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The fellowship is a one year program for physicians board certified or eligible in Clinical Pathology or Infectious Diseases that combines clinical, research and teaching responsibilities. The fellow's primary responsibilities are at Yale-New Haven Hospital, with rotation through a Public Health Laboratory.

The ACGME-accredited Medical Microbiology Fellowship training program at Yale New Haven Medical Center and VA Connecticut Healthcare is designed to provide a comprehensive experience in all aspects of diagnostic microbiology including consultative clinical practice, state-of-the-art diagnostic testing, multi-level teaching and an understanding of the principles of biomedical research. Instruction and practical experience occurs for all aspects of infectious disease diagnosis: bacteriology, mycology, mycobacteriology, parasitology, virology, serology, histopathology of infections, molecular diagnostics, and emerging technologies such as MALDI-TOF-MS and next-generation sequencing.

The microbiology fellow has responsibilities in the Clinical Microbiology, Virology, and Molecular Diagnostics laboratories of Yale-New Haven Hospital. A primary task is clinical management of difficult cases, including coordination and consultation with laboratory and clinical staff. Issues addressed by the fellow include indications for and interpretation of specialized assays (specialized antimicrobial susceptibility procedures, send-out tests, molecular diagnostic methods, etc.), the diagnostic approach to and specimen collection for unusual cases of infectious disease, and discussion of unusual organisms or test results. The medical microbiology fellow organizes and runs the daily teaching/clinical rounds with the infectious disease service. The fellow also participates in Yale-New Haven Hospital Epidemiology and Infection Control Committee meetings.

VA Connecticut Healthcare provides a second training site. In addition to bacteriology serving the local VA facility, VA Connecticut features mycobacteriology, virology, and molecular diagnostics reference laboratories serving the New England VA hospitals and other client. The VA training site provides trainees with a distinctly different training environment with different instrumentation, clinical population, and scope of services, broadening the fellowship experience.

The program envisions our trainees, and all clinical microbiologists, as being active members of the diagnostic and therapeutic team caring for patients with infectious disease. Close communication with colleagues is emphasized; the fellow participates in daily formal rounds with the infectious disease teams as well as providing other consultative services. The clinical microbiologist must also be an excellent teacher and communicator - hence the fellow is given significant responsibility for presenting at multidisciplinary conferences. Moreover, we believe that a clinical microbiologist should be able to understand and bring to his/her practice cutting edge diagnostic modalities that pass the test of "evidence-based" medical practice. Toward this end, the program provides training in some of the principles of state-of-the-art basic, clinical and translational research through active participation in a journal club, by providing for attendance at a national meeting, and by having the trainee carry out at least one significant clinically-oriented research project during their year of clinical training. In addition, the fellow is involved in clinical conferences, research conferences, and other academic activities of the Department of Laboratory Medicine.

Salary and Benefits

Salary is commensurate with the year of postgraduate training. The standard Yale University benefits package applies.


The arrangement of the fellowship is flexible and can be arranged to best suit the needs of individual fellows.

Other Opportunities

Rotations in Public Health Microbiology are scheduled via the Connecticut Public Health Laboratory, and the Connecticut Agricultural Experiment Station in New Haven.

A further opportunity to gain teaching experience in the laboratory portion of the Medical Microbiology course of the medical school is also part of the fellowship.

It is expected that the fellow will pursue a basic or applied research project during the fellowship. Funding is available for travel to present research results at a national meeting.


The Yale-New Haven Medical Center provides a rich clinical, educational, and research environment for fellowship training in medical microbiology.

The fellowship is centered at the Clinical Microbiology laboratory of Yale-New Haven Hospital. The laboratory provides state-of-the-art diagnostic microbiology services to the hospital's inpatient and outpatient care programs, which include active bone marrow, stem cell, and solid organ transplantation programs, HIV/AIDS care, cancer center, trauma center, and an active Tropical Medicine clinic.

Yale-New Haven Hospital is a primary clinical campus for Yale University School of Medicine. The medical school faculty has active research projects in many areas related to infectious disease. A partial list would include projects studying the pathogenesis of intracellular protozoal infections, molecular pathways of macrophage action, gene regulation of HIV infection and production of novel anti-HIV therapies, RNA metabolism in African trypanosomes, host-pathogen interactions in Salmonella infection, processing and presentation to T lymphocytes of antigens derived from intracellular pathogens, pathogenesis of pathogenesis of invasive fungal disease, and intracellular survival of Legionella, as well as many others. A wide variety of clinical research projects in infectious disease, especially protocols related to AIDS care, are ongoing at the medical center.

VA Connecticut provides primary and specialty care for Connecticut veterans within the larger integrated VA health care system. VA Connecticut laboratories function within Veteran’s Integrated Service Network 1 (VISN 1), serving Connecticut, Rhode Island, Massachusetts, Vermont, New Hampshire, and Maine. As part of the Network Consolidated Laboratories, VA Connecticut labs provide laboratory to both local VA CT patients and reference services within the VISN, and beyond.



Applications must be completed in the year prior to when the fellowship begins, however earlier completion is strongly encouraged.


Applicants must be physicians who are board eligible or certified in either Pathology by American Board of Pathology, or in either adult or pediatric Infectious Disease by the American Board of Medical Specialties or the American Board of Pediatrics. Graduates of our fellowship must be eligible for boards in Clinical Microbiology according to the American Board of Pathology (ABP) criteria.

Inquiries about eligibility should be addressed to the Fellowship Director, Dr. David Peaper, at

CAP Application

Complete the standardized CAP fellowship application. Please provide the documents requested on the application.

Please send a CV, the completed CAP fellowship application, and a statement of your interest in Medical Microbiology

We also require three letters of reference sent directly the One of those letters should be from the Chair or the residency director of your prior training program.

Fellowship application, letters of recommendation, and curriculum vitae should be sent to:

Microbiology Fellowship Director
Clinical Microbiology Laboratory
Yale-New Haven Hospital
20 York St. - PS 653a
New Haven, CT 06510-3202

Or electronically to: