Testing for Mycoplasma genitalium and Using Doxycycline as First-Line Therapy at Initial Presentations for Non-Gonococcal Urethritis (NGU) Correlate With Reductions in Persistent NGU.

We found that the odds of return clinic visits for persistent non-gonococcal urethritis (NGU) were significantly lower (odds ratio: .4; 95% confidence interval: .3-.6; P < .0001) after implementing (1) testing for Mycoplasma genitalium during initial evaluations for NGU and (2) switching from azithromycin to doxycycline as first-line NGU treatment.

Prevalence of Undiagnosed Monkeypox Virus Infections during Global Mpox Outbreak, United States, June-September 2022.

Since May 2022, mpox has been identified in 108 countries without endemic disease; most cases have been in gay, bisexual, or other men who have sex with men. To determine number of missed cases, we conducted 2 studies during June-September 2022: a prospective serologic survey detecting orthopoxvirus antibodies among men who have sex with men in San Francisco, California, and a retrospective monkeypox virus PCR testing of swab specimens submitted for other infectious disease testing among all patients across the United States. The serosurvey of 225 participants (median age 34 years) detected 18 (8.0%) who were orthopoxvirus IgG positive and 3 (1.3%) who were also orthopoxvirus IgM positive. The retrospective PCR study of 1,196 patients (median age 30 years; 54.8% male) detected 67 (5.6%) specimens positive for monkeypox virus. There are likely few undiagnosed cases of mpox in regions where sexual healthcare is accessible and patient and clinician awareness about mpox is increased.

COVID-19, HIV, and Syphilis Contact Tracing: What Have We Learned and Where Are We Headed?

ABSTRACT: Contact tracing is a core public health intervention for a range of communicable diseases, in which the primary goal is to interrupt disease transmission and decrease morbidity. In this article, we present lessons learned from COVID-19, HIV, and syphilis in San Francisco to illustrate factors that shape the effectiveness of contact tracing programs and to highlight the value of investing in a robust disease intervention workforce with capacity to pivot rapidly in response to a range of emerging disease trends and outbreak response needs.

Contact-Tracing Outcomes Among Household Contacts of Fully Vaccinated Coronavirus Disease 2019 (COVID-19) Patients: San Francisco, California, 29 January-2 July 2021.

BACKGROUND: The extent to which vaccinated persons diagnosed with coronavirus disease 2019 (COVID-19) can transmit to other vaccinated and unvaccinated persons is unclear. METHODS: Using data from the San Francisco Department of Public Health, this report describes outcomes of household contact tracing during 29 January-2 July 2021, where fully vaccinated patients with COVID-19 were the index case in the household. RESULTS: Among 248 fully vaccinated patients with breakthrough infections, 203 (82%) were symptomatic and 105 were identified as the index patient within their household. Among 179 named household contacts, 71 (40%) contacts tested, over half (56%) were fully vaccinated and the secondary attack rate was 28%. Overall transmission from a symptomatic fully vaccinated patient with breakthrough infection to household contacts was suspected in 14 of 105 (13%) of households. Viral genomic sequencing of samples from 44% of fully vaccinated patients showed that 82% of those sequenced were infected by a variant of concern or interest and 77% by a variant carrying mutation(s) associated with resistance to neutralizing antibodies. CONCLUSIONS: Transmission from fully vaccinated symptomatic index patients to vaccinated and unvaccinated household contacts can occur. Indoor face masking and timely testing of all household contacts should be considered when a household member receives a positive test result in order to identify and interrupt transmission chains.

HIV and Sexually Transmitted Infections Among Persons with Monkeypox - Eight U.S. Jurisdictions, May 17-July 22, 2022.

