Bacteria: Fecal Indicator Bacteria

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E. Coli Bacteria; Photo source:
Enterococcus Faecium Bacteria on Human Skin; Photo Source:


When we think of bacteria, especially with respect to beach water quality, we are usually concerned about the bacteria that cause infections and disease. In order to determine if a beach or waterway is safe to recreate in, state agencies and other water testing programs measure concentrations of fecal indicator bacteria present in water. The actual disease-causing agents (pathogens) are typically not analyzed because

  • there are many different types of pathogens that could potentially be in the water,
  • the difficulty and expense of analysis,
  • and the very low concentration of some pathogens in water, such as viruses, that can cause disease.

This article discusses fecal indicator bacteria, which may or may not be pathogenic (cause disease), but whose presence in water has been correlated with the presence of other bacteria, viruses, or protozoa that do cause disease. An ideal fecal indicator bacteria is one that is:

  • directly correlated with human illness,
  • survives in the environment for approximately as long as pathogens do (doesn’t die off quickly),
  • and is easy and inexpensive to detect.

Historically, several groups of bacteria have been used for water quality monitoring, including total coliform, fecal coliform, E. coli, and enterococcus. Common sources of fecal pollution include stormwater runoff, pets, wildlife, agriculture, and human sewage. If high concentrations of feces are present in recreational waters, and are ingested while swimming or enter the skin through a cut or sore, they may cause human disease (primarily gastroenteritis), infections, rashes, or worse. High concentrations of fecal indicator bacteria point to possible fecal pollution in a waterway or beach.Therefore, the public should not recreate in waterways where fecal indicator bacteria levels surpass state health standards. To see what your state’s health standards are, and what agency is monitoring your local beaches, refer to this resource.

Total Coliforms

Total coliforms are a group of bacteria that occur naturally in soils, plants, and in the intestines of warm-blooded animals. This group of bacteria was used as a bacterial indicator as early as the 1920’s, but because they can originate from both fecal and non-fecal sources, their correlation with human illness is not well established. Therefore, total coliform concentrations are no longer considered useful as an indicator for monitoring recreational waters; however, they are still used to measure the safety of drinking water, because their presence indicates contamination of the water supply from an outside source.

Relationships of fecal indicator bacteria

Fecal Coliform Bacteria

Fecal coliforms are a subset of coliform bacteria that are found primarily in the intestinal tracts of mammals and birds. These bacteria are released into the environment through human and animal feces, although some non-fecal sources of fecal coliforms do exist. Fecal coliforms, like total coliforms, were used as bacterial indicators since the 1920’s; however, fecal coliforms are more closely correlated with human health risk, since they are more likely to enter the environment through human or animal waste. Fecal bacteria were the primary indicator bacteria for monitoring recreational waters until epidemiological studies showed an even closer correlation for E. coli and enterococcus with human illness. In 1986, the Environmental Protection Agency (EPA) began recommending E.coli and enterococcus as superior indicators of human health risk in recreational waters. After the passage of the federal BEACH Act of 2000, all states were required to start using public health standards based on either E. coli or enterococcus (described below) in recreational waters, in order to receive federal grant monies through the EPA. Some states do continue to measure fecal coliforms, but typically as a measure of safety for shellfish harvesting areas. 

E. coli

One species of fecal coliform is the infamous Escherichia coli (E. coli) bacteria, which is commonly found in the intestines of warm-blooded animals and humans. In addition to E.coli, a number of other bacteria comprise the fecal coliform group. In other words, E. coli is not a direct substitute for fecal coliform monitoring, and can comprise anywhere from 5% to 90% of the fecal coliform in the water.

E.coli serves as a more useful fecal indicator bacteria in recreational waters compared to fecal coliform because it correlates with human recreational water illnesses. In 1986, the EPA conducted epidemiological studies and found that E.coli and and enterococcus reliably correlated with human gastrointestinal illness in fresh waters. If there are high concentrations of E.coli in a waterway, that is a strong indication of recent sewage pollution or animal waste contamination and the resulting risk to public health.


The enterococcus group is a subgroup of fecal streptococci bacteria. Similar to E. coli, enterococcus is a fecal indicator bacteria that naturally occurs in the intestines of warm-blooded animals (mammals and birds). Enterococcus is frequently used to measure recreational water safety across the country and around the world, because it serves as a proxy, or an indicator, for fecal contamination. According to studies conducted by the EPA, enterococci have a greater correlation with swimming-associated gastrointestinal illness in both marine and fresh waters than other bacterial indicator organisms, and are less likely to "die off" in saltwater.

In 1986, EPA established national recommendations for, health-based recreational water quality criteria that included a single sample maximum of 104 colony forming units (CFU) per 100 milliliters (ml)water sampled. In late 2012, EPA published new Recreational Water Quality Criteria Guidance that maintained enterococcus as the preferred indicator bacteria, but allowed states to choose different thresholds values based on varying degrees of public health risk. This is why different states currently use different water quality criteria to issue swim advisories and make decisions to open or close beaches.

Surfrider's Blue Water Task Force performs beach water quality testing for enterococcus, using IDEXX's Enterolert method, to evaluate the levels of these indicator bacteria in recreational waters. Note: The IDEXX tests report results as Most Probable Number (MPN) per 100 ml, which is equivalent to CFU per 100 ml. Results are shared online, with local communities, and with local water quality testing agencies to raise awareness of local pollution problems, and to bring communities together to implement solutions.

It is important to note that enterococcus and other fecal indicator bacteria can also sometimes be present naturally in the environment, without obvious sources of fecal pollution in a watershed. In some instances, enterococcus colonies can grow in warm, moist soils of tropical areas or in the seaweed wrack line during the hot summer season of temperate beaches, long past any initial contamination event. More research is needed to better understand the impacts of these natural processes on recreational water quality and public health risk, but health authorities continue to rely on concentrations of these bacteria in beach water to make decisions to protect public health because of the proven close association with human illness.

To learn more about enterococcus bacteria, click here.

Learn More

To learn about enterococcus and E.coli bacteria monitoring in coastal states, including which bacteria thresholds are used to determine beach water quality safety, check out Beach Water Quality Monitoring Programs in Coastal States. Also, see these articles on Epidemiological Studies, Health Threats from Polluted Coastal Waters, Environmental Protection Agency's (EPA) Fecal Bacteria article and University of Rhode Island Watershed Watch Bacterial Monitoring.

This article is part of a series on Clean Water which looks at various threats to the water quality of our oceans, and the negative impacts polluted waters can have on the environment and human health.

For information about laws, policies, programs and conditions impacting water quality in a specific state, please visit Surfrider's State of the Beach report to find the State Report for that state, and click on the "Water Quality" indicator link.