South Africa Field Epidemiology Training Program

Program overview

South Africa was one of the 15 focus countries at the launch of the President’s Emergency Plan for AIDS Relief (PEPFAR) in 2004 and was allotted the largest PEPFAR budget. Therefore, epidemiologists were in great demand due to the need to understand and effectively respond to South Africa’s HIV/AIDS epidemic. Beginning in 2005, South African health officials, together with the U.S. and locally-based CDC officials, discussed and defined the development of a South Africa Field Epidemiology and Laboratory Training Program (SAFELTP), which was subsequently launched in 2006.

SAFELTP began as an academic degree-granting program with a laboratory training component, similar to the Kenya and Tanzania FELTPs, and was supported as a collaboration between the National Department of Health (NDOH), the National Institute of Communicable Diseases (NICD), and the University of Pretoria School of Health Systems and Public Health, with technical and financial assistance from the U.S. Centers for Disease Control and Prevention (CDC) office in South Africa and PEPFAR. The South African Field Epidemiology Training Program (SAFETP) is a competency-based program that uses an established applied epidemiology curriculum, providing an accredited Masters in Science (MSc) degree from either the University of Pretoria (UP) or the University of the Witwatersrand (Wits) with mentored practical field experience. The program targeted physicians, nurses, laboratorians and other allied health professionals with a primary degree in the health sciences.

The skilled workforce is needed at every level to detect, analyse and respond to diseases of public health importance. In addition to the Advanced tier, SAFETP offers the Frontline and Intermediate tiers. The Frontline tier was launched in 2016. This is a three-month in-service training program and the first step in the three-tiered model of training. The Intermediate tier was launched in November 2021. This is a nine-month, in-service program designed for surveillance officers and public health professionals. Both tiers/levels equip participants with the essential skills used in surveillance, including the use of case definitions, disease detection and reporting.

Participants are taught how to summarise data using simple tables and graphs, conduct case investigation, outbreak investigation and response, data analysis and interpret data for decision-making. Participants at the Intermediate level trainees are also introduced to designing, conducting, analyzing and interpreting data from descriptive epidemiologic studies. These two levels are targeted at public health professionals working in the area of surveillance at national, provincial, district and local levels, to strengthen the country’s capacity to rapidly detect, respond to, and contain public health emergencies at their source. Moreover, they are designed to prevent the spread of diseases, and thereby enhance global health security. The target audience includes medical officers, nurses, infection control officers, surveillance officers, and environmental health officers.


Over 90 scientific manuscripts have been published in peer-reviewed scientific journals by SAFETP residents based on their activities during the training program. SAFETP trainees have made significant contributions in investigating and responding to numerous disease outbreaks and priority health conditions. Additionally, graduates have engaged in various activities throughout the country that have provided key inputs for local, provincial, and national public health decision-making. Selected examples include outbreaks of Rift Valley fever from 2008 to 2011 that led to greater collaborations with the veterinary and animal health sector, an outbreak of multi-drug resistant Pseudomonas aeruginosa in a hospital in Cape Town in 2010, and a diarrheal disease outbreak investigation in Free State that led to major improvements in the water treatment system. Others include the identification of the emergence of multi-drug resistant Candida auris fungal infections which led to the development of clinical and diagnostic guidelines for detection and investigation of future outbreaks, and the Listeriosis outbreak in 2017, which led to the inclusion of Listeriosis in the category 1 Notifiable Medical Conditions list in South Africa.

In addition, SAFETP trainees have also assisted in responding to outbreaks in other African countries in the region. Select examples of these include an outbreak of typhoid in Zimbabwe from 2011 to 2012 which highlighted the role of contaminated boreholes in continued transmission, an outbreak of diarrheal illness in Swaziland in 2014, and a 2017 investigation of a cluster of hydrocephalus cases in Lesotho. Finally, residents have completed analytic research studies on the determinants of loss to follow-up among HIV patients in South Africa on antiretroviral treatment enrolled in a pharmacovigilance cohort study from 2004 to 2012. The results helped bolster the strategy of community-based adherence support programs and integrated patient care that has been implemented by the South African HIV/AIDS treatment program. Residents also conducted analyses identifying risk factors for tuberculosis smear non-conversion in Western Cape Province from 2007 to 2013, helping health providers better target at-risk patients.

SAFETP trainees and graduates have played a significant role in strengthening public health surveillance programs within the country. The trainees have contributed to the design, implementation, and evaluation of various surveillance systems at all levels of the health system within the country. In 2015, a team of six SAFETP residents and seven alumni evaluated the National Notifiable Medical Conditions (NMC) surveillance system in the country. The findings from the evaluation have informed the re-engineering of the entire NMC surveillance system for South Africa.

In 2018, the SAFETP was accredited by the Training Programs in Epidemiology and Public Health Interventions Network (TEPHINET), and the SAFETP Alumni Association was established. As SAFETP’s reputation grows for producing competent field epidemiologists, the positions for which graduates are being hired suggests an increasing influence in a public health leadership capacity at program management levels. Furthermore, SAFETP graduates are increasingly involved in using applied epidemiology methods to address the key health burdens and initiatives in South Africa. To date, the program has more than 95 graduates who are employed in various sectors such as the public sector or ministry of health, private sector, public health institutes, Africa CDC, US CDC (in-country office), other national FETPs, WHO, etc. Currently, the program has 26 residents. More than 300 abstracts (from both Advanced and Frontline trainees) have been presented at major scientific conferences including AFENET, TEPHINET and EIS.

Another significant impact of SAFETP is the involvement of graduates and residents in COVID-19 response activities. More than 70 percent of the Provincial Epidemiology Team (PET) comprises SAFETP graduates who play a significant role in the Ministry of Health’s epidemiology, surveillance and outbreak response directorates.  

To strengthen the country capacity on public health surveillance, epidemic preparedness and response, the SAFETP team offers short courses on basic epidemiology to train and mentor health professionals in addition to training of the three tiers. Over 250 frontline health workers have been trained in all the various provinces and districts of the country. In November 2021, the program has enrolled and welcomed the first cohort for the Intermediate level (16 participants in Eastern Cape Province). The program continues to build field epidemiology capacity in neighbouring countries by training the specific countries’ health professionals (Lesotho, Malawi and Eswatini).