Is Doxy PEP Behind San Francisco’s Sharp Drop in STI Rates?

San Francisco has become the first major U.S. City to report a significant decline in bacterial sexually transmitted infections (STIs) following the widespread adoption of doxycycline post-exposure prophylaxis (doxy PEP). Fresh data from the San Francisco Department of Public Health (SFDPH) shows an 18% drop in chlamydia cases, a 24% reduction in syphilis, and a 5% decrease in gonorrhea between 2023 and 2024. Public health officials attribute much of this progress to doxy PEP, a preventive strategy that involves taking the antibiotic doxycycline within 72 hours after condomless sex to reduce the risk of infection.

As a physician and health journalist with over a decade of experience in infectious disease reporting, I’ve followed the rise of doxy PEP closely. The strategy has shown remarkable efficacy in clinical trials, particularly among men who have sex with men (MSM) and transgender women—groups disproportionately affected by bacterial STIs. However, the long-term implications of widespread antibiotic employ for prevention remain a topic of intense debate among public health experts. Here’s what we know so far about San Francisco’s encouraging results—and the questions that still need answers.

What Is Doxy PEP and How Does It Work?

Doxy PEP is a biomedical prevention strategy that uses the antibiotic doxycycline to reduce the risk of bacterial STIs after potential exposure. The approach is modeled after HIV post-exposure prophylaxis (PEP) but targets chlamydia, syphilis, and gonorrhea instead. Users take a single 200 mg dose of doxycycline within 72 hours after condomless oral or anal sex. Clinical trials have demonstrated its effectiveness in reducing STI incidence by up to 88% for chlamydia, 87% for syphilis, and 55% for gonorrhea in MSM and transgender women. However, studies have not found doxy PEP to be effective for cisgender women engaging in penis-in-vagina sex, likely due to differences in bacterial transmission dynamics.

It’s significant to note that doxy PEP does not prevent viral STIs such as HIV, herpes, or human papillomavirus (HPV). The strategy is recommended by the Centers for Disease Control and Prevention (CDC) for MSM and transgender women who have had an STI in the past year or who engage in condomless sex with multiple partners. San Francisco was among the first cities to formally endorse doxy PEP, launching a citywide rollout in late 2022. The strategy has since gained traction in other urban centers, including Seattle, Los Angeles, and New York City, though San Francisco remains the only city to report such dramatic declines in STI rates to date.

San Francisco’s STI Decline: A Closer Look at the Numbers

The SFDPH’s latest surveillance data, released in early 2025, reveals a striking reduction in bacterial STI cases across the city. Between 2023 and 2024, reported cases of chlamydia fell by 18%, syphilis by 24%, and gonorrhea by 5%. The declines were most pronounced among MSM and transgender women, the primary target populations for doxy PEP. For context, these reductions reverse a decade-long trend of rising STI rates in San Francisco, where syphilis cases had increased by nearly 300% since 2010.

Dr. Stephanie Cohen, director of STI and HIV prevention at SFDPH, stated in an official release: “The remarkable drop in STI cases in San Francisco is due in large part to the trailblazing work that made the rollout of doxy PEP possible. This strategy, combined with increased testing and community engagement, has given us a powerful new tool in the fight against STIs.” Dr. Susan Philip, San Francisco’s health officer, echoed this sentiment, emphasizing the importance of continued vigilance: “We encourage the public to keep up the momentum by taking actions—such as getting tested—to protect their sexual health.”

While the data is promising, public health experts caution against attributing the entire decline to doxy PEP alone. Other factors, such as increased STI testing, expanded access to PrEP (pre-exposure prophylaxis for HIV), and shifts in sexual behavior during and after the COVID-19 pandemic, may have also played a role. However, the timing of the decline—coinciding with the widespread adoption of doxy PEP—strongly suggests that the strategy has been a key driver of these improvements.

The Antibiotic Resistance Debate: A Looming Concern

Despite its effectiveness, doxy PEP has sparked concerns about the potential for increased antibiotic resistance. Gonorrhea, in particular, has already developed resistance to multiple classes of antibiotics, including tetracyclines like doxycycline. The World Health Organization (WHO) has classified gonorrhea as a “high priority” pathogen due to its ability to rapidly develop resistance, and some experts worry that widespread doxy PEP use could accelerate this trend.

A 2024 study published in *Clinical Infectious Diseases* found that doxy PEP use was associated with a slight increase in doxycycline-resistant gonorrhea strains in San Francisco. However, the study’s authors noted that the overall prevalence of resistance remained low and that the benefits of doxy PEP in reducing STI transmission likely outweighed the risks. “We’re monitoring resistance patterns closely,” said Dr. Cohen. “At this point, the data suggests that doxy PEP is a net positive for public health, but we must remain vigilant.”

The CDC’s current guidelines recommend doxy PEP for MSM and transgender women with a history of STIs or multiple sexual partners, but they also emphasize the need for ongoing surveillance of antibiotic resistance. Some public health experts argue that doxy PEP should be used judiciously, reserving it for individuals at the highest risk of infection rather than as a blanket prevention strategy.

Who Benefits from Doxy PEP—and Who Doesn’t?

Doxy PEP is not a one-size-fits-all solution. Clinical trials have shown that the strategy is highly effective for MSM and transgender women but not for cisgender women. This discrepancy is likely due to differences in how bacteria are transmitted during sex. For example, chlamydia and gonorrhea are more likely to infect the cervix in cisgender women, where doxycycline may not reach therapeutic levels as effectively as it does in the rectum or urethra.