High prevalences of HIV and other sexually transmitted infections (STIs) have been reported in the current global monkeypox outbreak, which has affected primarily gay, bisexual, and other men who have sex with men (MSM) (1-5). In previous monkeypox outbreaks in Nigeria, concurrent HIV infection was associated with poor monkeypox clinical outcomes (6,7). Monkeypox, HIV, and STI surveillance data from eight U.S. jurisdictions* were matched and analyzed to examine HIV and STI diagnoses among persons with monkeypox and assess differences in monkeypox clinical features according to HIV infection status. Among 1,969 persons with monkeypox during May 17-July 22, 2022, HIV prevalence was 38%, and 41% had received a diagnosis of one or more other reportable STIs in the preceding year. Among persons with monkeypox and diagnosed HIV infection, 94% had received HIV care in the preceding year, and 82% had an HIV viral load of <200 copies/mL, indicating HIV viral suppression. Compared with persons without HIV infection, a higher proportion of persons with HIV infection were hospitalized (8% versus 3%). Persons with HIV infection or STIs are disproportionately represented among persons with monkeypox. It is important that public health officials leverage systems for delivering HIV and STI care and prevention to reduce monkeypox incidence in this population. Consideration should be given to prioritizing persons with HIV infection and STIs for vaccination against monkeypox. HIV and STI screening and other recommended preventive care should be routinely offered to persons evaluated for monkeypox, with linkage to HIV care or HIV preexposure prophylaxis (PrEP) as appropriate.

Texting Lost-to-follow-up PrEP Patients from a San Francisco Sexual Health Clinic.

It is critical to understand what happens when PrEP patients are lost-to-follow-up (LTFU) and, where appropriate, attempt to re-engage them in care with the goal of preventing future human immunodeficiency virus (HIV) acquisition. We evaluated the benefits and limitations of using text-based outreach to re-engage with LTFU PrEP patients and offer re-initiation of PrEP care. Using text-messaging, we surveyed San Francisco City Clinic patients who started PrEP from January 2015 to October 2019 and were LTFU by October 1, 2020. Our goals were to better understand (1) whether our patients remained on PrEP through another provider or source, (2) why patients choose to discontinue PrEP, and (3) whether text-based outreach could successfully re-engage such patients in care. Multiple-choice survey questions were analyzed quantitatively to determine the proportion of respondents selecting each option; free-text responses were analyzed qualitatively using an inductive approach to identify any additional recurring themes. Of 846 eligible survey recipients, 130 responded (overall response rate 15.4%). Forty-two respondents (32.3%) were still on PrEP through another provider while 88 (67.7%) were not. Common reasons for stopping PrEP included: COVID-19-related changes in sex life (32.3% of responses), concerns regarding side effects (17.7%), and the need to take a daily pill (8.3%). Free text responses revealed additional concerns regarding risk compensation. While 32 participants agreed to be contacted by City clinic staff for PrEP counseling, only 6 were reached by phone and none of the six subsequently restarted PrEP. We learned that text messaging is a possible approach to survey certain PrEP program participants to determine who is truly LTFU and off PrEP, and to better understand reasons for PrEP discontinuation. While such information could prove valuable as programs seek to address barriers to PrEP retention, efforts to improve acceptability and increase response rates would be necessary. We were less successful in re-engaging LTFU patients in PrEP care, suggesting that text-messaging may not be the optimal strategy for this purpose.

Decreased Time From Human Immunodeficiency Virus Diagnosis to Care, Antiretroviral Therapy Initiation, and Virologic Suppression during the Citywide RAPID Initiative in San Francisco.

BACKGROUND: Early virologic suppression (VS) after human immunodeficiency virus (HIV) infection improves individual health outcomes and decreases onward transmission. In San Francisco, immediate antiretroviral therapy (ART) at HIV diagnosis was piloted in 2013-2014 and expanded citywide in 2015 in a rapid start initiative to link all new diagnoses to care within 5 days and start ART at the first care visit. METHODS: HIV providers and linkage navigators were trained on a rapid start protocol with sites caring for vulnerable populations prioritized. Dates of HIV diagnosis, first care visit, ART initiation, and VS were abstracted from the San Francisco Department of Public Health HIV surveillance registry. RESULTS: During 2013-2017, among 1354 new HIV diagnoses in San Francisco, median days from diagnosis to first VS decreased from 145 to 76 (48%; P < .0001) and from first care visit to ART initiation decreased from 28 to 1 (96%; P < .0001). By 2017, 28% of new diagnoses had a rapid start, which was independently associated with Latinx ethnicity (AOR, 1.73; 95% CI, 1.15-2.60) and recent year of diagnosis (2017; AOR, 16.84; 95% CI, 8.03-35.33). Persons with a rapid ART start were more likely to be virologically suppressed within 12 months of diagnosis than those with a non-rapid start (RR, 1.17; 95% CI, 1.10-1.24). CONCLUSIONS: During a multisector initiative to optimize ART initiation, median time from diagnosis to VS decreased by nearly half. Immediate ART at care initiation was achieved across many, but not all, populations, and was associated with improved suppression rates.

