Smart monitoring for microbial risk assessment

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Periodic catchment assessments are required as part of routine ‘operational monitoring’ under the Australian Drinking Water Guidelines framework. This is commonly achieved using a microbial Health-Based Targets (HBT) assessment, as referred to in the Health-Based Targets Manual.

The HBT manual, which has a particular focus on Cryptosporidium, prescribes the use of a sanitary survey and microbial indicators as part of the mandatory 'Tier 1' assessment of source water. An optional 'Tier 2' assessment using actual Cryptosporidium monitoring data can also be used, which may be required if microbial indicators (E. coli) are inconsistent with source vulnerability assessments (sanitary survey).

However, monitoring for Cryptosporidium is expensive and results often show ‘nil detects’ which may not be a true assessment of the risk. While new research provides support and guidance for consistency in the delivery of sanitary surveys along with developments in molecular techniques that offer alternative approaches to better characterise risk and improve the efficiency of monitoring, the water industry still identified need for improvement.

This project investigated a new method that uses genome sequencing to make a better, more accurate assessment of the microbial risk that different catchments pose to public health through drinking water. It developed and validated protocols for vertebrate faecal source tracking (FST) targeting mitochondrial DNA or “vDNA”, including sampling requirements, and quality standards and guidelines for data interpretation, with the objective to integrate this new profiling technique with existing source tracking techniques (E. coli typing and Bacteroides host markers). This new technology has the potential to enhance decision-making for water utilities about the most effective and efficient raw water treatment processes to apply in different areas.

Several insightful outcomes of this project, include:

• The selection, evaluation and establishment of qPACR markers that target DNA from mitochondria (faelcal DNA indicator) and Bacteroides (gut bacteria indicator).
• The determination that Bacteroides markers are robust indicators of recent faecal contamination while mitochondrial markers can indicate more persistent (historical) contamination.
• The generation of two highly precise DNA Standards in collaboration with the National Measurement Institute (NMI), which can now be used is assays for exceptionally accurate quantification.
• The establishment of a DNA diversity profiling platform for mitochondrial 12S vertebrate.
• The consideration of the capability of FST technologies and their influence on potential sampling strategies, in addition to the power of each indicator to be used in field settings across Australia.
• The determination of the robustness of methods (tested through interlaboratory trial).

This project is a first step in the process of deciding whether catchment genome sequencing will be used routinely across Australia to inform drinking water treatment.