The NICD’s flagship GERMS–SA surveillance programme celebrates its 21st anniversary since its establishment in 2003. GERMS-SA, coordinated and led by the NICD’s Division of Public Health, Surveillance and Response, provides strategic information on diseases of public health importance. For example, GERMS-SA has measured the impact of vaccines such as pneumococcal conjugate vaccine (PCV) and newly-introduced treatments such as flucytosine.
GERMS-SA has monitored antimicrobial-resistant infections caused by the ESKAPE bacterial pathogens, HIV-associated opportunistic infections such as cryptococcal meningitis and outbreak-prone diseases such as typhoid fever. GERMS-SA is primarily a laboratory-based surveillance programme in which laboratory-confirmed cases of infection are reported to the NICD by the National Health Laboratory Service (NHLS) and private microbiology laboratories.
NICD reference laboratories perform specialised testing such as serotyping and antimicrobial susceptibility testing on submitted pathogens linked to cases. In addition, GERMS-SA collects clinical data from case patients through interviews and medical record reviews at 30 enhanced sentinel sites nationally. The GERMS-SA network also provides a link between clinical microbiologists, health practitioners and the NICD reference centres.
We chat with the head of GERMS-SA, Dr Vanessa Quan, who reflects on the key milestones and challenges over the last 21 years and sheds light on future plans:
How did GERMS-SA surveillance come about?
It all started in August 1999 with a letter published in the South African Medical Journal written by renowned experts in the field of infectious diseases and public health: Robin Huebner, Keith Klugman, Ursheila Matai, Rudi Eggers, Greg Hussey and endorsed by their various institutions: the South African Institute for Medical Research, Medical Research Council, the Wits Pneumococcal Research Unit, the Department of Health Expanded Programme on Immunisation (EPI), the University of Cape Town Department of Paediatrics and Child Health; and the Haemophilus Surveillance Working Group.
What was the purpose of this letter?
The letter motivated for a laboratory-based surveillance system to measure the impact of the introduction of the Haemophilus influenzae type B (Hib) vaccine (to be given at 6, 10 and 14 weeks with no catch-up) into the SA Expanded Programme on Immunisation (EPI) in July 1999. An ongoing surveillance programme would be able to measure the impact of the Hib vaccine in preventing invasive Hib disease in infants to justify the expenditure of the vaccine, identify vaccine/programme failures, determine whether to include a booster dose at a later stage and potentially to establish a surveillance system for other pathogens which might be included in the EPI in future.
Dr Vanessa Quan reflects on the key milestones and challenges over the last 21 years and sheds light on future plans.
What are some of the key milestones for the GERMS-SA data?
The surveillance programme evolved quite quickly; by 2006, surveillance was conducted for nine bacterial and fungal pathogens causing pneumonia, meningitis, and enteric diseases.
By 2008, GERMS-SA had entered a stable phase. Data were being translated into information to influence public health policy related to HIV-associated opportunistic infections, for introducing PCV and a Hib booster into the South African EPI programme and for developing various disease guidelines.
In 2009, our surveillance system was robust enough to support nested studies. A case-control study was set up to estimate the effectiveness of the PCV against invasive pneumococcal disease amongst South African infants, and a post-discharge follow-up study was undertaken to determine the outcome of patients with cryptococcosis.
GERMS-SA has monitored the effect of EPI vaccines, such as PCV7, PCV13 and the Hib booster, on laboratory-confirmed pneumococcal disease. GERMS-SA has also monitored the impact of the SA antiretroviral treatment programme, national reflex cryptococcal antigen screening and new antifungal regimens on cryptococcal meningitis incidence and mortality.
By 2015, we could perform good quality audits, using the NHLS’s Corporate Data Warehouse, to establish the total number of cases in our public sector surveillance. By this stage, we had included syndromic surveillance as an arm of GERMS-SA, with pneumonia and influenza-like illness (SRI and ILI), diarrhoeal diseases, drug-resistant TB and HIV, sexually transmitted infections (STIs) and acute febrile illness in adults.
All these projects leverage the permanent staffing capacity of the GERMS-SA programme and are led by the various NICD centres. With the vaccines for the pneumococcus, Hib and rotavirus, we documented remarkable declines in invasive disease and for rotavirus particularly, many paediatric gastroenteritis wards are now empty. Data from syndromic surveillance have recently been used to motivate for maternal pertussis (whooping cough) vaccination.
When COVID-19 hit South Africa, the SRI syndromic surveillance programme, run by the NICD Centre for Respiratory Diseases and Meningitis (CRDM), was able to sustain the SRI system and do a nested study to identify risk factors for severe COVID-19 in people living with HIV, finding that there was prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in this hospitalised group, to identify risk factors for severe COVID-19 among children and adolescents, respiratory syncytial virus (RSV) disease and other respiratory-transmitted bacterial infections during the pandemic period. Conversely, GERMS-SA was able to show an increase in multi-drug resistant Candida auris and Candida parapsilosis bloodstream infections in healthcare settings during the pandemic.
The NICD Executive Director, Prof. Adrian Puren (holding a certificate) and Deputy Director, Dr Natalie Mayet (holding a trophy), with staff members who were at the forefront of the COVID-19 response.
Other studies building on surveillance data included a meningococcal carriage study in university students, which showed that there was a 200% increase in meningococcal carriage among first year students during their first week on campus. GERMS-SA also captures data on sequelae post-bacterial meningitis, and with our data, South Africa is part of the WHO’s “Defeating Meningitis by 2030” initiative.
Our national neonatal sepsis study (Baby GERMS-SA) shifted our surveillance approach from diseases to an at-risk population (i.e. hospitalised newborn babies) for the first time. Through this 2-tiered Baby GERMS-SA surveillance study, we showed high rates of Gram-negative bloodstream infections in lower-tier neonatal units as well as high multi-drug resistance rates, particularly among small, sick, premature babies. Our next step is to extend this novel surveillance approach to understanding the rates of life-threatening bacterial, fungal, and TB infections among people with advanced HIV disease, a national 3-tiered project called ADVANCE GERMS-SA.
Diarrhoeal diseases sentinel surveillance site.
What challenges have GERMS-SA faced over the past 21 years?
As the world adapts to the digital environment, GERMS-SA has had to follow suit. There was much resistance in the beginning when we moved from paper-based case report forms to collecting data electronically. And even now, improvements in cyberspace bring with it many adaptations and unseen complications that we need to overcome to ensure ongoing data collection, collation, analysis and reporting.
What are the plans for GERMS-SA in the short-term?
We aim to continue collecting robust surveillance data for public health action. In addition, we are working with the NICD Information Technology Department and the Notifiable Medical Conditions (NMC) surveillance platform to create a comprehensive and integrated system for surveillance.
Any message to colleagues, partners and supporters?
Reporting GERMS-SA cases and submission of isolates is very important to monitor the impact of changes in public health policies. For example, in 2024, the South African EPI changed from a 13-valent to a 10-valent PCV. The NICD reference laboratories are the only ones where routine serotyping of pneumococcal isolates takes place, and therefore, they need isolates to monitor the impact of this change on invasive pneumococcal disease in infants and the rest of the population.
All 21 years of the GERMS-SA surveillance data are stored securely by the NICD. These data belong to South Africans and, therefore, are available for analysis and write-up by students and scholars in the field. It is said that it takes a community to grow a child, and although I am the mother of GERMS-SA (as well as a granny to our Baby GERMS-SA), it is through our community of collaborators and network that GERMS-SA has achieved so many great things for public health in South Africa. GERMS-SA is grateful to all those who participate in this important programme, and you should be proud of your role in keeping our population safe and healthy.
