Coronado Mayor John Duncan challenged the validity of San Diego County’s public health safety testing for ocean water at the Aug. 18 City Council meeting.
The tense conversation focused on a relatively new testing protocol implemented in May 2022 to check the sewage levels coming from Tijuana.
Before adopting the method, known as Polymerase Chain Reaction (ddPCR), the county relied on Enterolert – a culture-based protocol standardized nationwide by the Environmental Protection Agency (EPA).
The EPA approved a pilot program for the ddPCR protocol in 2021 and stated that a study had “found good agreement” between the two methods.
However, beach closures in Coronado jumped significantly after the county started using the ddPCR testing.
While the Enterolert testing measures live enterococci bacteria and yields results in 24 to 48 hours, the county’s rapid ddPCR method delivers same-day results by detecting bacterial DNA from both living and dead cells.
According to the EPA, enterococci serve as an indicator for fecal contamination and other disease-causing pathogens. Because ddPCR captures dead or damaged DNA alongside active bacteria, it appears to report higher contamination levels.
In May 2022, the new data prompted 25 of 31 days of beach closures for Imperial Beach. Silver Strand Beach was closed for 16 of 31 days and Coronado’s shoreline closed for 11 days. There were zero closure days the previous year in May with the Enterolert testing.
According to a study published in the National Library of Medicine, Coronado conducted an independent experiment on their beaches in the summer of 2023 and concluded that when comparing beach closures on Enterolert and ddPCR, there was a false positive rate with ddPCR of 56.3%.
That means that according to the study, if the county had been using the old Enterolert test, the water would have been deemed safe over half of those times.
The tests do not match.Coronado Mayor John Duncan
“The tests do not match,” Duncan said at the council meeting, addressing Dr. Sayone Thihalolipavan, the county’s public health officer.
Thihalolipavan explained that beach closures were not triggered by test results, but due to confirmed sewage impacts like spills or visible contamination as required by state law, and that ddPCR testing is used to reopen beaches once the contamination clears.
The mayor explained that four years ago, two previous mayors, Coronado Mayor Richard Bailey and Imperial Beach Mayor Serge Dedina, sent a letter to the county demanding answers on the validity of the new ddPCR method.
Duncan claimed that the county stopped using Enterolert shortly after the concern was raised, solely basing water reopenings on ddPCR. He also said that the city never got a response from the county on this issue in the last four years.
“You stated that (ddPCR) is the safe way, and the Enterolert is not the safe way to do it,” Duncan said. “If your premise is that (Enterolert) is faulty, that means the EPA is jeopardizing everybody’s health, every other ocean in the entire country – except for Coronado’s and Imperial Beach’s and San Diego County.”
In response, Thihalolipavan neither confirmed nor denied whether Enterolert was faulty, but explained that the county worked with the state and the EPA to validate the ddPCR test.
We could not use these tests unless these were validated and approved from the EPA. (ddPCR) is a test that we have to go with because that is validated.
County public health officer Dr. Sayone Thihalolipavan
“We could not use these tests unless these were validated and approved from the EPA,” Thihalolipavan countered, but did not offer an answer as to why the test results between the two methods did not match. “(ddPCR) is a test that we have to go with because that is validated.”
Duncan pointed out that the Enterolert protocol is also validated.
The public health officer also said that the county could not change testing thresholds based on the study the city offered that claimed a false positive of 56%.
“Our technical review found several limitations of Coronado’s study,” Thihalolipavan said. “Samples were collected by different agencies, the length of the study was too brief and therefore the data sample size was too small … and errors in data output.”
While San Diego County currently enforces a standard safety limit of 1,413 copies/100 mL, city officials advocated for raising that threshold to 6,791 copies/100 mL based on the study. It reported that the lower threshold created an overly sensitive “false alarm” system, unnecessarily triggering hundreds of days of beach closures.
Setting the threshold at 6,791 would match the new testing with the EPA’s old protocol and therefore avoid closures, according to the study.
However, a letter sent from the county on Aug. 18 to the city and obtained by The Coronado News included an attachment from Sept. 2024 in response to the study that said that the county felt adopting less stringent water quality requirements for ddPCR enterococcal concentrations could pose a “substantial public health risk.”
It also said that the current threshold of 1,413 copies/100ml for the ddPCR test was set by California Department of Public Health and the county does not have the authority to change it.
In a letter from the EPA to the county, it stated ddPCR was reliable and effective.
“The county is not seeing an increase in closures occurring in other communities outside the South County region where there is not a known sewage pollution source even though the same testing methods are used at those beaches,” the letter stated.
Thihalolipavan said “ddPCR remains the most accurate, EPA-validated tool.”
Duncan later clarified during the meeting that the city wants the beaches closed if they are unsafe, and open when they are safe, but he also wants answers on why the county stopped using the Enterolert method.
Thihalolipavan did not give an answer at the meeting and the county did not respond on deadline.
The Enterolert tests live, growing enterococci bacteria in the water, producing results a day or two after taking the sample. The ddPCR tests have a much faster turnaround time and produce results within hours, but they capture enterococcus DNA from both live and dead or damaged cells, according to the Surfrider Foundation.
This means the ddPCR test usually identifies a higher level of bacteria in the water, leading to more frequent beach closures.
According to the EPA, testing for enterococci indicates possible contamination of waters by fecal waste and although the bacteria itself is typically not considered harmful to humans, “their presence in the environment may indicate that other disease-causing agents such as viruses, bacteria and protozoa may also be present,” and could sicken swimmers.
San Diego County was the first municipality in the U.S. to switch to the DNA-based test, according to the Southern California Coastal Water Research Project who developed the ddPCR method.
