GERMS-SA’s 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 and the burden of HIV-associated opportunistic infections (OI). 


The National Institute for Communicable Diseases (NICD) reference units report the GERMS-SA surveillance 2021 findings which continue to be valuable in reporting trends in pathogen specific data. The far-reaching impact of COVID – 19 continued to put extraordinary pressure on both healthcare systems and our routine GERMS-SA surveillance. Having experienced four waves by 2021 resources had to be shifted towards COVID-19-related activities. With easing of lockdown regulations, introduction of COVID-19 vaccination program and decline in COVID-19 cases, diagnosis rates of other infectious diseases increased, also the number of isolates received by NICD reference laboratories showed an increase as well as better quality isolate viability. Pressure in many clinical laboratories remained and impacted the rates of audit cases which are still out of target range. Therefore, we were unable to do antimicrobial susceptibility testing and serotyping/serogrouping on these missing isolates. The fire at CMJAH, deferment of patients to other hospitals and the NHLS laboratory being closed for a few months also impacted our statistics.

We urge all microbiology laboratories, in their challenged capacities, to continue to participate in laboratory surveillance so monitoring can continue and relevant, evidence-based policies can be made. The 2021 review also includes other NICD projects using the GERMS-SA platform; rotavirus/diarrhoeal aetiological surveillance. This project differs from the laboratory-based surveillance in that it is syndromic surveillance and specimens are taken from patients with diarrhoea.

To download and view past publications, go to Archives.