Mycology
Unit Mission Statement

The Mycology Reference Unit (MRU), within the Microbiology Division of the National Institute for Communicable Diseases (NICD) in Johannesburg, aims to contribute to the control of fungi of public health and clinical importance in South Africa, by undertaking relevant, laboratory-based surveillance and research projects, by functioning as a regional, reference laboratory in the field of clinical mycology, and by teaching laboratory, clinical and public health workers to diagnose and manage fungal infections.

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Staff

Publications

Awards

Overview



SANAS Accreditation

In 2008, the MRU surveillance laboratory was re-accredited by SANAS in accordance with ISO15189 standards.



Current Projects


The GERMS-SA Cryptococcal Surveillance Project
The cryptococcal surveillance project, managed by the MRU, is nested within a national, laboratory-based surveillance programme, coordinated by the Group for Enteric, Respiratory and Meningeal disease Surveillance in South Africa (GERMS-SA). The project was initiated in 2005, following successful implementation of laboratory-based, population-based surveillance for cryptococcosis in Gauteng province, 2002 through 2004. The main objective of the project is to estimate the burden of laboratory-confirmed cryptococcal disease in South Africa. From 1 July 2008, surveillance methodology for the project was changed to reduce the reporting burden on diagnostic laboratories. Only GERMS-SA enhanced surveillance sites (25 hospitals in 9 provinces), National Health Laboratory Service (NHLS) laboratories in KwaZulu-Natal, and laboratories in the private, mining, and military sectors are currently required to directly report case patients to NICD, whereas data from case patients, diagnosed with cryptococcosis at NHLS laboratories in the other 8 provinces, are obtained through audit of the NHLS Corporate Data Warehouse, a centralised, laboratory data repository. In total, 8,240 case patients with incident cryptococcosis were detected through the surveillance project in 2008. Cryptococcal isolates (n=1582), obtained from case patients at enhanced surveillance sites, were characterised by phenotypic and genotypic tests at MRU. A detailed report of surveillance findings for 2008 is contained within the GERMS-SA Annual Report 2008, which can be accessed on the GERMS-SA webpage.

Paediatric cryptococcosis
Cases of cryptococcosis in children (<15 years), reported to MRU between 1 January 2005 and 31 December 2007, have been compared to adult cases. A large series of paediatric cryptococcal cases has been identified and described.

Antifungal Susceptibility Testing of Incident Cryptococcal Isolates, 2002-2003 and 2007-2008
There have been no South African studies examining the prevalence of fluconazole non-susceptibility amongst incident episode isolates of Cryptococcus species. Population-based, laboratory-based surveillance for cryptococcosis, initiated in Gauteng in March 2002 and expanded nationally in 2005, provided the opportunity for this issue to be explored further. Clinical strains of Cryptococcus species were submitted to the NICD, phenotypically characterised and stored at -70 OC to maintain viability. We randomly chose 500 incident episode strains from surveillance case patients, diagnosed with cryptococcosis during 2 time periods (2002-2003 and 2007-2008), for fluconazole minimum inhibitory concentration (MIC) determination by various test methods. Laboratory work commenced in November 2008.

Molecular Epidemiology of Environmental and Clinical Cryptococcal Isolates
Isolates obtained from the environment as well as clinical surveillance isolates (obtained from adults and children through the GERMS-SA project) were characterised genotypically, in collaboration with investigators at Duke University Medical Centre, North Carolina, USA.

Estimation of the Current Global Burden of Cryptococcal Meningitis among Persons Living With HIV/AIDS Cryptococcal meningitis is an important AIDS-related opportunistic infection, especially in the developing world. In order to assist with development of global strategies and priorities for prevention and treatment, it is important to estimate the burden of disease. In collaboration with investigators at the U.S. Centers for Disease Control and Prevention, Atlanta and the University of Alabama, data from published studies were used to estimate the global burden of cryptococcal meningitis.  

TRAC-South Africa (Tracking Resistance to Antifungal drugs for Candida species in South Africa): A Laboratory-based Sentinel Surveillance Project for Candidaemia and Antifungal Drug Resistance in South Africa, 2009-2010
During 2008, a laboratory-based, sentinel surveillance project was designed by MRU, in collaboration with 20 public and private laboratory sites across South Africa, and the Centers for Disease Control and Prevention, Atlanta. The major objective of this project is to describe the species distribution of Candida spp. causing bloodstream infection at sentinel sites in South Africa, and to compare the species distribution during 2009-2010, to previous reports and between the public- and private-health sectors. Another major objective is to describe the prevalence of resistance to at least four antifungal drugs (fluconazole, voriconazole, amphotericin B, caspofungin), amongst invasive Candida spp. in 2009-2010, and to compare these antifungal drug resistance patterns to previous reports, where possible and between the public- and private-health sectors. Formal surveillance started on 1 February 2009.  

