Microbial source tracking: a forensic technique for microbial source identification?

Abstract

As the requirements of the Water Framework Directive (WFD) and the US Clean Water Act (USCWA) for the maintenance of microbiological water quality in 'protected areas' highlight, there is a growing recognition that integrated management of point and diffuse sources of microbial pollution is essential. New information on catchment microbial dynamics and, in particular, the sources of faecal indicator bacteria found in bathing and shellfish harvesting waters is a pre-requisite for the design of any 'programme of measures' at the drainage basin scale to secure and maintain compliance with existing and new health-based microbiological standards. This paper reports on a catchment-scale microbial source tracking (MST) study in the Leven Estuary drainage basin, northwest England, an area for which quantitative faecal indicator source apportionment empirical data and land use information were also collected. Since previous MST studies have been based on laboratory trials using 'manufactured' samples or analyses of spot environmental samples without the contextual microbial flux data (under high and low flow conditions) and source information, such background data are needed to evaluate the utility of MST in USCWA total maximum daily load (TMDL) assessments or WFD 'Programmes of Measures'. Thus, the operational utility of MST remains in some doubt. The results of this investigation, using genotyping of Bacteroidetes using polymerase chain reaction (PCR) and male-specific ribonucleic acid coliphage (F + RNA coliphage) using hybridisation, suggest some discrimination is possible between livestock- and human-derived faecal indicator concentrations but, in inter-grade areas, the degree to which the tracer picture reflected the land use pattern and probable faecal indicator loading were less distinct. Interestingly, the MST data was more reliable on high flow samples when much of the faecal indicator flux from catchment systems occurs. Whilst a useful supplementary tool, the MST information did not provide quantitative source apportionment for the study catchment. Thus, it could not replace detailed empirical measurement of microbial flux at key catchment outlets to underpin faecal indicator source apportionment. Therefore, the MST techniques reported herein currently may not meet the standards required to be a useful forensic tool, although continued development of the methods and further catchment scale studies could increase confidence in such methods for future application.

Quantitative catchment profiling to apportion faecal indicator organism budgets for the Ribble system, the UK's sentinel drainage basin for Water Framework Directive research

“…However, the use of chemical or microbial tracers is limited to following only a limited number of inputs at any one time whilst faecal pollution source tracking techniques are relatively new, no standard methods have yet been proposed, sample analysis is often complicated and requires costly analytical equipment and many techniques require reference libraries. The application of these latter methods on a catchmentwide basis is still uncertain and more comparison studies are required in order to determine which methods are best suited to catchment scale studies (Meays et al, 2004;Stapleton et al, 2007).…”

Discrimination of Viable and Dead Fecal Bacteroidales Bacteria by Quantitative PCR with Propidium Monoazide

“…In a recent watershed study, MST data using qualitative (presence/absence) markers of bovine-specific (CF128) and human-specific (HF183) Bacteroidales genotypes were more reliable on high-flow samples with higher concentrations of culturable fecal indicators and could not discriminate precisely between livestock-and human-derived feces in the larger land use pattern (17). The reason for this outcome may have been the use of nonquantitative MST data and/or the presence of free DNA or extracellular DNA, which can persist in marine water, freshwater, and sediment for up to 55 days, 21 days, or 40 days, respectively (6).…”

Spatial and temporal heterogeneity of bacteria across an intertidal shellfish bed: Implications for regulatory monitoring of faecal indicator organisms

“…Current routine monitoring protocols discourage sampling during the same tidal state, instead suggesting a minimum of seven days between sampling events, a procedure that is supported by our study (Anon, 2014). Sporadic and unpredictable rainfall events however, probably influence the concentrations of bacteria in shellfish harvesting waters more than tidal state alone, by increasing the levels of agricultural run-off and potential for partially treated sewage entering the sea (Henroth et al, 2002;Stapleton et al, 2007;Laws et al, 2008;Kay et al, 2005). …”

“…Subsequently, the classification grade assigned to an individual shellfish bed impacts not only consumers, but also the shellfish industry, as it dictates the level of post-harvest treatment required for shellfish products at each classification grading, and could promote either a change in management practice or a temporary closure of the harvesting area. Previous research has shown that environmental factors such as seasonality, tidal state and rainfall events may alter concentrations of E. coli detected within shellfish tissues and hence affect the classification assigned to a harvesting area (Stapleton et al, 2007;Riou et al, 2007;Kay et al, 2008a). Subsequently, the classification assigned to each shellfish harvesting area has substantial socio-economic implications (e.g.…”