The GERMS-SA programme, established in 2003, is a nationwide surveillance programme coordinated by the Division of Public Health Surveillance and Response at the NICD. Following the amalgamation of multiple, laboratory-based surveillance projects in 2012 and 2013, the name was modified to GERMS-SA.

Its main objective is to provide strategic information regarding trends in the pathogens of public health importance, e.g. vaccine-preventable diseases to measure the impact of vaccines, epidemic-prone diseases to monitor and respond to outbreaks, healthcare-associated bloodstream infections with the trend of antibiotics resistance, the burden of HIV-associated opportunistic infections (OI) and neglected tropical diseases to control and combat the impact in affected people.

 GERMS-SA exists:

• To deliver accurate, quality-controlled strategic surveillance information on selected organisms to participants and stakeholders, e.g. Department of Health;
• To improve laboratory participation in the surveillance programme;
• To improve clinical case data collection at enhanced surveillance sites;
• To improve and maintain surveillance data management procedures;
• To facilitate improved laboratory diagnosis of diseases under surveillance;
• To provide support to similar laboratory-based surveillance efforts by neighbouring African countries; and
• To undertake special research studies nested within the surveillance programme.

GERMS-SA ANNUAL SURVEILLANCE REVIEW

NICD has historically supported the National Department of Health (NDoH) in its roles of responding to priority diseases such as HIV and TB and to outbreaks of infectious diseases. Support to provincial DoH has primarily been from teams based at the NICD until 2014 when the NICD set up a provincial epidemiology team (PET) comprising of one senior epidemiologist based at the NICD and nine provincial field epidemiologists; one in each of the provincial DoH offices.

Currently, there are eight provincial epidemiologists except in Northern Cape. Having an NICD epidemiologist in each province ensures that epidemiology, public health, diagnostic and clinical expertise within the NICD is available to provinces in a timely manner to effectively support communicable disease surveillance, prevention and control, epidemiology research, training and outbreak response at provincial and district level.

Over the period 2023-2026, the PETs strategic plan will focus mainly on TB, Communicable Disease Control (CDC) and Outbreak Response. These priorities are hinged on three strategic objectives: 1. Public health surveillance 2. Outbreak response support, and 3. Epidemiological support to priority programmes (linkage of laboratory diagnosis to health care services). The PET provides expert technical advice and assistance on the design, maintenance, analysis and interpretation of surveillance databases. Additionally, they support synthesis and analysis of surveillance and routine clinical and NMC data collected at provincial, district and sub-district levels by both NICD and DoH to determine populations at risk, monitor disease trends and distribution, detect outbreaks and subsequently advise on interventions required to curb morbidity and address public health needs and resource allocation.

Provincial epidemiologists analyse data generated from NMC surveillance and the NICD centre for TB (CTB). Data from CTB is analysed to describe and report on trends and numbers of patients diagnosed with drug susceptible and drug resistant TB. These reports analysed together with provincial data from electronic TB registers showing the actual number of patients’ initiating TB therapy, are used to identify and address gaps in the TB treatment cascade.

The Outbreak Response Team is tasked with providing technical support for all aspects of communicable disease outbreak investigation and control in the nine provinces of South Africa, with particular emphasis on optimising the role of laboratory services during these events. The team aims to be a source of intelligence during outbreaks, and through working in close collaboration with the provincial and national Departments of Health, ensures a comprehensive outbreak response, as well as the development of systems for early detection and improved reporting. Through close partnerships with the NHLS diagnostic laboratories and reference units of the NICD, the team aims to facilitate appropriate laboratory diagnostic services during outbreaks and specialised diagnostics as required.

The Outbreak Response Team plays a crucial role in communications, with stakeholders such as the Department of Health, medical practitioners, media and the general public. The team publishes a monthly Communicable Diseases Communiqué for providing up-to-date information on communicable disease events in South Africa, as well as regularly produce various healthcare worker guidelines, handbooks, fact-sheets, etc., for outbreak-prone communicable diseases of high public health importance. The Team also plays a central role in capacity development by providing in-service training to SA-FELTP residents, public health specialist registrars and secondees from international partner organisations, and routinely provides Epidemic Preparedness and Response Training to the staff of the Department of Health.

The National Emergency Operations Centre (EOC), housed on the upper level of the PRF Training Centre, was created in 2014 in response to the Ebola outbreak in West Africa. The EOC operates under a memorandum of agreement, signed January 2015, with the government of the Republic of South Africa through its National Department of Health (NDoH) to act as a coordination centre for responses to public health emergencies such as the Listeriosis outbreak of 2017/2018, and is seen as a key strategic point for the country’s ability to build a resilient health system.

The EOC aims to collate, organise and deploy resources both internal and external to the NICD required to respond to a major infectious disease incident, outbreak or related event, which has been declared a Public Health Emergency by the Director-General of the NDoH.

During a declared public health emergency, the specific functions of the EOC are to:

• Maintain surveillance, verification and confirmation of the relevant infectious disease in South Africa, the African continent and internationally;
• Perform a coordination role, provide strategic management oversight, gather data on a daily basis and provide Provinces and the NDoH with strategic information to manage the incident;
• Provide a 24-hour hotline for advice and reporting of incidents relating to the declared Public Health Emergency;
• Organise for appropriate samples to be collected, transported to the laboratory and for appropriate diagnostics test to be carried out;
• Liaise with Port Health authorities in the establishment and evaluation of screening systems in at key entry points in South Africa;
• Organise and manage the monitoring of individuals returning from countries with, ongoing outbreaks of high-risk infectious diseases during a Public Health Emergency, with a specific focus on individuals who have been involved in healthcare, those in contact with a known or suspected case of the relevant disease;
• Provide a communications portal during ongoing outbreaks of high-risk infectious diseases during a Public Health Emergency, including updates, health promotion materials and travel advice and a public call centre where communities can obtain information of a particular incident or disease profile;
• When relevant during a Public Health Emergency, liaise with Department of Agriculture, Fisheries and Forestry on Zoonotic diseases that have potential to spread to humans;
• Use every Public Health Emergency as an opportunity to train South African and Southern African Development Countries’ scientists, technologists and epidemiologists in partnership with the NDoH and Provinces;
• Support the Government’s International Health Regulations reporting responsibilities; and
• Ensure that Department of Health Executive Management at National and in Provinces are regularly kept informed on progress in the management of any declared Public Health Emergency.