The Scholar track constitutes an individualized two-year training program based on a specific area of interest. This track includes additional selected hospital clinical rotations and/or expanded ambulatory experiences (HIV, transplant infectious disease, etc.), extended electives in special areas (e.g. Infection Control, Clinical Microbiology) and scholarly activity leading to publication. Additional infectious diseases rotations at specialty centers, in particular areas of infectious diseases (e.g. sexually transmitted diseases, pediatrics) can be arranged. A focused clinical research project, either a retrospective or prospective study, or a quality assurance exercise is required as part of this track.

Immunocompromised Host/Transplant ID Track

The Immunocompromised Host/Transplant Infectious Diseases Service at Beth Israel Deaconess Medical Center provides world-class care to hospitalized and non-hospitalized patients with a broad range of infectious diseases issues related to immunosuppression. We have active basic science investigations, clinical research, and clinical trials within our program. Carolyn Alonso’s research focuses on the epidemiology and outcomes of C. difficile infection among transplanted patients with the ultimate goal of developing novel preventative and curative therapies for C.difficile. Sabrina Tan’s laboratory investigates the immune response to BK virus in renal transplant patients and novel therapies for treatment of BK virus. Stephen Walsh’s laboratory studies immune responses induced by a novel smallpox vaccine and has clinical trials evaluating novel treatments for RSV infection in stem cell transplant recipients. Barbra McDonagh Blair (read more) is a master clinician-educator whose work focuses on curricular innovation and improvement in Transplant ID and Microbiology and who serves as a leader in medical education at BIDMC as Firm Chief of the Kurland Firm for the Department of Medicine Residency Program.

Immunocompromised Host (ICH)/Transplant ID Training Track

During year two of fellowship, fellows interested in pursuing this focused ID Transplant training will:

  1. Engage in continued intensive inpatient and ambulatory Transplant ID consultation to expand experience:
    • Inpatient Transplant ID consults (12 week minimum)
      • 4 additional weeks BIDMC ICH ID consult team
      • 4 weeks additional off-site* HSCT ID consult rotation to expand experience/practice
      • 4 weeks off-site* SOT ID consult rotation with a focus on heart, lung transplant experience (BIDMC performs kidney, liver, pancreas SOT on-site)
        *Off-site opportunities are arranged based on fellow interest and rotation/faculty availability at collaborating sites, either within the Harvard affiliated hospitals and/or at appropriate academic centers outside of Boston with active Transplant ID Fellowships or structured rotations
    • Transplant Clinic (1 half day per week in addition to 1 half day per week ID continuity clinic)
      • Every other week SOT clinic on Lowry Bldg 7th Floor mentored by Dr. Blair
      • Every other week BMT clinic Wed afternoons Shapiro 7 mentored by Dr. Alonso
    • Multidisciplinary Team rounds – Weekly Friday afternoon patient care rounds involving BMT, Hematology faculty, Advanced Practitioners, Transplant ID Faculty and Transplant ID Track Fellow
  2. Research (scholarly project will be required with plan to produce at least one abstract for presentation at national meeting/manuscript for publication) - options for scholarly work dependent on fellow interest
    • Clinical research project - in association with BIDMC ID Transplant or external faculty mentor
    • Medical education project – curriculum development within Transplant ID
    • Assistance with review/updates to Transplant ID BIDMC Standard Operating Procedures (SOPs)
    • Review articles/Case Reports


During the second year, fellows interested in developing an expertise in microbiology can do a one-year Committee on Postgraduate Educational Programs (CPEP)-approved fellowship by working in the microbiology lab under the supervision of Drs. James Kirby (read more), Qinfang Qian, and Ramy Arnaout (read more). The goal of the program is to:

  • Train fellows to assume leadership roles in academic, tertiary care, and public health microbiology laboratories through hands-on instruction in:
    • Microbiological methods
    • The consultative and administrative activities of the microbiology laboratory
    • The activities of the infectious diseases, pharmacy, and infection control/hospital epidemiology departments.
  • Fellows will also rotate at Children's Hospital Boston and the Massachusetts State Laboratory to gain a comprehensive education experience that includes adult, pediatric and public health microbiology.
  • For fellows who desire additional training beyond this, and want to qualify to sit for board certification in medical and public health microbiology, they can continue their medical microbiology training for a second year, after which may take the American Board of Medical Microbiology (ABMM) credentialing exam. However, at this time, additional sources of funding would be needed for fellows wishing to pursue a second year of microbiology training.
  • During training fellows are highly encouraged to participate in scholarly projects related to infectious disease diagnostics.

