Dept. Health Sciences
Biomedical Sciences Program
B10M 422
Syllabus
Spring 2010
810M 422 Diagnostic Microbiology, 2 Credit Hours
Pre-requist Medical Microbiology 810M 322 Lecture:
Sundays 10:00 am.
Lecture Room D 212
The practical sessions will be delivered at Hamad Medical Corporation
Premises (5th. Floor)
Instructor:
Adil Makkiya, Ph. D Science
Building SE 121 Office
Phone: 485 1952
Email.makkiya@qu.edu.qa
Office Hours:
Sundays: 11.00-12.00 Thursdays:
10.00-12.00 Required Text
Textbook: Textbook of Diagnostic Microbiology
Connie R. Mahon & George Manuselis 2nd• Edition 2000
W.B. Saunders Company
Reference: Koneman's Color Atlas and Textbook of Diagnostic
Microbiology Washington Winn, Stephen Allen, William Janda, Elmer
Koneman, Gary Procop, Paul Schreckenberger, Gail Woods 6th
Edition 2006
Lippincott Williams & Wilkins
Course Description: The different methods and techniques applied for the diagnosis of
pathogenic microorganisms isolated from different clinical specimens. Emphasizing on
both normal and transient flora of the human body. Methods of collection and handling of
different pathological specimens. Introduction to procedures and identification techniques
used to isolate and identify bacteria. Morphological, biological, and biochemical
characteristics of bacteria commonly isolated from clinical specimens.
Adil Makkiya
Page 10/9
Dept. Health Sciences
Biomedical Sciences Program
B10M 422
Objectives
1- To Introducing the understanding to the safety measures necessary to be
considered in a clinical microbiology lab. at the hospital (Hamad Medical
Corporation)
2- Assisting the students how to exclude normal microbial flora from pathogens in clinical
specimens.
3- Developing student's skills with theoretical and practical knowledge on collecting,
handling, culturing, and finally diagnosing the different pathogens in clinical
specimens.
4- To perform gram stain, streaking plates, isolation and identification of
microorganisms through biochemical and biological methodologies.
5- To asses and recommend course of action for laboratory diagnosis when
provided patient history and type of specimen.
6- Interpretation and reporting the clinical results of the specimen in a
professional manner.
OUTCOMES
Upon successful completion of this course the student will be able to:
1- Recognize the safety measures in a diagnostic microbiology laboratory.
2- Identify and differentiate between microbial flora and pathogens in the clinical
specimens delivered to the laboratory.
2.1 Identify normal flora at different sites of the human body. 2.2
Exclude the pathogens from flora.
3- Evaluate the ideal methods of collecting, handling and finally
culturing each clinical specimen delivered to the laboratory 3.1
Inspect the quality of the containers and collection protocols of the
specimen and prior to processing
3.2 Setting up the specimens on appropriate media
3.3 Discussing the incubation (aerobic / anaerobic),
temperature and time requirements
4-Checking the eligibility of the specimen
4.1 Method of transportation of the specimen
4.2 Specimen did suffer any spoilage or exposed to
environmental factors that could effect it's quality 4.3
Adequate informative labeling
4.4 Identify if the specimen was hazardous
5- Performing all the required direct examination as wet, gram stain
and ZN ..... etc
5.1 Interpretation of each of the direct exams and correctly related to
the specimen
5.2 Checking and confirming the gram stained smears following the
primary isolation of the specimen (culture) and it's relation to
earlier gram or any other in the direct smear
Adil Makkiya
Page 2 0/9
Dept. Health Sciences
Biomedical Sciences Program
B10M 422
6- Perform and interpret the laboratory procedures for the
identification of pathogens encountered in urinary tract
infections
6.1 Checking the eligibility of the specimen
6.2 Perform and understands the use of calibrated wire loop 6.3
Differentiating significant and non-significant bacteriuria 6.4
Defining sterile pyuria
6.5 Defining bacteriuria during pregnancy and children
6.6 Understanding the values of the general urine exams in view of its
microscopical (deposit), physical and chemical aspects
6.7 Discussing techniques used for examining and diagnosing renal
tuberculosis in the lab.
