Healthcare-Associated Infections, Antimicrobial Resistance & Mycoses

The NICD’s Centre for Healthcare-associated Infections (HAIs), Antimicrobial Resistance (AMR) and Mycoses serves as a national hub of expertise in the fields of:

  • Healthcare-associated infections (HAIs)
  • Antimicrobial resistance (AMR)
  • Mycoses

Relevant to these three focus areas, the Centre conducts/ provides:

  • Surveillance
  • Outbreak investigations
  • Public health-focused research
  • Reference laboratory diagnostic services

Strategic information from these activities is shared with the South African Department of Health and other major stakeholders.

Healthcare-associated infections (HAIs)

  • This is a new focus area for the Centre
  • Plans are afoot to pilot surveillance for HAIs at sentinel hospitals

Antimicrobial resistance (AMR)

  • The Centre works on AMR in bacterial and fungal pathogens causing human infections in healthcare facilities and in the community, spanning the public- and private-health sectors
  • The Centre has recently been named a World Health Organization Coordinating Centre for AMR
  • The Centre is also a National Coordinating Centre for the WHO Global Antimicrobial Resistance Surveillance System (GLASS)
  • Laboratory-based surveillance is conducted for a number of priority pathogens, including carbapenemase-resistant Enterobacteriaceae, ESKAPE pathogens, Candida auris
  • The Centre has two reference laboratories which provide support for outbreak and reference activities related to AMR.


  • Over the last 5 years, the Centre led implementation of a national cryptococcal antigen screening and pre-emptive treatment intervention, nested within the South African HIV treatment programme. The Centre is now involved in evaluating the effectiveness of this intervention to reduce mortality.
  • The Centre has contributed to discovery of emerging HIV-associated fungal pathogens such as the newly-described thermally-dimorphic fungus, Emergomyces africanus
  • The Centre has expertise in antimicrobial resistance (AMR) for fungal pathogens.

The National Stock Culture Collection (NSCC)

The National Stock Culture Collection was established in April 2004, with the mandate to provide a quality controlled and reliable source of reference bacterial, fungal and mycobacterial strains for NHLS laboratories. Microbiology laboratories that are accredited according to ISO15189 as diagnostic medical laboratories are required to control all procedures and tests. Certain procedures such as antimicrobial susceptibility testing and biochemical tests on bacteria require reference bacterial strains on which control tests are performed. The NSCC has an invaluable role to play in facilitating the NHLS laboratories’ compliance with accreditation requirements. Strains are also available for teaching, training and research purposes.
The services of the NSCC were re-launched in February 2014 with the development of streamlined online ordering system, accessible via the NHLS intranet homepage. This system requires laboratories to upload the relevant permits and registrations required by legislation and to select the strains they require. There is traceability of strains until the order is received and acknowledged in the laboratory.
Centre Leadership
Prof Nelesh Govender (Mycology surveillance, diagnostics and research)
Tel: 011 555 0353
Prof Olga Perovic (Antimicrobial resistance surveillance, diagnostics and research)
Tel: 011 386 6278