Coronado Mayor John Duncan confronted San Diego County's top public health official at the Aug. 18 City Council meeting, arguing that the county's DNA-based beach water testing disagrees with the older national standard more than half the time and has kept beaches closed when they should have been open.

"The tests do not match," Duncan told county Public Health Officer Dr. Sayone Thihalolipavan, summarizing the city's core complaint about the testing protocol that helps determine when Coronado's shoreline reopens after sewage contamination.

The dispute centers on a method called droplet digital PCR, or ddPCR, which San Diego County adopted in May 2022 to replace the older, culture-based Enterolert test. The county was the first municipality in the nation to make the switch, according to the Southern California Coastal Water Research Project, which developed the method.

Enterolert measures live enterococci bacteria and returns results in 24 to 48 hours. The ddPCR method detects bacterial DNA from both living and dead cells, delivering same-day results but registering higher contamination readings.

The consequences showed up immediately. In May 2022, the first month of ddPCR use, Imperial Beach was closed 25 of 31 days, Silver Strand Beach 16 of 31 days and Coronado's shoreline 11 days, The Coronado News reported. Under Enterolert testing the previous May, there were zero closure days.

A peer-reviewed study by researchers Matthew Verbyla and Rosanna Lacarra, published in January 2026 in the Journal of Microbiological Methods, analyzed Coronado beach samples from summer 2023 and found that ddPCR flagged unsafe conditions 56.3% of the time when Enterolert would have deemed the water safe. The city commissioned the research and is now pushing the county to raise the ddPCR safety threshold from 1,413 copies per 100 milliliters to 6,791 copies per 100 mL, a level the study found would align ddPCR results with the older EPA-standardized protocol.

Thihalolipavan pushed back on multiple fronts. She explained that beach closures are not triggered by test results alone but by confirmed sewage impacts such as spills or visible contamination, as required by state law. The ddPCR test is used to determine when beaches can reopen once contamination clears.

She also said the county's technical review found the Coronado-commissioned study's sample size too small, its study period too brief, its samples collected by different agencies and its data output containing errors. The California Department of Public Health sets the 1,413-copy threshold, she said, and the county lacks authority to change it.

"We could not use these tests unless these were validated and approved from the EPA," Thihalolipavan said. "(ddPCR) is a test that we have to go with because that is validated."

A county letter sent to the city on Aug. 18, with an attachment dated September 2024, warned that adopting less stringent water quality requirements could pose a "substantial public health risk." An EPA letter cited in the county's response noted that beaches outside the South County region, where no known sewage source exists, are not seeing increased closures under the same ddPCR testing.

Duncan pressed a broader point: if the county's position is that Enterolert is inadequate, then the EPA is putting public health at risk at every other beach in the country where Enterolert remains the standard.

He also noted that in July 2022, then-Mayor Richard Bailey and then-Imperial Beach Mayor Serge Dedina sent a letter to the San Diego County Board of Supervisors demanding answers about the new method. Duncan said the city never received a response in the four years since.

Thihalolipavan did not explain at the meeting why the county stopped using Enterolert. The county did not respond to The Coronado News by its deadline.

A Coronado councilmember published an op-ed in the Coronado Eagle & Journal on Aug. 19 calling for independent scientists to be convened to explain the discrepancies between the two methods rather than having elected officials choose a preferred conclusion.