7- Perform and interpret the laboratory procedures for the
identification of pathogens encountered in the CNS infection 7.1
Checking the eligibility of the specimen
7.2 Macroscopic observation of CSF
7.3 Cells and differentia counts
7.4 Performing direct serological diagnosis of CSF
7.5 Discussing Quellung reaction, CIE, and IFA technique 7.6
Correlation of culture results with cells count and
biochemical data of CSF following completion
7.7 Discussing agents of chronic meningitis
7.8 Performing body fluids (synovial, pleural, pericardial, ascitic,
and hydrocele fluids) diagnosis
7.9 Identifying the differences of exudates and transdutes
8- Perform and interpret the laboratory procedures for the
identification of pathogens encountered in blood
8.1 Checking the eligibility of the specimen
8.2 Phlebotomy of a blood
8.3 Identifying the important steps of skin disinfection prior to blood
withdrawal
8.4 Discuss mixing the blood specimen following inoculation of the
blood culture bottle
8.5 Importance of using of SPS as an anticlotting agent
8.7 Identifying the use of both the manual and the automated Bact /
Alert machine
8.8 Describing the follow up steps required for completing the
laboratory diagnosis of the causative agent
9- Perform and interpret the laboratory procedures for the identification
of pathogens encountered in the upper and lower respiratory
infection
9.1 Checking the eligibility of the specimen
9.2 Conduct a macroscopical examination for the quality of the
Specimen
9.3 Differentiating a real sputum from saliva specimens
Adil Makkiya
Page 3 0/9
Dept. Health Sciences
Biomedical Sciences Program
9.4 Identifying the mucupurelent part of the sputum
9.5 Defining antibacterial substances as diagnostic tool for
some pathogens
10- Perform and interpret the laboratory procedures for the
identification of pathogens encountered in the gastrointestinal
tract
10.1 Checking the eligibility of the specimen 10.2
Macroscopical examination of the specimen 10.3
Microscopical examination of the specimen
10.4 Discussing the different techniques for concentration of stool
specimens
10.5 Perform the rapid automated API 20E system
11- Perform and interpret the laboratory procedures for the
identification of pathogens encountered in the genital tract
11.1 Checking the eligibility of the specimen
11.2 Discussing agents involved in septic abortion
11.3 Assessment of direct smears in the diagnosis of sexually
transmitted diseases (STD)
11.4 Preparing and interpreting the germ tube test 11.5
Discussing other miscellaneous venereal diseases 11.6
Discussing agents in human abortion
12- Perform and interpret the laboratory procedures for the
identification of pathogens encountered in infected wounds,
burns, and sinuses
12.1 Discussing both exogenous and endogenous infected
Wounds
12.2 Macroscpical examination and reporting the color of pus
12.3 Identifying and describing the presence of granules and pus
consistency
12.4 Discussing the methods for identifying fungal agents
13- Performing and interpreting the Kirby-Bauer sensitivity test.
Adil Makkiya
Page 4 0/9
B10M 422
Dept. Health Sciences
B10M 422
Biomedical Sciences Program
Policie
s
A- Theoretical Lectures
Each student is provided with lecture schedule for the whole module on the
blackboard.
Students are expected to show on time before commencing of lectures, no
admittance shall be permitted with out valid reason. A missed lecture i s the
responsibility of student to compensate.
Students are encouraged to interrupt the lecture whenever they feel to ask or to discuss
matters related to topic of the lecture, and thus discussions are always welcomed.
There will be only one mid-term examinations (at the 8th week) and a final semester
examination. Dates and grades of these exams are already scheduled as indicated
below. Case studies will be included in all examinations. Students in this
course should be aware of the knowledge they acquired in all the previous
courses in Microbiology (1062 241 & BIOM 322) in the exams in this current
course since it's the last advanced and a professional requirement course
prior to graduation.
B- Laboratory Sessions
Hamad Medical Hospital Clinical Laboratory on the 5 th floor will be designated for
teaching this course.
Lab coat is a must in all microbiology labs. No admittance is permitted with out lab coat.
Each student will have her allocated place on the bench and her name will be displayed
where she carries her lab works and she will be:
1. Responsible on keeping cleanliness of her place from all aspects after each
laboratory session.
2. Should follow the lab safety measure offered on the first lab session with
diligence.
3. Each students is requested to prepare a clinical presentations on case study
of a given or selected topic by the students during the lab. sessions.
