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Bacterial Pathogen Genes in Streams related to Animal Type and Hydrologic Conditions

USGS scientist taking measurements of field parameters in a stream
The team of USGS scientists collected stream water samples before and after rainfall events for this study. In this photo a USGS scientist is taking measurements of field parameters (dissolved oxygen, water temperature, specific conductance, and pH) from New York Branch, Iowa, at low flow (baseflow) conditions. Photo Credit: Dana W. Kolpin, USGS.
A USGS scientist is getting ready to measure discharge in a stream
In this photo the USGS scientist is getting ready to measure discharge (flow) in the same stream as above (from New York Branch, Iowa), but after a rainfall event. Photo Credit: Dana W. Kolpin, USGS.

A U.S. Geological Survey (USGS) study elucidates the influence of animal type and environmental variables on bacterial pathogen occurrence in streams under typical watershed conditions.

In the United States, pathogens are a commonly reported stream impairment; however, pathogen impairment is assessed not by evaluating actual pathogens but by determining whether the concentration of fecal indicator bacteria (FIB) is acceptable with regard to applicable water standards. Although FIB provide a simple and inexpensive test, they do not indicate the source of pollution, have no specific relationship to pathogens, and unless epidemiological studies are performed, do not indicate health risk.

What They Did

Scientists measured pathogenic genes (shiga-toxin producing and enterotoxigenic Escherichia coli (E. coli), Salmonella, Campylobacter, and pathogenic and vancomycin-resistant enterococci) and fecal indicators (FIB, cholesterol, coprostanol, and hormones) in manure, stream water, and stream sediment samples to understand the occurrence, fate, transport, survival, and environmental sources of pathogens in 19 small watersheds in 12 U.S. States with either no major animal agriculture, or predominantly beef, dairy, swine, or poultry.

What They Determined

Scientists determined that the number and type of pathogenic genes differed among animal types and in stream water influenced by those wastes. The number of pathogen genes in manure was largest in, in descending order, dairy, beef, swine, and poultry. Stream water samples were influenced most by animal type, by local factors such as whether animals had stream access, and by the occurrence and degree of rainfall events. The occurrence of pathogen genes observed in this study is within the ranges of other watershed studies and indicates that pathogens are not typically ubiquitous in stream water or streambed sediment; however, many genes were from viable organisms, including several (shiga-toxin producing or enterotoxigenic E. coli, Salmonella, and vancomycin-resistant enterococci) that could potentially affect either human or animal health. There was no association between the total number of pathogen genes and any fecal indicator in samples collected during dry conditions; however, for samples collected post-rainfall, the number of pathogen genes detected was significantly correlated with cholesterol, coprostanol, and marginally with some FIB concentrations.

Environmental Health Considerations

This study provides specific data on pathogenic genes associated with animal types and insights into the influence of animal agriculture on stream water quality. The results indicate that pathogen gene profiles offer the potential to address both the source of and the human and ecological risks associated with fecal pollution. The inclusion of animal-specific genes, indicating the presence of pathogens, adds to the body of knowledge by providing information on potential health risks.

The study was supported by the USGS Toxic Substances Hydrology Program.


Haack, S.K., Duris, J.W., Kolpin, D.W., Focazio, M.J., Meyer, M.T., Johnson, H.E., Oster, R.J., and Foreman, W.T., 2016, Contamination with bacterial zoonotic pathogen genes in U.S. streams influenced by varying types of animal agriculture: Science of the Total Environment, v. 563–564, p. 340-350, doi:10.1016/j.scitotenv.2016.04.087.

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