Stephanie Cohen, MD

Volunteer Associate Clinical Professor

Stephanie Cohen, MD, MPH is the medical director of San Francisco City Clinic, the municipal STD clinic in San Francisco and an assistant professor at UCSF in the division of infectious diseases. She provides HIV primary care at City Clinic and the VA medical center. Her research focuses on using implementation science to guide the translation of STD and HIV prevention research into clinical and public health practice. She is currently a protocol Co-Chair and site Co-Principal Investigator of The Demo Project, an NIH-funded research study assessing the delivery of pre-exposure prophylaxis (PrEP) in STD and community health clinics. She is also the site co-PI of the STOP Study, which is evaluating the use of 4th generation HIV Ag/Ab tests and RNA pooling for the detection of acute HIV in high prevalence settings.
Education
Residency, - Internal Medicine, University of California, San Francisco
Publications

  1. Sankaran M, Glidden DV, Kohn RP, Nguyen TQ, Bacon O, Buchbinder SP, Gandhi M, Havlir DV, Liebi C, Luetkemeyer AF, Nguyen JQ, Roman J, Scott H, Torres TS, Cohen SE. Doxycycline Postexposure Prophylaxis and Sexually Transmitted Infection Trends. 2025. PMID: 39761052


  2. Barbehenn A, Shi L, Shao J, Hoh R, Hartig HM, Pae V, Sarvadhavabhatla S, Donaire S, Sheikhzadeh C, Milush J, Laird GM, Mathias M, Ritter K, Peluso MJ, Martin J, Hecht F, Pilcher C, Cohen SE, Buchbinder S, Havlir D, Gandhi M, Henrich TJ, Hatano H, Wang J, Deeks SG, Lee SA. Rapid biphasic decay of intact and defective HIV DNA reservoir during acute treated HIV disease. 2024. PMID: 39557853


  3. Perkins R, Beima-Sofie K, Christopoulos K, Cohen SE, Dright A, Dombrowski JC, Gougougui A, Kohler P, Luetkemeyer AF, Pintye J, Celum C. "Another tool for the sexual health toolkit": U.S. health care provider knowledge and attitudes about doxycycline post-exposure prophylaxis (doxy-PEP) to prevent bacterial sexually transmitted infections among men who have sex with men. 2024. PMID: 39481014


  4. Dombrowski JC, Donnell D, Grabow C, Cohen SE, Cannon CA, Brown CE, Buchbinder SP, Celum C, Luetkemeyer AF. Evidence-Informed Provision of Doxycycline Post-Exposure Prophylaxis for Prevention of Bacterial Sexually Transmitted Infections. 2024. PMID: 39478321


  5. Chu VT, Glascock A, Donnell D, Grabow C, Brown CE, Ward R, Love C, Kalantar KL, Cohen SE, Cannon C, Woodworth MH, Kelley CF, Celum C, Luetkemeyer AF, Langelier CR. Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome. 2024. PMID: 39363100


  7. Barbehenn A, Shi L, Shao J, Hoh R, Hartig HM, Pae V, Sarvadhavabhatla S, Donaire S, Sheikhzadeh C, Milush J, Laird GM, Mathias M, Ritter K, Peluso M, Martin J, Hecht F, Pilcher C, Cohen SE, Buchbinder S, Havlir D, Gandhi M, Henrich TJ, Hatano H, Wang J, Deeks SG, Lee SA. Rapid Biphasic Decay of Intact and Defective HIV DNA Reservoir During Acute Treated HIV Disease. 2024. PMID: 38585951


  8. Lieberman NAP, Reid TB, Cannon CA, Nunley BE, Berzkalns A, Cohen SE, Newman LM, Aldrete S, Xu LH, Thornlund CP, Pettus K, Lundy S, Kron M, Soge OO, Workowski K, Perlowski C, Hook EW, Dionne JA, Golden MR, Lieberman JA, Lee MK, Morshed M, Naidu P, Cao W, Pillay A, Giacani L, Greninger AL. Near-Universal Resistance to Macrolides of Treponema pallidum in North America. 2024. PMID: 38865666


