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Clinician Educator Track (2 years)


The Clinician Educator Track provides training to fellows interested in pursuing a career with a clinical, education, and/or leadership focus (more so than research).  The first year of this fellowship track is very similar in structure to that of fellows in the research track and consists primarily of inpatient consult rotations at our various training sites.  The second year of the fellowship is individualized based on the fellow's Area of Emphasis and career goals, and includes a combination of clinical rotations, coursework, and protected time for scholarly projects.  Potential Areas of Emphasis within the Clinician Educator Track include (but are not limited to):

  • Antimicrobial Stewardship
  • General Infectious Diseases
  • HIV Medicine
  • Infection Prevention and Hospital Epidemiology
  • Medical Education
  • Transplant ID (solid organ and bone marrow transplant)

Year 1 Clinician Educator Sample Schedule

General ID
Hillcrest8 weeks

Jacobs6-8 weeks
San Diego VA12 weeks
Antimicrobial Stewardship, Infection Prevention, and Quality ImprovementSan Diego VA6 weeks
HIV Medicine 4 weeks
Oncologic ID 6 weeks
Solid Organ Transplant ID 4 weeks
Microbiology Lab 2 weeks
ID Outpatient Clinic ½ day weekly
4 weeks

Year 2 Clinician Educator Sample Schedule

Area of EmphasisRotations, Clinic, Scholarship
HIV Medicine
·       4 months of inpatient HIV Medicine 
·       1 month of another inpatient ID service 
·       6 months of scholarly project 
·       Weekly HIV continuity clinic 
·       4 weeks of vacation/CME
Transplant ID ·       3 months of SOT ID 
·       3 months of Onc ID 
·       5 months of weekly SOT/Onc ID clinic 
·       5 months of scholarly project 
·       Weekly HIV continuity clinic 
·       4 weeks of vacation/CME 
Antimicrobial Stewardship / IPCE ·       1 month of General ID 
·       1 month of SOT 
·       1 month of Onc ID 
·       1 month of HIV Medicine 
·       7 months of scholarly project 
·       7 months of weekly ID clinic 
·       Weekly HIV continuity clinic 
·       4 weeks of vacation/CME 

Research Track (3 years)


The Research Track provides training for fellows interested in pursuing a research career (including basic, translational, clinical, epidemiology, and/or global health research).  The first year of this fellowship track is very similar to the first year of the Clinician Educator Track and consists primarily of inpatient consult rotations at our various training sites.  During the second and third years, fellows spend the majority of their time (~80%) working with a mentor on a research project.  Fellows are supported by T32 training grants during their 2nd and 3rd year of fellowship, focusing either on general infectious diseases and antimicrobial resistance or HIV. 

Year 1 Research Track Sample Schedule

General IDHillcrest4-8 weeks

Jacobs4-8 weeks
San Diego VA12 weeks
Antimicrobial Stewardship, Infection Prevention, and Quality ImprovementSan Diego VA12 weeks
HIV Medicine 4-6 weeks
Oncologic ID 4-6 weeks
Solid Organ Transplant ID 4-6 weeks
Microbiology Lab 2 weeks
ID Outpatient Clinic ½ day weekly
Vacation/CME 4 weeks


Year 2 Research Track Sample Schedule

Research42 weeks
Inpatient ID consult rotations6 weeks
HIV continuity clinic½ day weekly
Vacation/CME4 weeks


Year 3 Research Track Sample Schedule

Research44 weeks
Inpatient ID consult rotations4 weeks
HIV continuity clinic½ day weekly
Vacation/CME4 weeks

Research Mentors

The following provides a brief list of our research mentors within and outside of the ID division.  Mentors are divided here into three different cores (antimicrobial resistance, HIV and other pandemics, and Epidemiology/Global Public Health), however, fellows many have research mentoring teams that include mentors from different cores.  Fellows may work with mentors not included in these lists. 

