Course Description

Pathogenic Microbiology is a survey of microorganisms of medical importance. In this course, we study the physiology, pathogenesis, epidemiology, clinical presentation, laboratory diagnosis, treatment, prevention, and control of common bacterial and fungal pathogens with a special emphasis on case studies.

Course Objectives

After completing this course, students should be:

  1. able to describe the physiology, pathogenesis, epidemiology, clinical presentation, laboratory diagnosis, treatment, prevention, and control of common bacterial and fungal pathogens
  2. proficient in aseptic techniques for bacterial transfers and in the use of the light microscope
  3. familiar with common media and techniques used to isolate and identify some common bacterial pathogens
  4. able to clearly communicate laboratory findings in written and oral form

Course Format and Materials

This class consists of three, one-hour lectures and two, two-hour laboratories each week. Readings will be assigned from the primary scientific literature and discussed each week.

Laboratory Manual

The laboratory is an introduction to the common types of media and biochemical tests used to identify and isolate some common bacterial pathogens. In this lab, you will take the role of a medical laboratory technician and aid in the diagnosis and treatment of six different case study patients throughout the semester. For example:

Mary Mallon is a 22-year-old female who presents with abdominal cramps, diarrhea, and vomiting. Symptoms first appeared four days ago. She is a private chef.

Students will diagnose and offer a treatment plan for each case study by isolating and identifying the pathogen. In Mary’s case:

Mary has gastroenteritis caused by Salmonella. Salmonella bacteria were isolated from a fecal slurry[1] on XLD agar. Biochemical tests confirmed identification of Salmonella as non-lactose fermenting, Gram negative rods, that reduce sulfur and decarboxylate Lysine. The recommended treatment for Salmonella is pushing fluids and electrolytes; however, if symptoms persist or worsen, Ciprofloxacin can be prescribed.

For each exercise, the students pick one of eight case study patients and receive a simulated patient sample containing an unknown pathogen (e.g. artificial urine or simulated wound exudate), a transcript of a medical interview, the patient’s medical history, and a picture of the patient. Their goal is to isolate and identify the pathogen, then recommend a treatment plan. The students are responsible for the entire process, starting with how to isolate the bacteria, through identification using morphological/biochemical tests, and recommending treatment by conducting and interpreting antimicrobial sensitivity tests on their pathogen. The TAs and I are available to help by guiding them with a sensemaking approach, but otherwise, the students have access to a wide range of resources to solve their cases.

The students get 3-6 lab periods to create a diagnosis and treatment plan for their patients. On the final day of the exercise, the students use their results to create demo stations, and the class rotates through all eight patients to identify the pathogens for the other patients. They only required to diagnose five of the eight patients, but are encouraged to identify and treat all eight. Students that get all eight correct win a button, and there’s also a competition between sections.

Modules

  1. Fundamentals of the Microbiology Lab
  2. ELISA HIV Antibody Test
  3. Urinary Tract Infections
  4. Bacterial Pneumonia
  5. Bacteremia
  6. Skin and Soft Tissue Infections
  7. Multi-State Diarrhea Outbreak

Procedures