  9. Sugarman J, Taylor HA, Bachmann LH, Barbee LA, Cahill S, Celum C, Cohen SE, Faden RR, Luetkemeyer AF, Mayer KH, Mena L, Mermin J, Upshur R, Aral S. Ethical Considerations in Implementing Doxycycline Postexposure Prophylaxis for the Prevention of Bacterial Sexually Transmitted Infections. 2023. PMID: 38079243


  10. Minhaj FS, Singh V, Cohen SE, Townsend M, Scott H, Szumowski J, Hare CB, Upadhyay P, Reddy J, Alexander B, Baird N, Navarra T, Priyamvada L, Wynn N, Carson WC, Odafe S, Guagliardo SAJ, Sims E, Rao AK, Satheshkumar PS, Weidle PJ, Hutson CL. Prevalence of Undiagnosed Monkeypox Virus Infections during Global Mpox Outbreak, United States, June-September 2022. 2023. PMID: 37832516


  12. Sachdev D, Chew Ng RA, Hernandez K, Nguyen TQ, Cohen SE. COVID-19, HIV, and Syphilis Contact Tracing: What have we learned and where are we headed? 2022. PMID: 36538488


  13. Cohen SE, Stookey J, Anderson N, Morris D, Singzon T, Dann M, Burk K, Chen CC. Using Geocoding to Identify COVID-19 Outbreaks in Congregate Residential Settings: San Francisco's Outbreak Response in Single-Room Occupancy Hotels. 2022. PMID: 36239486


  14. Curran KG, Eberly K, Russell OO, Snyder RE, Phillips EK, Tang EC, Peters PJ, Sanchez MA, Hsu L, Cohen SE, Sey EK, Yin S, Foo C, Still W, Mangla A, Saafir-Callaway B, Barrineau-Vejjajiva L, Meza C, Burkhardt E, Smith ME, Murphy PA, Kelly NK, Spencer H, Tabidze I, Pacilli M, Swain CA, Bogucki K, DelBarba C, Rajulu DT, Dailey A, Ricaldi J, Mena LA, Daskalakis D, Bachmann LH, Brooks JT, Oster AM, Monkeypox, HIV, and STI Team. HIV and Sexually Transmitted Infections Among Persons with Monkeypox - Eight U.S. Jurisdictions, May 17-July 22, 2022. 2022. PMID: 36074735


  15. Sachdev DD, Chew Ng R, Sankaran M, Ernst A, Hernandez KT, Servellita V, Sotomayor-Gonzalez A, Stoltey J, Cohen SE, Nguyen TQ, Chiu C, Philip S. Contact tracing outcomes among household contacts of fully vaccinated COVID-19 patients - San Francisco, California, January 29-July 2, 2021. 2021. PMID: 34928340


  16. Johnson KA, Levy M, Brosnan H, Kohn RP, Cohen SE. Texting Lost-to-follow-up PrEP Patients from a San Francisco Sexual Health Clinic. 2022. PMID: 35841493


  17. Thurlow CM, Joseph SJ, Ganova-Raeva L, Katz SS, Pereira L, Chen C, Debra A, Vilfort K, Workowski K, Cohen SE, Reno H, Sun Y, Burroughs M, Sheth M, Chi KH, Danavall D, Philip SS, Cao W, Kersh EN, Pillay A. Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing. 2022. PMID: 35491834


  18. Stojanovski K, Decker A, Brosnan H, King EJ, Cohen SE, Fuchs JD, Sachdev D. Public Health Detailing on Sexual Health Care in San Francisco: Learnings From Real-World Implementation. 2022. PMID: 35264028


  19. Johnson KA, Graglia S, Lynch ED, De Mesa J, Antunez E, Torres S, Coffey S, Cohen SE. Concurrent COVID-19 and Acute HIV: A Case Report and Diagnostic Review. 2021. PMID: 34824585