For MSM and transgender women, however, doxy PEP offers a critical layer of protection, particularly for those who face barriers to consistent condom use or who have multiple sexual partners. “Doxy PEP has been a game-changer for my patients,” said Dr. Oliver Bacon, an infectious disease specialist at Zuckerberg San Francisco General Hospital. “Many of them report feeling more in control of their sexual health, which has led to increased testing and earlier treatment when infections do occur.”

Despite its benefits, doxy PEP is not without side effects. Common issues include nausea, photosensitivity (increased sensitivity to sunlight), and, in rare cases, esophageal irritation. Doxycycline can interact with other medications, such as antacids and blood thinners, so it’s essential for users to consult a healthcare provider before starting the regimen.

Global Implications: Could Doxy PEP Work Elsewhere?

San Francisco’s success with doxy PEP has drawn attention from public health officials worldwide. Cities like London, Paris, and Sydney are closely monitoring the strategy’s impact, with some already piloting similar programs. However, the approach is not without challenges. In countries with limited access to antibiotics or robust STI surveillance systems, the risks of resistance may outweigh the benefits.

The WHO has not yet issued formal guidelines on doxy PEP, but it is actively reviewing the evidence. In the meantime, some European countries, including France and the UK, have begun offering doxy PEP to high-risk populations on a case-by-case basis. “The global STI epidemic is worsening, and we need new tools to address it,” said Dr. Teodora Wi, a medical officer at the WHO’s Department of Sexual and Reproductive Health. “Doxy PEP shows promise, but we must balance its benefits with the potential for resistance.”

In the U.S., the CDC’s endorsement of doxy PEP has paved the way for broader adoption. However, access remains uneven, with many healthcare providers still unfamiliar with the strategy or hesitant to prescribe it. Advocacy groups, such as the National Coalition of STD Directors, are pushing for expanded education and training to ensure that doxy PEP reaches those who need it most.

What’s Next for Doxy PEP?

As doxy PEP continues to gain traction, researchers are exploring ways to optimize its use. One area of focus is the development of rapid diagnostic tests that could help users determine whether they’ve been exposed to an STI before taking doxycycline. This could reduce unnecessary antibiotic use and further mitigate the risk of resistance. Another promising avenue is the combination of doxy PEP with other prevention strategies, such as HPV vaccination and regular STI screening.

For now, San Francisco’s experience offers a glimpse of what’s possible when public health innovation meets community engagement. The city’s decline in STI rates is a testament to the power of proactive prevention—but it also serves as a reminder that no single strategy is a silver bullet. “Doxy PEP is not a replacement for condoms or regular testing,” said Dr. Philip. “It’s one tool in a larger toolkit, and we must use it wisely.”

Key Takeaways

• Doxy PEP is a preventive strategy that involves taking doxycycline within 72 hours after condomless sex to reduce the risk of chlamydia, syphilis, and gonorrhea.
• San Francisco reported an 18% drop in chlamydia, 24% in syphilis, and 5% in gonorrhea between 2023 and 2024, with the declines most pronounced among MSM and transgender women.
• Clinical trials indicate doxy PEP reduces STI risk by up to 88% for chlamydia, 87% for syphilis, and 55% for gonorrhea in high-risk populations.
• Doxy PEP is not effective for cisgender women engaging in penis-in-vagina sex, likely due to differences in bacterial transmission dynamics.
• Concerns about antibiotic resistance remain, particularly for gonorrhea, which has already developed resistance to multiple antibiotic classes.
• The CDC recommends doxy PEP for MSM and transgender women with a history of STIs or multiple sexual partners, but ongoing surveillance is critical.

Frequently Asked Questions

How effective is doxy PEP?

Doxy PEP has been shown to reduce the risk of chlamydia by 88%, syphilis by 87%, and gonorrhea by 55% in MSM and transgender women. However, it is not effective for cisgender women engaging in penis-in-vagina sex.

Does doxy PEP prevent HIV or other viral STIs?

No. Doxy PEP only prevents bacterial STIs (chlamydia, syphilis, and gonorrhea). It does not protect against HIV, herpes, HPV, or other viral infections.

What are the side effects of doxy PEP?

Common side effects include nausea, photosensitivity (increased sensitivity to sunlight), and, in rare cases, esophageal irritation. Doxycycline can also interact with other medications, so it’s important to consult a healthcare provider before use.

Is doxy PEP available outside of San Francisco?

Yes. The CDC has endorsed doxy PEP for MSM and transgender women in the U.S., and some cities, including Seattle, Los Angeles, and New York, have begun offering it. However, access varies by location, and not all healthcare providers are familiar with the strategy.

Could doxy PEP lead to antibiotic resistance?

There is a theoretical risk that widespread doxy PEP use could contribute to antibiotic resistance, particularly in gonorrhea. However, current data suggests that the benefits of reduced STI transmission outweigh the risks. Ongoing surveillance is critical to monitor resistance patterns.

What You Can Do

If you’re interested in doxy PEP, talk to your healthcare provider about whether it’s right for you. The CDC recommends the strategy for MSM and transgender women who have had an STI in the past year or who engage in condomless sex with multiple partners. Regular STI testing is also essential—San Francisco offers free or low-cost testing through City Clinic and other community health centers.

For the latest updates on doxy PEP and STI prevention, follow the CDC’s STI guidelines or consult your local health department. Together, we can help turn the tide on the STI epidemic—one informed decision at a time.

What are your thoughts on doxy PEP? Have you or someone you know used it? Share your experiences in the comments below, and don’t forget to share this article to spread awareness about this groundbreaking prevention strategy.