Healthcare-Associated Infections, Antimicrobial Resistance & Mycoses

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

  1. Healthcare-associated infections (HAIs)
  2. Antimicrobial resistance (AMR)
  3. Mycoses

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

  1. Surveillance
  2. Outbreak investigations
  3. Public health-focused research
  4. Reference laboratory diagnostic services
  5. Teaching and training

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

Healthcare-associated infections (HAIs)

  • HAIs are among the commonest complications of a hospital admission, are costly for the patient and overall healthcare system and may lead to patient deaths
  • This is an important new focus area for the Centre
  • Plans are afoot to pilot surveillance for HAIs at sentinel hospitals and detect outbreaks at facility level
  • The Centre is now involved in developing practical South African guidelines for hospital-level activities related to HAIs and AMR

Antimicrobial resistance (AMR)

  • AMR is associated with >700000 deaths every year, a number which could rise as high as 10 million in 2050
  • AMR is a major focus area of the South African Department of Health and the NICD
  • 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 was named a World Health Organization Coordinating Centre for AMR in 2017
  • CHARM is also a National Coordinating Centre for the WHO Global Antimicrobial Resistance Surveillance System (GLASS)
  • Senior members of the Centre represent NICD on the Ministerial Advisory Committee for AMR
  • Laboratory-based surveillance is conducted for priority pathogens, including carbapenemase-resistant Enterobacteriaceae, the “ESKAPE” bacterial pathogens and Candida auris. The Centre is also responsible for compiling electronic surveillance data from public- and private-sector laboratories across the country. Surveillance data support development of standard treatment guidelines for certain infectious diseases.The Centre has two reference laboratories which provide support for outbreak and reference activities related to AMR


  • Over the last 5 years, NICD 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 through an NIH R01-funded grant.
  • The Centre contributed to discovery of emerging HIV-associated fungal pathogens such as the newly-described thermally-dimorphic fungus, Emergomyces africanus
  • The Centre’s mycology reference laboratory has expertise in antimicrobial resistance (AMR) for fungal pathogens and conducts national surveillance for candidaemia
  • The Centre is involved in global efforts to improve access to antifungal medicines and fungal diagnostics

National stock culture collection (NSCC)

  • The NSCC was established in April 2004 and is now housed within CHARM
  • The Culture Collection provides a quality-controlled and reliable source of reference bacterial, fungal and mycobacterial strains to NHLS laboratories
    • Laboratories, which are accredited to ISO15189 as diagnostic medical laboratories, are required to control all procedures and tests.
    • Antimicrobial susceptibility and identification tests on bacteria/ fungi require reference strains on which control tests are performed.
  • Strains are also available for teaching, training and research purposes
  • The services of the NSCC were re-launched in February 2014 with development of a 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 management team 


Name Position Office Tel Email
Nelesh Govender Head of Centre

Section Lead: Mycoses

011 555 0353
Olga Perovic Section Lead: AMR 011 386 6278
Charlotte Sriruttan Team Lead: CrAg Screening
Ruth Mpembe Laboratory Manager: MRL 011 555 0325
Marshagne Smith Laboratory Manager: AMRL 011 555 0342
Ashika Singh-Moodley Medical Scientist: Molecular Laboratory 011 555 0342
Erika van Schalkwyk Centre Medical Epidemiologist
Mpho Thanjekwayo Centre Project Administrator 011 386 0396