Beach water quality monitoring typically tests for the presence of “indicator bacteria” (usually enterococcus or E. coli bacteria; sometimes total coliform or fecal coliform bacteria) whose presence has been correlated with the presence of human pathogens (disease-causing organisms) and therefore with actual human illnesses such as gastroenteritis, diarrhea, and various infections in Epidemiological Studies.
One of the limitations of all available and EPA-approved test methods is that the sample must be incubated for about 24 hours. So, we find out today that we shouldn't have gone in the water yesterday. And that warning sign on the beach may or may not be reflective of actual water quality because it's based on tests performed one or more days ago.
Because of this, there is a lot of research going on into developing what are generally termed "Rapid Indicator" tests that would give results in 1 to 4 hours. Below is information from the website of the Southern California Coastal Water Research Project (SCCWRP). As indicated, SCCWRP has conducted several rounds of testing on new methods. As they stated after tests in 2004, "two methods, dual wavelength fluorimetry (DWF) and quantitative PCR (qPCR), performed well enough to be optimistic that one or both methods could become available in the near future."
Subsequent to additional studies that were conducted in June 2005, two "finalists" (a qPCR method developed by University of North Carolina and Cepheid and a Genprobe Transcription Mediated Amplification (TMA) method) were invited back to perform a series of field tests where the TMA and qPCR methods were used on "real world" ocean samples also analyzed by "traditional" methods (the IDEXX method and the membrane filtration method). This testing was conducted in Spring 2006 by Orange County Sanitation District and County of Orange Public Health Laboratories and included several samples collected during rainy, polluted water conditions. Here's a 2007 report on that work. SCCWRP also has a Fact Sheet prepared in 2011 that discusses rapid methods.
A preliminary evaluation of the test methods by SCCWRP's "Beach Water Quality Workgroup" (Surfrider is a member of this) concluded that the best initial applications for these new test methods would probably be "special studies" as indicated below rather than routine beach monitoring:
It should also be recognized that although the per-test costs for these methods is roughly comparable (or even less) than current methods, the estimated cost for the test equipment may be $40,000 or more, making it out of reach of most volunteer groups. The training necessary to accurately perform these tests is also more extensive than required for existing methods.
Significant advances are being made in the development of rapid indicator tests and they are getting closer to general commercial application. EPA discussed the use of qPCR tests for enterococcus in their Recreational Water Quality Criteria released November 2012. The criteria document allows the use of qPCR, but does not require the use of this technology. The criteria document also fails offer incentives that would facilitate phase-in of rapid methods.
The qPCR test method was used alongside traditional methods during Epidemiological Studies conducted at three southern California beaches in 2008 and 2009. qPCR was also used in routine beach monitoring alongside traditional methods during a pilot test at three beach areas in Orange County, CA during July and August 2010. Further discussion of this pilot program and a similar testing program in Los Angeles County can be found on SCCWRP's website.
In 2012 EPA released their Recreational Water Quality Criteria. As part of the development of this guidance document, EPA developed and validated a molecular testing method using quantitative polymerase chain reaction (qPCR) as a rapid analytical technique for the detection of enterococci in recreational water (EPA Method 1611). For the purposes of beach monitoring, a state may use a qPCR method on a site-specific basis. For more details on this, see Section 5.2 of the guidance document and here. Also see Acceptability of the EPA qPCR Test at Your Beach.
More recently, a new PCR test method known as Droplet Digital PCR (ddPCR) has been developed that seems to offer advantages over earlier PCR technologies. Here is an abstract from a technical paper on initial testing of this technology. Field testing of ddPCR is being conducted as part of a Surfer Heath Study being performed by SCCWRP in San Diego, CA.
The subject of rapid indicator tests was also discussed in an article in the April 2007 issue of Surfrider Foundation's publication Making Waves.
Rapid Methods Demonstration (SCCWRP)