E. coli bacteria naturally populate the gastrointestinal tract of humans and animals; they are usually harmless and are commonly excreted. Faeces can also contain harmful microscopic pathogens, and this has led to the assumption that if harmless E. coli are found in water, that the drinking water has been contaminated with faeces that might also have contained pathogens that pose a risk to public health. Using E. coli as an indicator of faecal contamination was recently challenged by the finding that some E. coli strains live, grow and bloom in the environment, and their presence in water might not mean that the water has been contaminated with harmful pathogens. This research examined the environmental conditions associated with E. coli bloom formation in the context of climate-change adaptation and developed multiplex PCR tests which allow the identification of environmental and faecal E. coli. This information was added to a Utility Response Protocol.

‘Microbial source tracking’ (MST) is a technique that aims to identify the animal that excreted faeces and polluted water. There are a number of ways to do this, but the problem is that no one method accurately identifies the origins of faecal pollution in environmental water samples. This research found that faeces could be stored in a freezer or a laboratory -80°C cold-store for up to a month without changing the relative numbers of the different types of bacteria in the samples of faeces. Up to seven faeces samples from different animals were mixed together and examined using 17 techniques to identify the original animals. Three of the most accurate and reliable methods used mitochondrial DNA, the analysis of a bacterial enzyme sequence (beta-glucuronidase), and specific DNA sequences form bacteria known to come from humans, horses and cows. These three types of tests were selected for inclusion in a ‘Toolbox’ from which a combination of methods will allow accurate and reliable management of faecal contaminants in source waters.

Cryptosporidium, a microscopic single-cell parasite, forms an “oocyst” with a resistant outer layer analogous to an eggshell. Oocysts survive for a long time in the environment but UV in sunlight, and high temperatures that cause desiccation, kill them. If a mammal drinks water containing live oocysts, they embed in the gut wall and continue their lifecycle until eventually many more oocysts are excreted. There are 26 species of cryptosporidium but only five infect humans, and two; Cryptosporidium hominus and Cryptosporidium parvum, cause approximately 95% of all human infections. C. hominus occurs only in humans, but C. parvum is also found in cattle, sheep, and other animals. The problem is that human-infecting oocysts are excreted by animals in catchments and rain can wash live oocysts into water reservoirs. This research collated peer-reviewed published literature, and information and data collected by the water industry, then characterised the distribution of different Cryptosporidium species in Australian catchments. This led to recognition of a research need to track and predict live and dead oocyst transport during different weather events, and to model and evaluate catchment management initiatives such as excluding cattle from reservoir areas.