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 2022 findings that continue to be appreciated in reporting trends in pathogen-specific data. The beginning of 2022 saw the NHLS laboratories starting on their back foot, with NHLS Diagnostic Media Productions in Sandringham shutting down because of structural challenges.

This impacted negatively on the number of isolates received by NICD reference laboratories in terms of numbers and isolate viability. Despite the support of the GERMSSA rover technician in collecting isolates/samples and plates from the largest Johannesburg hospitals, along with case patient notification reports from the Surveillance Data Warehouse (SDW) and Notifiable Medical Conditions (NMC), the shortage of staff in reference laboratories persisted, affecting the proportion of submitted isolates.

Consequently, we were unable to do antimicrobial susceptibility testing and serotyping/serogrouping on these missing isolates. The Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM) requested the submission of Cryptococcus spp. isolates to monitor 5-flucytosine from the Western Cape Province and all other laboratories for sites implementing the use of 5FC for cryptococcal meningitis.

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. We thank you for your ongoing service to the health of all South Africans.

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