Clinical Microbiology and Immunology

Lauren Bertelle and Alan Lesse, MD.

“Your microbiology and immunology rotation teaches you how to analyze test results and apply them clinically,” says fellowship alum Lauren Ibrahim, MD, with Alan Lesse, MD.

During your laboratory-based clinical microbiology and immunology rotation, you will discover how to harness this critical infectious disease resource to optimize patient care.

Working in Erie County Medical Center’s microbiology lab, you’ll perform a wide variety of tests for common and uncommon infectious agents. This rotation gives you experience with four major areas of infectious disease lab work.

At the end of the rotation, you will understand the techniques used by the laboratory as well as:

  1. which tests identify a given infectious agent
  2. when to alert the laboratory for non-routine diagnostic modalities
  3. how long it will take for diagnostic information to become available

Week 1: Bacteriology

  • General collection and transport of specimens
  • Processing microbial specimens, including primary setup of various specimen types
  • Detection and characterization of medically important bacteria
  • Blood cultures
  • Antimicrobic susceptibility testing methods

Week 2: Diagnostic Immunology

  • General serologic and antigenic assays for infectious agents
  • Pneumocystis immunofluorescence
  • Hepatitis assays
  • HIV testing: HIV antibody, CD4/CD8, Western blot
  • PCR techniques: HIV, HCV, HIV Resistance Genotyping

Week 3: Mycobacteriology/Mycology and Parasitology

Special biosafety precautions; use of primary and secondary barrier protection; universal and respiratory precautions; disinfection and sterilization practices.

  • Specimen transport and processing
  • Differentiation and identification of mycobacterium spp
  • Antimicrobial susceptibility testing for mycobacterium tuberculosis and non-tuberculosis mycobacterium
  • Characterization and identification of systemic mycoses
  • Antifungal susceptibility testing
  • Parasitology: microscopic identification of classic and emerging pathogens

Week 4: Virology

  • Selecting appropriate viral specimens
  • General viral culture methods
  • Antigen detection: cytomegalovirus
  • Influenza surveillance
  • Chlamydia diagnosis; culture and PCR
  • C difficile toxin(s) assays
  • Human papilloma virus-Digene hybrid capture

Patient Population

We diagnose specimens from ECMC inpatients and outpatients. Because of this laboratory’s world-class capabilities, especially in mycobacteriology and virology, we also receive specimens from outside institutions.

Clinical Site