  20. Bacon O, Chin J, Cohen SE, Sachdev D, Coffey S, Scheer S, Hessol NA, Buchbinder S, Havlir DV, Hsu L. Decreased Time from HIV Diagnosis to Care, ART Initiation, and Virologic Suppression during the Citywide RAPID Initiative in San Francisco. 2020. PMID: 32449916


  21. Sachdev DD, Cohen SE, Scheer S. Factors Contributing to Missing COVID-19 Cases During Contact Tracing-Reply. 2021. PMID: 33720284


  22. Johnson KA, Chen MJ, Kohn R, Sachdev D, Bacon O, Lee S, Cohen SE. Acute HIV at the time of initiation of Pre or Post Exposure Prophylaxis: Impact on drug-resistance and clinical outcomes. 2021. PMID: 33512849


  23. Lee A, Gaither TW, Langston ME, Cohen SE, Breyer BN. Lubrication Practices and Receptive Anal Sex: Implications for STI Transmission and Prevention. 2021. PMID: 33789174


  24. Sachdev DD, Brosnan HK, Reid MJA, Kirian M, Cohen SE, Nguyen TQ, Scheer S. Outcomes of Contact Tracing in San Francisco, California-Test and Trace During Shelter-in-Place. 2021. PMID: 33136116


  26. Tang EC, Vittinghoff E, Philip SS, Doblecki-Lewis S, Bacon O, Chege W, Coleman ME, Elion R, Buchbinder S, Kolber MA, Liu AY, Cohen SE. Quarterly screening optimizes detection of sexually transmitted infections when prescribing HIV pre-exposure prophylaxis. 2020. PMID: 32205724


  27. Campbell EM, Patala A, Shankar A, Li JF, Johnson JA, Westheimer E, Gay CL, Cohen SE, Switzer WM, Peters PJ. Phylodynamic Analysis Complements Partner Services by Identifying Acute and Unreported HIV Transmission. 2020. PMID: 32012700


  28. Johnson KA, Hessol NA, Kohn R, Nguyen TQ, Mara ES, Hsu L, Scheer S, Cohen SE. HIV Seroconversion in the Era of Pharmacologic Prevention: A Case-Control Study at a San Francisco STD Clinic. 2019. PMID: 31192823


  30. Clemenzi-Allen A, Hartogensis W, Cohen SE, Gandhi M, Geng E, Christopoulos K. Evaluating the Impact of Housing Status on Gonorrhea and Chlamydia Screening in an HIV Primary Care Setting. 2018. PMID: 30383619


  31. Luo W, Sullivan V, Smith T, Peters PJ, Gay C, Westheimer E, Cohen SE, Owen SM, Masciotra S. Performance evaluation of the Bio-Rad Geenius HIV 1/2 supplemental assay. 2018. PMID: 30594702


  32. Cohen SE, Sachdev D, Lee SA, Scheer S, Bacon O, Chen MJ, Okochi H, Anderson PL, Kearney MF, Coffey S, Scott H, Grant RM, Havlir D, Gandhi M. Acquisition of tenofovir-susceptible, emtricitabine-resistant HIV despite high adherence to daily pre-exposure prophylaxis: a case report. 2018. PMID: 30503324


  33. Nguyen TQ, Kohn RP, Ng RC, Philip SS, Cohen SE. Historical and Current Trends in the Epidemiology of Early Syphilis in San Francisco, 1955 to 2016. 2018. PMID: 29787467


  34. Doblecki-Lewis S, Liu AY, Feaster DJ, Cohen SE, Elion R, Bacon O, Coleman M, Cardenas G, Kolber MA. Patterns and Correlates of Participant Retention in a Multi-City Pre-Exposure Prophylaxis Demonstration Project. 2018. PMID: 29771790


