The Blue Water Task Force (BWTF) Program has been monitoring the levels of fecal contamination at public beaches across San Diego County since 2001. Fecal contamination can come from a variety of sources such as sewage leaks, failing septic systems, pet waste, and agricultural runoff.  Exposure to fecal contamination while recreating at the beach can lead to serious medical ailments including gastrointestinal illness, skin and eye infections, rashes, and respiratory illness.

BWTF aims to keep San Diego informed about the status of fecal pollution at local beaches. However, the science behind our work is not as widely understood. Furthermore, the metric we use in our results – MPN/100mL – is not very clear or intuitive to most people. In this article, we are going to explore a bit of the science behind BWTF.

What are we testing for?

BWTF tests the water at public beaches for Enterococcus bacteria. Most Enterococcus species are not harmful to humans, but they are a reliable indicator that fecal contamination is present. If fecal contamination is high at beaches, it’s likely that more harmful bacteria, viruses, or other pathogens are also present. Some forms of contamination, such as sewage leaks, can lead to exposure of dangerous pathogens like Vibrio, MRSA, and Hepatitis A.

One of the reasons we look for a fecal indicator bacteria instead of the specific bacteria or viruses that make people sick is because there are too many kinds of harmful pathogens to test for everything dangerous. Another reason is that a lot of these harmful bacteria or viruses are either very difficult or very expensive to detect.

Enterococcus presence is the EPA’s gold standard for fecal pollution assessment at beaches. Studies have demonstrated that Enterococcus presence has a stronger correlation with swimming-associated gastrointestinal illness than any other fecal indicator bacteria.

How do we test for Enterococcus presence?

BWTF uses the IDEXX Enterolert system to test the samples we collect. This system is EPA-approved, is easy to use, and can provide results in 24 hours. For each water sample, we add media that is conducive for bacterial growth. This media includes a nutrient indicator specific to enterococci. This nutrient indicator is essentially a sugar molecule with an inactive visual indicator molecule attached. This indicator molecule can only be activated if it is broken off from the rest of the sugar. If enterococci are present in the sample, they will break the bond between the sugar and the indicator molecule and the now-active indicator will glow under UV light.

After this nutrient indicator is added to our water samples, we separate out each sample into a series of wells on a tray.  In these separate wells, the bacteria are left to grow overnight. If any viable Enterococcus cells are present in a particular well, they will reproduce and activate the indicator molecule. We can use the number of wells that glow to estimate how many Enterococcus cells are likely to be in our sample. We quantify this using an MPN/100mL metric. The more wells that glow, the more bacteria was present in the sample, and the higher the MPN/100ml value will be.

What does MPN mean?

The readout, MPN, stands for “Most Probable Number”. This is an estimate of how many individual bacteria cells are present in a particular volume of water. So if we got a value of 15 MPN/100mL, we expect 15 bacterial cells to be present in each 100mL of water from that beach. If the value were 500 MPN/100mL, we expect 500 bacterial cells to be present in every 100mL of water.

BWTF then classifies water samples as “Low”, “Medium” or “High” based on the Enterococcus MPN/100mL readout. These classifications are based on standards set by the California State Water Resources Control Board:

• “Low” Enterococcus counts (0-35 MPN/100mL) are safe for human contact. 
• “Medium” Enterococcus counts (36-104 MPN/100mL) the beach is still considered safe but caution is still advised. If the 30-day average MPN results for a beach exceed 35 it is considered unsafe for recreation.
•  “High” Enterococcus counts (over 104 MPN/100mL) exceed the state safety standards and it is advised to avoid contact with the water. 

San Diego County puts up beach advisory signs when enterococcus counts exceed these safety thresholds. For BWTF programs outside of California, “Low”, “Medium”, or “High” thresholds reflect the specific standards of the state where the sample is collected.

How is this system different from ddPCR?

Since 2022, the County of San Diego Department of Health and Environmental Quality has started using digital droplet polymerase chain reaction (ddPCR) methods to test for fecal pollution at beaches. This method measures the amount of DNA coming from enterococci in the water. It is targeting and quantifying the number of copies of a genetic sequence specific to Enterococcus in the sample. It is estimated that 1,413  DNA copies/100mL is roughly equal to 104 MPN/100mL when it comes to assessing exposure risk. This ddPCR estimate has a 6% false positive and 3.7% false negative rate compared to culture-based methods.

ddPCR is conceptually similar to the Enterolert system. It takes a sample of water and separates it into thousands of microscopic droplets. These droplets are so small that only a fraction of them are likely to contain the Enterococcus-specific gene. Then each droplet undergoes a chemical reaction that will cause only the Enterococcus-specific gene to replicate and the reaction adds a visual indicator molecule in the process. The indicator molecule will cause the droplet to glow if it initially contained a copy of Enterococcus-specific DNA. After the reaction, the proportion of droplets that do or do not glow will indicate the Enterococcus abundance in the sample. This is similar to how Enterolert uses the proportion of wells that do or do not glow to estimate Enterococcus abundance.

There are a lot of benefits to ddPCR testing compared to the Enterolert method. First, it is much faster. The ddPCR method can get results in around 3-10 hours while the Enterolert system takes at least 24 hours. ddPCR thus allows for same-day updates on the safety status of beaches. It is also very sensitive and can detect low levels of Enterococcus DNA. However, ddPCR is much more expensive than most culture-based methods and requires specialized training and equipment.

Another feature of ddPCR is that it can detect DNA from Enterococcus cells that have been damaged or cells that cannot be cultured. This may better reflect the true amount of fecal contamination in the water. However, this method cannot distinguish DNA from viable or damaged cells, which is important for assessing the health risks of contamination events.

Want to learn more?

Hopefully this article illuminated some of the science that makes it possible to monitor our beaches. If you have any questions about the topics in this article, please reach out to BWTF via email  at BWTF@sandiego.surfrider.org.

BWTF is run by a group of dedicated volunteers who participate in community science. We run three labs across the County: in Carlsbad as a partnership with REEF, Hillcrest at the Surfrider San Diego office, and in Imperial Beach at YMCA Camp Surf. Through these three labs and committed volunteers we can ensure that water quality monitoring can happen across our 70-mile coastline!