Honors & Awards

  • Post-doctoral Fellow, Stanford Spectrum KL2 Mentored Career Development Award (10/2015-)
  • Research Fellow, Doris Duke International Clinical Research Fellowship (7/2008-6/2009)

Boards, Advisory Committees, Professional Organizations

  • Member, IDSA (2015 - Present)

Professional Education

  • Medical Education:University of California at San Francisco School of Medicine (2010) CA
  • Board Certification, American Board of Internal Medicine, Infectious Diseases (2015)
  • Board Certification: Internal Medicine, American Board of Internal Medicine (2013)
  • Fellowship:Stanford University - Infectious Diseases (2016) CA
  • Internship, New York University, Internal Medicine (2011)
  • Residency, New York University, Internal Medicine (2013)
  • Doctor of Medicine, University of California San Francisco (2010)
  • Bachelor of Science, University of California Davis (2004)

Stanford Advisors

Community and International Work

  • Ebola Response Clinician, Port Loko, Sierra Leone


    Provided clinical care for patients infected with EVD in Sierra Leone

    Partnering Organization(s)

    Partners in Health

    Populations Served

    Ebola-infected patients



    Ongoing Project


    Opportunities for Student Involvement


Service, Volunteer and Community Work

  • HIV/AIDS Physician, PACE Clinic - Santa Clara Valley Medical Center

    Provide care for patients with HIV/AIDS


    San Jose, CA

Research & Scholarship

Current Clinical Interests

  • Infectious Diseases


Graduate and Fellowship Programs


All Publications

  • HIV-1 drug resistance and resistance testing. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Clutter, D. S., Jordan, M. R., Bertagnolio, S., Shafer, R. W. 2016


    The global scale-up of antiretroviral (ARV) therapy (ART) has led to dramatic reductions in HIV-1 mortality and incidence. However, HIV drug resistance (HIVDR) poses a potential threat to the long-term success of ART and is emerging as a threat to the elimination of AIDS as a public health problem by 2030. In this review we describe the genetic mechanisms, epidemiology, and management of HIVDR at both individual and population levels across diverse economic and geographic settings. To describe the genetic mechanisms of HIVDR, we review the genetic barriers to resistance for the most commonly used ARVs and describe the extent of cross-resistance between them. To describe the epidemiology of HIVDR, we summarize the prevalence and patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) in both high-income and low- and middle-income countries (LMICs). We also review to two categories of HIVDR with important public health relevance: (i) pre-treatment drug resistance (PDR), a World Health Organization-recommended HIVDR surveillance metric and (ii) and pre-exposure prophylaxis (PrEP)-related drug resistance, a type of ADR that can impact clinical outcomes if present at the time of treatment initiation. To summarize the implications of HIVDR for patient management, we review the role of genotypic resistance testing and treatment practices in both high-income and LMIC settings. In high-income countries where drug resistance testing is part of routine care, such an understanding can help clinicians prevent virological failure and accumulation of further HIVDR on an individual level by selecting the most efficacious regimens for their patients. Although there is reduced access to diagnostic testing and to many ARVs in LMIC, understanding the scientific basis and clinical implications of HIVDR is useful in all regions in order to shape appropriate surveillance, inform treatment algorithms, and manage difficult cases.

    View details for DOI 10.1016/j.meegid.2016.08.031

    View details for PubMedID 27587334

  • Response to Therapy in Antiretroviral Therapy-Naive Patients With Isolated Nonnucleoside Reverse Transcriptase Inhibitor-Associated Transmitted Drug Resistance JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES Clutter, D. S., Fessel, W. J., Rhee, S., Hurley, L. B., Klein, D. B., Ioannidis, J. P., Silverberg, M. J., Shafer, R. W. 2016; 72 (2): 171-176


    Nonnucleoside reverse-transcriptase inhibitor (NNRTI)-associated transmitted drug resistance (TDR) is the most common type of TDR. Few data guide the selection of antiretroviral therapy (ART) for patients with such resistance.We reviewed treatment outcomes in a cohort of HIV-1-infected patients with isolated NNRTI TDR who initiated ART between April 2002 and May 2014. In an as-treated analysis, virological failure (VF) was defined as not reaching undetectable virus levels within 24 weeks, virological rebound, or switching regimens during viremia. In an intention-to-treat (ITT) analysis, failure was defined more broadly as VF, loss to follow-up (LTFU), and switching during virological suppression.Of 3,245 patients, 131 (4.0%) had isolated NNRTI TDR. 122 received a standard regimen comprising two NRTIs plus a boosted protease inhibitor (bPI; n=54), an integrase strand transfer inhibitor (INSTI; n=52), or an NNRTI (n=16). The median follow-up was 100 weeks. In the as-treated analysis, VF occurred in 15% (n=8), 2% (n=1) and 25% (n=4) of patients in the bPI, INSTI and NNRTI groups, respectively. In multivariate regression, there was a trend toward a lower risk of VF with INSTIs than with bPIs (HR 0.14; 95% CI, 0.02,1.1; p = 0.07). In ITT multivariate regression, INSTIs had a lower risk of failure than bPIs (HR 0.38; 95% CI, 0.18,0.82; p = 0.01).Patients with isolated NNRTI TDR experienced low VF rates with INSTIs and bPIs. INSTIs were non-inferior to bPIs in an analysis of VF but superior to bPIs when frequency of switching and LTFU were also considered.

