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Lab work in the Clinical Microbiology program

Clinical training

Mayo Clinic's campus in Rochester, minnesota, offers two Clinical Microbiology Postgraduate Fellowships: the Ph.D. (CPEP) program and the M.D. (ACGME) program.

CPEP program

The two-year Clinical Microbiology Ph.D. (CPEP) Postgraduate Fellowship leads to certification by the American Board of Medical Microbiology (ABMM) in Medical and Public Health Laboratory Microbiology.

First year

During your first year of training, you will rotate through the bacteriology, mycobacteriology, mycology, molecular microbiology, virology, parasitology, and infectious disease serology laboratories. These rotations emphasize the practical aspects of clinical microbiology. You become proficient in pre-analytical, analytical, and post-analytical phases of diagnostic testing, including processing specimens, performing procedures at the bench, and result reporting and interpretation.

The first year also has a strong didactic component, with interactive lectures, small group discussions, and one-on-one education. As a fellow, you will gain additional knowledge and experience through providing case-based clinical presentations and error/event analysis. In addition to microbiology-specific education, training is provided in leadership management and the pathology of infectious diseases.

Second year

You will have a broad range of experiences during your second year of training:

  • Division of Infectious Diseases. As a fellow, you will spend at least three months rotating with our infectious disease clinicians. While there, you will learn how results from the clinical microbiology laboratory are interpreted and applied for patient care. Additionally, you will learn to integrate clinical and microbiological data for diagnostic, interpretive, and prognostic purposes.
  • Hospital infection control. During this two-week assignment, you learn about the specific functions and daily responsibilities of a nurse epidemiologist. This includes recognizing and controlling nosocomial infections and using proper methods to sterilize hospital equipment and supplies.
  • Minnesota Department of Health. During the second year of training, you will spend two weeks training in St. Paul, Minnesota, at the Minnesota Department of Health Infectious Disease Laboratory. You will work in laboratory management, epidemiology, and the state laboratory quality assurance program. At the bench level, you will learn procedures for collecting and processing food and stool specimens for pathogenic microorganisms, the principles of water bacteriology, and detection techniques for the rabies virus.
  • Test development and research. After completing the previous rotations, you will spend the rest of your second year participating in the development and implementation of a new diagnostic test or completing an independent research project. 
  • External Laboratory Directorship Rotation. Fellows may select a one-month rotation in the clinical microbiology laboratory at either the Mayo Clinic campus in Scottsdale, Arizona, or Jacksonville, Florida.

ACGME program

The Clinical Microbiology M.D. (ACGME) Postgraduate Fellowship 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). 

This one-year training program generally matches the first year of the CPEP Fellowship, but your schedule can be modified based on your prior training, experience, and specific areas of interest. Individuals with anatomic pathology experience have the opportunity to actively participate in the infectious diseases pathology consult service. 

Didactic training

As a fellow in the Clinical Microbiology, M.D. (ACGME) or Ph.D. (CPEP) Postgraduate Fellowship, you will participate in the following didactic training opportunities:

  • Clinical microbiology rounds. Presentation and discussion of current cases and interesting laboratory aspects.
  • Clinical microbiology journal club. Monthly one-hour meeting led by fellows.
  • Infectious disease conference. Weekly one-hour presentation given by consultants or fellows.
  • Laboratory Leadership and Management course. Series of sessions given by consultants from the Department of Laboratory Medicine and Pathology.
  • Test development conference. Monthly one-hour meeting for brief updates about special projects carried out by fellows and others in the division.
  • Core curriculum. Intensive core curriculum didactic course in all areas of diagnostic microbiology.
  • Infectious diseases pathology core curriculum. Interactive, case-based course in covering the histopathology and cytopathology of infectious diseases.
  • Small group reading/review sessions. One-hour sessions, three times per week, with consultants for board preparation. 

To support your educational experience, you have access to Mayo Clinic's medical library as well as the learning resources available in the fellows' resource room, where individual desks and computers are provided for each trainee.

Research and test development training

Research is an important component of the Clinical Microbiology, M.D. (ACGME) or Ph.D. (CPEP) Postgraduate Fellowship. You will complete a research project in which you will develop or evaluate new tests, assess existing tests, evaluate new or existing antimicrobial agents, and/or analyze the clinical value of specific laboratory tests.

Early in the program, you will meet with consultants to discuss available projects to allow for time to begin your project and collect sufficient data for submission of meeting abstract(s) and completion of your project by the end of the program. An introduction to the IRB system, the Mayo Clinic library, and the department's Biorepository Laboratory services will also be provided.

We have a tremendous number of resources to support research at Mayo Clinic, including readily-accessible statistical support, graphic design and media services, and publication services. We also have the DLMP Research Innovation Office (RIO) which provides support for drafting and submitting IRB protocols. These services facilitate research, taking care of the administrative aspects, and allowing the fellow to focus on the scientific aspects of the project.

You will have the opportunity to submit abstracts to regional, national, or international meetings in clinical microbiology/infectious diseases, and/or publish your studies in peer-reviewed journals.

Call frequency

You will be responsible for taking call on a weekly (i.e., 24/7 calls for seven days) rotational basis. This includes:

  • Assisting in the resolution of laboratory problems
  • Contacting clinical services about important laboratory findings or problems
  • Obtaining clinical histories of patients with important or unusual laboratory findings
  • Presenting these problems and histories at laboratory rounds

Teaching opportunities

As a fellow, you will help to teach pathology residents and other trainees rotating in clinical microbiology. 

You will be responsible for reviewing and discussing clinical cases with residents during the clinical microbiology rotation. The resident participates in all aspects of the services, including laboratory rotations, taking call, and presenting at rounds. 

You will also provide didactic lectures and assist with wet lab activities in a supervisory/teaching role for medical students, the clinical laboratory science program, and global health training sessions.


You will be evaluated at the completion of each rotation, which may range in length from four to 16 weeks. Evaluations assess fellow competence in:

  • Patient care
  • Medical knowledge
  • Professionalism
  • Systems-based practice
  • Practice-based learning and improvement
  • Interpersonal and communication skills

Evaluations are also completed for all fellow presentations, such as laboratory rounds and journal club.

The program director will meet with you quarterly to review your evaluations and discuss professional growth. In addition, allied health staff and residents are asked to evaluate your performance periodically. You will be able to view your evaluations electronically. Final written summative evaluations are completed for each fellow upon completion of the Clinical Microbiology, M.D. (ACGME) or Ph.D. (CPEP) Postgraduate Fellowship.