  35. Tang EC, Vittinghoff E, Anderson PL, Cohen SE, Doblecki-Lewis S, Bacon O, Coleman ME, Buchbinder SP, Chege W, Kolber MA, Elion R, Shlipak M, Liu AY. Changes in Kidney Function Associated With Daily Tenofovir Disoproxil Fumarate/Emtricitabine for HIV Preexposure Prophylaxis Use in the United States Demonstration Project. Volume 77 of Issue 2. 2018. PMID: 28991887


  36. Hughes SD, Sheon N, Andrew EVW, Cohen SE, Doblecki-Lewis S, Liu AY. Body/Selves and Beyond: Men's Narratives of Sexual Behavior on PrEP. 2018. PMID: 29257911


  37. Henrich TJ, Hatano H, Bacon O, Hogan LE, Rutishauser R, Hill A, Kearney MF, Anderson EM, Buchbinder SP, Cohen SE, Abdel-Mohsen M, Pohlmeyer CW, Fromentin R, Hoh R, Liu AY, McCune JM, Spindler J, Metcalf-Pate K, Hobbs KS, Thanh C, Gibson EA, Kuritzkes DR, Siliciano RF, Price RW, Richman DD, Chomont N, Siliciano JD, Mellors JW, Yukl SA, Blankson JN, Liegler T, Deeks SG. HIV-1 persistence following extremely early initiation of antiretroviral therapy (ART) during acute HIV-1 infection: An observational study. Volume 14 of Issue 11. 2017. PMID: 29112956


  38. Gandhi M, Murnane PM, Bacchetti P, Elion R, Kolber MA, Cohen SE, Horng H, Louie A, Kuncze K, Koss CA, Anderson PL, Buchbinder S, Liu A. Hair levels of preexposure prophylaxis drugs measure adherence and are associated with renal decline among men/transwomen. 2017. PMID: 28832411


  39. Krakower DS, Cohen SE, Mayer KH. Top Questions in ID: Pre-exposure Prophylaxis for HIV. 2017. PMID: 29026872


  40. Doblecki-Lewis S, Liu A, Feaster D, Cohen SE, Cardenas G, Bacon O, Andrew E, Kolber MA. Healthcare Access and PrEP Continuation in San Francisco and Miami After the US PrEP Demo Project. Volume 74 of Issue 5. 2017. PMID: 27861236


  41. Marson KG, Marlin R, Pham P, Cohen SE, Jones D, Roemer M, Peters PJ, Haller B, Pilcher CD. Real-world performance of the new US HIV testing algorithm in medical settings. Volume 91. 2017. PMID: 28434809


  42. Masciotra S, Luo W, Westheimer E, Cohen SE, Gay CL, Hall L, Pan Y, Peters PJ, Owen SM. Performance evaluation of the FDA-approved Determine™ HIV-1/2 Ag/Ab Combo assay using plasma and whole blood specimens. 2017. PMID: 28372891


  43. Adams S, Luo W, Wesolowski L, Cohen SE, Peters PJ, Owen SM, Masciotra S. Performance evaluation of the point-of-care INSTI™ HIV-1/2 antibody test in early and established HIV infections. 2017. PMID: 28372890


  44. Wu H, Cohen SE, Westheimer E, Gay CL, Hall L, Rose C, Hightow-Weidman LB, Gose S, Fu J, Peters PJ. Diagnosing acute HIV infection: The performance of quantitative HIV-1 RNA testing (viral load) in the 2014 laboratory testing algorithm. 2017. PMID: 28342746


  45. Bacon O, Gonzalez R, Andrew E, Potter MB, Iñiguez JR, Cohen SE, Liu AY, Fuchs JD. Brief Report: Informing Strategies to Build PrEP Capacity Among San Francisco Bay Area Clinicians. Volume 74 of Issue 2. 2017. PMID: 27654813


  47. Marcus JL, Volk JE, Pinder J, Liu AY, Bacon O, Hare CB, Cohen SE. Successful Implementation of HIV Preexposure Prophylaxis: Lessons Learned From Three Clinical Settings. Volume 13 of Issue 2. 2016. PMID: 26898645


