Clinical Microbiology Rotation

During the two-month training in Clinical Microbiology, residents gain experience in the isolation and identification of medically important microorganisms and in the interpretation and application of laboratory results. Residents have assigned responsibilities in each area in Microbiology with emphasis on acquisition of technical experience and clinical application of the data provided to the attending physician.


The goal of the two-month Clinical microbiology rotation is to provide a broad-based training program in laboratory microbiology, which includes all subspecialties of that discipline. The focus of the training program is laboratory diagnosis of infectious diseases and clinical interpretation of microbiologic results. 


At the end of the rotation, the residents should be able to:

  • Describe the approaches for evaluation of specimens submitted for aerobic and anaerobic microbiology, mycology, mycobacteriology, parasitology, virology, and serology.
  • State the principles associated with requirements for specific sample submissions including rationale for requiring specific volumes, transportation conditions, and the rationale for use of selective versus non-selective culture conditions.
  • Understand the basic diagnostic approaches for the work up of specimens from different sites (blood, exudates, respiratory specimens, etc.) and the algorithm used for identification of gram positive and gram negative bacteria.
  • Understand the clinical significance of serology results of major clinical infectious diseases syndromes (hepatitis panel, HIV western blot, etc.)
  • Learn the basic morphology characteristics of yeasts and filamentous fungi.
  • State the principles of antimicrobial susceptibility testing and evaluate the interpretation of the results.
  • Correlate the finding of histology examination with microbiologic culture when appropriate.  
  • Understand the principles and requirements for molecular testing.

Resident Responsibilities

  1. Attend the scheduled bench rotation for the different sections of the clinical microbiology laboratory.
  2. Present cases/situations that come up during on call duties or micro rotation for CP conference on Thursdays
  3. Attend the Infectious Diseases Case Conference Monday at noon (3rd floor Hanes Conference Room 3042). One presentation every other week (10 minutes talk).
  4. Prepare presentations (path slides) for the Infectious Disease Case Conference and M&M conference in Infectious Diseases when needed: 5-6 cases every three month.
  5. Serve as a consultant by recommending appropriate cultures and culture processing for autopsies.
  6. Correlate mycology/AFB results with Path reports.
  7. Prepare a presentation for the laboratory personnel focusing in methods of diagnostic, microbiology.
  8. Serves as a consultant for evaluation of send out test related to infectious diseases.


Medical Microbiology (Part VI): In Clinical Diagnosis and Management by Laboratory Methods. Henry J (ed)

Bailey & Scott Diagnostic Microbiology: Baron E, Peterson L, Finegold S (eds)

Koneman’s Color Atlas and Textbook of Diagnostic Microbiology

Online resources

Centers for Disease Control and Prevention

Doctor Fungus

CDC Parasitology Diagnostic Website