BIO580 MEDICAL
MICROBIOLOGY
Syllabus Fall
2008
A. General information
Infection is a conflict
between a host and a microorganism with two possible outcomes, resistance or disease,
dependent on interactions between the infectious agent and the host’s immune
response. Medical microbiology, therefore, is a discipline that includes the
study of the microorganisms, the host immune system, and interactions between
the two. Although bacteria and viruses are the most numerous and most important
pathogens and are emphasized in this course in lecture and clinical case
studies, fungi and protozoa are also included. The goal of this course is to provide a foundation of concepts in host-microbe
interactions that will allow students to understand the diseases facing humans
today and be prepared for the diseases coming tomorrow.
Medical Microbiology is an
advanced course and will be taught at a rigorous level. Most of the students
who take this course are interested in pursuing a career in health related
fields or are graduate students in microbiology and are ready for a course that
requires synthesis, integration, and application.
B. Course
logistics.
Lectures meet Mon. and Wed from
Course
instructor:
Dr. Elizabeth Alm
Teaching
assistant:
Erica Clark
Office hours: Office
hours are posted. Dr. Alm will have a sign-up sheet outside Brooks 157.
E-mail: alm1ew@cmich.edu (Note:
this is the easiest way to reach me). Important: If you have a BIO580 question,
put "BIO580" as the beginning of the subject line of your e-mail
message. I get about 100 e-mail a day, much junk that I trash in batches. If
you fail to include this header I may accidentally trash your e-mail.
Example:
To: Elizabeth.W.Alm <alm1ew@cmich.edu>
From: Susan B. Student <stude1sb@cmich.edu>
Subject: BIO580: questions on today’s lecture
Prerequisites: BIO 208 (General Microbiology)
and BIO 392 (Mammalian Physiology). BIO 324 (Cell Biology) is also recommended.
C. Required
materials
Textbook: Mims, Playfair, Roitt,
Wakelin, and Williams. (2004) Medical
Microbiology 3rd Ed., Mosby Europe Limited,
Access to the
World Wide Web and an E-mail account. I will be posting many class materials on the
course website via Blackboard, and expect every student to check for
announcements/assignments a couple times a week. I can be reached more easily
by e-mail than by any other method, and will reply to any concern or question
you raise if you reach me by e-mail.
Finally, there is a Medical Microbiology group on Facebook, which you will be invited to join. This is totally optional, but I hope you will
use it as an additional resource during this semester and as a means to connect
with professional alumni.
D. Laboratory
All organisms handled in the laboratory have the
potential to cause illness, especially in compromised individuals (about half
of the organisms are classified as Biological Safety Level 2). Compromising
conditions include cancer, chemotherapy, diabetes, HIV positivity, open wounds,
pregnancy, steroid use, etc. See me if you have concerns about your safety in
laboratory. All inquiries will be confidential.
E. Clinical
Cases
Three important skills in medical microbiology are
problem-solving, interacting with other professionals, and oral and written
communication skills. Development of these skills is also an objective in this
course. Written communication skills will be developed throughout the semester
in essay exam questions. The other skills will be emphasized in the second half
of the semester. For the first half of the semester, both the lecture and
laboratory will emphasize basic concepts and skills and will operate fairly
independent of one another. After the Midterm exam, the labs and lectures will
be integrated by way of clinical cases. Case study groups will consist of 4-5 students.
Clinical cases will be handed out to each group in lecture at the beginning of
the week. Some cases will be accompanied by a clinical sample that you will
receive and work with in the laboratory. At least some members of the group
will need to come in at times other than scheduled lab times to continue
identification of the unknown. Case reports will be collected and graded. One
report for the group will be turned in and all members of the group will
receive the same grade.
F. Reading
assignments
G. Grades
Quizzes and
Tests:
10-15 point quizzes may consist of a mixture of material from lectures and
laboratories. Tests may include a mixture of different types of questions, such
as short-answer, multiple-choice, true-false, and/or short essay. There will be a Midterm laboratory
practical; a makeup will not be possible for this test under any circumstances.
Final Exam: The final exam is
comprehensive.
Grading:
|
|
Undergraduates |
Graduates |
|
Quizzes |
10% |
8% |
|
Lecture Test One |
15% |
13% |
|
Lecture Test Two |
15% |
13% |
|
Lab Practical |
15% |
13% |
|
Case Reports |
25% |
23% |
|
Final Comprehensive Exam |
20% |
18% |
|
Additional
Required Elements |
|
12% |
Grading Scale:
|
94+ = A |
80-83.9 = B- |
|
90-93.9 = A- |
77-79.9 = C+ |
|
87-89.9 = B+ |
74-76.9 = C |
|
84-86.9 = B |
70-73.9 = C- |
H. Students
requiring accommodations
CMU provides students with disabilities reasonable
accommodation to participate in educational programs, activities or services. Students
with disabilities requiring accommodation to participate in class activities or
meet course requirements should first register with the office of Student
Disability Services (250 Foust Hall, telephone #989-774-3018, TDD #2568), and
then contact me as soon as possible.
