and supporting health leaders to build country capacity to achieve lasting health improvement.


SMDP is a program of the U.S Centers for Disease Control and Prevention which supports AFENET in strengthening programs to produce public health leaders and managers by enhancing management capacity of Ministry of Health (MoH) staff from the Planning and Surveillance units.

SMDP conducts management workshops for MoH staff especially at the district level. This model involves:

  • Team building
  • Leadership
  • Communication
  • Priority setting and planning
  • Performance assessment
  • Problem solving


  • Support improvement of Health Management Information Systems (HMIS) in Zimbabwe
  • Organized first short course on Improving Management of Public Health Interventions (IMPHI) in Ghana

Uganda Immunization Training Program (UITP)

The Uganda Immunization Training Program (UITP) aims at training mid-level immunization personnel and managers of the Expanded Program on Immunization (EPI) in Uganda, with skills in immunization service delivery and vaccine management through short training programs.


Started in December 2007,UITP is a collaboration of the Task Force for Global Health, Makerere University School of Public Health (MakSPH), Uganda Ministry of Health, and the Uganda National Expanded Program on Immunization (UNEPI). The project is funded by the Merck Company Foundation under its Merck Vaccine Network Africa (MVN-A) branch.

To achieve its objectives UITP is addressing some of the challenges in EPI training using materials adapted from WHO AFRO and conducting cascade training on immunization service delivery for national and district level managers. The long term goal is to train all EPI staff in Ministry of Health facilities in Uganda.

  • Reviewed and adopted training materials
  • Participated in polio eradication campaigns
  • Conducted operational-level trainings
  • Trained district and health sub-district mid-level managers in immunization service delivery


Upcoming Events

Board of Directors Meeting
Date: 24 - 27 August 2015
Venue: Kampala, Uganda


Date: 7 - 11 September 2015
Mexico City, Mexico

European Scientific Conference on Applied Infectious Disease Epidemiology (ESCAIDE)
Date: 11 - 13 November 2015
Venue: Stockholm, Sweden


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