The Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM) was established in April 2017. CHARM hosts two national reference laboratories and is supported by an epidemiology section. The centre was designated as a World Health Organization (WHO) Collaborating Centre for AMR (WHO SOA-43) in June 2017.

Healthcare-associated infections (HAIs) are among the commonest complications of hospital admission, are costly for the patient and the overall healthcare system, and may lead to patient deaths. This is an important new focus area for the centre. Antimicrobial resistance (AMR) is estimated to be associated with over 700 000 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. CHARM  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 is supporting the “One Health” programme including surveillance for AMR in humans and animals.

Fungal diseases (mycoses) are responsible for an estimated 1.5 to 2 million deaths annually, including nearly half of those dying of AIDS and many of those with sepsis. Over the last seven years, the centre has led the scaling up of a 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 national intervention to reduce mortality through a US National Institutes of Health R01-funded grant.

The national stock culture collection (NSCC) was established in April 2004 and is housed within CHARM. The NSCC provides a quality-controlled and reliable source of reference bacterial, fungal and mycobacterial strains to the National Health Laboratory Service laboratories.


The objectives of CHARM are:

  • To conduct surveillance of healthcare-associated infections and detect outbreaks;
  • To conduct surveillance for antimicrobial-resistant bacterial and fungal pathogens at public- and private-sector laboratories across the country;
  • To conduct surveillance and public health research for mycoses;
  • To use surveillance data to support the development of standard treatment guidelines for certain infectious diseases and to evaluate relevant public health programmes;
  • To improve access to essential medicines and diagnostics including identification of emerging pathogens;
  • To provide reference laboratory functions for identification, susceptibility testing and genotyping of bacteria and fungi; and
  • To serve as a repository of reference bacterial, fungal and mycobacterial strains.


  • The Centre works on preventing life-threatening fungal diseases of public health importance in South Africa:
    • Cryptococcal meningitis, a deadly brain infection that affects persons living with advanced HIV disease (AIDS);
    • Other life-threatening opportunistic fungal infections that occur with AIDS;
    • Candidaemia, a healthcare-associated bloodstream infection that occurs among critically-ill patients and patients with certain cancers; and
    • Invasive and chronic infections caused by Aspergillus.
  • Led efforts to implement and evaluate a laboratory-based reflex cryptococcal antigen screening programme across South Africa. This programme aims to prevent deaths associated with cryptococcal meningitis.
  • Involved in developing South African and international clinical guidelines for management of fungal infections.
  • Offers a specialised mycology reference service to diagnostic medical laboratories, including phenotypic and sequence-based identification of unusual or difficult-to-identify fungi and antifungal susceptibility testing of yeasts and moulds.
    • Please consult the NICD handbook for a list of tests that are offered.
  • Research activities are focused on developing and validating new diagnostic assays and defining risk factors for fungal diseases and antifungal drug resistance.
  • The mycology reference laboratory holds a large collection of pathogenic fungi of medical importance.

Antimicrobial resistance poses a major threat to the health of individuals and populations worldwide. Antimicrobials are not only essential for the treatment of community-associated infections such as pneumonia and meningitis but also healthcare-associated infections. These infections are commonly caused by bacteria or fungi which are killed or inhibited by antibiotics or antifungals, unless they develop resistance due to inappropriate use or abuse of these agents.

In a healthcare setting, medical procedures such as the insertion of intravascular or urinary catheters, intubation or surgery break the body’s natural barriers to infection and allow pathogens direct access to sites such as the bloodstream, urinary tract, lung or abdominal cavity. Patients with healthcare-associated infections require prolonged care in hospitals, serving as a source of cross-infection to other patients.

The emergence and widespread occurrence of multidrug-resistant bacteria and fungi threatens the ability of antimicrobials to act against these bacteria and fungi.

New resistance mechanisms in bacteria and fungi are emerging and spreading across the world. Some bacteria are naturally resistant to antibiotics and others develop resistance through genetic changes. Misuse, overuse and inappropriate use of antibiotics accelerates this process.

