Canadian recreational water quality guidelines - Indicators of fecal contamination: Alternative indicators

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Organization: Health Canada

Published: 2023-02-xx

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The Guidelines for Canadian Recreational Water Quality are comprised of multiple guideline technical documents that consider the various factors that could interfere with the safety of recreational waters from a human health perspective. This includes technical documents on understanding and managing risks in recreational waters, indicators of fecal contamination, microbiological sampling and analysis, cyanobacteria and their toxins, physical, aesthetic and chemical characteristics, and microbiological pathogens and other biological hazards. These documents provide guideline values for specific parameters used to monitor water quality hazards and recommend science-based monitoring and risk management strategies.

Recreational waters are any natural fresh, marine or estuarine bodies of water used for recreational purposes; this includes lakes, rivers and human-made systems (for example, stormwater ponds, artificial lakes) that are filled with untreated natural waters. Jurisdictions may choose to apply these guidelines to other natural waters for which limited treatment is applied (for example, short-term use of disinfection for an athletic event). Applying the guidelines in these scenarios should be done with caution. Some disease-causing microorganisms (for example, protozoan pathogens) are more difficult to disinfect than fecal indicator organisms and may still be present even if disinfection has reduced the fecal indicators to acceptable levels.

Recreational activities that could present a human health risk through intentional or incidental immersion and ingestion include primary contact activities (for example, swimming, wading, windsurfing and waterskiing) and secondary contact activities (for example, canoeing, boating or fishing).

Each guideline technical document has been established based on current, published scientific research related to health effects, aesthetic effects and beach management considerations. The responsibility for recreational water quality generally falls under provincial and territorial jurisdiction, therefore the policies and approaches, as well as the resulting management decisions, may vary between jurisdictions. The guideline technical documents are intended to guide decisions by provincial, territorial, and local authorities that are responsible for the management of recreational waters.

This document focuses on the indicators of fecal contamination. For a complete list of the guideline technical documents available, please refer to the Guidelines for Canadian Recreational Water Quality summary document available on the website (in publication). For issues related to drinking water, please consult the Guidelines for Canadian Drinking Water Quality – Guideline Technical Document on Escherichia coli (Health Canada, 2020b) and Guidance on the use of Enterococci as an Indicator in Canadian Drinking Water Supplies (Health Canada, 2020a).

Using indicators of fecal contamination for recreational water quality management

This document outlines how indicators of fecal contamination can be used as one component of a preventive risk management approach alongside other activities, such as environmental health and safety surveys (EHSS) and, in some cases, microbial source tracking (MST) investigations. Recreational waters may be impacted by fecal material containing enteric pathogens from numerous sources, including discharged sewage, treated wastewater effluent, stormwater runoff from agricultural or urban areas, industrial processes, wild or domesticated animals and even fecal shedding by swimmers. The degree of risk from enteric pathogens varies between sources of fecal contamination, with sewage sources generally considered the most significant (in terms of the highest concentrations of infectious enteric viruses, bacteria and parasitic protozoa). Routine testing of recreational waters for pathogens is generally impractical, due to the variability in the types and quantities of pathogens present at any one time and the degree of difficulty associated with many of the detection methods. Consequently, as part of a risk management approach for recreational waters, authorities monitor for fecal indicators that are present in high numbers in both human and animal feces. Elevated numbers of these indicators in the aquatic environment are used to indicate fecal contamination and an elevated risk of illness.

Guideline values have been developed for Escherichia coli (E. coli) and enterococci. The values consider both the potential health risks associated with recreational activities and the benefits of recreational water use in terms of physical activity and enjoyment. These guideline values are considered to represent an acceptable level of risk for recreational activities for the general public.

E. coli and enterococci are recommended as primary indicators of possible fecal contamination and of potentially elevated gastrointestinal illness (GI) risk in recreational waters impacted by human enteric pathogens. Quantitative microbial risk assessment studies have shown that, similar to waters contaminated with human sewage, waters impacted by ruminants (for example, cattle feces) may also present a significant risk to human health. Recreational areas that are not impacted by human or ruminant fecal sources generally contain lower levels of human pathogens, compared to those impacted by human and ruminant feces, at similar levels of E. coli and enterococci. Detection of E. coli and enterococci at the guideline levels, in water sources that are not impacted by human and ruminant feces, may therefore represent a lower level of risk to human health. Alternative water quality criteria may be developed for these potentially lower risk recreational waters on a site-specific basis. However, care is needed to ensure that the risk of illness associated with any new criteria does not exceed the acceptable level of risk. Recreational area managers are encouraged to determine the sources of fecal contamination impacting a recreational water site. A variety of options are available, such as EHSS and MST methods, as well as alternative indicators, to determine the sources of contamination and the remediation priorities to improve the water quality for recreators.

