D3-Microbiology-Course-Syllabus-2013-2014

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Kingdom of Saudi Arabia
The National Commission for Academic Accreditation &
Assessment
COURSE SYLLABUS
Program: Dentistry
Course Name: Microbiology
Course Code: D3-MICR
ACADEMIC YEAR 2013-2014
P. O. Box 6231, Jeddah 21442 Saudi Arabia
www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415
Revised November 20, 2012
1
Microbiology Course Syllabus
ACADEMIC YEAR 2013-2014
I. COURSE IDENTIFICATION
Program/Department: Dentistry / Microbiology
Program Year: 2013-2014
Course Title & Code: Microbiology & D3-MICR
Credit Hours: one theoretical & one practical
Pre-requisites: NAD
Course Requirements:NAD
II. PROFESSOR/INSTRUCTOR’S PROFILE
Name: Ass. Prof. Dr. Manal El Said
Title: Head of Microbiology Department
Office Location: Female First Corridor
Extension No.: 1671
Office Hours: Sat-Wen: 2pm-4 pm- Thu:11 am-1pm
Email: microbiology 3.jed@bmc.edu.sa
III. COURSE DESCRIPTION
This course provides learning opportunities in the basic principles of medical
microbiology and infectious disease. It is designed to contain the conceptual basis for
understanding pathogenic microorganisms and the mechanisms by which they cause
disease in the human body. It also develops a knowledge base of principles of microbial
taxonomy, structure, physiology and function, familiarity with the major types of
pathogenic microorganisms and the diseases that they produce in humans.
This course provides description of the structure and functions of viruses,
distinguish diverse characteristics of viruses – host range, target tissues, replication
strategy, transmission. Explain the various techniques for detecting and treating viral
diseases. It will also provide students with an overview of the major fungus diseases or
mycoses that threaten human health. The causal agents, symptoms, modes of infections,
and treatment of fungus-related illness will be discussed and explored.
The course will deals with an introduction to the general biology of the parasitic
protozoans, and helminths of humans and emphasize the morphology, form and function,
life cycles, symptomatology, and pathogenesis of representative taxa from these major
parasitic groups. It also deals with the knowledge of general categories of therapeutic
modalities available to treat infections.
The course covers the ability to use the laboratory to diagnose infections, including
appropriate specimen collection and test ordering and demonstrate the ability to interpret
laboratory findings in the context of the patient’s presentation and findings.
P. O. Box 6231, Jeddah 21442 Saudi Arabia
www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415
Revised November 20, 2012
2
III. COURSE OBJECTIVES
After student studied the course and according to their acquired knowledge and
understanding, he should be able to:
 Recognize general and fine structure of bacteria.
 Classify bacteria.
 Recognize genetics, metabolism and growth of bacteria.
 Identify medically important bacteria, viruses and parasites that cause human
diseases as regard their morphology, pathogenecity, manifestations, diagnosis and
management.
 Practical Skills: At the end of the course the students should be able to:
- Identify different bacteria as regard their shape, arrangement and staining
characters.
- Do Gram staining which is the most important staining in identifying different
bacteria.
- Recognize bacteria which are in need for special staining methods.
- Recognize different types of culturing media and their uses.
- Culturing and identify the bacterial colonies.
- Perform antibiotic sensitivity testing and serological tests.
- Examination of Faeces For Parasites
- Examination of blood for parasites
V.
