The Establishment of the National Public Health Institute (NPHI) in South Sudan

Introduction

Following the establishment of the Africa Centres for Disease Control and Prevention (Africa CDC) within the African Union in 2016, it was mandated to support the creation of National Public Health Institutes (NPHIs) in African Union (AU) member states. In 2018, the Africa CDC published a framework for the development of NPHIs. That same year, a high-level meeting was held at the National Public Health Laboratory (NPHL) involving the Ministry of Health (MOH), the US CDC, and the World Health Organization (WHO), which affirmed the commitment to establishing an NPHI for South Sudan.

Country profile

South Sudan is located in the eastern African region between latitudes 3° and 13°N, and longitudes 24° and 36°E. It is bordered by the Sudan to the north, Central African Republic and Democratic Republic of the Congo to the west, Ethiopia to the east, and Uganda and Kenya to the south. The country has a surface area of about 619,745 square kilometres comprising tropical forest, swamps and grassland. The White Nile flows through the country, passing the capital, Juba. Administratively, the country is divided into 10 States and 3 Administrative Areas, each with several Counties subdivided into Payams, within three major administrative regions of Equatoria, Bahar El Ghazal, and Upper Nile. South Sudan joined the East African Community (EAC) of partner states in March 2016.

NPHI establishment

The NPHI in South Sudan was established on February 11, 2019, through Ministerial Order Number 004/2019, as an autonomous entity with perpetual succession and legal personnel. As provided for in the South Sudan National Public Health Act 2023, the NPHI’s primary objectives include enhancing disease surveillance and response systems, fostering a sustainable public health workforce, and collaborating with stakeholders to improve environmental and occupational health. Its structure comprises two main directorates: the Technical Directorate, which encompasses departments focused on surveillance, emergency preparedness, public health research, and laboratory systems, and the Directorate of Administration & Finance, which manages human resources, finance, procurement, and ICT.

The Institute was envisioned to serve as a centre of excellence in the following thematic areas:

• Thematic Area 1: Surveillance and Disease Intelligence
• Thematic Area 2: Emergency Preparedness and Response and EOCs 
• Thematic Area 3: Laboratory Services and Public Health Diagnostics
• Thematic Area 4: Public Health Workforce Development
• Thematic Area 5: Non-Communicable Disease and Injuries
• Thematic Area 6: Public Health Research and Ethics

The development of health research is part of the mandate of the NPHI. Research activities will ensure that health research agendas and research resources focus on priority health problems in the country.

NPHI scope

The scope of the NPHI extends to generating knowledge for better health outcomes, understanding the determinants of health, and innovating interventions that address the health challenges faced by the South Sudanese population. It focuses on:

• Generating knowledge to enhance health outcomes and promote individual, community and population health 
• Understanding health determinants by analysing how biological, social, cultural, and environmental factors interact to influence population welfare.
• Creating health innovations by developing interventions needed to improve health outcomes for the population of South Sudan.

Through these functions, the NPHI is pivotal in strengthening the Nation’s public health infrastructure and addressing critical health issues.

Progress and milestones accomplished

The establishment of the NPHI was significantly advanced by a ministerial order that facilitated the formation of a steering committee tasked with providing oversight, high-level guidance, and advocacy among stakeholders. To ensure technical oversight during the institute’s creation, a 15-member Technical Working Group (TWG) was established. In October 2019, the Minister of Health appointed an Interim Director to coordinate stakeholder engagement and manage the establishment process effectively. 

With funding from the US CDC, a benchmarking visit to Ethiopia was conducted in late September and early October 2019, involving nine members from the steering committee and TWG. This visit aimed to gather insights and best practices for the development of the NPHI.

In November 2019, with support from Africa CDC, US CDC, WHO, and Intra-Health International, the legal framework for the NPHI was developed. Subsequently, in October 2021, the Ministry of Justice and Constitutional Affairs presented the NPHI to the Governance Cluster, which passed it with amendments. This passage transformed the legal framework into a Bill, which was tabled before the Council of Ministers and unanimously passed in September 2022.

