Due to the high cost of analysis, the routine monitoring of manures or surface waters for specific pathogens is prohibitively expensive. Consequently, “indicators” of fecal contamination, such as fecal coliform bacteria, Escherichia coli, and/or Enterococcus are routinely used to assess contamination. However, the reliability of these “indicator” assays is limited. One reason for their limitation is that they cannot distinguish between the different sources of microbial contamination (e.g., cattle manure versus wildlife feces). Although methods are currently being developed to differentiate one source from another (known as source tracking), they have yet to be thoroughly validated. In addition, no established correlations exist between any of these “indicators” and any specific pathogen/parasite. Consequently, there are no simple or easy methods for determining the extent or source(s) of pathogen contamination. The only way to ensure that manures are not a source of pathogens is to employ various treatment practices that have been documented to destroy pathogens, e.g., composting or anaerobic digestion. Additional Reading Waterborne Pathogens in Agricultural Watersheds, USDA Watershed Science Institute Technical Note 2, http://forestry.berkeley.edu/rangelandwq/pdfs/Atwillwssitn21.pdf

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