COURSE OUTLINE (Lecture Course Outline, Lab Course Outline, Clinical Course
Outline)
1-Bacteria
 Bacterial Classification, Morphology & Cell Structure
 Bacterial Metabolism & Growth
 Bacterial Genetics & Mechanisms of Bacterial Pathogenesis
 The Gram-Positive Cocci –I (Staphylococcus)
 The Gram-Positive Cocci – II (Streptococcus)
 The Gram-Positive Bacilli: Aerobic ,Anerobic and branched
 The Gram-Negative Cocci :Aerobic & Anaerobic
 Enterobacteriaceae: Lactose fermenter and non lactose
 Gram negative bacilli: non fermenters- fastidious, bacilli with pointed ends & Bacilli
with curved ends
 Gram negative anaerobic Bacilli, Spirochete, Rickettsial,Chlamydial &Mycobacterium
2-Viruses
 Viral Classification, Structure ,Replication& Mechanisms of Viral Pathogenesis
 DNA viruse: Adenoviridae, Herpesviridae, Poxviridae, Parvoviridae, Papovaviridae &
Hepadnaviridea
P. O. Box 6231, Jeddah 21442 Saudi Arabia
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Revised November 20, 2012
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 RNA viruses: Orthomyxoviridae, Paramyxoviridae, Coronaviridae,Togaviridae,
Picornaviridae & Reoviridae, Retroviridae, Flaviviridae, Bunyaviridae ,Caliciviruses,
Astroviridae, Arenaviridae, Rhabdoviridae, Filoviridae, Bornaviridae& Proines
3-Mycology
 Basic Biology of Fungi, Superficial, Cutaneous & Subcutaneous Mycoses
 Systemic and Opportunistic Mycoses
4- Parasitology
 Intestinal, Urogenital, Blood & Tissue Protozoa
 Cestodes, Trematodes & Nematodes
5- Immunology
 Introduction to immunity:
- Innate & Adaptive Immunity, Active & Passive Immunity
- Cellular Basis of the Immune Response
 Antibodies, Humoral & Cell-Mediated Immunity
 Major Histocompatibility Complex
 Transplantation
 Complement
 Hypersensitivity
 Tolerance & Autoimmune Disease
 Tumor Immunity
 Immunodeficiency
Practical:
 Microbiology Laboratory Safety Measures & Microscopy
 Morphology of microorganisms: Size- shape - arrangements & staining properties
 Microscopical techniques used in microbiology: Gram staining technique & Hot and cold
Ziehl Neelsen staining technique.
 Culturing bacterial Pathogens:
- Different types of culture media
- How to prepare, Sterilize and dispense, labeling and storage of culture media.
 Specimens collections & processing
 Culturing blood & Possible pathogens isolated from blood
 Culturing bacterial Pathogens: How to inoculate culture media, Enumeration of
microorganisms, Incubation of Inoculated Media & Culturing of anaerobes
 Biochemical reaction
 Antibiotics susceptibility tests
 Sterilization and disinfections
 Perform and Interpret the results of serological tests
P. O. Box 6231, Jeddah 21442 Saudi Arabia
www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415
Revised November 20, 2012
4
Batterjee Medical College
For Sciences and Technology
Course Outline
Program Name:
Year Level:
Course / Subject:
Pls. tick/check: √
Week
Dentistry
Academic Year 2013-2014
D3
Semester:
1ST
Microbiology
Lecture: √ Clinical __ Practical: __ Others: __
Whole Year __√_ / Semester
Professor / Lecturer / Instructor
Week 1
Ass. Prof .Dr. Manal EL Said
Week 2
Ass. Prof .Dr. Manal EL Said
Week 3
Ass. Prof .Dr. Manal EL Said
Topics/Skills Covered
Introduction to the Course:
Learning objectives; course format; evaluation,
testing, and grading, policies expectations.
Bacterial Classification, Morphology & Cell
Structure:
 Medically important groups of microorganisms
 Classification (taxonomy) of bacteria
 Morphology (cell shapes, Gram stain)
 Ultrastructural
features
(cytoplasm,
cell
envelope, external features) & Bacterial spores.
Lecture -2
Bacterial Metabolism & Growth:
 Nutrient requirements of bacteria
 Aerobic & anaerobic respiration & fermentation
 Bacterial growth.
Bacterial Genetics
 Bacterial genome
 DNA replication (binary fission)
 Gene transfer (transposons, extrachromosomal
elements and mechanisms of DNA exchange).
Mechanisms of Bacterial Pathogenesis:
 Entry into the human body
 Adhesion, colonization & invasion
 Pathogenic actions of bacteria
Commensal & Pathogenic Human Microflora:
 Normal microflora of the human body
Ass. Prof .Dr. Manal EL Said
Week 4
P. O. Box 6231, Jeddah 21442 Saudi Arabia
www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415
Revised November 20, 2012
5
 Normal flora of major human body systems.
Week 5
Week 6
Week 7
The Gram-Positive Cocci (Staphylococcus):
 Staphylococcus aureus , Methicillin-resistant S.
aureus & glycopeptides resistance in S. aureus
 Coagulase negative Staphylococcus
 Staphylococcus epidermidis
 Staphylococcus saprophyticus
The Gram-Positive Cocci (Streptococcus):
 Streptococcus pyogenes (group A Streptococcus)
 Streptococcus agalactiae (group B Streptococcus)
The Gram-Positive Cocci (Streptococcus):
 Streptococcus pneumoniae
 Streptococcus bovis &viridans Streptococcus
 Enterococcus
Ass. Prof. Dr. Manal EL Said
Ass. Prof .Dr. Manal EL Said
Ass. Prof .Dr. Manal EL Said
Week8
EID VACCATION
Week 9
EID VACCATION
Week10
Week 11
Week 12
The Gram-Positive Bacilli:
Aerobic
 Bacillus spp.
-B. anthracis
-B. cereus
 Corynebacterium.ssp.
- C. diphtheria
- Non-diphtheria Corynebacteria
 Listeria monocytogenes, Erysipelothrix &
Rhodococcus
The Gram-Positive Bacilli:
Anaerobic
 Clostridium spp.
-Clostridium perfringens
-Clostridium tetani,
-Clostridium botulinum
-Clostridium difficile
The Gram-Positive Bacilli:
Anaerobic
Propionobacterium ssp.
The Gram-Positive Bacilli:
Branching
 Actinomyces
 Nocardia ssp.
 Actinomadura
 Streptomyces
Ass. Prof .Dr. Manal EL Said
Ass. Prof .Dr. Manal EL Said
Ass. Prof .Dr. Nadeem
P. O. Box 6231, Jeddah 21442 Saudi Arabia
www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415
Revised November 20, 2012
6
Week 13
Week 14
Week 15
Ass. Prof .Dr. Nadeem
Ass. Prof .Dr. Manal EL Said
Ass. Prof .Dr. Manal EL Said
Week 16
Question & Answer Sessions
Course Outline (revised: May 12, 2013)
Program Name:
Year Level:
Course / Subject:
Pls. tick/check: √
Week
Week 1
The Gram-Negative Cocci
a-Aerobic
 Neisseria gonorrhoeae
 Neisseria meningitides
 Moraxella catarrhalis
b- Anaerobic
Veillonella
The Gram-Negative Bacilli
a- Enterobacteriaceae
Lactose fermenter
 Escherichia coli & Citrobacter
 Klebsiella, Enterobacter & Serratia
The Gram-Negative Bacilli
a- Enterobacteriaceae
Non-Lactose fermenter
 Proteus, Morganella & Providencia
 Salmonella
 Shigella
 Yersinia
Gram negative bacilli –non fermenters
 Pseudomonas aeruginosa, Stenotrophomonas
maltophilia & Burkholderia
 Acinetobacter
Course Outline (revised: May 12, 2013)
Dentistry
Academic Year 2013-2014
D3
Semester:
2nd
Microbiology
Lecture: √ Clinical __ Practical: __ Others: __
Whole Year ___ / Semester √
Professor / Lecturer /
Instructor
Ass. Prof .Dr. Manal EL Said
Topics/Skills Covered
C-Fastidious gram negative rods Coccobacilli
 Haemophilus
 HACEK Organisms(Haemophilus, Actinobacillus
Cardiobacterium, Eikenella & Kingella)
 Gardnerella
 Bordetella pertussis
P. O. Box 6231, Jeddah 21442 Saudi Arabia
www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415
Revised November 20, 2012
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Week 2
Ass. Prof .Dr. Manal EL Said
Week 3
Ass. Prof .Dr. Manal EL Said
Ass. Prof .Dr. Manal EL Said
Week 4
Week 5
Ass. Prof .Dr. Manal EL Said
 Brucella
 Pasteurella
 Francisella tularensis
Bacilli with pointed ends:
 Legionella pneumophila
 Capnocytophaga
Bacilli with curved ends:
 Vibrio, Aeromonas & Plesiomonas
 Campylobacter
 Helicobacter
D- Gram negative anaerobic Bacilli:
 Bacteroides
 Prevotella
 Porphyromonas
 Fusobacterium
Spirochete, Rickettsial
 Spirochetes: Treponema , Borrelia & Leptospira
 Rickettsia: rickettsiae, prowazekii &Rickettsia typhi
 Coxiella burnetii
 Bartonella spp.
 Mycoplasma
Chlamydial & Mycobacterium
 Chlamydia: trachomatis, Chlamydophila pneumoniae &
psittaci
 Tuberculosis, leprosy& non- tuberculosis
Viral Classification, Structure & Replication-I:
 Basic characteristics , classification of viruses & structure
(non-enveloped & enveloped viruses)
 Viral replication:
- Uncoating
- Macromolecular
synthesis
(general
information,
transcription and replication of DNA and RNA viral
genomes, production of viral proteins)
- Assembly
- Release from host cell.