4. Made up quizzes could be made randomly with out prior notification during
both the practical and/or the lectures sessions.
Failure of students to comply with 1 and 2 above would subject her to marks
deduction (3-5 marks).
Grading System:
Mid-Term Examination
=30%
Practical Examination
=30%
-Mid -Term ..................................... = 8
-Lab. Note Book Reports .................... = 3
-Final Prado Exam ............................. = 14
-Clinical Presentation ............................ = 3
- Quiz 1-2 ....................................... = 2
=40%
Final Examination
Adil Makkiya
Page 5 0/9
Dept. Health Sciences
Grade
Biomedical Sciences Program
Will be
Reported as:
A
B+
B
90-100%
85-90%
80-85%
C+
75-80%
C
70-75%
D+
65-70%
D
F
Adil Makkiya
60-65%
<60%
Page 60/9
B10M 422
Dept. Health Sciences
Month
B10M 422
Biomedical Sciences Program
Day
Chapter and Title
21
-Course orientation, review syllabus
28
-Chapter 6 Host -Parasites Interaction
7
-Chapter 7 General Concepts in Specimen -Collection & Handling
14
-Chapter 8 Microscopic Examination of Infected Materials
21
- Cont'd Chapter 7and Chapter 8
28
-Chapter 31 Urinary Tract Infections (UTI)
4
-Cha pter 31 Cont'd UTI
18
- Mid-Term Exam
25
Chapter 29 Infections of the CNS
2
Chapter 30 Bacteriaemia
9
16
23
Chapter 26 Upper & Lower Respiratory tract Infections
Chap. 19 Anaerobes of Clinical Importance &-33 Infections in Special
Patients population.
-Chapter 28 Gastrointestinal Infections & Food Poisoning,
30
-Chapter 32 Sexually Transmitted
4
Chapter 35 Ocular Infections
February
March
April
May
June
Final Exam.
Adil Makkiya
Page 70/9
Diseases
Dept. Health Sciences
Biomedical Sciences Program
Cou rse Objectives
Identify the safety measures
necessary to be considered in a
clinical microbiology lab. in the
hospital (Hamad Medical Corporation)
Learning Outcomes
Acquire knowledge and know
the skills and tools required by
the hospital (HMC) to protect
health care workers from
spread of organisms or
specimens to the environment.
B10M 422
Assessment tools
Exams
Quizzes
Assignments
Presentations
Recognize the proper methodology for
specimens collection and subsequent
Acquire knowledge and know
the skills and tools for the
proper methods collecting and
Exams
Quizzes
Assignments
Presentations
handling.
handling the clinical specimens
Lab experiments
Exams
Acquire the knowledge and
Evaluate and differentiate between
microbial flora of the human body
and the pathogens.
earns the skills and tools
necessary to confirm the
pathogens in the clinical
Quizzes
Assignments
Presentations
Lab experiments
specimens.
Describe the basic steps in the
complete identification of pathogens
through manual, and automated
methods.
Conducting through the
acquired knowledge and the
ski lis a II the test necessa ry
steps to complete the
identification of all the
pathogens incriminated in
Exams
Quizzes
Assignments
Presentations
Lab experiments
process of human infections.
Identify the antibiotics sensitivity test
for the pathogens isolated.
Adil Makkiya
Acquire the knowledge, and
know the skills and the tools
required in the lab. perform
Exams
Quizzes
Assignments
the antibiotics sensitivity test.
Presentations
Page 8 0/9
Dept. Health Sciences
Biomedical Sciences Program
B10M 422
Sources for Electronic Information
www.asmusa.org (
American Society for Microbiology) www.cdc.gov ( Centers for Disease
Control and Prevention) www.cdc.gov/ncidod/index.htm( CDC National
Center for Infectious Diseases)
www.ohsu.edu/c1inweb (Oregon Health Sciences University)
www.phls.co.uk ( Public Health Laboratory Service)
www.socgenmicrobiol.org.uk ( Society for General Microbiology)
www.who.intlhome-page/( World Health Organization)
http:// ezproxy.qu.edu.qa/login?url = http://www.pubmedcentral.nih.gov /
http://ezproxy.qu.edu.qa/ login?url = http://www.biomedcentral.com/
Adil Makkiya
Page 9 0/9