    View details for Web of Science ID 000378059300017

    View details for PubMedID 26855248

  • Genetic Variability of HIV-1 for Drug Resistance Assay Development. Viruses Clutter, D. S., Sánchez, P. R., Rhee, S., Shafer, R. W. 2016; 8 (2)


    A hybridization-based point-of-care (POC) assay for HIV-1 drug resistance would be useful in low- and middle-income countries (LMICs) where resistance testing is not routinely available. The major obstacle in developing such an assay is the extreme genetic variability of HIV-1. We analyzed 27,203 reverse transcriptase (RT) sequences from the Stanford HIV Drug Resistance Database originating from six LMIC regions. We characterized the variability in a 27-nucleotide window surrounding six clinically important drug resistance mutations (DRMs) at positions 65, 103, 106, 181, 184, and 190. The number of distinct codons at each DRM position ranged from four at position 184 to 11 at position 190. Depending on the mutation, between 11 and 15 of the 24 flanking nucleotide positions were variable. Nonetheless, most flanking sequences differed from a core set of 10 flanking sequences by just one or two nucleotides. Flanking sequence variability was also lower in each LMIC region compared with overall variability in all regions. We also describe an online program that we developed to perform similar analyses for mutations at any position in RT, protease, or integrase.

    View details for DOI 10.3390/v8020048

    View details for PubMedID 26875985

  • Fidaxomicin versus Conventional Antimicrobial Therapy in 59 Recipients of Solid Organ and Hematopoietic Stem Cell Transplantation with Clostridium difficile-Associated Diarrhea ANTIMICROBIAL AGENTS AND CHEMOTHERAPY Clutter, D. S., Dubrovskaya, Y., Merl, M. Y., Teperman, L., Press, R., Safdar, A. 2013; 57 (9): 4501-4505


    The feasibility of fidaxomicin versus vancomycin and metronidazole (conventional therapy) was assessed in 59 transplant recipients with 61 episodes of Clostridium difficile-associated diarrhea (CDAD). Overall clinical cure was achieved in 86% of episodes, and in 7% of episodes, infection recurred. Fidaxomicin was well tolerated. Clinical cures were not significantly different compared with conventional therapy (67% versus 89%, respectively; P = 0.06). Univariate analysis of predictors for lack of clinical cure included continued use of broad-spectrum systemic antibiotics (P = 0.026) and prior diagnosis of CDAD (95% confidence interval, 1.113 to 19.569; odds ratio, 4.667; P = 0.041). New-onset vancomycin-resistant Enterococcus (VRE) colonization was not noted after fidaxomicin therapy alone. However, this occurred in 10 of 28 patients (36%) following conventional therapy, and 2 of 3 patients with subsequent bacteremia died.

    View details for DOI 10.1128/AAC.01120-13

    View details for Web of Science ID 000323285500052

    View details for PubMedID 23836168

  • Investigation of a novel, heritable bleeding diathesis of thoroughbred horses and development of a screening assay JOURNAL OF VETERINARY INTERNAL MEDICINE Norris, J. W., Pratt, S. M., Auh, J., Wilson, S. J., Clutter, D., Magdesian, K. G., Ferraro, G. L., Tablin, F. 2006; 20 (6): 1450-1456


    Bleeding in racing horses associated with exercise appears to be multifactorial, and clinical investigation into severe cases rarely occurs. Previously, we reported a severe bleeding diathesis in a Thoroughbred mare. Herein, we describe the cellular physiology of this defect, provide a diagnostic tool for identifying it, and demonstrate that the dysfunction is heritable.The subject has a heritable defect in platelet secretion that reduces thrombin generation in the absence of additional plasma factors and delays the onset of thrombin production even in the presence of these factors.The study included 3 clinically normal Thoroughbred horses: the subject and her offspring.Washed platelets were examined for their ability to (1) translocate phosphatidylserine to the outer leaflet of the platelet membrane as determined by annexin-V binding, (2) generate thrombin as assessed by the activity of the prothrombinase enzyme complex, and (3) bind fibrinogen and form aggregates as determined by flow cytometry.Subject and offspring platelets created procoagulant surfaces by translocating phosphatidylserine. The subject's platelets demonstrated reduced prothrombinase activity, resulting in decreased production of thrombin relative to control platelets. Subject and offspring platelets bound less fibrinogen than control platelets when stimulated with thrombin.The subject mare has a transmissible defect that involves reduced generation of thrombin by activated platelets, resulting in decreased aggregation and ineffective clotting. A flow cytometric assay of fibrinogen binding to washed platelets discriminates individuals with this platelet dysfunction and may be useful for discerning subclinical congenital or acquired platelet dysfunctions.

    View details for Web of Science ID 000242567200028

    View details for PubMedID 17186864

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