Mechanisms of Viral Pathogenesis:
- Acquisition & infection of target tissue, cytopathogenesis
(lytic & nonlytic infections, oncogenic viruses), human
host defenses against viral infection, immunopathology,
epidemiology of viral diseases, (age, immune status &
other host factors), control of viral spread.
P. O. Box 6231, Jeddah 21442 Saudi Arabia
www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415
Revised November 20, 2012
8
Week 6
Week 7
Week8
Ass. Prof .Dr. Manal EL Said
Ass. Prof .Dr. Manal EL Said
Ass. Prof .Dr.Nadeem
Week 9
MID SEMESTER /SPRING VACTION
Week10
Ass. Prof .Dr.Nadeem
Week 11
Ass. Prof .Dr.Nadeem
Week 12
Week 13
DNA Enveloped viruses
1-Poxvirus
2-Hepadnaviridea
3-Herpesviridae
DNA non-Enveloped viruses
1-Adenovirus
2-Parvoviridae
3- Papillomaviridae
4- Polyomaviridae
RNA viruses
1- Orthomyxoviridae
2- Paramyxoviridae
3- Coronaviridae
4- Togaviridae
5- Picornaviridae
6- Reoviridae
7- Caliciviruses
8-Astroviridae
 Introduction to immunity
 Antibodies, Humoral & Cell-Mediated Immunity
Ass. Prof .Dr. Manal EL Said
Ass. Prof .Dr. Manal EL Said
 Major Histocompatibility Complex
 Transplantation
 Complement
 Hypersensitivity:
 Tolerance
 Autoimmune Diseases
 Tumor Immunity
 Immunodeficiency
Basic Biology of Fungi:
General characteristics, classification, medical importance
of major fungal groups, fungal cell structure, fungal
morphology & pathogenesis.
Superficial, Cutaneous & Subcutaneous Mycoses:
 Superficial mycoses
 Cutaneous mycoses
 Subcutaneous mycoses
Systemic and Opportunistic Mycoses:
 Histoplasmosis
 Blastomycosis
 Paracoccidioidomycosis& Coccidioidomycosis
 Cryptococcosis
 Candidiasis
 Aspergillosis
 Zygomycosis
P. O. Box 6231, Jeddah 21442 Saudi Arabia
www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415
Revised November 20, 2012
9
Dr. Faten Hasan
Week 14
Dr. Faten Hasan
Week 15
Week 16
Question & Answer Sessions
Course Outline (revised: May 12, 2013)
Program Name:
Year Level:
Course / Subject:
Pls. tick/check: √
Week
 Pneumocystis Carinii
 Intestinal & Urogenital Protozoa
 Blood & Tissue Protozoa
 Cestodes, Trematodes & Nematodes
Dentistry
Academic Year 2013-2014
D3
Semester:
1ST
Microbiology
Lecture:
Clinical __ Practical: √ Others: __
Whole Year __√_ / Semester
Professor / Lecturer
/ Instructor
Topics/Skills Covered
Theoretical
Session -1
 Microbiology Laboratory Safety Measures.
Session -2
 Microscopy:
1- The light microscopes
Week 1
Microbiology staff
Microbiology
staff
Week 2
-
Bright filed microscope
Phase contrast microscope
Dark field microscope
Florescence microscope
Differential interference contrast microscope
2- Electron microscope
3- Confocal scanning laser microscope
Practical
A-Components of Bright filed microscope
1. Framework the arm and base.
2. Stage the mechanical stage,
3. Light Source
4. Lens Systems Oculars, objectives, and condenser.
5. Focusing Knobs: coarse adjustment and fine adjustment knobs
6. Ocular Adjustments
B- Calculation of Magnifications
Theoretical
Session -1
Morphology of microorganisms
Size- shape - arrangements & staining properties
Session -2
Microscopical techniques used in microbiology:
1.Examination of pathogens in wet preparations
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2.How to prepare and fix smears prior to staining
3.Precautions to take when staining smears
4.Staining technique
-
Gram stain
Ziehl-Neelsen technique to detect AFB
Auramine-phenol technique to detect AFB
Methylene blue technique
Wayson’s bipolar staining of bacteria
Albert staining of volutin granules
Giemsa technique
Acridine orange fluorochrome staining.
Toludine blue-0 staining of P. jiroveci cysts
Polychrome Loeffler methylene blue staining of anthrax bacilli
Practical
1-Using a microscope to identify different bacterial shapes and
arrangements.
