Identify Sources of Fecal Contamination using Molecular (DNA) Approaches

Many surface waters and beaches do not meet water quality standards due to elevated levels of fecal indicator bacteria (e.g. E.coli). Microbial source tracking employing DNA based methods can aid in identifying sources of fecal pollution so that control measures can be implemented to protect our waters.

More than 30 years after the Clean Water Act, approximately 13% of US surface waters are included on the 303(d) list of impaired waters and beach closures and advisories exceeded 20,000 days in each of the past 4 years with more than 60% caused by fecal pollution. The problem continues due to the inability of traditional methods to identify fecal contamination sources so that control measures can be promptly implemented.

In a typical watershed, contamination of surface waters can stem from a myriad of potential point and non-point sources containing fecal material from:

  • humans (sewer leaks, sanitary sewer overflows, septic system failures, stormwater),
  • dogs and other domestic animals (stormwater, urban runoff),
  • livestock (confined animal feeding operations), and
  • wildlife

Traditionally, water quality has been assessed by cultivation-based enumeration of fecal indicator bacteria such as fecal coliforms and E. coli. Monitoring fecal indicator bacteria can identify impaired waterbodies and aid in protecting human health. However, traditional approaches have no real diagnostic power to identify the source of fecal pollution and direct corrective actions to improve water quality. Recognition of the limitations of traditional culture-dependent methods and indicator organisms has spawned an entire field of study termed microbial source tracking (MST) which employs cultivation-independent methods to not only assess water quality more accurately but also to identify the source of fecal contamination.

Microbial Insights (MI) has developed and licensed quantitative polymerase chain reaction (qPCR) assays for microbial source tracking of fecal contamination of surface waters. PCR is a molecular method in which a specific gene can be amplified permitting detection and quantification of a target DNA marker in a mixture of non-target DNA sequences. Since the target DNA can be extracted directly from environmental samples, cultivation of the indicator organism is not required thus eliminating culture bias while providing rapid detection with greater sensitivity and throughput.

Microbial Source Tracking Services include:

Currently, MI is offering MST CENSUS assays for water contamination testing.


MI Code 

  Relevance / Data Interpretation

General BacteroidesGenBACOne of the prominent bacterial groups inhabiting the intestinal tracts of warm blooded animals including humans, cattle, swine, horses, and dogs. Quantification of total Bacteroides provides a general indicator of fecal contamination.
Total EnterococcusTENTEnterococci, a subset of fecal streptococci, are found in the feces of all warm blooded animals and are believed to have higher survival rates in water than fecal coliforms.  As with total Bacteroides, the total Enterococcus assay provides a general indicator of fecal contamination.
Total E. ColiTECOLIThe total E. coli assay also provides a general indicator of fecal contamination.
Human BacteroidesHBACQuantification of genetic markers of fecal Bacteroides from humans.
Ruminant BacteroidesBACRQuantification of two genetic markers of fecal Bacteroides from a variety of grazing animals.
Canada Goose BacteroidesCGBQuantification of two genetic markers of fecal Bacteroides from Canada Geese.
Dog BacteroidesDBACQuantification of a genetic marker of fecal Bacteroides from dogs.
Seagull CatellicoccusGULLQuantification of a genetic marker of Catellicoccus marimammaliumshown to be an indicator of gull fecal contamination.
Human PolyomavirusHPyVsEvidence indicates that more than 70% of humans harbor and shed polyomaviruses in their urine.

CENSUS – Based on quantitative polymerase chain reaction (qPCR), CENSUS is a nucleic acid based approach to quantify host specific genetic markers to identify sources of fecal contamination.