I. Makeup
policy
Makeup exams are available only to students who have
a legitimate excuse for missing an exam, such as personal illness or injury,
sanctioned athletic team event out of town, or death in the immediate family.
If you know in advance that you must miss an exam, see me in advance and bring
documentation to support your anticipated absence. If you miss an exam
unexpectedly because of last-minute illness or accident, contact me when you
return to campus (or by e-mail or phone if you will be away for some time) with
documentation of your situation. Make-ups for the final exam will be scheduled
for Friday of exam week.
J. Extra
credit
Students wishing to make up for poorer than expected
exams may write essays for a maximum addition of 10 points to the total course
points.
Essays - You may write up to three
short (2-3 pages, double-spaced) essays on Medical Micro related topics during
the semester. All essays are due 2 weeks
prior to the final exam. Each essay submitted will earn up to 5 points
added to the total course points, as follows:
·
5 points - good work, appropriate references,
·
2-4 points - basically acceptable content but marred by mechanical
problems such as incorrect spelling or grammar, or lack of clarity in explaining
the topic, lack of or inappropriate references,
·
0 points - unacceptable or plagiarized.
**Any evidence of plagiarism will result in zero points for all
students involved and denial of any extra credit points otherwise earned in the
course. Essays should integrate at least two articles from the primary
literature, not textbooks or internet sources.
K. How to
succeed in this course
As you proceed upward in course level difficulty
from 100 to 200 to 300, and so on, you need to develop greater responsibility
for your own learning. The ultimate goal of college is to develop independent
learners and critical thinkers. Therefore, you will find that less structured
learning assistance is provided for you in this course. This does not mean that
I am not still happy to help you with any material during my office hours.
In order to succeed in this course you should plan
to attend all lectures, allow ample time to read and study assigned material
and turn assignments in on time. You will get more out of lectures if you read
(or at least skim) the assigned readings before lecture and then reread
relevant material carefully soon after lecture.
You should plan on spending a minimum of two hours
of study time for each hour of lecture. This is standard academic advice you
will find in any book on how to study. This is a minimum requirement for
most students to perform satisfactorily (B level). If you desire an
"A", you will probably need to put in more time than this minimum
recommendation. If you begin to fall behind, make every effort to catch up
quickly, otherwise you may find yourself swamped with too much material to
assimilate before a test. Tips for
studying for the sciences and how to study
actively.
Many of you will find attending lectures and reading
the text is all the support you will need to do well in the course. Some of you
may have problems with some of the material. I offer several forms of
assistance to help you with difficulties you may experience in this course.
1. I will be happy to repeat
information and/or answer questions during lecture, please do not hesitate to
ask me to do so. Also feel free to e-mail questions to me at any time.
2. The textbook provides
concept guides throughout the chapter as well as chapter end questions. The
questions in the chapter should help guide your reading. If you can't answer
the questions, then you should re-read that section more closely. Use the
chapter end questions to practice writing essays over the material.
3. A web page, linked to
Blackboard, is available for this course: http://www.cst.cmich.edu/users/alm1ew/Medimicro.html.
This web page will contain links to additional internet resources.
4. There is an extra credit
possibility in this course. See J. above for more information.
5. I am available for
individual consultation regarding any aspect of the course. If you have
unanswered questions or concerns, or are in serious academic trouble, see me! I
will provide whatever assistance I can to help you do well in this course;
however, ultimately the grade you earn is your responsibility.
L. Recommended
and optional material
Your grade will be based on how well you master the
required elements listed above. In addition to required elements that all
students must undertake, this course will provide recommended and optional
elements. Recommended reading material marked FYI will be provided for students
who are interested in exploring a particular topic in a little more detail.
Optional material will be provided upon request for students with further interest
or aptitude in medical microbiology or in particular topics. Undertaking
recommended and optional material will not add to or subtract from your grade.
This is purely a means for students to take the subject of medical microbiology
as far as they are interested. If you have ideas about optional material,
please feel free to come see me.
