Surveillance of Invasive Bacterial Diseases: Vaccine-Preventable & Epidemic-Prone Pathogens
The GERMS-SA surveillance system is a national, active, laboratory-based surveillance system that has been in place since 2003. GERMS-SA monitors invasive bacterial infections caused by pathogens of public health importance in South Africa. Data are collected from both public and private laboratories across South Africa, with clinical isolates and specimens sent to the National Institute for Communicable Diseases (NICD) for further characterisation. Additionally, the Surveillance Data Warehouse (SDW) is used to identify unreported cases, referred to as audit cases.
The Centre for Respiratory Diseases and Meningitis (CRDM) quarterly report on laboratory-based surveillance for invasive bacterial disease caused by vaccine-preventable or epidemic-prone pathogens summarises trends in invasive disease caused by Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Streptococcus agalactiae, and Streptococcus pyogenes. The report includes the number of episodes identified by age and province, submission rates to NICD, organism viability, as well as serotyping/serogrouping characterisation.
This report covers the reporting period from 01 January 2015 to 30 June 2026
Highlights
- In 2026, up to the end of quarter 2, 739 episodes of invasive Streptococcus pneumoniae, 124 episodes of invasive Haemophilus influenzae, 65 episodes of invasive Neisseria meningitidis, 435 episodes of invasive Streptococcus agalactiae and 406 episodes of invasive Streptococcus pyogenes were reported to GERMS-SA.
- The proportion of episodes where no isolate/specimen was received ranged from 2% (1/65) for N. meningitidis to 31% (136/435) for S. agalactiae.
- Serogroup B N. meningitidis continues to dominate, followed by serogroups W and Y. The number of serogroup B episodes has increased compared with the corresponding quarters of previous years; however, the numbers are small, and this finding should be interpreted with caution.
- Serotyping data entry for S. agalactiae and S. pneumoniae has been delayed due to staff shortages. Serotyping results are therefore incomplete and should be interpreted with caution. It is anticipated that outstanding results will be updated by the end of quarter 3.
- All microbiology laboratories are encouraged to submit isolates for serotyping.