Surveillance is a key component of the strategy to combat antimicrobial resistance. The centre leads the national effort to conduct surveillance for AMR infections through establishment of a national diagnostic laboratory surveillance network. Several approaches are currently used for laboratory-based surveillance:

  • National or sentinel surveys: bacterial and fungal isolates cultured from patients with bloodstream infections are submitted to CHARM’s reference laboratories for identification, antimicrobial susceptibility testing and genotyping;
  • Enhanced surveillance: detailed clinical information is collected from patients admitted to sentinel hospitals who meet the surveillance case definitions throughout GERMS programme; and
  • Electronic surveillance: data from public- and private-sector diagnostic laboratory information systems are compiled annually and reported as tables and resistance maps.

The Centre was named a World Health Organization (WHO) Coordinating Centre for AMR in 2017. CHARM is a National Coordinating Centre for the WHO Global Antimicrobial Resistance Surveillance System. Senior members of the Centre represent NICD on the Ministerial Advisory Committee (MAC) for AMR and the WHO Strategic and Technical Advisory Group (STAG) for AMR.

The Centre uses several methods, including real time surveillance to detect outbreaks of healthcare-associated infections; reporting on relatedness between strain causing outbreaks and advising on responses. A team of trained epidemiologists within the centre investigate and respond to such outbreaks

The centre offers a specialised bacteriology and mycology reference service to diagnostic medical laboratories, including:

  • Phenotypic, mass spectrometric and sequence-based identification of bacteria and unusual or difficult-to-identify fungi;
  • Antibiotic susceptibility testing of bacteria and antifungal susceptibility testing of yeasts and molds;
  • Genotyping of bacteria and fungi; and
  • Molecular mechanisms of antimicrobial resistance.

Please consult the NICD handbook for a list of tests that are offered

The Antimicrobial Resistance Laboratory and Culture Collection in the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (AMRL-CC/CHARM) is designated as World Health Organization (WHO) Collaborating Centre (CC) for Antimicrobial Resistance (AMR) under the WHO reference number SOA-43.

One of its activities is to build microbiology laboratory capacity and to improve surveillance for AMR in the WHO African region. It is are committed to providing teaching, training and an External Quality Assessment Programme (EQAP) to facilitate good laboratory practice.  EQA panels are sent twice a year to participants that are nominated by the Ministry of Health in each African country. Participating laboratories process samples sent and submit results for evaluation. Participants are assessed against the intended response, which is verified by referee laboratories.

Feedback on individual laboratory performance is provided to each participant along with the overall participant performance for the challenge in the survey. This programme is published in the WHO EQA Annual Report. EQA is a key element for the total Quality Management System (QMS) of a laboratory and is compulsory for laboratories who pursue accreditation

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Leadership and Team

Centre Head: Prof Nelesh Govender

Prof Govender began his career in public health in 2006 when he joined the NICD as Head of GERMS surveillance. He now heads CHARM. In this position, he works closely with the Department of Health to generate evidence to guide government policy. His particular area of expertise is in medical mycology and in the field of antimicrobial resistance (AMR) wherein his work has focused largely on the neglected area of antifungal resistance.

He is a member of the Ministerial Advisory Committee on AMR and
President of the Federation of Infectious Disease Societies of Southern Africa

Prof Govender led implementation and evaluation of a national
cryptococcal disease screen-and-treat intervention in South Africa in
partnership with the Department of Health, of which he was co-chair of the
South African cryptococcal disease guidelines panel and a member of the WHO
cryptococcal disease and advanced HIV disease guidelines panel.

He is currently Principal Investigator on two large projects, funded by
the US National Institutes of Health and the US CDC).

He is an Associate Professor in the Department of Clinical Microbiology
and Infectious Diseases at the University of the Witwatersrand and Honorary
Associate Professor in the Division of Medical Microbiology at the University
of Cape Town.

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Project Administrator
Mpho Thanjekwayo
Tel: +27 11 555 0396
Email: mphot@nicd.ac.za

Section Lead – AMR
Prof Olga Perovic
Email: olgap@nicd.ac.za

Team Lead – crAg Screening
Greg Greene
Email: gregg@nicd.ac.za

Laboratory Manager – MRL
Ruth Mpembe
Email: ruthm@nicd.ac.za

Laboratory Manager – AMRL
Marshagne Smith
Email: marshagnes@nicd.ac.za

Medical Scientist – Molecular Laboratory
Ashika Singh-Moodley
Email: ashikas@nicd.ac.za

Senior Medical Epidemiologist

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