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Abstract
The contamination of water catchments by non-point source faecal pollution is a major issue affecting the microbial quality of receiving waters, and is linked to the occurrence of a range of enteric illnesses in humans. The potential sources of faecal pollution in surface waters are diverse, including urban sewage leaks, surface runoff and wildlife contamination, and may contain faecal inputs from a range of hosts. Effective management of this public health concern requires that the major contributing hosts be identified in order to launch targeted mitigative action. In this thesis, a range of Microbial Source Tracking (MST) approaches were investigated for their potential to distinguish between human and non-human associated Faecal Indicator Bacteria (FIB) from surface waters in Sydney, Australia. In this study, a PCR-based method targeting the plc gene of Clostridium perfringens was successfully used to detect this FIB from environmental water samples. Further investigation into the host-specificity of the plc gene indicated that C. perfringens may not be suitable for MST purposes. Subsequently, two high-performing existing MST assays, HF183 and BacCan-UCD, were assessed for their ability to detect host-specific Bacteroides 16S rRNA markers for faecal pollution in a 12-month study of an urban coastal lagoon in Sydney, Australia. The markers were assessed for their performance against local inputs, and the lagoon was found to contain year-round high numbers of human and canine faecal markers, as well as traditional FIB counts. Correlations between MST markers, traditional FIB measurements, and physico-chemical parameters suggested that high turbidity may be a potential early-warning indicator for low microbial water quality in the study lagoon. Finally, three new assays were developed for the multiplex qPCR detection of human- and canine-associated Bacteroides 16S rRNA gene markers for faecal contamination. The outcomes of this study contribute to the wider body of research in this exciting and rapidly expanding field, and represent a significant step in closing the gap between public health policy and microbiological research.