A significant number of households in rural South Africa rely on roof-harvested rainwater (RHRW) for domestic purposes. Although, there is a general public health perception that RHRW is safe to drink, the presence of potential pathogens has been reported in this water source. Generally, the microbiological methods used to evaluate water quality depend on conventional culturing methods, which may underestimate total pathogen content and diversity and, thus limit the extent to which one can fully understand potential infectious risks from RHRW use. However, the use of high-throughput next-generation sequencing, (pyrosequencing) offers an alternative, in which detailed community structure can be achieved in combination with a fairly high taxonomic resolution. Not only does high-throughput next-generation sequencing allow for the detection and identification of dominant bacteria phylotype profiles within a sample but the high sequence numbers produced allows for the detection of rare species including pathogens within bacterial communities.
The quality of the essential commodity water is being compromised by contaminants originating from anthropogenic sources, industrial activities, and agriculture amongst others. Water scarcity and severe drought in many regions of the world also represents a significant challenge to the availability of this resource. Domestic rainwater harvesting (DRWH), which involves the collection and storage of water from rooftops and diverse surfaces, is successfully implemented worldwide as a sustainable water supplement. In South Africa, a water-scarce country, the use of domestic rainwater harvesting is predominantly practised by communities situated in KwaZulu-Natal and the Eastern Cape. While the use of DRWH tank systems can definitely suffice and serve as an alternative water supply, there is a health risk associated with the use of this water source for drinking purposes, especially if the water is used untreated. Currently the information available on the microbial and chemical quality of harvested rainwater in South Africa is limited.