MEDICAL MICROBIOLOGY

Undergraduate: MEDS3024C, Graduate: PMM7004C 3 credits, Fall Semester 2016 Lectures: M, W, F 3:00-3:50 p.m., Medical Sciences Building E-161 Labs: Cardiovascular Center (CVC), G-level Course Director: David S. Askew, Ph.D. [email protected] Office: MSB 1256A, 558-2395 Course Description:

Medical Microbiology is a branch of microbiology that is concerned with the biology of microbial pathogens and how it relates to the diagnosis, prevention and treatment of infectious diseases. How does a microbe interact with the human host? Why do some microbes cause life-threatening infections and others only mild, transient ones? What is the role of the normal microbiota? How does can the understanding of a disease process impact infection control measures? This course will introduce students to the major classes of bacterial and fungal pathogens that infect humans.

The course is divided into four modules. The first module will cover fundamental concepts in microbiology that are necessary to understand how specific microbes cause disease. The subsequent three modules will go through the major bacterial and fungal pathogens that infect humans. Each module will comprise a mix of didactic lectures, hands-on laboratory exercises in microbiology, and problem-based learning in a clinical case format. Clinical cases will be directed by clinicians who are board-certified in infectious diseases or clinical laboratory diagnosis. Learning Outcomes:

After taking this course, the students will be able to:  Describe the pathogenesis of infections caused by the major bacterial and fungal pathogens.  Compare and contrast the structure of bacteria and fungi.  Describe the mechanism of action of the major classes of antibacterial and antifungal drugs  List the principle organisms associated with infection of a specific organ system.  Correlate clinical manifestations with laboratory information to establish a diagnosis.  List the clinical, research, and allied health careers in medical microbiology. Required Textbook:

Medical Microbiology (Sherris. 6th Ed), available online at no charge to U.C. students. http://accessmedicine.mhmedical.com/book.aspx?bookID=1020

How This Course Fits with Your Other Courses:

Medical Microbiology is a discipline of the medical sciences that integrates microbial biology with clinical and laboratory diagnosis. As such, it fits into any curriculum that prepares students for entry into health professions or biomedical PhD programs. The prerequisite is introductory college-level biology, but previous coursework in immunology or biochemistry would be useful. The course is primarily geared towards undergraduate students, but is open to graduate students. Electronic Communications Policy:

Powerpoint presentations will be posted to Canopy prior to each lecture and students may bring laptops to class if they wish. There are no formal office hours, but students are welcome to make appointments.

Directions to the Medical Sciences Building (MSB):

1

Exit the Eden Avenue shuttle, cross street (Eden Avenue) and go up the wide steps. Enter through glass doors. You will be in the CARE building. When you enter CARE building, cross the large atrium into the Medical Sciences Building (E- level). Lectures will be in MSB E-161, and labs will be in the adjacent Cardiovascular Center (CVC, G-level).

Attendance Policy:

Since classes may contain review sessions, regular attendance is strongly recommended, but not required. Attendance at all clinical cases and laboratory exercises is required to obtain 5% attendance credit at the end of the course. An excused absence requires prior permission from the course director, and will involve additional makeup work. Excused absences will require timely notification and acceptable documentation of the reason:  Personal illness, accident or a major catastrophic event  Urgent medical evaluations  Death or serious illness of immediate family members Each unexcused absence will reduce the 5% attendance credit by increments of 2.5% percent (i.e. one absence=2.5% credit, two absences=zero credit). The exams are online and are open for 2 days to accommodate student schedules. Under exceptional circumstances, a student may petition the director to take the exam before the scheduled dates. Unexpected absences due to medical emergencies must be reported to the course director as soon as possible. Academic Integrity:

The University Rules, including the Student Code of Conduct, and other documented policies of the department, college, and university related to academic integrity will be enforced. Any violation of these regulations, including acts of plagiarism or cheating, will be dealt with on an individual basis according to the severity of the misconduct.

Special Needs and Accommodations:

If you have any special needs related to course participation (visual/hearing impairment, physical disability, ommunication disorder, or learning disability), you should meet with the instructor prior to the start of class to arrange for reasonable provisions to meet course requirements. Some accommodations may require prior approval by U.C. Disability Services.