Research Faculty Mentors for Antimicrobial Resistance Core

Participating Faculty
Degree(s)RankPrimary Department or ProgramResearch Interest
Ayres, JanellePhDAdjunct ProfessorBiologyEvolutionary theory to understand microbe regulation of host physiology
Benson, ConstanceMDProfessorMedicineHIV/AIDS, viral hepatitus, influenza, TB clinical and translational research
Bradley, JohnMDProfessorPediatricsInnovative therapies for bacterial and viral infections
​Carlin, Aaron
​MD, PhD
​Assistant Professor
​Emerging Infectious Diseases, Host-pathogen interactions, genome-wide approaches to understanding pathogenesis; developing novel diagnostics and antimicrobials
Chu, HuitungPhDAssistant ProfessorPathologyCommensal microbe communication with Immune System
Crotty, ShanePhDAdjunct ProfessorMedicineVaccine Immunology
Dorrestein, PieterPhDProfessorSkaggs School of Pharmacy and Pharmaceutical SciencesMass Spectrometry characterization of metabolic interactions between cell populations
Fraley, StephaniePhDAssistant ProfessorBioengineeringMechanisms of cell migration, developing clinical profiling technologies
Gallo, RichardMDProfessorDermatologySkin biology and innate host defense
Gilbert, JackPhDProfessorPediatricsHospital microbial community in disease transmission and AMR gene reservoir
Glass, ChristopherMD,PhDProfessorCellular and Molecular MedicineRegulation of inflammation
Knight, RobPhDProfessorPediatricsComputational Biology, Genomics, and Human Microbiome
Ley, KlausMDAdjunct ProfessorBioengineeringControl of host inflammation in response to infection
Liu, GeorgeMD,PhDProfessorPediatricsHost pathogen interactions of MRSA, GBS, P. acnes
McKerrow, JamesMD,PhDProfessorSkaggs School of Pharmacy and Pharmaceutical SciencesDiscovery and Development of new drugs for neglected tropical diseases
Moore, BradleyPhDProfessorSkaggs School of Pharmacy and Pharmaceutical SciencesMechanisms in microbial antibiotic production, bioactive natural products
Nizet, VictorMDProfessorPediatricsBacterial Pathogenesis, Innate Immunity, novel aproaches to combat AMR
Palsson, BernhardPhDProfessorBioengineeringSystems Biology studys of genome to phenotype
Pogliano, JosephPhDProfessorBiologyCell biological tools to study mechanisms of antibiotic targeting of essential cellular processes
Pride, DavidMD,PhDAssociate ProfessorPathologyRNA and DNA virus contribution to pathogenesis and affect on host bacterial communities
Raffatellu, ManuelaMDProfessorPediatricsImmune response to mucosal pathogen infection
Rana, TariqPhDProfessorPediatricsRNA, stem cell, and chemical biology to discover pathways of human vial infections
Sakoulas, GeorgeMDAdjunct ProfessorPediatricsDrug synergies with host innate immunity
Schooley, RobertMDProfessorMedicineGlobal Infectious Disease, antiviral nanotherapies, phage therapy
Shresta, SujanPhDAssociate ProfessorMedicineImmunology and Virology of mosquito-borne pathogens
Siddiqui, AleemPhDProfessorMedicineMolecular Virology, hepatitus viruses and hepatocellular carcinoma
Steinmetz, Nicole PhDProfessorNanoengineeringDesign, development, and testing of biologics derived from plant viruses
Tan, GenePhDAssistant Adjunct ProfessorMedicineVirus-host interaction analyses
Winzeler, ElizabethPhDProfessorPediatricsGenome-wide methods identifying antimalarial drug resistance genes
Zhang, LiangfangPhDProfessornanoengineeringBiomimetic nanomedicine for drug delivery, detoxification, and vaccination

