Methodology for Laboratory-based Surveillance

1.     To provide accurate quality-controlled strategic information to clinicians and public health policy-makers to assist with patient management and health practice planning, implementation and evaluation for the infections under surveillance. Such strategic information includes:

§  Estimates of disease burden
§  Epidemiological trends
§  Organism/ pathogen characterisation
§  Impact of the South African Comprehensive Care, Management and Treatment Programme for HIV and AIDS on opportunistic infections
§  Impact of vaccines on vaccine-preventable diseases
§  Antimicrobial susceptibility patterns

2.     To identify areas of interest for further investigation from analysed surveillance data and to initiate and coordinate studies to address important and relevant research questions.

3.     To provide key contacts for response to issues of public health importance

Surveillance Population
The total population for disease surveillance in South Africa was estimated to be around 53 million in 2013. Population data are obtained from Statistics-SA, which is in line with the National Department of Health’s population data.

*See GERMS-SA case definition posters* under PATHOGENS
Data collection 
1. Isolate collection and information
When a participating laboratory has identified a case, the laboratory submits the corresponding isolate or specimen, along with the TrakCare laboratory form, to the reference laboratory at the NICD, Johannesburg. The basic demographic data from the laboratory form are entered onto our GERMS-SA databases.

2. Enhanced surveillance clinical information
GERMS-SA has enhanced surveillance at 25 public-sector hospitals in all 9 provinces of South Africa. The surveillance officers at certain sites obtain additional clinical information from cases of Streptococcus pneumoniaeNeisseria meningitidisHaemophilus influenzaeCryptococcus species (only for the first 3 months of every year), candidaemia, Staphylococcus aureus, CRE and rifampicin-resistant TB (from Gene Xpert). Surveillance officers conduct an interview with the case patient and capture data in a case report form (either paper based or on an electronic data collection tool). If the patient has been discharged or has died, the surveillance officer performs a medical record review or consults the attending clinician to obtain the required information for the case report form. The case report form includes additional information on antimicrobial use, patient outcome, vaccination data, HIV status and previous hospital admissions.
Surveillance evaluation
Laboratory Audits
Participating public-sector (NHLS) laboratories are audited by the coordinating unit of GERMS-SA, on a quarterly basis. The audits compare the number of cases detected by a participating laboratory on the Corporate Data Warehouse of the NHLS with the number of cases reported to the NICD reference laboratories (COTHI - AMRRL, COTHI – MRL, CED, CRDM, CTB).

The objective of these audits is: 

  • To assess the quality of the data sample.
  • To ensure that all isolates/ specimens for diseases under surveillance are being reported to the GERMS-SA network
  • To ascertain the percentage of missed isolates to monitor representativeness and efficacy of national surveillance
  • To use the percentage of those missing to ascertain a ‘correction factor’, to be used in data dissemination and publications
  • To aid laboratories which may have difficulties in any of the steps of collection of data