Implementation of pre-exposure prophylaxis at a community pharmacy through a collaborative practice agreement with San Francisco Department of Public Health.

OBJECTIVE: To discuss the design and implementation of a community pharmacy-initiated HIV pre-exposure prophylaxis (PrEP) and postexposure prophylaxis (PEP) program developed in collaboration with the San Francisco Department of Public Health (SFDPH). SETTING: A community pharmacy in San Francisco and the SFDPH developed a collaborative practice agreement (CPA) that allowed community pharmacists to initiate PrEP and PEP to prevent HIV acquisition and increase uptake in vulnerable populations. PRACTICE DESCRIPTION: A community pharmacy in San Francisco's Mission District, an urban, historically Hispanic/Latino/Latinx neighborhood. The primary collaborative practice team consisted of 1 community pharmacy technician, 4 community pharmacists, and 1 designated overseeing physician at SFDPH. PRACTICE INNOVATION: The pharmacy and the SFDPH collaborated together for 20 months from start to implementation of the CPA and the PrEP program. An interdisciplinary team of pharmacists, pharmacy personnel, public health physicians, and health department staff members worked together to design, launch, and maintain the program. Pharmacists were trained by SFDPH staff members on HIV testing and counseling and implementation of the PrEP protocol, including PEP initiation and sexually transmitted disease testing. A Department of Public Health secure portal was used to share patient information. An SFDPH physician reviewed patients' charts regularly and communicated with PrEP pharmacists as needed. RESULTS: Between April 2018 and the end of March 2019, 6 patients received PEP and 53 patients completed a PrEP initiation visit, of whom 96% (n = 51) filled their prescription. Approximately 47% (n = 24) of clients who started PrEP self-identified as Hispanic or Latino, 10% (n = 5) were black or African American, and 82% (n = 42) identified as men who have sex with men. CONCLUSION: Implementation of a CPA between a community pharmacy and a local health department enabled the launch of pharmacist-delivered PrEP, further expanding the landscape of access points to vulnerable populations in San Francisco.

Evaluating the Impact of Housing Status on Gonorrhea and Chlamydia Screening in an HIV Primary Care Setting.

INTRODUCTION: Gonorrhea and chlamydia (GC/CT) testing falls below recommended rates for people living with HIV (PLWH) in routine care. Despite evidence that homelessness and unstable housing (HUH) negatively impacts clinical outcomes for PLWH, little is known about GC/CT screening for HUH-PLWH in routine care. METHODS: Using an observational cohort of PLWH establishing care at a large publicly funded HIV clinic in San Francisco between February 2013 and December 2014 and with at least 1 primary care visit (PCV) before February 2016, we assessed GC/CT testing for HUH (staying outdoors, in shelters, in vehicles, or in places not made for habitation in the last year) compared with stably housed patients. We calculated (1) the odds of having GC/CT screening at a PCV using logistic regression with random effects to handle intrasubject correlations and (2) the percent of time enrolled in clinical care in which patients had any GC/CT testing ("time in coverage") based on 180-day periods and using linear regression modeling. RESULTS: Of 323 patients, mean age was 43 years, 92% were male, 52% were non-Latino white, and 46% were HUH. Homeless and unstably housed PLWH had 0.66 odds of GC/CT screening at a PCV than did stably housed patients (95% confidence interval, 0.44-0.99; P = 0.043). Time in coverage showed no difference by housing status (regression coefficient, -0.93; 95% confidence interval, -8.02 to 6.16; P = 0.80). CONCLUSIONS: Homeless and unstably housed PLWH had 34% lower odds of GC/CT screening at a PCV, demonstrating a disparity in routine care provision, but similar time in coverage. More research is needed to effectively increase GC/CT screening among HUH-PLWH.

