Opportunistic, Tropical and Hospital Infections

Opportunistic, Tropical and Hospital Infections


The Centre for Opportunistic, Tropical and Hospital Infections aims to prevent and control opportunistic, tropical and hospital infections in South Africa by providing:
• Strategic information obtained through surveillance and research, to the Department of Health and other major stakeholders
• Technical support for public health programmes, such as the malaria control programme and the cryptococcal screening programme
• Reference laboratory services in the fields of parasitology, mycology, entomology and bacteriology
• Laboratory support for outbreak response
• Training for clinical, laboratory and public health personnel to ensure optimal diagnosis and control of diseases
The Centre focuses its efforts on opportunistic infections, particularly those that are HIV related; tropical infections, especially malaria and its vectors; and nosocomial infections, concentrating on antimicrobial resistance in the hospital setting.
The Centre has the following working groups:

The group provides a specialised parasitology reference service for routine diagnostic medical laboratories. Specialised parasitological diagnostic and confirmatory tests are offered by the laboratory. In addition, certain important pathogens form the focus of its surveillance, research and teaching activities. Surveillance is currently being done on the unconventional opportunistic pathogen Pneumocystis jirovecii that causes the important AIDS-defining infection, Pneumocystis pneumonia (PcP). The estimation of the burden of parasites in children less than 5 years of age presenting with diarrhoea, is the aim of another surveillance project carried out at sentinel sites in South Africa. Surveillance of drug-resistant malaria in South Africa is new exciting project beginning in 2014. Research and development of new identification techniques for human parasites is on-going and currently includes projects on opportunistic diseases such as microsporidiosis, toxoplasmosis, and free-living amoeba infections.

Vector Control
Malaria is the major vector-borne disease in Africa, killing close to 1 million people annually, most of them children under the age of five. In South Africa, malaria transmission is confined to the low-lying border areas in the northeast of the country. The Vector Control Reference Laboratory (VCRL) focuses on the anopheline mosquitoes responsible for malaria transmission and houses a unique collection of live mosquito colonies of the three most important vector species in Africa, namely Anopheles gambiae, An. arabiensis and An. funestus, plus the minor vector An. merus, and the non-vector species of the An. gambiae complex, An. quadriannulatus. Three colonies of An. funestus from Mozambique and Angola continue to provide us with a unique resource for research into insecticide resistance in this important malaria vector. This places the VCRL in a unique position to provide operational support to the National and provincial malaria control programmes, to offer collaborations with international institutions investigating similar problems and to play a role in influencing policy decisions on vector control strategies in the southern African region. In addition, the VCRL houses the largest museum collection of African arthropods of medical importance in Africa, the third largest such collection in the world. The high level of expertise in the VCRL has been recognized by the University of the Witwatersrand and it now forms part of the Wits Research Institute for Malaria (WRIM).

The mycology working group focuses on laboratory-based surveillance for fungal diseases of public health importance in South Africa. These include cryptococcal meningitis, candidaemia and infections caused by Aspergillus and thermally-dimorphic fungi. In collaboration with the Department of Health and other partners, the group is also leading 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. Development of South African and international clinical guidelines for management of fungal infections is an important activity. A specialised mycology reference service is provided to diagnostic medical laboratories – including phenotypic and sequence-based identification of unusual or difficult-to-identify fungi and antifungal susceptibility testing. Research activities are focused on developing and validating new diagnostic assays and defining risk factors for fungal diseases and antifungal drug resistance. The reference laboratory also holds a large collection of pathogenic fungi of medical importance.

Antimicrobial Resistance
The group is responsible for laboratory-based surveillance of nosocomial infections caused by ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). Sentinel site surveillance for Staphylococcus aureus and Klebsiella pneumoniae has been piloted.  Molecular characterization of these organisms currently include confirmation of resistance genes, SCCmec typing, spa-typing and multilocus sequence typing of S. aureus and confirmation of resistance genes, and multilocus sequence typing of  K. pneumonia and P. aeruginosa. In addition, the laboratory processes highly-antimicrobial resistant pathogens by referral from diagnostic medical laboratories. These include the molecular detection of various carbapenemase resistance genes.

Staphylococcus aureus can cause skin and soft tissue infections, pneumonia, arthritis, endocarditis, osteomyelitis, foreign-body infections and sepsis; these can range from mild to severe and potentially fatal. However, risk groups include newborn infants, breast feeding women and individuals with chronic comorbid conditions such as diabetes, cancer, vascular disease and lung disease. K. pneumoniae can cause different types of healthcare-associated infections, including pneumonia, bloodstream infections, urinary tract infections, wound or surgical site infections, and meningitis. K. pneumoniae infections are often seen in individuals with compromised immune systems and those with diabetes, malignancy, renal failure, liver disease and chronic obstructive pulmonary disease (COPD). Hospitalised patients are also at risk as they can acquire infection through invasive medical devices such as ventilators, intravenous catheters, etc. Surveillance for antimicrobial resistance is fundamental component for antimicrobial stewardship programs.
P. aeruginosa is a well-known organism causing infections in immunosuppressed patients, such as neutropenic, chemotherapy, and cystic fibrosis patients, and patients with long hospitalization. 

Proficiency testing

The Centre contributes to the NHLS proficiency testing programme by providing expertise and technical support for two schemes related to communicable diseases, bacteriology and parasitology.

To read more click: http://www.nhls.ac.za/?page=proficiency_testing&id=42
The Quality Assessment Programme is provided in the disciplines of bacteriology and parasitology (enteric pathogens, bacterial meningitis, general bacteriology, plague, tuberculosis and malaria microscopy) to 81 laboratories, from 45 countries in the WHO African Region. The programme has been in operation for 12 years.
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. 
For Publications of the Centre for Opportunistic,Tropical and Hospital Infections click on link below:

Centre Leadership team

Associate Prof. John Frean (Parasitology surveillance, diagnostics and research)
Dr. Basil Brooke (Entomology service and research)
Dr. Nelesh Govender (Mycology surveillance, diagnostics and research)
Associate Prof. Olga Perovic (Antimicrobial resistance surveillance, diagnostics and research)

Contact details:

A/Prof. John Frean  
Tel: 011 555 0308  
Email: johnf@nicd.ac.za 
Dr. Basil Brooke
Tel: 011 386 6483
Email: basilb@nicd.ac.za
  A/Prof. Nelesh Govender 
Tel: 011 555 0353 
Email: neleshg@nicd.ac.za 
A/Prof. Olga Perovic
Tel: 011 386 6278
Email: olgap@nicd.ac.za