Research Faculty Mentors for HIV and other Pandemics Core

NameDegree(s)RankPrimary Department or ProgramResearch Interest
Bamford, LauraMDAssociate ProfessorMedicineHIV and HCV treatment and prevention in individuals with a history of opioid use disorder and injection drug use
Benson, ConstanceMDProfessorMedicineAntiretrovirals therapeutics, TB and HIV-related coinfections and comorbidities
Bharti, AjayMDAssociate ProfessorMedicineAdverse effects on brain function of co-infections such as hepatitis C, toxoplasmosis, malaria, and latent TB among persons living with HIV
Brouwer, KimberlyPhDProfessorSPHHIV epidemiology, Social and spatial epidemiology among marginalized populations; access to care
​Carlin, Aaron
​MD, PhD
​Assistant Professor
Emerging Infectious Diseases, Host-pathogen interactions, genome-wide approaches to understanding pathogenesis; developing novel diagnostics and antimicrobials
Chanda, SumitPhDResearch Assistant ProfessorSanford BurnhamHIV-host interactions
Crotty, ShanePhDProfessorLJICD4 T cell and germinal center reponses to candidate HIV vaccines
De Gruttola, VictorSc.D.Research Professor & Visiting ScholarMedicine/HarvardClinical and epidemiological research on HIV infection prevention and treatment
Ellis, RonaldMD, PhDProfessorNeuroscienceNeurological complications of HIV infection and substance use
Garfein, RichardPhD, MPHProfessorSPHInvestigation and intervention on the infectious disease consequences of substance Use
Gianella Weibel, SaraMDAssociate ProfessorMedicineTranslational virology, molecular biology and immunology, viral co-infections
Guatelli, JohnMDProfessorMedicineThe molecular virology and cell biology of two accessory genes of HIV-1: vpu and nef
Letendre, ScottMDProfessorMedicinePathogenesis and treatment of HIV comorbidities and neurologic infections
Little, SusanMDProfessorMedicineTranslational research related to transmission, prevention and pathogenesis of major viral pathogens
Looney, DavidMDAssociate ProfessorMedicineGene theraphy of HIV/AIDS using lentiviral vectors expressing RNAs (ribozymes, antisense RNA or siRNA
Martin, NatashaPhD, DPhilAssociate ProfessorMedicineEpidemic and economic modeling of HIV and related infectious disease transmission and prevention
Mehta, SanjayMDAssociate ProfessorMedicineMolecular epidemiology of HIV
Moore, DavidPhDProfessorPsychiatryCo-occuring conditions among persons with HIV, including mood disorders and substance use
Morris, SheldonMDAssociate ProfessorMedicinePrEP, STD
Nizet, VictorMDProfessorPediatricsbacterial pathogenesis and the innate immune system, with focus on human streptococcal and staphylococcal infections and emerging antibiotic-resistant pathogens
Richman, DouglasMDProfessor EmeritusPathologyHIV latency
Rodwell, TimothyMDAssociate ProfessorMedicineInfectious disease diagnostics with an emphasis on the development and implementation of rapid molecular diagnostics for TB
Schooley, RobertMDProfessorMedicineViral pathogenesis and therapy
Smith, DaveyMD, MASProfessorMedicineSexual transmission of HIV, acute HIV infection, drug resistance, genetic networks, virology
Stockman, JamilaPhD, MPHAssociate ProfessorMedicineHIV prevention and treatment research in the context of gender-based violence, substance abuse, mental health, and socio-structural barriers
Strathdee, SteffaniePhDProfessorMedicineHIV prevention among substance using populations
Wertheim, JoelPhDAssociate ProfessorMedicineHIV molecular epidemiology


Research Faculty Mentors for Epidemiology, Behavioral Science, and Global Public Health Core

NameDegree(s)RankPrimary Department or ProgramResearch Interest
Ayers, JohnPhDAssociate professor MedicineOnline network and social media predictors of public health
Borquez, AnnickPhDAssistant ProfessorMedicineSubstance use and HIV epidemiology
Bazzi, Angela (nee Robertson)
PhDAssociate ProfessorMedicineImprove the utilization of pre-exposure prophylaxis (PrEP) for HIV prevention in PWID
Blashill, Aaron J.PhDAssistant ProfessorPsychology (SDSU)Steroid use, sexual minorities, HIV risk behaviors
Brouwer, Kimberly C.PhDAssociate ProfessorFamily Medicine and Public HealthHIV epidemiology, Spatial and molecular epidemiology among substance user.
Chambers, ChristinaPhD, MPH