2- Observe the demonstration slides of:
- Basic shapes of bacteria
- Different arrangements of cocci
- Different arrangements of bacilli
- Appearance of typical yeast.
-Differentiation of yeast from a coccus-shaped bacterium by its size
Microbiology
staff
-Requirements
-Method
- Results
- Variations in Gram reactions
-Quality Control
Week 3
Microbiology staff
Week 4
Theoretical
Session
Gram staining technique and Hot and cold Ziehl Neelsen
staining technique:
Practical
1- Perform a gram staining techniques
2- Determine if a bacterium is gram-positive or gram-negative
when microscopically viewing a gram stain preparation
3- State the shape and arrangement of the organism
4- Perform cold Ziehl Neelsen staining technique
5- Observe the demonstration slide of acid fast bacilli
Theoretical
Session
Culturing bacterial Pathogens
Different types of culture media
1-The main types of culture media
-
Basic
Enriched
Selective
Indicator
Transport
Identification
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2-Culture media classification
according to consistency :
- Solid
- Semi-solid
- Fluid
Week 5
Microbiology staff
Microbiology
staff
Week 6
Microbiology
staff
Week 7
Week8
Week 9
Week10
Microbiology
Practical
Observe and identify the demonstration plates of main types of
culture media
Theoretical
Session
Culturing bacterial Pathogens
- How to Prepare, Sterilize and Dispense Culture Media
- Labelling and storage and Test of culture media
Practical
Preparation, sterilization and dispensing :
- Nutrient Agar
- Nutrient broth
Theoretical
Session
 Specimens collections
 Specimens processing
 Culturing blood & Possible pathogens isolated from blood
Practical
 Blood culture :
- Collect blood and inoculate culture media
- Examine the specimen microscopically
- Examine and report the cultures
Theoretical
Session
Culturing bacterial Pathogens
How to inoculate culture media
- Aseptic techniques
- Inoculation of media in petri dishes
- Inoculation of slopes
- Inoculation of stab media (deeps)
- Inoculation of fluid media
Practical
1- Using an inoculating loop, demonstrate how to aseptically
remove some inoculum from either a broth tube, slant tube, stab
tube, or petri plate, and inoculate a sterile broth tube, slant tube,
stab tube, or petri plate without introducing outside
contamination.
2-Label all tubes and plates and place them on the proper shelf in
the incubator.
Eid
Eid
Theoretical
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Revised November 20, 2012
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staff
Microbiology
staff
Week 11
Microbiology
staff
Week 12
Microbiology
staff
Week 13
Session
Enumeration of microorganisms
a. Plate count
b. Direct microscopic method
c. Turbidity
Practical
Perform a serial dilution of a bacterial sample and plate out
samples of each dilution.
Theoretical
Session
Culturing bacterial Pathogens
Incubation Of Inoculated Media
-Temperature of incubation
-Humidity
-Gaseous atmosphere
Culturing of anaerobes
A-Techniques for obtaining anaerobic conditions:
- Commercially produced sachets containing oxygen removing
chemicals and anaerobic container.
- Reducing agents in culture media.
B-Culturing in carbon dioxide
Practical
- Culturing of anaerobes using commercially produced sachets
containing oxygen removing chemicals and anaerobic container.
- Culturing in carbon dioxide
Theoretical
Session
1. Beta-glucuronidase: identify E. coli
2. Bile solubility: differentiate S. pneumoniae from other alphahaemolytic streptococci
3. Catalase: differentiate staphylococci from streptococci
4. Citrate utilization: differentiate enterobacteria
5. Coagulase: identify S. aureus
Practical
Perform the method of testing:
1. Catalase
2. Citrate utilization
3. Coagulase
Session
6. Indole : differentiate Gram negative rods, particularly E. coli
7. Litmus milk : identify decolorization Enterococcus and some
clostridia
8. Lysine decarboxylase: assist in identification of salmonellae
and shigellae
9. Oxidase: help identify Neisseria, Pasteurella, Vibrio,
Pseudomonas
10. Urease : identify Proteus, Morganella, Y. enterocolitica, H.
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Revised November 20, 2012
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Microbiology
staff
Week 14
Week 15
Microbiology staff
Week 16
Program Name:
Year Level:
Course / Subject:
Pls. tick/check: √
Week
pylori
11. TSI
Practical
Perform the method of testing:
4. Indole
5. Oxidase
6. Urease
7. TSI
Theoretical
Session
Antibiotics susceptibility tests:
1-Disc diffusion method
2- Tube dilution method
2- E test
Practical
- Perform and interpret the results of a Bauer-Kirby antimicrobial
susceptibility test when given a Mueller-Hinton agar plate, a
metric ruler, and a standardized zone-size interpretation table.
