Is the beach open? Get an answer faster – with help from PCR

For years, polymerase chain reaction (PCR) technology has been working hard behind the scenes to monitor everything from SARS-CoV-2 in municipal wastewater to harmful marine algal blooms. Now, scientists in San Diego are using it let you know if it’s safe to go swimming.

With the new program, San Diego becomes the first coastal county in the nation to use droplet digital PCR (ddPCR) methods for beach water sampling. Among the many benefits is the ability for authorities to issue or lift beach advisories on the same day the samples are collected, reducing the amount of time the public could be at risk of contact with dirty water—or the amount of time that otherwise clean beaches need to be closed.

The program is being run on a pilot basis by the state and the federal government, and positive results could mean the technology goes nationwide some day soon.

Beach cleanliness is a big deal in Southern California, where the allure of pristine beaches is a major draw for both locals and tourists. To date, many local beaches have been out of compliance with state bacteria standards, and considerable local resources are devoted to informing the public about what beaches are safe to visit and which have unhealthy levels of E. coli and enterococci. Most of those nasties end up in the water thanks to storm-related flows from the nearby Tijuana River, which has the unfortunate distinction of carrying untreated wastewater, trash, and sediment into the Pacific Ocean.

As explained in the San Diego Union-Tribune in 2021, beaches in San Diego County, which run from the Mexican border in the south to Trestles Beach in the north, had 104 advisories issued, but about half of those lasted only for a day or slightly more. The county, said Heather Buonomo, division director for the county’s Department of Environmental Health and Quality, wanted the ability to quickly test and then report which beaches were not in compliance or list restrictions on those that had been out of compliance.

What is PCR? 

Polymerase chain reaction (PCR) is a technology dating back to 1969, when a researchers discovered bacteria living near the boiling waters of geysers in Yellowstone National Park. It was refined in the 1980s by Kary Mullis, a California researcher who won the Nobel Prize in Chemistry in 1993. The technology is used to make millions and even billions of copies of a specific DNA sample. Within the sample, a small amount of DNA is amplified to permit easier studying. It’s fast, cheap, and effective.

While PCR has been hard at work in labs for decades, its breakout role came in 2020 when it landed a star part in COVID-19 testing. Today, reverse transcription polymerase chain reaction-based diagnostic tests are considered to be the standard bearer for detection of the current SARS-CoV-2 infection.

PCR in wastewater testing 

Using PCR to trace pathogens is not a new concept. The technology was called on in the early 1990s to track and prevent new polio outbreaks, for example. Quantitative polymerase chain reaction (qPCR) testing for poliovirus RNA was estimated at up to five times more sensitive in predicting outbreaks than monitoring based on cases alone. For polio, where it’s common for some individuals to be asymptomatic, the study of wastewater samples enabled large-scale community surveillance without actually having to test people—researchers just had to wait for them to flush their toilets.

At the beach, the old testing method had researchers collecting a sample, then growing the bacteria and waiting during an incubation period. Now, with PCR, they can test the water at 6 a.m. and have results up on their website before you are done waxing your surfboard.

In San Diego, fixing the polluted Tijuana River has been estimated to be a $630 million job. While the digital droplet PCR (ddPCR) testing program does not yet have a price tag, it is every bit as effective as the old method, the U.S. Environmental Protection Agency has reported.

The method, the agency said, was developed for beach use by the Southern California Coastal Water Research Project and put into action by a collaboration between that group and the California Department of Public Health.

“By using this digital test to measure bacterial DNA in beach water, San Diego County beach managers will be able to provide same-day notices of beach water quality,” the agency said in a press release.

The pilot program was fine-tuned over the course of two years, during which researchers took samples from 70 miles of coastline in the county. Final approval of the technology will be based on the success of this pilot program, the EPA said—meaning that same-day testing results could soon be coming to a beach near you.