PediatricsEnvironmental causes of birth defects
Corliss, Heather L.MPH, PhDProfessorPublic Health (SDSU)Epidemiology of substance use & mental health, sexual minorities, stigma
Davidson, Peter J.PhDAssociate ProfessorMedicineHarm reduction and HIV, overdose, research ethics, mixed methods
De Gruttola, VictorScDVisiting ScholarFamily Medicine and Public HealthClinical and epidemiological research on HIV infection prevention and treatment
Fielding-Miller, RebeccaPhDAssistant ProfessorMedicineSocial and structural drivers of HIV, gender based violence, and COVID-19 in the United States and sub-Saharan Africa.
Gaines, TommiPhDAssociate ProfessorMedicineStatistical and spatial methodologies to examine patterns of infectious disease and illicit substance use
Garfein, Richard S.PhDProfessorMedicineInvestigation and Intervention on the Infectious Disease Consequences of Substance Use
Grelotti, David J.MDAssistant Clinical ProfessorPsychiatryEmergence of illicit drug cocktails mixed with ARVs, treatment of HIV psychosocial syndemics
Horvath, KeithPhDAssociate ProfessorPsychologymHealth interventions to address the HIV prevention and care continuum for sexual minority men.
Jain, SoniaPhDProfessorFamily Medicine and Public HealthBiostatistics and clinical trials for HIV/infectious diseases populations
Kiene, Susan M.PhDAssociate ProfessorPublic Health (SDSU)Alcohol and HIV prevention, substance use and HIV co-infections, maternal/child health
Martin, Natasha K.PhDAssociate Professor and Associate DirectorMedicineEpidemic and economic modeling of HIV and related infectious disease transmission and prevention
Patterson, Thomas L.PhDProfessor and Co-directorPsychiatryBehavioral interventions among substance users, RCT design and analysis, psychometrics
Pines, Heather A.PhDAssistant ProfessorMedicineHIV/STI transmission dynamics among substance users, molecular epidemiology, Social network analyses
Pitpitan, Eileen V.PhDAssociate ProfessorMedicineStructural interventions, mediator/moderator analyses
Reed, Elizabeth A.ScDAssociate ProfessorPublic Health (SDSU)Evaluation of economic and structural interventions; HIV, gender-based violence, and substance use
Reed, Mark B.PhDProfessorSocial Work (SDSU)Substance use etiology, young adult use trajectories, person-environment and gene-environment interactions and substance use
Shi, YuyanPhDAssociate ProfessorPublic HealthRegulatory, physical, economics, and marketing environments in relation to drug abuse and related consequences
Silverman, JayPhDProfessorMedicine

HIV risks related to sex trafficking and substance

use, gender-based violence, adolescent HIV/STI prevention

Skaathun, BrittPhDAssistant ProfessorMedicineUsing social, sexual, substance and molecular networks for HIV prevention and care
Smith, David M. MD, MASProfessorMedicineSexual transmission of HIV, acute HIV infection, drug resistance, genetic networks, virology
Smith, Laramie R. PhDAssistant ProfessorMedicineAccess to HIV care among substance users
Strathdee, Steffanie A. PhDProfessorMedicine

Epidemiology of bloodborne pathogens, injection drug use,

design and evaluation of behavioral and structural interventions

Strong, David R. PhDAssociate ProfessorPublic HealthSmoking, behavioral interventions, scale development
Stockman, Jamila K.PhDAssociate ProfessorMedicineGender-based violence and HIV; HIV and stress
Tsuyuki, KiyomiPhDAssistant ProfessorMedicineSocio-structural barriers and syndemic barriers to HIV testing, ART adherence, and HIV viral suppression
Urada, LiannePhDAssistant ProfessorSocial Work (SDSU)Homelessness during COVID-19: Exploring the usability and effects of telehealth interventions on buprenorphine treatment
Vaida, FlorinPhDProfessorFamily Medicine and Public HealthMixed-effects models, proportional hazards mixed-effects models, model selection, and clinical trials
Vasylyeva, TetyanaPhDAssistant ProfessorMedicinePhylodynamics and phylogeography to investigate how social, behavioral and biological factors affect HIV epidemics
Werb, Daniel M.PhDAssistant ProfessorMedicineInitiation of drug use and HIV; drug policy evaluation
Wynn, AdrianePhDAssistant ProfessorMedicineHarmful alcohol use, HIV, and other sexually transmitted infections in resource-limited
Zuniga, Maria L.PhDProfessorSocial Work (SDSU)Behavior among HIV+ Latino/a substance users, HIV stigma, qualitative analysis