Historical and Current Trends in the Epidemiology of Early Syphilis in San Francisco, 1955 to 2016.

BACKGROUND: Seventeen years into a sustained epidemic, early syphilis (ES) rates in San Francisco (SF) are continuing to increase and the demographics of the affected population are changing. We provide a historical overview of ES in SF among men who have sex with men (MSM) and describe trends in the epidemiology and disease investigation outcomes. METHODS: We examined data from the SF Department of Public Health's patient-based registry of integrated STD surveillance, clinical, and field investigation data to describe demographic and behavioral characteristics of ES cases, as well as outcomes of syphilis partner services (PS). χ Tests were performed to examine categorical differences across periods. Analysis of variance was used to examine differences in continuous variables. RESULTS: In 2016, 1095 ES cases were reported among males in SF, a 219% increase from the 343 cases identified 10 years ago. Between 1996-1999 and 2010-2016, an increasing proportion of ES cases were among MSM younger than 25 years, nonwhite, and HIV negative (P < 0.05). A decreasing proportion of ES cases were assigned for PS, among whom a smaller proportion of reported sex partners were identified by name, resulting in an overall decline in the proportion of cases who had at least one named partner treated as a result of PS (Disease Intervention Rate) from 30.5 in 2000-2004 to 14.8 in 2010-2016. CONCLUSIONS: Syphilis case rates continue to increase in SF and the epidemic is expanding beyond a core population. Additional resources and innovative prevention approaches are needed to reduce the burden of syphilis among MSM.

HIV-1 persistence following extremely early initiation of antiretroviral therapy (ART) during acute HIV-1 infection: An observational study.

BACKGROUND: It is unknown if extremely early initiation of antiretroviral therapy (ART) may lead to long-term ART-free HIV remission or cure. As a result, we studied 2 individuals recruited from a pre-exposure prophylaxis (PrEP) program who started prophylactic ART an estimated 10 days (Participant A; 54-year-old male) and 12 days (Participant B; 31-year-old male) after infection with peak plasma HIV RNA of 220 copies/mL and 3,343 copies/mL, respectively. Extensive testing of blood and tissue for HIV persistence was performed, and PrEP Participant A underwent analytical treatment interruption (ATI) following 32 weeks of continuous ART. METHODS AND FINDINGS: Colorectal and lymph node tissues, bone marrow, cerebral spinal fluid (CSF), plasma, and very large numbers of peripheral blood mononuclear cells (PBMCs) were obtained longitudinally from both participants and were studied for HIV persistence in several laboratories using molecular and culture-based detection methods, including a murine viral outgrowth assay (mVOA). Both participants initiated PrEP with tenofovir/emtricitabine during very early Fiebig stage I (detectable plasma HIV-1 RNA, antibody negative) followed by 4-drug ART intensification. Following peak viral loads, both participants experienced full suppression of HIV-1 plasma viremia. Over the following 2 years, no further HIV could be detected in blood or tissue from PrEP Participant A despite extensive sampling from ileum, rectum, lymph nodes, bone marrow, CSF, circulating CD4+ T cell subsets, and plasma. No HIV was detected from tissues obtained from PrEP Participant B, but low-level HIV RNA or DNA was intermittently detected from various CD4+ T cell subsets. Over 500 million CD4+ T cells were assayed from both participants in a humanized mouse outgrowth assay. Three of 8 mice infused with CD4+ T cells from PrEP Participant B developed viremia (50 million input cells/surviving mouse), but only 1 of 10 mice infused with CD4+ T cells from PrEP Participant A (53 million input cells/mouse) experienced very low level viremia (201 copies/mL); sequence confirmation was unsuccessful. PrEP Participant A stopped ART and remained aviremic for 7.4 months, rebounding with HIV RNA of 36 copies/mL that rose to 59,805 copies/mL 6 days later. ART was restarted promptly. Rebound plasma HIV sequences were identical to those obtained during acute infection by single-genome sequencing. Mathematical modeling predicted that the latent reservoir size was approximately 200 cells prior to ATI and that only around 1% of individuals with a similar HIV burden may achieve lifelong ART-free remission. Furthermore, we observed that lymphocytes expressing the tumor marker CD30 increased in frequency weeks to months prior to detectable HIV-1 RNA in plasma. This study was limited by the small sample size, which was a result of the rarity of individuals presenting during hyperacute infection. CONCLUSIONS: We report HIV relapse despite initiation of ART at one of the earliest stages of acute HIV infection possible. Near complete or complete loss of detectable HIV in blood and tissues did not lead to indefinite ART-free HIV remission. However, the small numbers of latently infected cells in individuals treated during hyperacute infection may be associated with prolonged ART-free remission.

