Animal Waste, Water Quality and Human Health

288Animal Waste, Water Quality and Human Health8.2.3 Alternative or secondary indicators of faecalcontaminationSurvival rates of microbiological pathogens vary from organism to organismand are influenced by environmental conditions (see: Chapter 7). This paradigmalso holds true for pathogens associated with manure from domestic animalsand livestock (Pachepsky et al. 2006). As a result, a single indicator organism isunlikely to reliably predict the presence of all enteric pathogens for all typesof waters and faecal contamination associated with different hosts (Hörmanet al. 2004). The application of combined conventional and alternativeindicators and/or methods of detecting faecal contamination increases sensitivityand specificity and may enhance the ability to predict and reduce health riskassociated with the use of surface waters (Savichtcheva & Okabe 2006).Alternative or secondary indicators (see: Chapter 9) may include faecalanaerobes (Bacteriodales/ Bacteroides spp., Bifidobacterium spp. andClostridium perfringens), viral indicators (Bacteroides fragilis bacteriophageand F-specific RNA coliphage), chemical compounds (caffeine, opticalbrighteners and faecal sterols) and many other anthropogenic markers associatedwith human activity (Leeming et al. 1996, Calci et al. 1998, Gardinali &Zhao 2002, Scott et al. 2002, Hörman et al. 2004, Savichtcheva & Okabe2006, Schulz et al. 2006, Sobsey et al. 2006, Cao et al. 2009). Sourceattribution employing the combined use of traditional and secondary oralternative faecal indicators is often referred to as microbial source tracking(MST) (Bitton 2005).8.2.4 Source attribution (microbial source tracking, MST)In addition to alternative faecal indicators, MST is increasingly informed by the useof modern techniques taken from molecular biology, such as DNA fingerprintingby polymerase chain reaction (PCR), developing assay, or antigen electrochemicalrapid methods (Jones & Smith 2004, Ruecker et al. 2007). The aim of MST is toidentify the original host animal group(s) of faecal bacteria found in water. Forexample, this could be at the human or animal level (ruminant, non-ruminant),or to elucidate the contributions from specific animal groups for example, cow,sheep, dog, or avian species. A variety of faecal bacteria exist. Those typicallyused for regulatory purposes (e.g. E. coli or intestinal enterococci) have at leastsome properties of indicators, and as such allude to the possible presence ofpathogens. The only way to be certain that MST data relate directly to the faecalbacteria used for regulation would be to attribute those same bacteria to a hostsource. However, to date, methods to obtain MST information directly from