Animal Waste, Water Quality and Human Health

332Animal Waste, Water Quality and Human HealthHarwood 2007). These ideal conditions do not hold true for traditional FIOs and,potentially, for many of the alternative organisms employed in source attributiontechniques. It is, therefore, very important to understand the assumptions andlimitations associated with each faecal source tracking tool and its application.The issues of host-specific marker survival, correlation with FIOs andpathogens, and quantitative source detection are interrelated in these assumptions.Many source attribution methods have relied on library-dependent orlibrary-independent methods utilizing FIOs used for regulatory purposes such asE. coli and enterococci (reviewed in Simpson et al. 2002, Scott et al. 2002,Genthner et al. 2005, Field & Samadpour 2007, Stoeckel & Harwood 2007).Library-dependent methods are based on the development of a database ofisolates (usually bacterial) from known host sources. The isolates are typed(“fingerprinted”) by phenotypic or genotypic methods, and the patternsgenerated make up the library. Isolates from the environmental samples aresubsequently typed and compared to the library by a variety of statisticalmatching methods (Wiggins 1996, Hagedorn et al. 1999, Parveen et al. 1999,Harwood et al. 2000, Harwood et al. 2003, Ritter et al. 2003, Stoeckel et al.2004). The database of DNA fingerprints from known sources is frequentlyconstructed through the collection of geographically-related isolates, that is,local human sewage, ruminant manure, and wild or urbanized faecal samplesfrom a variety of animal populations. Therefore, by their very nature,library-dependent methods are limited by the strength of the library and itsrelevance to the water body under investigation (Wiggins et al. 2003, Mooreet al. 2005). While employed with some success, libraries based on phenotypicor genotypic characteristics of FIOs (such as antibiotic resistance) are subjectto cross-reactivity between co-habitating species. Therefore, whilelibrary-dependent MST methods may be useful in determining pollutant sourceswithin a suite of monitoring techniques, quantitative assumptions and the costsassociated with assembling a library with sufficient assembly size and scope toassign a host source with some degree of certainty must be considered (Stewartet al. 2003).Because of the limitations imposed by library-dependent methods that rely ontyping cultured FIOs, alternative methods focusing on different faecal (bacterial)groups, such as the Bacteroidetes (or Bacteroidales), have been explored(Bernhard & Field 2000b, Field et al. 2003, Shanks et al. 2010). Otheralternative targets include Brevibacterium for poultry faeces (Weidhaas et al.2010) and viruses such as polyomaviruses (McQuiag et al. 2006, Hundesa et al.2009). The use of MST targets other than regulatory FIOs introduces anadditional level of uncertainty due to the already uncertain relationship betweenthe marker-carrying organisms, FIOs and pathogens. The ecology of many