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Are Fecal Indicator Bacteria Effective Indicators of Chemical and Pathogenic Contaminants Associated with Human and Animal Waste?

USGS scientist prepares to analyze bacterial DNA extracted from water samples
USGS scientists use a variety of microbiological and chemical methods to evaluate the microbiological quality of water. In this photo, a USGS scientist prepares to analyze bacterial DNA extracted from water samples.

U.S. Geological Survey (USGS) scientists have evaluated 100 chemical indicators (including human and veterinary pharmaceuticals, personal care products, and other organic wastewater chemicals) and multiple gene-based indicators of fecal contamination for their effectiveness in providing an early warning of human or animal fecal contamination in drinking water sources. The scientists analyzed water from 18 public drinking-water sources (samples collected at the point of intake and before treatment) in the United States. The study was conducted in collaboration with the USGS source-water reconnaissance, which explored the presence and magnitude of emerging contaminants in surface water and groundwater used as drinking water in 25 States across the Nation.

The genes in bacterial DNA that the scientists tested include the esp gene (which indicates human-pathogenic enterococci) and nine genes associated with various animal sources of shiga toxin-producing Escherichia coli (STEC). STEC is a type of bacteria that can cause human illness ranging from mild intestinal disease to severe kidney complications. One or both of the gene- or chemical-based indicators were detected in 14 of 18 samples that tested positive for fecal indicator bacteria (specifically, fecal coliform). Total Escherichia coli (E. coli) concentrations, another indicator of the presence of pathogenic E. coli, were not consistent with the presence of fecal-source chemicals or genes. In samples from 13 drinking water sources with the lowest (<50 per 100 milliliter (mL)) E. coli concentrations, human pharmaceuticals or other chemical indicators of wastewater treatment plant effluent occurred in six, veterinary antibiotics were detected in three, and stx1 or stx2 genes (indicating varying animal sources of STEC) were detected in eight. Only one of the targeted STEC genes (the eaeA gene) consistently occurred in samples with fecal indicator bacteria. The analyses from this study demonstrate that standards for fecal indicator bacteria are not consistent with the occurrence of chemical indicators of fecal contamination or with genetic indicators of human pathogenic bacteria. The study emphasizes the potential use of gene- and chemical-based tests as indicators of specific contaminant sources and reflects the ongoing need for more robust and precise indicators of pathogenic and chemical contaminants in water used for drinking water and recreation.


Haack, S.K., Duris, J.W., Fogarty, L.R., Kolpin, D.W., Focazio, M.J., Furlong, E.T., and Meyer, M.T., 2009, Comparing wastewater chemicals, indicator bacteria concentrations, and bacterial pathogen genes as fecal pollution indicators: Journal of Environmental Quality, v. 38, no. 1, p. 248-258, doi:10.2134/jeq2008.0173.

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