- Interpret the results of E test.
Revision
Question & Answer Sessions
Course Outline (revised: May 12, 2013)
Dentistry
Academic Year 2013-2014
D3
Semester:
2nd
Microbiology
Lecture: Clinical __ Practical: √ __ Others:
Whole Year √ / Semester
Professor / Lecturer
/ Instructor
Week 1
Microbiology staff
Week 2
Microbiology staff
Topics/Skills Covered
Theoretical Session
Sterilization and disinfections
1-Physical means of sterilization
- Radiation
- Filtration
- Heat: dry heat
Practical
- Hot air oven: method of applying dry heat
Theoretical Session
Sterilization and disinfections
1-Physical means of sterilization:
Heat: moist heat
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Revised November 20, 2012
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Week 3
Microbiology staff
Week 4
Microbiology staff
Week 5
Microbiology staff
Week 6
Microbiology staff
Week 7
Microbiology staff
2-Chemical means of sterilization
Practical
Autoclave: method of applying moist heat &the process of
autoclaving (pressure, time, and temperature).
Theoretical Session
Antigen antibodies reaction
1-agglutination
2-precipitation
Practical
Perform and Interpret the results of the following serological
test:
 Widal test
- Salmonella typhi O
- Salmonella typhi H
- Salmonella paratyphi A
- Salmonella paratyphi B
- Salmonella paratyphi C
Theoretical Session
Antigen antibodies reaction
3-complement fixation
4-Toxin antitoxin neutralization
Practical
Perform and Interpret the results of the following serological
test:
- ASOT
Theoretical Session
Antigen antibodies reaction
5-virus neutralization
6- Immunefluorescence
Practical
Perform and Interpret the results of the following serological
tests:
- CRP
Theoretical Session
Antigen antibodies reaction
7- Enzyme linked immunesorbant assay (ELISA)
Practical
Perform and Interpret the results of the following serological
tests:
- RPR
Theoretical Session
Antigen antibodies reaction
8-Radioimmunoassay
Practical
Perform and Interpret the results of the following serological
tests:
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Revised November 20, 2012
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- Blood grouping
Week8
Microbiology staff
Week 9
Microbiology staff
Week10
Microbiology staff
Week 11
Microbiology staff
Week 12
Week 13
Microbiology staff
Week 14
Microbiology staff
Theoretical Session
Antigen antibodies reaction
9-Flow cytometry
Practical
Perform and Interpret the results of the following serological
tests:
- Rh grouping
Theoretical Session
Molecular diagnosis of microorganisms
Polymerase chain reaction (PCR)
Practical
Demo-videos for PCR
Theoretical
Examination of Faeces For Parasites
 Collection of fecal specimen for parasitic examination.
Practical
Examination of faeces for parasites.
Theoretical
Examination of Faeces For Parasites
 Faecal concentration techniques
1-Formol ether concentration technique
Practical
Reporting the appearance of the specimen and identifying any
parasitic worms.
Theoretical
Examination of Faeces For Parasites
 Faecal concentration techniques
1.Zinc sulphate floatation technique
2.Saturated sodium chloride floatation technique.
Practical
 Examining the stool specimen microscopically.
Theoretical
Examination of blood for parasites
1.Detecting and identifying malaria parasites microscopically in
blood films.
2.Reporting blood films for malaria parasites.
Practical
 Thin blood film preparation.
Theoretical
Examination of blood for parasites
1. Examination of blood for T. cruzi.
2. Examination of blood for microfilariae.
Practical
 Thick blood film preparation
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Revised November 20, 2012
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Week 15
Week 16
Microbiology staff
Revision
Question & Answer Sessions
Course Outline (revised: May 12, 2013)
VI. COURSE CONTENTS
Main topics and subtopics of course material in outline format matching the sequence
of the main topics given in the Course Outline.
I-Introduction to the course:
Learning objectives; course format; evaluation, testing, and grading, policies
expectations.