More details on risk management of recreational water quality are available in the Guidelines for Canadian Recreational Water Quality – Guideline Technical Document on Understanding and Managing Risks in Recreational Waters technical document (Health Canada, 2023).

No single microorganism is able to fill all of the roles of what might be considered a perfect indicator of recreational water quality, one that models all of the known pathogens, provides information on the degree and source of fecal pollution and communicates the potential risk of illness for recreational water users. This would require multiple indicators, each with unique characteristics that enable them to perform specific roles (Ashbolt et al., 2001). Although E. coli and enterococci are the indicators routinely used for monitoring recreational beaches, there are limitations to the information provided by these microorganisms (see Significance of E. coli and enterococci in recreational waters). Other microorganisms have been widely discussed as alternatives to monitoring E. coli and enterococci or as supplementary indicators to better characterize potential risks. These include Bacteroides spp., spores of Clostridium perfringens, male-specific and somatic coliphages (bacteriophages infecting E. coli) and bacteriophages infecting Bacteroides fragilis. A summary of the characteristics of the recommended and potential indicator microorganisms is presented in Table 3.

The potential roles of these alternative indicators vary. For example, enteric viruses represent the most significant health risk in many recreational waters impacted by human fecal sources, and although E. coli and enterococci are good indicators of fecal contamination, they alone may not be adequate indicators of human enteric pathogenic viruses. Alternative indicators, such as the coliphages, bacteriophages of Bacteroides spp. or human sewage markers can provide additional information on the potential human health risks associated with a beach area (Nelson et al., 2018; Boehm et al., 2020). In addition, the fecal sources may not be known at many beaches and therefore the potential human health risks may not be fully assessed. As suggested in Applying the guidelines, the use of microbial source tracking markers from microorganisms such as the Bacteroides spp. can help provide valuable information on the sources of fecal contamination (Boehm et al., 2018). They may also help determine whether site-specific alternative guideline values would be beneficial. Risk-based threshold values have been proposed for fecal markers (for example, HF183) that target Bacteroides spp. (Boehm et al., 2018; Boehm and Soller, 2020). Further information on microbial source tracking and understanding and managing risks in recreational areas can be found in the guideline technical document on Understanding and Managing Risks in Recreational Areas (Health Canada, 2023).

Table 3. Characteristics of recommended and potential indicator microorganisms


Indicator microorganism



E. coli Enterococci C. perfringens Bacteroides spp. Coliphages Bacteriophages of Bacteroides spp.
Brief description Gram-negative, non-spore forming bacteria Gram-positive, non-spore forming bacteria; comprised of >30 species, E. faecalis and E. faecium more frequent in aquatic environments Gram-positive, spore-forming, anaerobic bacteria Gram-negative, non-spore-forming, anaerobic bacteria; dominant species - B. fragilis, B. vulgatus, B. distasonis and B. thetaiotaomicron Two main types (1) somatic – diverse group that can infect various members of Enterobacteriaceae family, and (2) male-specific (F+) coliphages Bacteriophage host strains most often used are for B. fragilis and B. thetaiotaomicron; crAssphage is a member of this group of bacteriophages
Includes members that are not human pathogens Yes Yes Yes Yes Yes Yes
Includes human pathogenic members Yes Yes Yes No No No
Found within the intestinal tract of humans and warm-blooded animals 107–109 cfu/g feces in humans; 103–109 cfu/g feces in animals human and animal feces contain 103–107 cfu/g

In humans: 103–108 cells/g feces;
In dogs, cats, sheep: 105–108 cells/g feces; always found in human sewage collection systems