Successful Implementation of HIV Preexposure Prophylaxis: Lessons Learned From Three Clinical Settings.

The past 3 years have marked a transition from research establishing the safety and efficacy of HIV preexposure prophylaxis (PrEP) to questions about how to optimize its implementation. Until recently, PrEP was primarily offered as part of randomized controlled trials or open-label studies. These studies highlighted the key components of PrEP delivery, including regular testing for HIV and other sexually transmitted infections (STIs), adherence and risk-reduction support, and monitoring for renal toxicity. PrEP is now increasingly provided in routine clinical settings. This review summarizes models for PrEP implementation from screening through initiation and follow-up, focusing on the strengths and weaknesses of three delivery systems: a health maintenance organization, an STI clinic, and a primary care practice. These early implementation experiences demonstrate that PrEP can be successfully delivered across a variety of settings and highlight strategies to streamline PrEP delivery in clinical practice.

Sexual Behavior, Risk Compensation, and HIV Prevention Strategies Among Participants in the San Francisco PrEP Demonstration Project: A Qualitative Analysis of Counseling Notes.

Pre-exposure prophylaxis (PrEP) is a viable HIV prevention strategy but risk compensation could undermine potential benefits. There are limited data that examine this phenomenon outside of clinical trials. We conducted a qualitative analysis of counseling notes from the San Francisco site of the US PrEP demonstration project to assess how men who have sex with men used PrEP as a prevention strategy and its impact on their sexual practices. Four major themes emerged from our analysis of 130 distinct notes associated with 26 participants. Prevention strategy decision-making was dynamic, often influenced by the context and perceived risk of a sexual encounter. Counselors noted that participants used PrEP in conjunction with other health promotion strategies like condoms, asking about HIV status of their sex partners, and seroadaptation. With few exceptions, existing risk reduction strategies were not abandoned upon initiation of PrEP. Risk-taking behavior was 'seasonal' and fluctuations were influenced by various personal, psychosocial, and health-related factors. PrEP also helped relieve anxiety regarding sex and HIV, particularly among serodiscordant partners. Understanding sexual decision-making and how PrEP is incorporated into existing prevention strategies can help inform future PrEP implementation efforts.

Lymphogranuloma Venereum 2015: Clinical Presentation, Diagnosis, and Treatment.

Lymphogranuloma venereum (LGV) has emerged as an important cause of proctitis and proctocolitis in men who have sex with men; classical inguinal presentation is now increasingly uncommon. We report summary findings of an extensive literature review on LGV clinical presentation, diagnosis, and treatment that form the evidence base for the 2015 Centers for Disease Control and Prevention treatment guidelines for sexually transmitted diseases. Proctitis and proctocolitis are now the most commonly reported clinical manifestations of LGV, with symptoms resembling those of inflammatory bowel disease. Newer molecular tests to confirm LGV infection are sensitive and specific, but are generally restricted to research laboratory or public health settings. Doxycycline (100 mg twice daily for 21 days) remains the treatment of choice for LGV. Patients with rectal chlamydial infection and signs or symptoms of proctitis should be tested for LGV, or if confirmatory testing is not available, should be treated empirically with a recommended regimen to cover LGV infection.

Insurance among patients seeking care at a municipal sexually transmitted disease clinic: implications for health care reform in the United States.

