CSIR Microbiology and Parasitology Laboratory

The CSIR Microbiology and Parasitology Laboratory has played a key role in the development of wastewater-based epidemiology disease tracking and monitoring approaches during the Covid-19 pandemic. This added to the laboratory’s reputation, acquired over more than two decades, as a specialised and reliable provider of tests for niche waterborne pathogens. The facility focuses on niche waterborne microbes, like viruses and parasites, that require specialised equipment and approaches.

Disease-causing microbes are often spread through water, with cholera bacteria thriving in environmental waters (like rivers and lakes) when conditions favour the bacteria, and certain parasites and viruses being prevalent in wastewaters. It is therefore imperative that water resources are regularly tested, to make sure that these infective microbes are absent and pose no risk to water users.

There are many laboratories that test for microbial indicators in South Africa, and the most widely used indicator is a bacteria called Escherichia coli. The use of indicator organisms, like E. coli, has many advantages that include cost savings and simplicity of testing methodologies. The approach provides valuable information and is especially useful for the detection of sewage contamination. However, there are many scenarios where an indicator organism approach is not sufficient; for instance, when dealing with microbes that are more robust than E. coli and can therefore remain viable for much longer times. The CSIR Microbiology and Parasitology Laboratory focuses on these unique microbes, which require special consideration, because the risks associated with them are not adequately covered using the widely utilised indicator-organism testing approach.

The CSIR has been providing these specialised testing services (and method development) to the water sector for over two decades. The laboratory is a leader in the field of waterborne virology, having developed methods for detecting these pathogens since the 1990s and is continuing to expand in this field using modern molecular approaches as they become available. The virus testing capability has also been useful during the Covid-19 pandemic, with the laboratory being involved in the development of wastewater-based epidemiology disease tracking and monitoring approaches that can be applied during the pandemic. Using this approach, molecular detection techniques are utilised to detect and quantify Covid-19 viral matter from communities (as opposed to the practice of detecting it from individuals) based on the viral RNA signatures in wastewater effluents. Parasites are also difficult to analyse for, but the CSIR Microbiology and Parasitology Laboratory is proficient in testing for these pathogens, having offered this SANAS-accredited testing service to the water sector for many years now. The laboratory is also skilled in the testing methods for a variety of other niche waterborne pathogens, for instance those that cause cholera and dysentery.

The laboratory undertakes water testing specifically for the following:

• Cytopathogenic viruses using a tissue culture method;

• Protozoan parasites (Giardia and Cryptosporidium) using immunomagnetic separation and fluorescence microscopy (SANAS Accredited);
• Enterovirus, norovirus and SARS-CoV-2 using polymerase chain reaction;
• , Shigella and Vibrio cholerae (the causative agent of cholera) using polymerase chain reaction; and
• Helminth ova (intestinal worm eggs) and bilharzia larvae using light microscopy.

The laboratory services water utilities, municipalities, bottled water companies, health facilities and various companies within the food production and mining sector within southern Africa. Companies interested in using these specialised services are invited to contact the laboratory manager.

Contact details

Wouter le Roux: Laboratory Manager
Email: Wleroux@csir.co.za
Tel: +27 (12) 841 2189

Lisa Schaefer: Technical Signatory
Email: Lschaefer@csir.co.za
Tel: +27 (12) 841 4279