1011 cells/g feces (except in some birds) In humans: 101–104 PFU/g feces; animals: <10–107 PFU/g feces; raw sewage 106 PFU/g, In human feces: 10–102 PFU/g feces, variable isolation; sewage: < 10–105 phages/100 mL; not detected in animals
Present in waters with recent fecal contamination at higher numbers than enteric pathogens Yes Yes Dependent upon source of contamination Insufficient data Dependent upon source of contamination. Dependent upon source of contamination
Capable of growth in the aquatic environment Yes, under specific conditions Yes, under specific conditions No No Somatic may grow if host bacteria is growing in the environment; F+ not likely to grow; appreciable regrowth is not expected for either No
Capable of surviving longer than pathogens Similar to bacterial pathogens Similar to bacterial pathogens Yes Insufficient data Similar to enteric viruses Similar to enteric viruses
Applicable to fresh, estuarine and marine waters YesFootnote 1 Yes Yes Yes Yes Yes
Exclusively associated with animal and human feces No No No Insufficient data. Yes Yes
Association between GI and the indicator Yes Yes Yes, although association weak in some studies Weak associations, more studies with human-specific marker (HF183) needed Yes No
Host-specific characteristics for microbial source tracking No No No Yes Maybe (for F+ coliphages) Maybe (some cross-reactivity reported)
Rapid, easy, inexpensive, culture-based method available Yes Yes Yes No Yes No
Well-established molecular method available NoFootnote 2 Yes Yes Yes No Yes
Currently suggested role Primary indicator Primary indicator Secondary indicator (for example, sewage inputs) Microbial source tracking; secondary indicator Secondary indicator (human fecal inputs); microbial source tracking Secondary indicator (human fecal inputs)
  • Dufour, 1984;
  • Edberg et al., 2000;
  • Solo-Gabriele et al., 2000;
  • Ashbolt et al., 2001;
  • Leclerc et al., 2001;
  • Wade et al., 2003;
  • Marion et al., 2010;
  • Byappanahalli et al., 2012b;
  • Ervin et al., 2013
  • Bartram and Rees, 2000;
  • Edberg et al., 2000;
  • Ashbolt et al., 2001;
  • Wade et al., 2003;
  • Wade et al., 2006;
  • Wade et al., 2008;
  • Verhougstraete et al., 2010;
  • Byappanahalli et al., 2012a;
  • Ervin et al., 2013;
  • Staley, et al., 2014
  • Fujioka and Shizumura, 1985;
  • Ashbolt et al., 2001;
  • Lipp et al., 2001;
  • Hörman et al., 2004;
  • Fernandez-Miyakawa et al., 2005;
  • Wiedenmann et al., 2006;
  • Carman et al., 2008;
  • Mueller-Spitz et al., 2010;
  • Wade et al., 2010;
  • Viau et al., 2011;
  • Vierheilig et al., 2013;
  • Jacob et al., 2015
  • Bernhard and Field, 2000a, 2000b;
  • Wade et al., 2006;
  • Hong et al., 2008;
  • Ballesté and Blanch, 2010;
  • Wade et al., 2010;
  • McQuaig et al., 2012;
  • Cao et al., 2016;
  • Lloyd-Price et al., 2016;
  • Hughes et al., 2017;
  • Napier et al., 2017
  • Cole et al., 2003;
  • Muniesa et al., 2003;
  • Luther and Fujioka, 2004;
  • Nappier et al., 2006;
  • Colford et al., 2007;
  • Wade et al., 2010;
  • Lee and Sobsey, 2011;
  • Wu et al., 2011;
  • Haramoto et al., 2012;
  • Plummer et al., 2014;
  • U.S. EPA, 2015;
  • Griffith et al., 2016;
  • Jofre et al., 2016;
  • Benjamin-Chung et al., 2017;
  • Jebri et al., 2017;
  • Nappier et al., 2019
  • Puig et al., 1999;
  • Mocé-Llivina et al., 2005;
  • Payan et al., 2005;
  • McLaughlin and Rose, 2006;
  • Ebdon et al., 2012;
  • Harwood et al., 2013;
  • McMinn et al., 2014;
  • Sirikanchana et al., 2014;
  • Stachler and Bibby, 2014;
  • Diston and Wicki, 2015;
  • McMinn et al., 2017;
  • Dias et al., 2018;
  • Korajkic et al., 2020
Footnote 1

E. coli should only be used in estuarine and marine waters if it has been demonstrated to provide comparable results to enterococci

Return to footnote 1 referrer

Footnote 2

A molecular method is in development

Return to footnote 2 referrer

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