Rates of syphilis and chlamydia in San Francisco have been trending down since the start of 2023, city data shows. But gonorrhea is proving to be a much more pernicious opponent for public health.
The city's department of public health issued the last 2023 monthly sexually transmitted infection report in June of this year, and has also released the first four months of data for 2024. Reported chlamydia cases went from 6,465 at the end of 2022 to 5,634 at the end of 2023, including cases of rectal chlamydia, which went from 2,064 to 1,438.
Reported adult syphilis cases went from 1,559 to 1,162 from the end of 2022 to the end of 2023. (Cases in cisgender females went up, from 153 to 176.)
From January through April of 2024, there were 323 reported cases of chlamydia compared with 465 in the first four months of 2023 (for rectal cases that's 70 in 2024 compared to 123 in 2023). Turn to adult syphilis and it's 78 reported cases compared with 101 (with cisgender women, cases went up, from 13 to 15).
But the numbers for gonorrhea tell a different story — 5,247 reported cases at the end of 2022 became 5,012 reported cases at the end of 2023. By April 2024 there were 1,555 reported cases compared to 1,647 at the same time in 2023. That's a slight decline but not at the same level as the other infections.
The San Francisco Department of Public Health declined to provide an expert to speak with the Bay Area Reporter for this report, but did provide a statement from the director of health, Dr. Grant Colfax, who is gay.
"The sharp decline in chlamydia and early syphilis infections in San Francisco demonstrates just how effective doxyPEP is as a sexual health tool," Colfax stated. "The San Francisco Department of Public Health, including the San Francisco City Clinic, played a critical role in the implementation of doxyPEP, and our community outreach and education continues."
Mayor London Breed's bond measure — including funding for City Clinic — will be included on the November ballot after it was approved by the San Francisco Board of Supervisors June 25.
Medical experts the B.A.R. has spoken with think the introduction of doxyPEP in late 2022 — a novel way of treating bacterial sexually transmitted infections with the antibiotic doxycycline (a type of tetracycline) after unprotected sex — is the key to understanding what's happening.
DoxyPEP has been approved for men who have sex with men and for trans women, which explains the concurrent rise in cases in cis women even as cases go down generally.
It also explains why gonorrhea isn't budging as much.
"Gonorrhea has a real potential to develop [antibiotic] resistance, although doxycycline is not something we use for gonorrhea anymore because the cat is out of the bag there," Dr. Matt Spinelli, a UCSF assistant professor and medical lead of the PrEP clinic at Ward 86 told the B.A.R.
Jorge Roman, a gay man who oversees clinical services at Magnet, the sexual health clinic at the San Francisco AIDS Foundation's Strut health center in the Castro LGBTQ neighborhood, told the B.A.R. that "tetracyclines have not been used for or against gonorrhea for a very long time, and so I think that's part of it; that's a big piece of it. It's not necessarily a surprise."
A study of doxyPEP efficacy showed an 80% drop in syphilis and chlamydia but only a 55% drop in gonorrhea, according to findings presented by Dr. Annie Luetkemeyer of UCSF at the 2022 International AIDS Conference, as reported on by the B.A.R. earlier this year, and which Spinelli cited.
Health Commissioner Cecilia Chung, a trans woman who is a longtime HIV/AIDS advocate who is HIV-positive, agreed with Spinelli and Roman in a statement to the B.A.R. and thanked the LGBTQ community for embracing doxyPEP.
"The reduction in chlamydia and syphilis rates in MSM [men who have sex with men] and trans women is a testament to the innovation of the San Francisco Department of Public Health, which was the first in the nation to research and put out guidelines for this innovative prevention tool," Chung stated. "Credit must also be given to our MSM and trans women communities, who were quick to adopt DoxyPEP as part of their sexual practices."
Rectal cases of gonorrhea showed some improvement last year — 1,597 cases in 2023 compared to 1,916 in 2022. But this year it's slightly up — 562 in 2024 compared to 549 at the same point in 2023.
Dr. Dan O'Neill, the chief medical officer at the San Francisco Community Health Center, was less bullish than Spinelli or Roman on doxyPEP — but he did state, as a potential explanation for the gonorrhea persistence, that it's possible the bacteria is becoming more resistant to tetracyclines in the population.
"While I feel certain doxyPEP is a contributing factor, causality can be tricky to pin down with such a complex topic," O'Neill stated in an email to the B.A.R. "It is also still relatively early to know how this new intervention will play out, as the full story of doxyPEP is yet untold. In particular, evidence of growing population-level tetracycline resistance is concerning for both the STD gonorrhea, which doxyPEP has been less helpful in curbing."
This isn't just a problem for the bacteria that causes gonorrhea but also Staphylococcal aureus, or MRSA, a common staph bacteria that causes skin infections, O'Neill said, among the health center's patient population, which he stated is "largely houseless folks or those struggling with addiction."
'Really exciting time for STI prevention'
Roman said that the general trends the city is seeing are also the case at Magnet, saying his was the first of San Francisco's larger providers to see more doxyPEP uptake before primary care doctors started prescribing it. Roman and Spinelli agreed it's a compelling time for the frontlines of combatting sexually transmitted infections.
"It's a really exciting time for STI prevention — there was a lot of frustration our public health efforts [condoms, asymptomatic testing] were not making an impact, and it's such a great time to have a highly effective, biomedical preventative tool making improvements on the population level," Spinelli said.
There is even hope for the fight against gonorrhea, Spinelli said.
"There was hope a Meningitis group B vaccine — they [meningitis and gonorrhea] have some similarities in that they are the same genus — there was hope a vaccine would have an impact on gonorrhea, and the data was presented and, unfortunately, it did not have an effect but it trended toward benefit," he said, adding that now researchers are working on a gonorrhea vaccine, which is currently on an FDA fast-track following a phase 1 trial.
Roman said that in the interim, doctors and the public should build on the momentum they are gaining in the fight against STIs. One way Magnet does that is by having clinicians have "conversations with all of our clients in shared decision making as to whether it'd [doxyPEP] help on an independent basis in their sexual networks, who they are engaging in sexual relationships with, and so understanding that and having open dialogue with our clients will help build on that momentum in terms of who would benefit from it."
Spinelli said that work needs to be done to see how cisgender women would benefit from doxyPEP.
"Globally, it's a really important population," he said. "Some providers are speaking with women who've had a prior STI and doing patient-centered decision-making. We measured the adherence in the study in women and that adherence was very low — that's why the study failed."
A study of female sex workers in Tokyo Spinelli referred to showed evidence of doxyPEP efficacy in that population without affecting vaginal bacteria.
Spinelli said another potential field of study is whether a 200-milligram dose of doxycycline could be taken before unprotected sex.
"There is a lot of plausibility it would work that way," he said.
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