Tentative
schedule - any schedule changes will be posted on the course web site
|
DATE |
LECTURE TOPIC |
|
LABORATORY TOPIC |
|
M Aug 25 |
Course
introduction; Dynamics of infectious disease – CC 1 |
Ch.1 |
DIAGNOSTIC PRINCIPLES Lab
1 - Gram stain and streak plate isolation |
|
W Aug 27 |
UNIT 1 - THE PLAYERS Part A - Review of the microbes Viruses
and bacteria - CC 2 available online. |
|
Lab
2 - Colony morphology |
|
M Sep 1 |
Labor
Day - No Class |
|
|
|
W Sep 3 |
Eucaryotic
microbial pathogens and normal microbiota |
Ch.4
- 8 |
Lab
3 - Initial grouping of clinical isolates |
|
M Sep 8 |
Part B - Host defenses Nonspecific
host defenses against microbial invaders – CC 3 available online. |
Ch
9 |
Lab
4 - Identification of Gram-positive cocci |
|
|
Nonspecific
defenses continued |
|
Lab
5 – GPC continued |
|
M Sep 15 |
Specific
host defenses against microbial invaders – CC 4 available online |
Ch.10,
11 |
QUIZ
1 - Labs 1-5 Lab
6 - Identification of Enterobacteriaceae |
|
T Sep 16 |
|
|
Read
KIA results from Lab 6 |
|
W Sep 17 |
Specific
defenses continued |
|
Lab
7 – GNR continued |
|
M Sep 22 |
TEST ONE - UNIT ONE - MC and SA |
|
TEST ONE - UNIT ONE CON’T - essays AND
Lab 8 - Identification of Oxidase-positive Gram-negative Rods |
|
W Sep 24 |
UNIT 2 - HOST AND PATHOGEN CONFLICTS How
are pathogens acquired and transmitted? |
Ch.12,
13 |
Lab
8 – Identification of Gram-negative cocci Lab
9 - Identification of Gram-positive Rods |
|
M Sep 29 |
Topic
continued - CC 5 available online |
Ch.14,
15 |
Lab
10 - Introduction to Anaerobes AND Bacterial Unknown assigned to Grad
students |
|
W Oct 1 |
How
do pathogens escape nonspecific host defenses? |
|
QUIZ
2 - Labs 6-10 Lab
11 - Intro to yeasts |
|
M Oct 6 |
Grads
- Unknown Report due 1pm How
do pathogens escape specific host defenses? - CC 6 available online. |
Ch
16 |
Lab
12 - Intro to Molds |
|
W Oct 8 |
What
are the pathological consequences of infection? |
Ch.17 |
Lecture
will continue during lab if necessary; remaining lab time will be for
practical review |
|
M Oct 13 |
No
lecture |
|
LABORATORY PRACTICAL EXAM Laboratories
1 through 12 |
|
W Oct 15 |
TEST TWO - UNIT TWO – MC and SA Comprehensive with an emphasis on Unit 2 |
|
TEST TWO - UNIT TWO CON’T – essays No lab following Test Two |
|
M Oct 20 |
UNIT 3 - CLINICAL MANIFESTATIONS OF INFECTION Intro
to Clinical Case Problem-Solving; how to work through a case, practice case |
Ch
24 |
Infections
of the Nervous System – lecture, case 1 assigned, clinical specimen received |
|
T-F |
No
lecture |
|
Work
on solving cases |
|
M Oct 27 |
Clinical
Case 1 due 1 pm QUIZ
3 -NS Infections of the
Urinary Tract and Sexually Transmitted Infections; Case 2 assigned |
Ch.20,
21 |
Clinical
specimen received |
|
T-F |
No
lecture |
|
Work
on solving cases |
|
M Nov 3 |
Clinical
Case 2 due 1 pm QUIZ
4 -UTI and STI Respiratory Tract
Infections; Case 3 assigned |
|
Clinical
specimen received |
|
T-F |
No
lecture |
|
Work
on solving cases |
|
M Nov 10 |
Clinical
Case 3 due 1 pm QUIZ
5 - RTI Gastrointestinal
Tract Infections; Case 4 assigned |
Ch.22 |
Clinical
specimen received |
|
T-F |
No
lecture |
|
|
|
M Nov 17 |
Clinical
Case 4 due 1 pm QUIZ
6 - GI Infections
of the skin and wounds; Case 5 assigned |
Ch.26 |
Clinical
specimen received |
|
T-F |
No
lecture |
|
Work
on solving case |
|
M Nov 24 |
Clinical
Cases 5 due 1 pm UNIT 4 –
CONTROL OF MICROBIAL INFECTIONS Antimicrobial
action |
|
Lab
24 |
|
W Nov 26 |
Antimicrobial
action continued |
|
Lab
24 – continued – this lab may be completed during scheduled lab on Wed or
anytime on T Nov 26 that the room is available |
|
R Nov 27 |
Thanksgiving |
|
|
|
M Dec 1 |
Antimicrobial
resistance |
|
Lab
25 - Transfer of Antibiotic Resistance |
|
T Dec 2 |
|
|
Check
lab results |
|
W Dec 3 |
Immunization
strategy |
Ch.34 |
Lab
26 - continued |
|
W Dec 10 |
FINAL EXAM Comprehensive with an emphasis on Units 3 and 4 BR 201 |
|
|