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Faecal Source Tracking

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

What Did We Do?

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.

Research Updates

Norsewood and Districts’ School use Te Miro Farm as an outside classroom

Oct 6 2021

Protecting the Source of the Manawatū River

The source of the Manawatū River, hidden away in the Ruahine mountain range, is a ...
Faecal source tracking and sampling in Mākirikiri Reserve near Dannevirke

Oct 4 2021

How To Identify Sources of Faecal Contamination

Regional and city council staff now have a documented process to follow when faecal contamination ...
Probably possum poo, in the Mākirikiri Stream.

May 25 2021

Pests Poo Too! The Role of Introduced Predators on Water Quality Assessments

The poo of ruminant animals, especially cows, is often under the spotlight when it comes ...
Testing for E.coli

Dec 5 2019

Pūhoro Student Internships: In Their Own Words

Two Pūhoro STEM Academy students, Ella Cameron-Smith (Ngāti Raukawa, Ngai Te Rangi) and Meschka Seifritz ...
Kura students in the Hopkins Lab

Jun 13 2019

School Holiday Sampling: A Case Study of Community Engagement in Research

The Faecal Source Tracking project used DNA sequencing to identify 23 strains of ‘naturalised’ Escherichia ...

How Can The Research Be Used?

  • 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'.

In the Media

Trapping in Mākirikiri Reserve

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"

Stream Monitoring for Community Groups: A Crash Course in Practical Citizen Science

Monicalogues blog, 22 October 2017

This blog describes how Nelson community group Friends of the Matai are testing two methods for detecting E. coli


Community Involvement

  • 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

Team Snapshot

Research Outputs


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

Adrian L. Cookson, Jonathan C. Marshall, Patrick J. Biggs, Lynn E. Rogers, Rose M. Collis, Megan Devane, Rebecca Stott, David A. Wilkinson, Janine Kamke, Gale Brightwell
Environmental Microbiology, April 2022

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 New Zealand landscape is dominated by livestock farming, and previous work has demonstrated that “recreational exposure to water” is a risk factor for human infection by Shiga toxin-producing Escherichia coli (STEC). Though STEC isolates were rarely isolated from water samples, STEC-associated virulence factors were identified more commonly from water sample culture enrichments and were associated with increased generic E. coli concentrations. Whole-genome sequencing data from both E. coli and newly described Escherichia spp. demonstrated the presence of virulence factors from E. coli pathotypes, including extraintestinal pathogenic E. coli. This has significance for understanding and interpreting the potential health risk from E. coli where water quality is poor and suggests a role of virulence factors in survival and persistence of E. coli and Escherichia spp.

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

A. Cookson, D. Lacher, F. Scheutz, D. Wilkinson, P. Biggs, J. Marshall, G. Brightwell
American Society for Microbiology Microbiology Resource Announcements, August 2019

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 the hypervariable gnd gene and describe a database containing 534 distinct partial gnd sequences and associated O groups for use with culture-independent E. coli community analysis. The DNA sequences of the 534 distinct gSTs are available in FASTA format from GitHub (


Refinement of the Framework for Assessment of Recreational Water Quality

Megan Devane, Margaret Leonard, Carla Eaton
Report for Our Land and Water, June 2021

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

Marie Moinet, Lauren Gadd, Megan Devane, David Wood, Brent Gilpin, Adrian Cookson
Report for Our Land and Water, June 2021


Conference presentations

The next steps for sites with elevated E. coli concentrations above water quality guidelines

Adrian Cookson, Marie Moinet, Lauren Gadd, Megan Devane, David Wood, Brent Gilpin
30 September 2021

Presentation to SWIM special interest group of policy planners and scientists from across 15 regional authorities.

Framework assessment for water quality

Megan Devane, Carla Eaton, Margaret Leonard, Brent Gilpin
30 September 2021

Presentation to SWIM special interest group of policy planners and scientists from across 15 regional authorities.

Faecal Source Tracking, OLW Symposium

Adrian Cookson and Arapera Paewai
Our Land and Water Symposium, August 2019

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