The NPHI Bill was then passed by the National Parliament in June 2023 and received Presidential assent on the 7th of July, 2023. It was officially printed and disseminated as the NPHI Act, 2023, in August 2024. Following this significant legislative milestone, an Acting Executive Director and an Acting Deputy Executive Director were appointed in July 2024, marking a new phase in the operationalization of the NPHI.

Achievements

In October 2021, with support from Africa CDC, the NPHI conducted two high-level advocacy meetings targeting senior leadership from the Ministry of Health and leaders from various line ministries, including the Ministries of Water, Environment, and Livestock, as well as Members of Parliament in the Health Committee and representatives from the Universities of Juba and Upper Nile.

During the same month, the NPHI developed a strategic plan for the years 2022-2026. The Institute also identified budget priorities for the fiscal year 2024-2025, successfully incorporated these priorities into the health sector budget, and secured funding from the Ministry of Finance and Planning for the NPHI Directorate of Administration & Finance for FY 2024-2025.

With assistance from Intra-Health International, US CDC, Africa CDC, the African Field Epidemiology Network (AFENET), WHO, and the University of Juba, the NPHI designed and established several fellowship programs, including:

1. Data Management (DM)
2. Leadership Management and Governance (LMG)
3. Field Epidemiology Training Programmes (FETP)

On the 3rd June, 2022, 42 health workers graduated from the DM and LMG programmes (20 from DM and 22 from LMG). Additionally, eight cohorts of the Frontline FETP (F-FETP) were trained, resulting in the graduation of 66 frontline field epidemiologists. Supported by the Global Fund through UNDP, an Intermediate-FETP (I-FETP) cohort has commenced in January 2025.

Furthermore, the NPHI launched its official website at https://phi.gov.ss , which is linked to the Ministry of Health website https://moh.gov.ss enhancing its online presence and accessibility.

Next Steps

The following priorities have been identified for the NPHI:

• Appointment of the Board of Directors: Establishing a governing body to provide oversight and strategic direction. See Figure 1.
• Change Management: Facilitating a smooth transition of departments and units from the Ministry of Health (MOH) to the NPHI.
• Operationalization of the Directorate of Technical Services: Ensuring that this key directorate is fully functional and integrated into the institute’s operations.
• Review and Update of the Strategic Plan 2022-2026: Assessing and refining the existing strategic plan to ensure its relevance and effectiveness in guiding the NPHI’s activities.
• Development of Infrastructure: Building and enhancing the physical and organizational infrastructure necessary for the NPHI to operate effectively.

Figure 1. Governance Structures: NPHI Organogram

Summary

The establishment and operationalization of the NPHI in South Sudan involved a series of strategic steps aimed at enhancing public health capabilities:

• A dedicated 15-member TWG was established to provide technical oversight during the creation of the NPHI.
• The TWG conducted assessments to identify public health needs and gaps, clarifying how the NPHI would contribute to improving health outcomes in the country.
• A comprehensive plan was developed to guide the establishment of the NPHI, ensuring alignment with national health priorities.
• The core functions of the NPHI were outlined to focus on key public health areas.
• A review was conducted to determine which current functions from the MOH would transition to the NPHI while identifying major gaps that needed to be addressed.
• The NPHI developed a strategic plan for 2022-2026, which included identifying budget priorities for 2024-2025, successfully integrating these into the health sector budget.
• Resources were identified to support the operationalization of the NPHI, including funding allocations from the Ministry of Finance and Planning.
• Two high-level advocacy meetings were held with senior leadership from the MOH and other line ministries, as well as universities, to foster collaboration and support.
• With support from various partners, including Africa CDC and WHO, the legal framework for the NPHI was developed and subsequently passed into law as the NPHI Act, 2023.
• A structured change management process is currently being implemented to facilitate the smooth transition of departments and units from the MOH to the NPHI.
• The institute was officially inaugurated, marking a significant milestone in public health governance.

The NPHI is now actively engaged in the change management phase, as specified in Article 39 of the NPHI Act, 2023, which outlines transitional provisions. Ongoing dialogue and advocacy within the health sector are crucial to ensure a seamless transition. The NPHI is set to absorb the existing workforce from various departments and units earmarked for transfer, thereby strengthening its operational capacity to address public health challenges effectively.

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