Cryptococcosis and tuberculosis (TB) co-infection at Charlotte Maxeke Johannesburg Academic Hospital, South Africa, January 2005 to December 2007: a record review
The main objectives of this cross-sectional, retrospective study were to describe patients at Charlotte Maxeke Johannesburg Academic Hospital who were treated for both cryptococcosis and TB between 2005 and 2007 in terms of demography, method of diagnosis, treatment and outcome of cryptococcosis, and to define the basis for the TB diagnosis amongst these patients and to categorise according to the strength of TB diagnosis.  

Prospective, Serum Cryptococcal Antigen Screening at HIV Clinic at Chris Hani Baragwanath Hospital
Since January 2009, the MRU has tested serum specimens for cryptococcal antigen from patients, newly-enrolled into the CHBH HIV Clinic.


Capacity building


Mycology External Quality Assessment (MEQA) Programme
In 2008, the MRU coordinated 3 MEQA surveys for 104 laboratories in the southern African region participating in the yeast sub-programme, and for 49 laboratories participating in the mould sub-programme.  

Specialist Registrar Training
The MRU participates in the NICD training programme for medical doctors, specialising in the fields of pathology and public health. Training includes practical identification of clinically important yeasts and moulds, a review of antifungal susceptibility test methods, an introduction to molecular epidemiology and molecular diagnostic techniques as well as an overview of relevant clinical infectious disease issues.

South African Field Epidemiology and Laboratory Training Programme
The MRU participates in teaching residents from this NICD-based training programme.

Advanced Mycology Workshop
The week-long workshop aims to increase expertise in mycology laboratory techniques in referral diagnostic laboratories in South Africa, and is primarily intended to provide laboratory workers with the skills to identify clinically important fungi and to understand the major concepts required for performance, quality control and interpretation of antifungal drug susceptibility testing. During 24-28 November 2008, 4 laboratory workers attended the first course.  

Participants in the Advanced Mycology Workshop, Mycology Reference Unit, 24-28 November 2008

Contact us

Please direct any queries via one of the following:


e-mail:
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Staff
Nelesh Govender,
MBBCh, F. C. Path (SA) Micro, DTM&H, Dip HIV Man (SA)

Unit Head e-mail:

Nelesh Govender obtained his Bachelor of Medicine and Bachelor of Surgery (MBBCh) degree at the University of the Witwatersrand (WITS) in 1997, and specialised in clinical microbiology at WITS and the National Health Laboratory Service. Dr. Govender is currently Head of the Mycology Reference Unit (MRU) & National Microbiology Surveillance Unit (GERMS-SA) at the NICD. With colleagues in Johannesburg, as well as national and international collaborators, Dr. Govender directs and manages national, laboratory-based, surveillance programmes for bacterial and fungal diseases, including cryptococcosis and candidiasis.
Jaymati Patel,,
Nat Dip Med Tech (Micro)

Unit Manager

e-mail:

Jaymati Patel obtained her national diploma in microbiology. She is currently in a lab manager’s position in the MRU department at NICD.
Marelize van Wyk, ,
MSc. Microbiology

Molecular Laboratory Manager

e-mail:

Marelize obtained her degrees at the University of Pretoria (UP). Her BSc. was obtained in Microbiology. In her BSc. (Hons.) Microbiology she specialized in Virology. In her MSc. she specialized in mycology. Currently she is busy finishing her Ph.D. in Mycology in the faculty of Genetics at UP. She is the molecular laboratory manager and has a couple of projects she is working on. The projects focus on the molecular identification and typifying of Cryptococcus serotypes in South Africa and the identification of Candida spp.
Nevashan Govender ,
MSc. Medical Microbiology

Intern Scientist

e-mail:

His studies were done at The University of the Witwatersrand (WITS). He obtained his BSc. in Zoology and Advanced Biology. His BSc. (Hons.) was obtained in Zoology specializing in Histology. He has just completed his MSc. in Medical microbiology specializing in Enteric Diseases at NICD. In the mycology unit he will complete his internship under the GERMS-SA unit.
Thokozile Gloria Zulu,
Dip Med Tech

Medical Technologist (Surveillance Unit)

e-mail:

Thokozile Gloria Zulu obtained her national diploma at the Cape Peninsula University of Technology in Microbiology in 2007. She is currently employed as a medical technologist in MRU. Her job description entails surveillance work and managing the microbiology external quality assessment programme (MEQA). She is also doing a study on cryptococcal antigen testing with Dr. Allan Karsteadt.
Bulelwa Zigana,
Dip Office Admin

Laboratory Clerk

e-mail:

Bulelwa Zigana after completing her matric worked in a hospice careing for people with HIV and Aids for 4 years. Thereafter she worked with people with Disabilities: Mentaly & Physicaly Challanged. She got her Diploma and worked for a year as a Junior Bookkepper. She joined NICD in July 2008. She is currently a Laboratory Clerk where they collect information on Meningitis for Surveillance.
Dumisani Mlotshwa,
Matriculation Certificate