INTRODUCTION: Limited data exist on insured patients who receive care at publically funded sexually transmitted disease (STD) clinics, despite having access to a primary care provider. In this analysis, we compare patients with and without health insurance who sought services at City Clinic, the San Francisco municipal STD clinic. METHODS: We analyzed San Francisco City Clinic patients between August 1, 2011, and December 31, 2012. Insurance was self-reported and included both private and public insurance. Variables from the clinic electronic medical record were examined and included basic demographic and risk behavior questions, as well as positivity among patients tested for chlamydial and gonoccocal infection. We compared the characteristics of insured and uninsured patients using χ test. RESULTS: There were 13,104 patients in this analysis, of whom 4981 (38%) were categorized as insured and 8123 (62%) as uninsured. Overall, insured patients were older, more likely to be male, more likely to be white, and less likely to be Hispanic compared with uninsured patients (all P < 0.05). In addition, insured patients were more likely to be among men who have sex with men and among HIV-infected individuals compared with uninsured patients (all P < 0.0001). Insured patients were less likely to have a diagnosis of chlamydia at any site or a diagnosis of rectal gonorrhea. CONCLUSIONS: In our municipal STD clinic, more than one-third of patients report currently having insurance, yet still choose to seek care at the STD clinic. The different characteristics between insured and uninsured patients may reflect reasons other than affordability; therefore, STD clinics remain an important source of care for at-risk populations. These data suggest that the expansion of access to insurance may not result in a reduced need for categorical STD services. Maintaining access to high-quality sexual health services should remain a priority in the era of expanded health care access.

Identifying syphilis risk networks through venue attendance in San Francisco.

BACKGROUND: Prioritizing interventions for patients with syphilis who are part of large or interconnected sexual networks may be high yield for partner services, and identifying venues named by patients with syphilis who report high numbers of partners may help identify such networks. In this analysis, we explore differences between interviewed patients with early syphilis regarding where they met sex partners. METHODS: With a cross-sectional design, we examined the distribution of total reported sex partners from male index patients with early syphilis interviewed through the San Francisco Department of Public Health partner services program and the self-reported venues named as places they met sex partners. Based on the median number of total partners among male cases of syphilis who named each venue, we categorized venues into 3 levels of partner frequency: high (>15 partners reported), medium (6-15 partners reported), and low (<6 partners reported). Interviewed patients with early syphilis were then classified into these venue categories, and sociodemographic and risk behaviors from electronic medical records and interviews were compared using χ tests. RESULTS: In 2011, 433 male patients with early syphilis named 32 venues. One hundred forty-three (32.3%) patients were categorized as high, 226 (51.0%) as medium, and 74 (16.7%) as low partner frequency venue users. Patients with early syphilis who reported meeting partners at high partner frequency venues were generally older, more likely to be white, have a previous syphilis infection, use methamphetamines in the previous year, and be HIV infected (all P < 0.05) compared with those who reported meeting partners at medium-frequency and low-frequency venues. CONCLUSIONS: Venues where partners are met may be an appropriate proxy for network membership. Targeting additional resources, outreach, and services to clients who attend high-frequency venues may have a positive impact on syphilis prevention efforts.

Rapid Biphasic Decay of Intact and Defective HIV DNA Reservoir During Acute Treated HIV Disease.

Antiretroviral therapy (ART) is not a cure. Upon ART cessation, virus rapidly rebounds from latently-infected cells ("the HIV reservoir"). The reservoir is largely stabilized at the time of ART initiation and then decays slowly. Here, leveraging >500 longitudinal samples from 67 people with HIV (PWH) treated during acute infection, we developed a novel mathematical model to predict reservoir decay using the intact proviral DNA assay (IPDA) from peripheral CD4+ T cells. Nonlinear generalized additive models adjusted for initial CD4+ T count, pre-ART viral load, and timing of ART initiation demonstrated rapid biphasic decay of intact DNA (week 0-5: t1/2 ~0.71 months; week 5-24: t1/2 ~3.9 months) that extended out to 1 year of ART, with similar trends for defective DNA. Predicted reservoir decay were faster for participants individuals with earlier timing of ART initiation, higher initial CD4+ T cell count, and lower pre-ART viral load. These estimates are ~5-fold faster than prior reservoir decay estimates among chronic-treated PWH. Thus, these data add to our limited understanding of host viral control at the earliest stages of HIV reservoir stabilization, potentially informing future HIV cure efforts aimed at diverse, global population of PWH initiating ART at varying stages of disease.