Page 15: Guidelines for Canadian Recreational Water Quality – Third Edition

Part II: Guideline Technical Documentation

10.0 Faecal pollution source tracking


A wide variety of faecal sources are capable of contaminating recreational waters. Faecal pollution can come from sewage treatment plant effluents, stormwater and combined sewer overflows, faulty or improperly designed septic tanks, improper farming practices, intensive livestock and poultry operations, local wildlife (e.g., geese and gulls) and even recreational water users themselves. Understanding the specific sources of faecal contamination can help to assess public health risks and target appropriate risk management barriers. These, in turn, can reduce beach postings and prevent potential waterborne disease outbreaks.

Faecal source tracking can be performed by a variety of chemical and microbiological methods.

Chemical methods

Numerous chemical compounds have been investigated as potential markers for human sources of faecal pollution. Chemical methods of analysis are based on the detection of chemical compounds known to be present in faecal material as a result of human activities--either through consumption and/or metabolism and the subsequent excretion in faeces, or via disposal as sewage wastes. Caffeine, detergents, laundry brighteners, fragrance materials, faecal sterols and faecal stanols have been proposed as markers of faecal pollution from sewage treatment plants (Glassmeyer et al., 2005). Chemical tracers such as dyes have also been used to confirm suspected point sources of contamination, such as wastewater outfalls. A noted advantage of using chemical markers is that the time required for analysis is shorter than that for many microbial methods. There are still a number of information gaps regarding the use of chemical markers in terms of presence and fate in the environment and the sensitivity of the detection methods. More research is currently needed to clarify some of the uncertainties surrounding their use as potential faecal source indicators.

Microbial methods

Microbial source tracking (MST) is an emerging field. Methods are based on comparing the similarity of microorganisms in water samples with those from known faecal sources to make inferences about the source of faecal pollution. In recent years, a growing number of microbiological methods have been developed (Scott et al., 2002; Simpson et al., 2002; Meays et al., 2004; Edge and Schaefer, 2006). Consequently, more attention has been focused on microbial methods than on chemical methods.

Microbial methods can be divided into library-dependent and library-independent methods. To date, library-dependent methods have been more widely used in microbial source studies, although library-independent methods are increasingly under investigation. Library-dependent methods are based upon choosing a faecal indicator microorganism (e.g., E. coli or enterococci) and establishing a reference library of characteristics of individual isolates obtained from known faecal pollution sources. For example, a library could be a database of antibiotic resistance profiles or DNA fingerprints of E. coli isolates obtained from animal faeces and municipal wastewater effluent (Wiggins, 1996; Dombek et al., 2000; Carson et al., 2001). The similarity of the profiles or fingerprints of E. coli isolates obtained from recreational waters ("unknowns") can then be compared with the profiles or fingerprints in the library ("knowns") to make statistical inferences about the source of the waterborne E. coli isolates.

Library-independent methods are based upon detecting host-specific markers to indicate the presence of faecal contamination from a specific human or animal host in the water. Most library-independent methods rely on PCR to detect the host-specific markers in water samples. Host-specific markers may be such things as toxin genes (Khatib et al., 2002, 2003), genes for virulence factors (Scott et al., 2005) or highly conserved DNA sequences (Bernhard and Field, 2000a). Some of the most promising results to date for developing host-specific markers for faecal pollution source tracking involve 16S rDNA markers within the genus Bacteroides. These anaerobic bacteria comprise a very large portion of the faecal flora in warm-blooded animals. Bernhard and Field (2000b) developed Bacteroides 16S rDNA PCR assays specific to ruminants and humans, and such assays have been applied successfully to MST studies in recreational waters (Boehm et al., 2003; Bower et al., 2005; Noble et al., 2006).

An important aspect of MST has been discriminating between human and animal faecal contamination. This is because faecal pollution from a human source (e.g., sewage) may present human health risks different from those associated with faecal pollution from animal sources. Viruses that infect humans are more likely to occur in human faecal wastes. However, wildlife species can carry pathogens such as Campylobacter, Cryptosporidium and Giardia, which can pose a risk to human health.

Studies in the late 1990s had raised considerable expectations for microbial source tools to resolve problems in faecal pollution source identification. Recent publications (Griffith et al., 2003; Stoeckel et al., 2004) have pointed out some of the limitations associated with the use of microbial methods. Library-based methods require very large reference libraries and can have high misclassification rates. Non-library-based methods currently suffer from gaps in the information on the host specificity of the markers. Additional research is required to understand more fully the advantages and limitations of MST methods.

Current state of the science

Current thinking is that while many methods exist in the current MST toolbox, there is no universally accepted best method. While some methods have achieved a level of maturity where they could be considered for standardization, others are still experimental or research-grade tools (Edge and Schaefer, 2006). It is further felt that with any MST study, it is advisable to have multiple lines of evidence before making inferences about sources of faecal contamination.

Some recent MST studies have been perceived to have placed a "wet blanket" on the field by illustrating some of the significant challenges associated with these types of undertakings. These include the high costs of analysis and the difficulties encountered when using these technologies in watersheds that have numerous faecal sources. Nevertheless, there have been successful applications of MST in field studies. MST methods have been used to identify unexpected faecal pollution sources, to verify information from other lines of evidence, to resolve local beach closure problems involving limited contamination sources and to break down large source tracking problems into more manageable studies. Edge and Hill (2007) demonstrated the application of two library dependent MST methods for determining that bird droppings, rather than municipal wastewater, were the primary source of faecal pollution responsible for beach postings in Hamilton Harbour.

The field of MST is still evolving, and the MST toolbox is getting better. Novel molecular tools such as DNA microarrays (Hamelin et al., 2006; Soule et al., 2006) and protozoan genotyping methods (Jiang et al., 2005; Ruecker et al. 2007) could lead to the identification of new host-specific DNA markers. Other tools based on DNA markers for host cells in faeces may also prove useful for faecal pollution source tracking in the future (Martellini et al., 2005).

Application of microbial source tracking

MST studies can be expensive and time-consuming. As well, the current state of the science is such that the methods may not be able to completely resolve all of the sources contributing to the faecal contamination of the watershed and the recreational water area.

A good understanding and formulation of the nature of the faecal contamination problem are required before considering the need for an MST study. The Environmental Health and Safety Survey is a useful tool and an important first step for helping recreational water area operators, service providers and local authorities identify the sources of contamination that are relevant to their recreational water area.

At present, it is not possible to recommend a standard faecal source identification approach and method that would be applicable to any situation in recreational waters. The decision of which MST method to use will be influenced by factors such as the potential complexity and number of faecal pollution sources, the geographic and temporal considerations for the study area, and the available funds, equipment and expertise to conduct the study. For individuals wishing to pursue this approach, some guidance for the selection of an appropriate MST approach can be found in publications from the U.S. EPA (2005b) and the U.S. Geological Survey (Stoeckel, 2005).

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