Surveillance for Antimicrobial Resistance in South Africa-Report

27 Mar 2019
Surveillance for Antimicrobial Resistance in South Africa-Report Following a global initiative of combating antimicrobial resistance, South Africa developed the Antimicrobial Resistance National Strategic Framework, 2014-2024. The AMR Strategy Framework consists of five objectives: 1. Diagnostic stewardship 2. Enhanced surveillance for AMR 3. Antimicrobial stewardship 4. Prevention including IPCs 5. Vaccination. 

The enhanced surveillance report aimed to generate a consolidated observation of susceptibility pattern to antimicrobials in humans and animals. In addition, this report presents antimicrobial use in humans and animals. Unfortunately, no data on AMR surveillance in animals have been available and an initiative to integrate these two sectors is under review. Antimicrobial resistance in humans This report facilitated by the South African Society for Clinical Microbiology (SASCM), presented data from blood culture specimens for all public and the majority of private healthcare facilities that are served by four private laboratory groups (Lancet, Ampath, Vermaak and Partners and PathCare). The custodian of this data is the National Institute for Communicable Disease (NICD) and this dynamic interactive search on drug/bug combination can be obtained at the website: We report on ESKAPE organisms: Enterococcus faecalis and Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. 

We report susceptibility trends over a six-year period. 

Key findings include: 

  1. Improved susceptibility to cloxacillin in Staphylococcus aureus (i.e. reduced MRSA) in both sectors. 
  2. Improved susceptibility to carbapenems in Pseudomonas aeruginosa 
  3. Decreased susceptibility to carbapenems in Klebsiella pneumoniae, in both sectors 

There are a number of limitations that need to be acknowledged: 

  1. Data may have been incomplete due to missing cases not captured on the laboratory informatics system (LIS) or non-standardised coding of ESKAPE pathogens and antimicrobial agents at diagnostic laboratories. 
  2. Testing methods and microbiological practice may have varied between laboratories and this could account for variations in the results presented in this report. 
  3. Confirmatory antimicrobial susceptibility testing (AST) methods have not been performed or recorded for any of these ESKAPE pathogens as the results presented here were reported as captured on the LIS by diagnostic laboratories. 
  4. We have not been able to report on colistin AST as new methods have been recommended by CLSI and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines; which were not fully implemented by diagnostic laboratories during the period of analysis. 
  5. Data were omitted for those sentinel hospitals that tested fewer than 30 ESKAPE pathogens for a particular antimicrobial agent. 
  6. Results for carbapenemase-producing Enterobacterales (CPE) are not available in this report as not all carbapenem resistant Enterobacterales (CRE) isolates are tested for carbapenemase-producing genes. This report reflects on the AMR strategic framework objective to report on surveillance of AMR in order to provide reliable data to optimize policy decisions on antimicrobial therapy and impact on IPC measures.