Clinical microbiology fellow pipetting in the lab

Graduate medical education in laboratory medicine and pathology at Mayo Clinic

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The Clinical Microbiology Fellowship at Mayo Clinic's campus in Rochester, Minnesota, is designed to provide extensive training in medical microbiology. This fellowship develops your knowledge and skills in diagnostic microbiology, clinical consultation related to microbiology and infectious diseases, and clinical laboratory management. A strong emphasis is also placed on laboratory research, particularly on the development, validation, verification, and implementation of new diagnostic tests.

You receive training in all areas of clinical microbiology, including the isolation, identification, and antimicrobial susceptibility testing of bacteria, mycobacteria, fungi, and viruses, and the detection and identification of parasites, using traditional and novel techniques.

The Clinical Microbiology Fellowship also includes training in immunodiagnostic procedures for the diagnosis of bacterial, fungal, viral, and parasitic infections. You receive training in the use of molecular diagnostic techniques, including real-time polymerase chain reaction (PCR), DNA sequencing, mass spectrometry, and other molecular methods.

Special emphasis is placed on clinical-laboratory correlation, interpretation of laboratory results, and the planning, organization, performance, and analysis of new diagnostic tests. Strong mentorship is provided through daily interactions with the medical laboratory directors and education specialists.

Individuals appropriate for the program are those interested in gaining knowledge and experience to help them direct clinical microbiology laboratories and become eligible for board certification in this specialty.

Mayo Clinic offers two clinical microbiology fellowship programs:

  • Ph.D. program. The Ph.D. program is a two-year program designed for fellows with a doctoral degree who want specific training in clinical microbiology.
  • M.D. program. The M.D. program is a one-year program designed for fellows with a medical degree and acceptable previous residency training in the U.S. or Canada in pathology or an infectious diseases fellowship.

Both programs provide comprehensive training and hands-on experience and have a strong clinical component, which includes on-call responsibilities with each rotation. Both programs also include laboratory and management training, including participation in a laboratory medicine leadership course and a laboratory directorship rotation.

When you successfully complete either program, you will be prepared for a career as a director of a clinical microbiology laboratory that diagnoses infections caused by bacteria, fungi, mycobacteria, parasites, and viruses.

In both the one- and two-year programs, you learn:

  • Principles and procedures involved in the proper selection and collection of specimens
  • Methods to perform immunoassays to detect antibodies formed against bacterial, viral, fungal, and parasitic pathogens
  • Methods used to cultivate microorganisms
  • The detection process for microbial antigens, nucleic acids, or metabolic products
  • The significance and interpretation of laboratory results as they pertain to various host populations
  • Principles of laboratory management, including quality system essentials, leadership, conflict resolution, finance and budgeting, coding, personnel management, and laboratory safety


The Ph.D. program is accredited by the Committee on Postgraduate Educational Programs of the American Society for Microbiology.

The M.D. program is accredited by the Accreditation Council for Graduate Medical Education (ACGME) and meets the certification requirements of the American Board of Pathology (in Medical Microbiology).


When you successfully complete Mayo Clinic's Clinical Microbiology Fellowship Ph.D. program and the experience requirement, you will be eligible for certification by the American Board of Medical Microbiology.

When you successfully complete the M.D. program, you will be eligible for certification by the American Board of Medical Microbiology and the American Board of Pathology (in Medical Microbiology).

Bobbi Pritt, M.D., (left) is the director of the M.D. fellowship and Elli Theel, Ph.D., (right) is the director of the Ph.D. fellowship.

Meet the Faculty

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Choosing Mayo Clinic

Mayo Clinic campus in Rochester, Minnesota.
Campus and community

Rochester, MN

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Stipend and benefits