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New Rapid Tests at San Diego Beaches Focus Attention on Border Sewage Problems

*originally posted by Mara Dias on This version provides a few more resources for San Diego locals

Since the passage of AB 411 in 1999, county health agencies like the County of San Diego Department of Environmental Health and Quality have been conducting weekly testing of water quality at California’s beaches and providing notification to the public when pollution levels exceed state health standards. California, like all coastal states since the passage of the federal BEACH Act in 2000, monitors recreational waters at the beach for the presence of fecal indicator bacteria, namely enterococcus in marine water.  Enterococcus is plentiful in the guts of humans and other warm-blooded animals. While most species of enterococcus don’t make people sick, when it is found in high concentrations, it is a good indication that there is fecal pollution in the water that can contain a wide variety of illness-causing bacteria, viruses or parasites commonly found in human and animal waste.

When enterococcus levels measured at the beach exceed state water quality criteria, swim advisories are issued to warn people of the potential health threat. When the source of the high bacteria counts is known to be a sewage spill or other human source, then the health agency will close the beach until bacteria levels fall below the health standard once again. This approach to public health protection has generally worked well, but has been hindered by culture-based, testing methods which take at least 24 hours before results are available and informed beach management decisions can be made. Thus, people find out that they shouldn’t have been in the water yesterday if test results come back high, and conversely it can also take an extra day to reopen beaches once pollution events have passed.

This spring, after receiving approval from both the State Water Board and the USEPA, San Diego County started using a new, DNA-based, rapid method to detect fecal indicator bacteria in beach water samples. While the intent of this transition was meant to provide more timely information to protect public health at the beach, its implementation has caused some confusion by members of the public who were not expecting to see beach closures and advisories issued at the beaches they frequent in Southern San Diego at this time of year. Read more about these community concerns in this San Diego Union-Tribune article. Keep reading below to learn more about digital droplet PCR and its implications for public health protection at California’s most southerly beaches.

What is ddPCR?

Digital Droplet PCR is a genetic/DNA-based method used to detect and measure fecal contamination at beaches and in coastal recreational waters. It can provide test results in as little as 3 hours after samples arrive at the lab, and is now being used by the County of San Diego Department of Health and Environmental Quality to monitor beaches and post same day swim advisories and beach closures to protect public health from exposure to sewage and other sources of fecal pollution.

How does this new rapid method change how beaches are tested and how decisions are made to issue swim advisories and close beaches? 

Health officials are now able to make same day decisions to open or close a beach with test results available within hours of sampling. Previously, there was a 24-hour lag until results were available using culture based testing methods, and thus changing water quality conditions at the beach could leave public health unprotected or beaches unnecessarily closed while officials waited for test results.

county employee testing water at Imperial Beach pier
A County employee collects a sample at the Imperial Beach pier. Source: SD County

Why is the new genetic method resulting in more beach closures in South County then we normally see this time of year? 

Culture methods only measure bacteria cells that are able to grow in the laboratory and that have not been damaged by the environment or altered by wastewater treatment processes. The new ddPCR method is more sensitive and can pick up DNA from damaged cells that would not grow in culture. Because of this, the water quality criteria that is used to issue swim advisories or beach closures for ddPCR (1,413 DNA copies enterococcus/100 ml water) has been adjusted and is over 10Xs higher than the standard used by culture methods (104 colony forming units enterococcus/100 ml water). This new standard was determined to represent an equivalent health risk after several years of side-by-side testing was conducted between the two methods.

This relationship seems to be holding up well throughout most of San Diego County, however the use of ddPCR at South County beaches has resulted in more beach closures than we normally expect to see during May and June. The new genetic testing methods are showing us that the water along this stretch of coast is more polluted than we realized before. In fact, more than 20 million gallons of sewage per day are discharged into the Pacific Ocean just five miles south of the U.S.-Mexico border. This partially treated effluent regularly flows north and pollutes beaches in southern San Diego County during summer south swells. The more sensitive detection methods, however, are showing us that this contamination doesn’t just come up with southern swells, but can bounce around in the near-shore coastal zone longer than we originally thought. Circulation patterns in this zone are complicated and difficult to understand and predict.

While it can be disappointing to see beach closure signs posted at your favorite beach, what would be worse is for you or your family to get sick from trying to enjoy a day at the beach.  Rashes, ear infection, flu-like symptoms and gastro-intestinal discomfort are some of the more common illnesses that people can develop after recreational exposure to sewage, but people are also at risk of developing more serious yet rare illnesses like vibrio, hepatitis A or MRSA. The San Diego Health Department is using these new rapid methods to better protect you and your family’s health and to open up beaches quicker once water quality conditions improve.  

The Surfrider Foundation hopes that greater awareness of just how polluted our waters are in Southern San Diego, will help generate the political will necessary to solve the border sewage crisis that has been plaquing the region for decades.  With the recent resolution of a lawsuit brought forth to force federal and international authorities to stop the flow of untreated sewage into the Tijuana River Valley and the Pacific Ocean and the EPA’s selection of a comprehensive suite of infrastructure solutions, we are positioned well to finally improve water quality conditions. However, there remains a huge need for additional funding to complete the needed infrastructure improvements. Surfrider will continue to work with our elected officials and community partners to secure the remaining funding through available federal, state and local funding sources. Visit our webpage to learn more about the Clean Border Water Now campaign.  

To learn more about how San Diego’s beaches are monitored and the new ddPCR testing method, read the San Diego County Beach & Bay Water Quality Program’s Frequently Asked Questions.

Surfrider will continue to monitor the science, and you can help.

San Diego County is the first county in the U.S. to deploy ddPCR rapid testing to determine fecal bacteria levels at our local beaches. ddPCR is backed by solid science; despite some initial skepticism from local leaders in Coronado and Imperial Beach, Surfrider sees no reason at this time to doubt that recent test results are accurate. Thanks to our water quality illness reporting form, we do have anecdotal evidence from an Imperial Beach resident who fell ill from surfing on June 3, 2022, a day that County ddPCR results showed extremely high levels across the entirety of Imperial Beach. That said, we will continue to monitor ddPCR water quality results and compare them with our own results, plus those of other agencies who use the previous methods.

If you’ve fallen ill or developed any symptoms after surfing or swimming in the ocean in San Diego County, please report your illness (see Google Form below or visit this link)  - it's extremely valuable information to us. Please note that we strongly advise adhering to water quality advisories and beach closures.