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LABORATORY-BASED SURVEILLANCE

GERMS-SA is a nationwide network of clinical microbiology laboratories (in the public and private-sector) which participate in an active laboratory-based surveillance programme for pathogens of public health importance. Annually approximately 50 labs that do culture on CSF and blood send us specimens (from both private and public sector), however the drainage area for our surveillance specimens includes all ~150 NHLS microbiology laboratories as there is a set referral system for the flow of microbiology cultures. GERMS-SA relies not only on participating laboratories to submit isolates, but also makes use of the NHLS Corporate Data Warehouse to ensure that all cases meeting the case definition are included in the database.

 The SA population under surveillance is estimated to be about 53 million.  The reference laboratories at the National Institute for Communicable Diseases (NICD) receive isolates for confirmation and further characterisation. In addition, at 25 hospitals in all 9 provinces (our "enhanced" or “sentinel" sites), GERMS-SA has employed professional and enrolled nurses as Surveillance Officers (SOs).  The SOs collect additional clinical and epidemiological information on the laboratory-confirmed cases.

GERMS-SA has an extensive repository of data and isolates related to important communicable diseases in South Africa. This allows GERMS-SA to provide essential public health information to the Department of Health and other stakeholders.
 The pathogens under GERMS-SA surveillance were chosen from 4 broad categories, namely:
◾ AIDS-related opportunistic infections
 Cryptococcosis, salmonellosis, invasive pneumococcal disease, rifampicin-resistant TB
◾ Epidemic-prone diseases
 Cholera, typhoid fever, meningococcal disease, shigellosis, diarrhoeal disease due to diarrhoeagenic E. coli (EHEC), Campylobacter and Listeria spp
◾ Vaccine-preventable diseases
Haemophilus influenzae type b disease, invasive pneumococcal disease
◾ Nosocomial infections
 Bacteraemia due to Candida spp, Staphylococcus aureus and other ESKAPE organisms (Enterococcus, Klebsiella, Acinetobacter, Pseudomonas and ESBL (Enterobacter and E. coli), Carbapenem Resistant Enterobacteriaceae
 



 
NICD/GERMS-SA Annual Surveillance Review 27-28 October 2015
 
CLINIC SURVEILLANCE
Since late 2014 clinic surveillance sites (1-2 per province) were selected throughout the country for 2 projects
1. Sentinel Surveillance of Sexually Transmitted Infection Syndrome Aetiologies and HPV Genotypes among Patients attending Public Health Facilities in South Africa
 
2.  Prospective Sentinel Surveillance of Tuberculosis and Human Immunodeficiency Virus in South Africa and Related Drug Resistance
And a third project only based at a rural clinic in Mpumalanga: Hluvukani clinic which is part of the University of Pretoria’s Mnisi One Health Community Programme.
3.  Identifying zoonotic aetiologies in adults with acute febrile illness and baseline seroprevalence for selected zoonotic conditions at the human-wildlife-livestock interface, Mpumalanga, South Africa.

As of March 2016 we are running in the Eastern Cape (2 clinics), KZN (2 clinics), MP (2 clinics), Gauteng (1 clinic) and NW (1 clinic).