Animal Waste, Water Quality and Human Health

Indicators, sanitary surveys and source attribution techniques 335as E. coli and enterococci sometimes demonstrate a lack of correlation to eachother as well as to pathogens such as Salmonella spp., Campylobacter spp.,human viruses and coliphages (Savichtcheva & Okabe 2006, Field &Samadpour 2007). These examples are likely to reflect differential survivalbetween pathogens and FIOs, and their different distributions in hostpopulations. A study by Weaver et al. (2005) of E. coli and enterococci infresh and dry cow, sheep and horse manure demonstrated this phenomenon andconfirmed the results of a previous source-tracking proficiency study targetingE. coli and enterococci levels in faecal samples from a number of host species(Field 2004).9.4.4 Quantification of source specific markersAdvancements have been made in the field of source attribution and the ability tonot only assign a host source but to quantify those host-specific markers usingtechniques such as nucleic acid sequence-based amplification (NASBA) andquantitative real-time PCR (QPCR) (Dick & Field 2004, Choi & Jiang 2005, He& Jiang 2005, Gregory et al. 2006, Layton et al. 2006, Ogorzaly & Gantzer2006, Reischer et al. 2006, Khan et al. 2007, Kildare et al. 2007, Kirs & Smith2007, Okabe et al. 2007, Rajal et al. 2007a, Wolf et al. 2007, Caldwell &Levine 2009, Hundesa et al. 2009, McQuaig et al. 2009, Mieszkin et al. 2009a).For example, a QPCR method for detecting poultry (chickens and turkeys)pollution was developed based on a Brevibacterium avium-like 16S rRNA genesequence (MacBeth et al. 2008, Weidhaas et al. 2010). The marker was detectedin poultry faeces, poultry litter, soil on which litter had been spread and insurface waters close to areas where poultry litter was applied to the land. Aswith qualitative techniques, result interpretation may not be straightforward.Assumptions underlying quantitative source detection include (1) host-specificmarkers have similar environmental survival rates, fate and transport, (2) eachspecies sheds a similar amount of its host-specific marker, and (3) eachhost-specific marker has a similar prevalence and proportional distributionamong individuals within the species.Leach et al. (2008) used a modelling approach to test the effects of multiplevariables on the quantitative abilities of source tracking including: prevalenceor amounts of host-specific markers among individuals of the same species;specificity of markers; proportions of markers shed by different species;proportion of faecal contamination in the environment; decay rates; andevenness of environmental distribution on the ability of quantitative sourcetracking to correctly estimate relative contributions from different sources andthe percentage error likely to result from each of these factors in quantitative