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Using E. Coli Like a Fingerprint

Updated: Apr 20, 2022

Escherichia coli (E. Coli) can live in surface waters like streams and lakes where they can make swimmers, boaters, and anglers sick. While these bacteria can be very common, finding where they come from can help understand how to make water cleaner.

Why look for E. coli?

These bacteria are a common disease causing agent, and are a good indicator of water where disease causing agents may be more common. Traditionally, recreational use sampling of streams, pools, and lakes consists of collecting a few ounces of water from the water source and growing up cells in a lab using food the E. coli need to grow. These bacteria grow in a cluster of cells called colonies. When over 200 colonies of these little bacteria are grown from just a single milliliter of water it indicates that the water is more likely to make you sick.

How do E. coli get in the water?

Did you know that E.Coli live in your gut? Yep it's true. These little bacteria that can make you sick live inside you, your neighbor, your dog, the song bird on the telephone wire, and in livestock like cows, pigs, and poultry. Although E. coli can live in surface soils, high concentrations of E. coli generally enter the waterway through untreated sewer water, flood water, agriculture practices, or from leaky septic systems. In 2008 The EPA estimated that 23% of U.S. waterways are impaired by bacteria, and further estimate that 40% of streams are impaired for nutrients that can promote E. coli growth meaning there is a growing potential that future streams may continue to be impaired. The threat of bacterial contamination continues to plague recreational safety, and identifying sources of bacteria contamination can be important for generating cleaning water sources.

Thankfully we can identify sources!

Turns out the E.Coli living in your gut are unique to people! Neat right?! It gets better. The E.Coli in pigs, sheep, cows, horses, and birds are all unique to them too! So now with a special technique called qPCR quantitative polymerase chain reaction that allow differences among E. coli DNA to be used to determine where the E. coli originates from. This means that we can find out what is making the water polluted and potentially offer solutions to fix the problem!

What is being done to clean up E. coli in streams?

With the aid of several agencies and organizations farmers have been establishing fencing along streams, increasing stream vegetation, installing animal crossings, and optimizing their management of animal waste. Cities have been improving sewer infrastructure to decrease discharges of untreated water, and improvements to permitting and inspections have improved the overall quality of private septic systems.

To learn more about agriculture resources available to reduce animal fecal waste in streams and promote healthy stream banks visit the NRCS/USGS website.

For more details on national water quality you can view this EPA report

Deshmukh, Rehan A et al. “Recent developments in detection and enumeration of waterborne bacteria: a retrospective minireview.” MicrobiologyOpen vol. 5,6 901-922. 10 Jul. 2016, doi:10.1002/mbo3.383 (

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