The Identification of Predominant Faecal Contamination Sources in Water Using Host-Specific Genetic Markers in Water-Stressed Rural Communities of Vhembe District Municipality, South Africa

It is critical to attribute faecal contamination to its original source in order to assess public health risks and implement effective interventions to mitigate future contamination. This study aimed to identify the primary sources of faecal contamination in water using microbial source tracking markers in water-stressed rural communities. A total of 1128 water samples were collected sequentially from the main source (river/borehole) to the households. Six host-specific genetic markers were used to detect faecal contamination in the water samples (BacHum and HF183, BacCow, Pig-2-Bac, Cytb and BacCan). Of the 564 water samples tested during the wet season, 37.94% (n = 214) were positive for human and animal-specific Bacteroidales marker genes, while 31.73% (n = 179) of the 564 tested during the dry season were also positive. During the wet season, animal faecal contamination was more prevalent among the positive samples (Cytb: 20.56%, n = 44; BacCan: 19.16%, n = 41). By contrast, human-origin faecal contamination was dominant during the dry season (BacHum: 23.46%, n = 42; HF183: 21.23%, n = 38). Identifying the origin of faecal contamination will assist in implementing targeted intervention strategies for the effective prevention of pathogen transmission in water-stressed rural communities in order to protect public health.