Fellows interested in developing expertise in HPV and high resolution anoscopy (HRA) during year two of fellowship will work under the mentorship of Dr. Ami Multani at Fenway Community Health Center to develop the clinical skills needed to evaluate patients at risk for significant disease due to anogenital HPV infection, and obtain training to perform HRA in the clinical setting. Fellows will engage in hands on clinical/procedural training an average of 1-2 sessions/week (5-6 sessions per month x 10months).

Fellows will (during year 2):

  • Attend the American Society for Colposcopy and Cervical Pathology (ASCCP) Course
    • 4 day course with colposcopy and HRA training, typically in late July
  • Engage in HRA hands on clinical/procedural training – September – June
    • 1-2 clinic sessions/week with Dr. Multani and possibly other certified HRA providers as schedules allow
  • Goal is for trainee to graduate with competence in HRA diagnostic and treatment interventions so he/she can become an independent HRA provider and explore this as a potential clinical ID career avenue, with the objective to become certified with the AIDS Malignancy Consortium (AMC)
  • Develop and conduct a research or QI project focused on HPV or anal dysplasia and present findings at a national conference or publish findings in a peer-reviewed journal
  • Present at fellow/faculty teaching conferences both BIDMC and Fenway Community Health

Medical Education

Fellows interested in developing expertise in medical education will work under the mentorship of Dr. Wendy Stead (read more). This track is designed for those interested in clinician-educator career paths, so fellows will also identify an area of clinical focus in ID to be further developed by specialty clinic experiences during year two of fellowship. Fellows in this track will apply to the Department of Medicine’s BIDMC Clinician Educator Track ( and, if accepted, will take part in the longitudinal medical education curriculum, in addition to completing a mentored medical education research project, during year two.  Outline of track structure below:

Clinical Activities

  • 2-3 clinics per week
    • ID continuity clinic
    • Specialty clinics to be determined based on fellow's clinical interest (examples include HIV, hepatitis, HPV/HRA, TB, Transplant, Refugee Health, Travel)
  • Additional 5-6 weeks of ID inpatient consult service time 
    • At least 2 of these weeks as "supervising" fellow (junior fellows present cases to supervising fellow for teaching/guidance under the supervision of service attending)
  • Medical education fellow will be expected to provide advanced level teaching to junior fellows and will receive formal feedback by supervising attending.

Medical Education Scholarly Activities

  • Apply to BIDMC Department of Medicine Clinician Educator Track (CET) for Fellows
  • Develop and conduct a focused medical education project in a designated area of interest with plans to disseminate findings at a national meeting and/or in a peer-reviewed journal
    • Examples of recent projects completed by ID medical education track fellows:
      • A workshop to improve communication and reduce stigma and implicit bias in the care of patients with opioid use disorder (Colleen Kershaw MD, 2018 graduate)
      • An opioid overdose curriculum for medical residents: Impact on naloxone prescribing, knowledge, and attitudes (Alison Rapoport MD, 2017 graduate)
      • Survey and needs assessment of resident expectations for elective subspecialty rotations at BIDMC followed by development of web-based core curriculum for medical students and residents rotating on the ID consult service –  (Andy Hale MD, 2017 graduate)
  • Develop and lead lectures for ID clinical conferences with post-lecture formal feedback on teaching skills
  • Participate in medical student teaching opportunities (patient-doctor courses, participation in preclinical ID curriculum at Harvard Medical School)
  • Become a member of the BIDMC Academy of Medical Educators ( and participate regularly in medical education symposia and lectures

Antimicrobial Stewardship Scholar Track

This is a 1-2 year track for a senior ID fellow interested in a future ID career with an AST component. The training will encompass all aspects of stewardship including pre-prescriptive review of antibiotic choices with weekly feedback with the Director of the AST program (Dr. Howard Gold), training courses such as the SHEA Antibiotic Stewardship Training Course, participation in teaching of the AST curriculum to fellows, housestaff, and interprofessional learners, interfacing with the microbiology lab to develop and interpret antibiograms, as well as working with the hospital-wide committees such as the antibiotic subcommittee of the P&T Committee which determines which antibiotics should be on formulary.

For a one year experience (during the second year of the ACGME ID Fellowship training), funding will be provided by the ID division. For fellows desiring a third year of training, either hospital funding or independent funding will need to be secured by the fellow and his/her mentor.