  48. Liu AY, Cohen SE, Vittinghoff E, Anderson PL, Doblecki-Lewis S, Bacon O, Chege W, Postle BS, Matheson T, Amico KR, Liegler T, Rawlings MK, Trainor N, Blue RW, Estrada Y, Coleman ME, Cardenas G, Feaster DJ, Grant R, Philip SS, Elion R, Buchbinder S, Kolber MA. Preexposure Prophylaxis for HIV Infection Integrated With Municipal- and Community-Based Sexual Health Services. Volume 176 of Issue 1. 2016. PMID: 26571482


  50. Woolston S, Cohen SE, Fanfair RN, Lewis SC, Marra CM, Golden MR. A Cluster of Ocular Syphilis Cases - Seattle, Washington, and San Francisco, California, 2014-2015. 2015. PMID: 26469141


  51. Cohen SE, Vittinghoff E, Doblecki-Lewis S, Coleman M, Bacon O, Elion R, Kolber MA, Buchbinder S, Liu AY. Authors' Reply: Race and the Public Health Impact Potential of Pre-Exposure Prophylaxis in the United States. Volume 70 of Issue 1. 2015. PMID: 26049284


  52. Cohen SE, Vittinghoff E, Bacon O, Doblecki-Lewis S, Postle BS, Feaster DJ, Matheson T, Trainor N, Blue RW, Estrada Y, Coleman ME, Elion R, Castro JG, Chege W, Philip SS, Buchbinder S, Kolber MA, Liu AY. High interest in preexposure prophylaxis among men who have sex with men at risk for HIV infection: baseline data from the US PrEP demonstration project. Volume 68 of Issue 4. 2015. PMID: 25501614


  53. Stoltey JE, Cohen SE. Syphilis transmission: a review of the current evidence. 2015. PMID: 25702043


  54. McMahon JM, Myers JE, Kurth AE, Cohen SE, Mannheimer SB, Simmons J, Pouget ER, Trabold N, Haberer JE. Oral pre-exposure prophylaxis (PrEP) for prevention of HIV in serodiscordant heterosexual couples in the United States: opportunities and challenges. 2014. PMID: 25045996


  55. Stephens SC, Fann CK, Strona FV, Wolf W, Cohen SE, Philip SS, Bernstein KT. Identifying syphilis risk networks through venue attendance in San Francisco. 2014. PMID: 24722390


  57. Marcotte T, Lee Y, Pandori M, Jain V, Cohen SE. Lymphogranuloma venereum causing a persistent genital ulcer. 2014. PMID: 24622642


  58. Cohen SE, Klausner JD, Engelman J, Philip S. Syphilis in the modern era: an update for physicians. 2013. PMID: 24275265


  59. Das M, Christopoulos KA, Geckeler D, Huriaux E, Cohen SE, Philip S, Shade S, Moss NJ, Morin SF, Charlebois ED. Linkage to HIV care in San Francisco: implications of measure selection. Volume 64 Suppl 1. 2013. PMID: 24126446


  60. Cohen SE, Liu AY, Bernstein KT, Philip S. Preparing for HIV pre-exposure prophylaxis: lessons learned from post-exposure prophylaxis. 2013. PMID: 23253767


  61. Korthuis PT, Feaster DJ, Gomez ZL, Das M, Tross S, Wiest K, Douaihy A, Mandler RN, Sorensen JL, Colfax G, McCarty D, Cohen SE, Penn PE, Lape D, Metsch LR. Injection behaviors among injection drug users in treatment: the role of hepatitis C awareness. 2011. PMID: 22209655


  62. Cohen SE, Chew Ng RA, Katz KA, Bernstein KT, Samuel MC, Kerndt PR, Bolan G. Repeat syphilis among men who have sex with men in California, 2002-2006: implications for syphilis elimination efforts. 2011. PMID: 22095364


  63. Yuhara H, Steinmaus C, Cohen SE, Corley DA, Tei Y, Buffler PA. Is diabetes mellitus an independent risk factor for colon cancer and rectal cancer? 2011. PMID: 21912438