Using Fecal Source Tracking to Detect and Identify Fecal Contamination and Protect Public Health

Clean water is fundamental to healthy communities, thriving ecosystems, and safe recreation. One of the greatest threats to water quality is contamination from fecal matter, which can carry harmful bacteria, viruses, and parasites. In this post, we provide an introduction to Fecal Source Tracking: what it is, how it’s done, and how it can be used to protect water quality and public health.  

What Is Fecal Source Tracking? 

Fecal Source Tracking is used to pinpoint the origin of fecal contamination. Potential sources include humans, livestock, wildlife, and pets. While all fecal contamination can create health issues, human fecal matter is considered the most dangerous as it can carry harmful pathogens like bacteria (e.g., E. coli, Salmonella, Shigella), viruses (e.g., norovirus, hepatitis A, rotavirus), and parasites (e.g., Giardia and Cryptosporidium). 

Fecal Source Tracking is a specialized subset within the broader field of Microbial Source Tracking, which encompasses analysis of a diverse range of microorganisms beyond those associated with fecal contamination. Examples include environmental bacteria (e.g., Pseudomonas, Legionella), cyanobacteria responsible for harmful algal blooms, industrially relevant microbes, and fungi or molds. Additionally, Microbial Source Tracking can be used to detect and identify antibiotic-resistant bacteria and microbes involved in natural or man-made pollution events, such as those originating from soil, decaying vegetation, wastewater effluent, or industrial runoff.  

How Fecal Source Tracking is Used 

Fecal Source Tracking is crucial across a variety of real-world scenarios in which identifying the origin of contamination can help inform effective remediation strategies.  

Recreational Water – Fecal Source Tracking is widely used to ensure public safety in recreational waters, including public beaches and swimming pools. Contamination in these areas can stem from a variety of causes, such as sewage overflows, urban runoff, and animal waste. 

Flood Remediation – Excessive precipitation and waterline breaks heighten the risk of sewage entering surface waters or stormwater systems. Fecal Source Tracking can rapidly detect the presence of fecal matter and identify its source, enabling emergency responders to issue the appropriate advisories, prioritize cleanup efforts, and prevent widespread outbreaks of waterborne diseases.  

It should be noted that many bacteria, viruses, and parasites found in fecal matter can survive on dry surfaces, sometimes for days, weeks, or even longer, depending on the organism and environmental conditions. Specialized swabbing techniques can be used to sample dried surfaces for fecal contamination. 

Sewage spills – Groundwater is a vital source of drinking water in many regions. When contamination occurs due to failing septic systems or leaking sewer lines, Fecal Source Tracking can determine the source and inform corrective actions.  

Agricultural runoff – Runoff from fields and pastures can also lead to groundwater contamination. Identifying human versus animal sources is essential for preventing long-term exposure to pathogens and ensuring regulatory compliance for drinking water safety. 

By applying Fecal Source Tracking methods to these scenarios, public health officials, environmental agencies, and water utilities can take precise, informed actions to safeguard both people and ecosystems against the risks posed by fecal contamination. 

Detecting Fecal Contamination  

Fecal indicator bacteria provide a better means of assessing the presence of fecal matter in recreational and drinking water. There are three main types: 

Enterococci are frequently used to monitor fecal contamination in both marine and freshwater environments. We are frequently asked to analyze for Enterococci in recreational water samples as this bacterium is strongly associated with gastrointestinal illness. However, because the Enterococcus bacterium is found in the digestive tract of both humans and animals, it cannot indicate the source of the contamination. 

Fecal coliforms are a broad group of bacteria that thrive in the intestines of humans and animals. As a category, they can indicate the presence of fecal matter, but do not provide clues to its source. In addition, despite the name, a few organisms in this category are found in the natural environment, so without more precise identification, fecal coliform testing is not a precise indicator of fecal contamination. Fecal coliforms are occasionally referenced in water quality regulations; however, testing for total coliforms and E. coli is more frequently mandated.

E. coli, a type of fecal coliform, is found only in the digestive system of warm-blooded animals, so it is one of the best indicator bacteria for fecal contamination. E. coli analysis is almost always the preferred analysis for freshwater samples, including drinking water and recreational water, as the infection rate and severity of illness can be greater than that of Enterococci. However, more advanced analysis is usually required to determine the source.

It should be noted that we also do a lot of testing for total coliforms in drinking water at Pace® as it is frequently required for water quality compliance and baseline safety. However, while total coliforms include bacteria found in the digestive tract, they also encompass species commonly present in soil, water, and vegetation that have no connection to fecal matter. Therefore, their presence alone does not necessarily indicate fecal contamination. 

Determining the Source of Fecal Matter 

As noted in the last section, fecal indicator bacteria are used to detect fecal contaminations, but they are not sufficient for determining the source of the contamination, i.e., human or animal.  

Bacteroides are a group of bacteria predominantly found in the intestines of warm-blooded animals. Unlike broad indicator organisms, Bacteroides species are highly host-specific, meaning certain strains are unique to humans while others are found only in particular animal species.  

This specificity allows scientists to use molecular techniques, such as quantitative PCR assays (qPCR), to detect and identify Bacteroides DNA from various sources. By targeting genetic markers unique to human-associated Bacteroides, researchers can pinpoint contamination events linked to sewage or failing septic systems. Likewise, animal-specific markers can reveal agricultural runoff or wildlife contributions.  

Safeguarding Water Quality Through Fecal Source Tracking 

Effective Fecal Source Tracking protects public health. By leveraging both traditional fecal indicator bacteria and advanced molecular tools, communities can better identify contamination sources and develop targeted solutions. For more information or to connect with a Pace® laboratory specializing in Fecal Source Tracking, please reach out to us.