II-Bacteriology
1-Bacterial Classification, Morphology & Cell Structure:
1.1. Medically important groups of microorganisms
1.2. Classification (taxonomy) of bacteria
1.3. Morphology (cell shapes, Gram stain)
1.4. Ultrastructural features (cytoplasm, cell envelope, external features)
1.5. Bacterial spores.
2-Bacterial Metabolism & Growth:
2.1. Nutrient requirements of bacteria
2.1. Aerobic & anaerobic respiration & fermentation
2.3. Bacterial growth.
3-Bacterial Genetics
3.1. Bacterial genome (chromosome & extrachromosomal elements).
3.2. DNA replication (binary fission)
3.3.Gene transfer (transposons, extrachromosomal elements and mechanisms of
DNA exchange).
4-Mechanisms of Bacterial Pathogenesis:
4.1. Entry into the human body
4.2. Adhesion, colonization & invasion
4.3. Pathogenic actions of bacteria
5-Commensal, Pathogenic Human Microflora &Antimicrobial Drugs:
5.1.Normal microflora of the human body
5.2.Normal flora of major human body systems
5.3.Antimicrobial Drugs: Mechanism of Action &Resistance
5.4.Bacterial Vaccines
5.5.Sterilization & Disinfection
6-The Gram-Positive Cocci –I (Staphylococcus):
6.1.Staphylococcus aureus , Methicillin-resistant S. aureus & glycopeptides resistance in
S. aureus
6.2. Coagulase negative Staphylococcus
6.2.1.Staphylococcus epidermidis
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6.2.2. Staphylococcus saprophyticus
7-The Gram-Positive Cocci – II (Streptococcus):
7.1.Streptococcus pyogenes (group A Streptococcus)
7.2.Streptococcus agalactiae (group B Streptococcus)
7.3.Streptococcus pneumoniae
7.4.Streptococcus bovis &viridans Streptococcus
7.5.Enterococcus
8-The Gram-Positive Bacilli:
8.1.Aerobic
8.1.1.Bacillus spp.
8.1.2.Corynebacterium.ssp.
8.1.3.Listeria monocytogenes, Erysipelothrix & Rhodococcus
8.2. Anaerobic
8.2.1.Clostridium spp.
8.2.2.Propionobacterium ssp.
8.3.Branching
8.3.1.Actinomyces
8.3.2.Nocardia ssp.
8.3.3.Actinomadura
8.3.4.Streptomyces
9-The Gram-Negative Cocci
9.1. Aerobic
9.1.1. Neisseria gonorrhoeae
9.1.2. Neisseria meningitides
9.1.3.Moraxella catarrhalis
9.2.Anaerobic
9.2.Veillonella
10-The Gram-Negative Bacilli
10.1.Enterobacteriaceae
10.1.1.Lactose fermenter
10.1.1.1. Escherichia coli & Citrobacter
10.1.1.2. Klebsiella, Enterobacter & Serratia
10.1.2. Non-Lactose fermenter
10.1.2.1. Proteus, Morganella & Providencia
10.1.2.2.Salmonella
10.1.2.3.Shigella
10.1.2.4.Yersinia
10.2. Gram negative bacilli –non fermenters
10.2.1.Pseudomonas aeruginosa, Stenotrophomonas maltophilia
(cepacia,peudomallei & mallei)
10.2.2. Acinetobacter
10.3. Fastidious gram negative rods
10.3.1.Coccobacilli
10.3.1.1.Haemophilus
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Burkholderia
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10.3.1.2.HACEK Organisms(Haemophilus, Aggregatibacter Cardiobacterium, Eikenella &
Kingella)
10.3.1.3.Gardnerella
10.3.1.4.Bordetella pertussis
10.3.1.5.Brucella
10.3.1.6.Pasteurella
10.3.1.7.Francisella tularensis
10.4.Bacilli with pointed ends:
10.4.1.Legionella pneumophila
10.4.2.Capnocytophaga
10.4.3.Vibrio, Aeromonas & Plesiomonas
10.4.4.Campylobacter
10.4.5.Helicobacter
10.5.Gram negative anaerobic Bacilli:
10.5.1.Bacteroides
10.5.2.Prevotella
10.5.3.Porphyromonas
10.5.4.Fusobacterium
11-Spirochete, Rickettsial
11.1.Spirochetes: Treponema , Borrelia & Leptospira
11.2.Rickettsia: rickettsiae, prowazekii &Rickettsia typhi
11.3.Coxiella burnetii
11.4.Bartonella spp.