Pass/fail option, audit policy, and withdrawal policy:

There are no pass/fail or audit options for this class. Withdrawal procedures follow U.C. guidelines. http://www.uc.edu/registrar/policies_and_procedures/withdrawal_procedures.html

Grading:

Undergraduate students Graduate students Module 1 exam: fundamentals 15% of final grade 10% of final grade Module 2 exam: 20% of final grade 20% of final grade Module 3 exam: 20% of final grade 20% of final grade Module 4 exam (cumulative): 35% of final grade 35% of final grade Attendance:* 5% of final grade 5% of final grade Lab challenges: 5% 5% Term paper:** - 5% of final grade

*Attendance at all clinical cases and laboratory exercises. **Graduate students will write a short (3 page) review paper on some aspect of medical microbiology, similar to review articles published in the journal Current Opinion in Microbiology. The topic is selected by the student and approved by the course director. Students must submit a draft of their paper to the course director before the Module 2 exam. The paper will be returned with feedback for improvement. The final paper is due before the Module 4 exam.

The final grade will be determined using the following scale:

A 94-100 B+ 87-89 C+ 77-79 D+ 67-69 F 0-59 A- 90-93 B 84-86 C 74-76 D 64-66 B- 80-83 C- 70-73 D- 60-63

2

Date Chapter Lecturer MODULE 1: Fundamental concepts M 8-22 The nature of infection & the microbiome 1, 3, 22 Askew W 8-24 Bacterial structure & principals of biological risk assessment 22 Askew/Espinola F 8-26 Bacterial growth & genetics 22 Choi M 8-29 Immune responses & infection 2 Choi W 8-31 Immune responses & infection 2 Choi F 9-2 Antibiotics & mechanisms of resistance 23 Mortensen M 9-5 No class – labor day W 9-7 LAB 1: Intro to working with bacteria: streak-plating - Askew F 9-9 LAB 2: Principles of differential & selective media - Askew M 9-12 LAB 3: Tour of the clinical microbiology lab, UC Health - Rhodes Module 1 exam (online: 9-14 to 9-16) MODULE 2 W 9-14 Staphylococci 24 Mortensen F 9-16 Haemophilus & Bordetella 31 Weiss M 9-19 Streptococci & enterococci 25 Askew W 9-21 Corynebacterium, Listeria, & Bacillus 26 Askew F 9-23 Mycobacteria 27 Askew M 9-26 Clinical case presentations by an ID physician - Robertson W 9-28 LAB 4: The gram stain - Askew F 9-30 LAB 5: Horizontal gene transfer & antibiotic resistance - Askew/Sandhu M 10-3 LAB 6: Gram stained specimens from the clinical lab/data analysis - Askew Module 2 exam (online: 10-5 to 10-7) MODULE 3 W 10-5 STDs: Neisseria 30 Hassett F 10-7 STDs: Chlamydia & Treponema 37, 39 Askew M 10-10 Anaerobes: Clostridium & Bacteroides 29 Madan W 10-12 Vibrio, Campylobacter & Helicobacter 32 Askew F 10-14 No class – fall reading days 10-13/14 W 10-19 Enterobacteriaceae 33 Askew F 10-21 Enterobacteriaceae 33 Askew M 10-24 Clinical case presentations by an ID physician - Luckett W 10-26 LAB 7: Antibiotic susceptibility testing - Askew F 10-28 LAB 8: Introduction to fungi: yeasts and molds - Askew M 10-31 LAB 9: Fungal data analysis/microbial identification by 16S rDNA - Askew Module 3 exam (online 11-2 to 11-4) MODULE 4 W 11-2 Legionella, Pseudomonas & Burkholderia 34, 35 Romick-Rosendale F 11-4 Zoonotic infections: plague, tularemia, & brucellosis 36 Askew M 11-7 Mycoplasma & Rickettsia 38, 40 Askew W 11-9 Cutaneous fungal pathogens: dermatophytes, Malasezzia, Sporothrix 42, 45 Askew F 11-11 No class – veterans day M 11-14 Opportunistic fungal pathogens: Aspergillus, Candida, Pneumocystis 46 Askew W 11-16 Systemic fungal pathogens: Histoplasma, Coccidioides, Cryptococcus 47 Askew F 11-18 Microbes & bioterrorism - Stringer M 11-21 Clinical case presentations by an ID physician - Robertson W 11-23 No class – Thanksgiving F 11-25 No class - Thanksgiving M 11-28 LAB 10: The human & environmental microbiota - Askew W 11-30 LAB 11: The human & environmental microbiota - Askew F 12-2 LAB 12: Microbial identification by MALDI-TOF mass spectrometry - Mortensen Module 4 exam (exam week)

3