Faecal Source Tracking

Identifying the sources of faecal contamination in waterways, and identifying naturalised Escherichia coli to help establish water quality for swimming

Project Details Ngā taipitopito

Project Status:
Challenge funding:
Research duration:
July 2017 – December 2019

Collaborators Ngā haumi

AgResearch | Auckland University | Department of Conservation | ESR | Horizons Regional Council | Manawatu Citizen Science | Massey University | NZ Landcare Trust | Pūhoro STEM Academy | Pūkaha Mount Bruce | Rangitāne o Tamaki nui a Rua | Rangitāne o Wairarapa | Te Kāuru

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What are we doing?E aha ana mātou?

A key indicator of swimmable water quality in New Zealand’s lakes and rivers is the minimal presence of E.coli (Escherichia coli). This bacteria naturally occurs in the gastro-intestinal tract of animals and its presence in water generally indicates faecal contamination, which can make humans sick.

However, E. coli can also be present naturally in soil and water, with no risk to human health (non-pathogenic). The presence of this naturalised Escherichia, rather than faecal contamination, may cause some waterways to fail to meet water quality standards. Faecal Source Tracking research identified potential sources of faecal contamination impacting waterways in New Zealand, and investigated the presence of naturalised Escherichia.

The Faecal Source Tracking project used DNA sequencing to identify 23 strains of E.coli that are not associated with risk to human health. This work is a significant contribution to the evidence base that ensures New Zealand’s water quality standards for “swimmability” are appropriately protective of human health and recreational values.

How can the research be used? Ka pēhea e whai take ai te rangahau?

  • Using microbiological culture methods, Faecal Source Tracking researchers found naturalised coli at several sample sites, including those in water catchments situated in closed canopy native bush with intensive pest management. In catchments with agricultural land use, E. coli originating from the gastro-intestinal tract of warm-blooded animals predominate.
  • This project’s genome sequencing data of 23 naturalised Escherichia strains suggests they represent a distinct evolutionary population. Faecal Source Tracking researchers have sequenced the genomes of a further 218 coli, and sequenced over 1.1 billion DNA base pairs.
  • Further work identified traits that may be used to rapidly distinguish naturalised Escherichia from coli associated with faecal contamination, for use by stakeholders and catchment communities to establish water quality and ecological health of freshwater environments. This work will contribute to robust risk assessments and help ensure targeted mitigation steps are implemented.
  • This research will continue for a further three years following a successful bid for Smart Idea funding through the 2019 Endeavour Fund. This further research is titled ‘Novel discriminatory tests for E.coli to improve water quality assessments’.

Participation & engagement Te hunga i whai wāhi mai

  • Early dialogue with iwi and Regional Councils at an initial hui identified project sampling sites and social processes to underpin stakeholder engagement. Long-term aspirations for co-developing solutions, such as tools for assessing land-use suitability, were agreed beyond the life of the current project.
  • Faecal Source Tracking researchers participated in the Citizen Science Community Freshwater monitoring day at Pūkaha Mount Bruce organised by Landcare Trust NZ. This provided an opportunity to provide information on the project to members of the public, Fish & Game and Horizons Regional Council.
  • This research team contributed to building the capabilities of future researchers by partnering with the Pūhoro STEM Academy to support the students’ science study with emphasis on water quality measurements and te ao Māori, through internships, field studies and lab analysis opportunities. Read more

Research team Te hunga i whai wāhi mai

Research Lead
Adrian Cookson
Patrick Biggs
Massey University
Jonathan Marshall
Massey University
Rebecca Stott
Megan Devane

Tools & resources Ngā utauta me ngā rauemi


Te Miro Farm Community Project

This short video, shot at Te Miro Farm, shows researchers from the Faecal Source Tracking project joining hapū groups, dairy farmers and the local school…
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The next steps for sites with elevated E. coli concentrations above water quality guidelines

Presentation to SWIM special interest group of policy planners and scientists from across 15 regional authorities.
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Framework assessment for water quality

Presentation to SWIM special interest group of policy planners and scientists from across 15 regional authorities.
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Refinement of the Framework for Assessment of Recreational Water Quality

Regional and city council staff now have a documented process to follow when faecal contamination is identified in freshwater, created by ESR researchers involved in…
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Academic outputs He whakaputanga ngaio

Journal Article

Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use

This study takes a systematic sampling approach to assess the public health risk of Escherichia coli recovered from freshwater sites within forest and farmland. The…
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Technical Report

Faecal source tracking and the identification of naturalised Escherichia coli to assist with establishing water quality and faecal contamination levels

E. coli are routinely measured as faecal indicator bacteria (FIB) to provide indications of microbial water quality in parallel with other physico-chemical parameters. Recent evidence…
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Technical Report

Faecal source tracking to understand the role of introduced predators and avian species on water quality assessments in the Makiriri Reserve, Dannevirke

Escherichia coli are used as indicators of faecal contamination in water quality assessments, but ‘naturalised’ non-faecal E. coli and non-pathogenic E. coli-like bacteria can confound…
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Journal Article

gndDb, a Database of Partial gnd Sequences To Assist with Analysis of Escherichia coli Communities Using High-Throughput Sequencing

The use of culture methods to detect Escherichia coli diversity does not provide sufficient resolution to identify strains present at low levels. Here, we target…
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Journal Article

Indirect faecal source tracking methods to elucidate critical sources and contaminant transfers through catchments – a review

In New Zealand, there is substantial potential for microbial contaminants from agricultural fecal sources to be transported into waterways. Understanding contaminant transport pathways from catchment…
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In the media Mai i te ao pāpaho

Good Nature blog, 16 November 2020
"As well as this valuable research the aim of Te Kauru is to have the river returned to its original purpose as a place of mana and pride for the region"
Monicalogues blog, 22 October 2017
This blog describes how Nelson community group Friends of the Matai are testing two methods for detecting E. coli
REX Rural Exchange podcast, 19 May 2023

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