Stephanie Cohen, MD

Associate Clin Prof Volunteer

Infectious Diseases

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.

Residency, - Internal Medicine, University of California, San Francisco
  1. 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. The New England journal of medicine 2024. PMID: 38865666

  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 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. medRxiv : the preprint server for health sciences 2024. PMID: 38585951

  3. 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. Sexually transmitted diseases 2023. PMID: 38079243

  4. 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. Emerging infectious diseases 2023. PMID: 37832516

  5. Johnson KA, Sankaran M, Kohn RP, Bacon O, Cohen SE. 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. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022. PMID: 36575605

  6. 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? Sexually transmitted diseases 2022. PMID: 36538488

  7. 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. Public health reports (Washington, D.C. : 1974) 2022. PMID: 36239486

  8. 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. MMWR. Morbidity and mortality weekly report 2022. PMID: 36074735

  9. 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

  10. Johnson KA, Levy M, Brosnan H, Kohn RP, Cohen SE. Texting Lost-to-follow-up PrEP Patients from a San Francisco Sexual Health Clinic. Prevention science : the official journal of the Society for Prevention Research 2022. PMID: 35841493

  11. 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. mSphere 2022. PMID: 35491834

  12. 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

  13. 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

  14. 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. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020. PMID: 32449916

  15. Sachdev DD, Cohen SE, Scheer S. Factors Contributing to Missing COVID-19 Cases During Contact Tracing-Reply. Volume 181 of Issue 7. 2021. PMID: 33720284

  16. Johnson KA, Chen MJ, Kohn R, Sachdev D, Bacon O, Lee S, Cohen SE. Acute HIV at the Time of Initiation of Pre-exposure or Post-exposure Prophylaxis: Impact on Drug Resistance and Clinical Outcomes. 2021. PMID: 33512849

  17. Lee A, Gaither TW, Langston ME, Cohen SE, Breyer BN. Lubrication Practices and Receptive Anal Sex: Implications for STI Transmission and Prevention. Volume 9 of Issue 3. 2021. PMID: 33789174

  18. 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. JAMA internal medicine 2020. PMID: 33136116

  19. Cohen SE, Kelley CF. Is the United States Ready for Event-Driven Human Immunodeficiency Virus Preexposure Prophylaxis? Volume 71 of Issue 2. 2020. PMID: 31436811

  20. 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. AIDS (London, England) 2020. PMID: 32205724

  21. 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. Volume 12 of Issue 2. 2020. PMID: 32012700

  22. 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. Volume 82 of Issue 2. 2019. PMID: 31192823

  23. Lopez MI, Cocohoba J, Cohen SE, Trainor N, Levy MM, Dong BJ. Implementation of pre-exposure prophylaxis at a community pharmacy through a collaborative practice agreement with San Francisco Department of Public Health. Volume 60 of Issue 1. 2019. PMID: 31405804

  24. 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. Sexually transmitted diseases 2018. PMID: 30383619

  25. 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. Volume 111. 2018. PMID: 30594702

  26. 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. The lancet. HIV 2018. PMID: 30503324

  27. 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. Volume 45 of Issue 9S Suppl 1. 2018. PMID: 29787467

  28. 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. Journal of acquired immune deficiency syndromes (1999) 2018. PMID: 29771790

  29. 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. Journal of acquired immune deficiency syndromes (1999) 2018. PMID: 28991887

  30. 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. Volume 37 of Issue 5. 2018. PMID: 29257911

  31. 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. PLoS medicine 2017. PMID: 29112956

  32. 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. AIDS (London, England) 2017. PMID: 28832411

  33. Krakower DS, Cohen SE, Mayer KH. Top Questions in ID: Pre-exposure Prophylaxis for HIV. Volume 4 of Issue 4. 2017. PMID: 29026872

  34. 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. Journal of acquired immune deficiency syndromes (1999) 2017. PMID: 27861236

  35. 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. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017. PMID: 28434809

  36. 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. Volume 91. 2017. PMID: 28372891

  37. 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. Volume 91. 2017. PMID: 28372890

  38. 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. Volume 93. 2017. PMID: 28342746

  39. 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. Journal of acquired immune deficiency syndromes (1999) 2017. PMID: 27654813

  40. Carlo Hojilla J, Koester KA, Cohen SE, Buchbinder S, Ladzekpo D, Matheson T, Liu AY. Sexual Behavior, Risk Compensation, and HIV Prevention Strategies Among Participants in the San Francisco PrEP Demonstration Project: A Qualitative Analysis of Counseling Notes. Volume 20 of Issue 7. 2016. PMID: 25835463

  41. 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. Current HIV/AIDS reports 2016. PMID: 26898645

  42. 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. JAMA internal medicine 2016. PMID: 26571482

  43. Stoner BP, Cohen SE. Lymphogranuloma Venereum 2015: Clinical Presentation, Diagnosis, and Treatment. Volume 61 Suppl 8. 2015. PMID: 26602624

  44. 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. Volume 64 of Issue 40. 2015. PMID: 26469141

  45. 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. Journal of acquired immune deficiency syndromes (1999) 2015. PMID: 26049284

  46. 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. Journal of acquired immune deficiency syndromes (1999) 2015. PMID: 25501614

  47. Stoltey JE, Cohen SE. Syphilis transmission: a review of the current evidence. Volume 12 of Issue 2. 2015. PMID: 25702043

  48. 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. Volume 28 of Issue 9. 2014. PMID: 25045996

  49. Stephens SC, Fann CK, Strona FV, Wolf W, Cohen SE, Philip SS, Bernstein KT. Identifying syphilis risk networks through venue attendance in San Francisco. Volume 41 of Issue 5. 2014. PMID: 24722390

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

  51. Cohen SE, Klausner JD, Engelman J, Philip S. Syphilis in the modern era: an update for physicians. Volume 27 of Issue 4. 2013. PMID: 24275265

  52. 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. Journal of acquired immune deficiency syndromes (1999) 2013. PMID: 24126446

  53. Cohen SE, Liu AY, Bernstein KT, Philip S. Preparing for HIV pre-exposure prophylaxis: lessons learned from post-exposure prophylaxis. Volume 44 of Issue 1 Suppl 2. 2013. PMID: 23253767

  54. 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. Volume 37 of Issue 4. 2011. PMID: 22209655

  55. 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. Volume 102 of Issue 1. 2011. PMID: 22095364

  56. 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? Volume 106 of Issue 11. 2011. PMID: 21912438