Laboratory Clerk

e-mail:

Dumisani Mlotshwa was born in Pietermaritzburg (KZN) where he studied and matriculated at Siyahlomula High School. He has worked for different companies in the data management field including the Human Science Research Council (HSRC) as a data technician and for the Centre for Aids Programs of Research in South Africa (CAPRISA) as Data encoder. Currently he is a Laboratory clerk for MRU.
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Publications
Journal articles

  2009
  • Harrison T. The burden of HIV-associated cryptococcal disease (editorial comment). AIDS 2009;23:531-532. Download
  • Park BJ, Wannemuehler KA, Marston BJ, Govender N, Pappas PG & Chiller TM. Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS. AIDS 2009;23:525-530. Download
2008
  • McCarthy KM , Cohen C, Schneider H, Gould SM, Brandt ME & Hajjeh RA. Cryptococcosis in Gauteng: Implications for monitoring of HIV treatment programmes. S Afr Med J 2008;98:452-454.   Download
2007
  • Govender N . HIV-associated opportunistic fungal infections: A guide to using the clinical microbiology laboratory. S Afr J HIV Med 2007;Spring edition:18-22. Download
  • McCarthy KM, et al. Guidelines for the Prevention, Diagnosis and Management of Cryptococcal Meningitis and Disseminated Cryptococcosis in HIV-infected patients. S Afr J HIV Med 2007;Spring edition:25-35. Download
2006
  • McCarthy KM , Morgan J, Wannemuehler KA, Mirza SA, Gould SM, Mhlongo N, Moeng P, Maloba BR, Crewe-Brown HH, Brandt ME & Hajjeh RA. Population-based surveillance for cryptococcosis in an antiretroviral-naive South African province with a high HIV seroprevalence. AIDS 2006;20:2199–2206 Download
  • Morgan J, McCarthy KM, Gould SM, Fan K, Arthington-Skaggs B, Iqbal N, Stamey K, Hajjeh RA & Brandt ME. Cryptococcus gattii Infection: Characteristics and Epidemiology of Cases Identified in a South African Province with High HIV Seroprevalence, 2002–2004. Clin Infect Dis 2006; 43:1077–1080 Download

Presentations at international congresses

2008
  • Park BJ, Wannemuehler K, Marston BJ, Govender N, Pappas P, Chiller T. Estimating the Global Burden of Cryptococcal Meningitis. Abstract. HIV/AIDS Implementers’ Meeting June Kampala, Uganda, June 3-7, 2008
  • Litvintseva AP, Rossouw J, Thakur R, Govender N, Mitchell T.Cryptococcus neoformans var. grubii in Africa. Abstract SY-12-03. 7 th International Conference for Cryptococcus and Cryptococcosis September Nagasaki, Japan, September 11-14, 2008.
  • Govender N , Cohen C, Meiring S, Quan V, Patel J, et al. Surveillance for cryptococcosis in South Africa, 2005-2007. Abstract P-B-32. 7 th International Conference for Cryptococcus and Cryptococcosis September Nagasaki, Japan, September 11-14, 2008.
  • Govender N , Patel J, Rossouw J, Quan V, Meiring S. Recurrent cryptococcosis caused by Cryptococcus neoformans in three cases with incident Cryptococcus gatti infection. Abstract P-A-32. 7 th International Conference for Cryptococcus and Cryptococcosis September Nagasaki, Japan, September 11-14, 2008.
  • Govender N , Patel J, Rossouw J, Quan V, Meiring S. Dual infection with Cryptococcus neoformans and Cryptococcus gattii, South Africa. Abstract P-C-31. 7 th International Conference for Cryptococcus and Cryptococcosis September Nagasaki, Japan, September 11-14, 2008.
  • Miglia KJ, Meiring S, Govender Net al. Molecular characterisation of 82 strains of Cryptococcus species obtained from South African paediatric patients during 2005 and 2006. Abstract P-C-33. 7 th International Conference for Cryptococcus and Cryptococcosis September Nagasaki, Japan, September 11-14, 2008.
  • Govender N , Cohen C, Meiring S, Quan V, et al. A comparison of cryptococcal cases with and without recurrent disease in South Africa, 2005-2006. Abstract M-1851. 48 th Annual Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC) and the Infectious Disease Society of America (IDSA) 46 th Annual Meeting October Washington, D.C., U.S.A., October 25-28, 2008.
  • Park BJ, Wannemuehler KA, Marston BJ, Govender N, Pappas P, Chiller T. Refocusing on a re-emergent Disease: the current global burden of cryptococcal meningitis among persons living with HIV/ AIDS. Abstract M-1848. 48 th Annual Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC) and the Infectious Disease Society of America (IDSA) 46 th Annual Meeting October Washington, D.C., U.S.A., October 25-28, 2008.
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Awards
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