A Cross Comparison of QPCR to Agar-Based or Defined Substrate Test Methods for the Determination of Escherichia Coli and Enterococci in Municipal Water Quality Monitoring Programs

Water Res. 2009 Nov;43(19):4967-79. doi: 10.1016/j.watres.2009.08.010. Epub 2009 Aug 14.


Molecular methods such as quantitative, real-time polymerase chain reaction (QPCR) are intended to shorten the period between sampling and publicly available results. Cross comparison studies in Racine, WI, USA evaluated QPCR against agar-based (US EPA Method 1600) and defined substrate (IDEXX Colilert-18) methods for the detection and quantification of Escherichia coli and enterococci in a variety of aqueous environments (wastewater, stormwater, and surface water). Regulatory outcomes were also compared based on choice of indicator and method. Positive correlation was seen between QPCR cell equivalents and viable cells through the wastewater treatment process and in all surface water samples (river or freshwater bathing beach) but not in direct stormwater discharge. For surface water samples, correlation improved with the application of a site-specific corrective factor, with regulatory action correctly predicted 98% of the time at bathing beaches. This study suggests the potential utility of QPCR for certain water quality monitoring applications.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Agar
  • Bathing Beaches
  • Cell Culture Techniques / methods
  • Culture Media
  • Enterococcus / genetics
  • Enterococcus / isolation & purification*
  • Environmental Monitoring / methods*
  • Escherichia coli / genetics
  • Escherichia coli / isolation & purification*
  • Fresh Water / microbiology*
  • Reverse Transcriptase Polymerase Chain Reaction / methods
  • Waste Disposal, Fluid
  • Water Pollutants / isolation & purification*


  • Culture Media
  • Water Pollutants
  • Agar