County launches new DNA-based ocean water testing system, including at two La Jolla sites

Ocean water is tested using San Diego County's new system May 4.
(Courtesy of San Diego County)

Two La Jolla beaches are among the sites where San Diego County has started using new ocean water-quality testing technology intended to produce faster results and earlier warnings when bacteria reach unhealthy levels.

During a rollout of the DNA-based technology last week, county Board of Supervisors Vice Chairwoman Nora Vargas said the county plans to expand its use of the testing technology, known as droplet digital polymerase chain reaction, or ddPCR, to more than 70 miles of shoreline that the county samples and tests to help protect the public.

In La Jolla, county testing sites include the end of Avenida de la Playa in La Jolla Shores and Black’s Beach. Other beach sites are tested by the city rather than the county.

“I’m happy to announce [that] with today’s sampling, San Diego becomes the first coastal county in the nation to implement the ddPCR method for beach water sampling,” Vargas said during the launch May 4. “Faster results are going to allow the county to issue or lift beach advisories on the same day samples were collected. And it reduces the time the public could unknowingly be at risk and when the water is contaminated.”

Officials said the DNA-based system is more sensitive to bacteria levels than the older method, which required growing bacterial cultures from water samples in petri dishes.

“In San Diego we had 104 advisories in 2021, and about half lasted a day or a little more, so it’s important that we are able to test, retest and report and lift advisories as needed,” said Heather Buonomo, division director for the county’s Department of Environmental Health & Quality.

La Jolla’s Children’s Pool is under an ongoing advisory due to the harbor seals there and the bacteria associated with their fecal matter.

To determine bacteria levels under the new system, samples are collected early in the morning and, using the ddPCR method, DNA is reproduced in a lab.

“This is different from the culture method we would use before, where we would grow the bacteria and wait during the incubation period,” Buonomo said. “The new method gives us the information much quicker. So we can test at 6 a.m., get it back by 8 or 9 so we can have the results the same day.”

The testing sites are chosen based on accessibility for samplers and where there might be a storm drain or runoff that contains bacteria. The results apply only to that geographic area.

Getting to this point was a decade in the making.

“It’s been a long time coming. We started thinking about this in 2012,” Buonomo said. “Even back then, we were looking for faster ways to get information out there.

“We worked with state health officials and conducted analyses to see if it would work. Once they had the data, they had to get state law changed to use this new method. It’s very exciting.”

The information collected is posted to, which provides a listing of all active water-quality advisories. ◆