11.5.Mycoplasma
12-Chlamydial & Mycobacterium
12.1. Chlamydia: trachomatis, Chlamydophila pneumoniae & psittaci
12.2. Tuberculosis, leprosy& non- tuberculosis
III-Virology
13-Viral Classification, Structure & Replication
13.1. Basic characteristics, classification of viruses & structure (non-enveloped &
enveloped viruses)
13.2. Viral replication:
14-Mechanisms of Viral Pathogenesis:
- Acquisition & infection of target tissue, cytopathogenesis (lytic & nonlytic infections,
oncogenic viruses), human host defenses against viral infection, immunopathology,
epidemiology of viral diseases, (age, immune status & other host factors), control of
viral spread.
15. DNA Enveloped viruses
15.1.Poxvirus
15.2.Hepadnaviridea
15.3.Herpesviridae
16.DNA non-Enveloped viruses
16.1. Adenovirus
16.2. Parvoviridae
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16.3. Papillomaviridae
16.4. Polyomaviridae
17-RNA viruses
17.1. Orthomyxoviridae
17.2. Paramyxoviridae
17.3. Coronaviridae
17.4. Togaviridae
17.5. Picornaviridae
17.6. Reoviridae:
17.7. Caliciviruses:
17.8. Astroviridae
17.9. Retroviridae
17.10.Flaviviridae
17.11. Bunyaviridae
17.12.Arenaviridae (Rodent-borne)
17.13. Rhabdoviridae:
17.14.Filoviridae:
17.15.Bornaviridae
17.16. Proines
IV-Mycology
18-Basic Biology of Fungi:
General characteristics, classification, medical importance of major fungal groups,
fungal cell structure, fungal morphology & pathogenesis.
19-Superficial, Cutaneous & Subcutaneous Mycoses:
19.1. Superficial mycoses
19.2. Cutaneous mycoses
19.3.Subcutaneous mycoses
20-Systemic and Opportunistic Mycoses:
20.1. Histoplasmosis
20.2.Blastomycosis
20.3.Paracoccidioidomycosis
20.4.Coccidioidomycosis
20.5.Cryptococcosis
20.6.Candidiasis
20.7.Aspergillosis
20.8.Zygomycosis
20.9.Pneumocystis Carinii
V-Parasitology
21.1.Intestinal & Urogenital Protozoa
21.2.Blood & Tissue Protozoa
21.3.Cestodes
21.4.Trematodes
21.5Nematodes
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IV-Immunology
1-Introduction to immunity
2-Antibodies, Humoral & Cell-Mediated Immunity
3-Major Histocompatibility Complex
4-Transplantation
5-Complement
6-Hypersensitivity
7-Tolerance & Autoimmune Disease
8-Tumor Immunity
9-Immunodeficiency
Practical:
 Microbiology Laboratory Safety Measures & Microscopy
 Morphology of microorganisms: Size- shape - arrangements & staining properties
 Microscopical techniques used in microbiology: Gram staining technique & Hot and
cold Ziehl Neelsen staining technique.
 Culturing bacterial Pathogens:
- Different types of culture media
- How to prepare, Sterilize and dispense, labeling and storage of culture media.
 Specimens collections & processing
 Culturing blood & Possible pathogens isolated from blood
 Culturing bacterial Pathogens: How to inoculate culture media, Enumeration of
microorganisms, Incubation of Inoculated Media & Culturing of anaerobes
 Biochemical reaction
 Antibiotics susceptibility tests
 Sterilization and disinfections
 Perform and Interpret the results of serological tests
 Examination of Faeces For Parasites
 Examination of blood for parasites
VII. COURSE SCHEDULE
State number of hours spent in the following areas per week for 15 weeks each
semester:
Lectures: 15
Lab: 30
Clinical: __________ Other: ____________

Instruct students to view the ELMS for their comprehensive class schedule.
VIII. EVALUATION METHOD
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1.
2.
Grade Distribution (FAST, Clinical, M1M2D1D2, Scientific Subjects)
Grading System
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IX.
COURSE POLICIES
1.
Submission of projects/assignments: what, when, to whom, and where?
2.
Laboratory requirements, plan & assignments:
3.
Quiz & Examination Policy:
3.1. Quizzes
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3.1.1.
3.1.2.
3.1.3.
3.1.4.
3.1.5.
3.1.6.
3.1.7.
3.1.8.
3.1.9.


The time of quizzes must be clearly stated in the Course
Outlines (Lecture, Lab or Clinical) for the students.
The Course Outlines must be included in the Course
Syllabus for uploading on the ELMS before the start of
the academic year.
The time of quizzes must also be submitted to the
Academic Office before the start of the each semester.
3 quizzes per semester must be given for a one
semester course.
2 quizzes per semester must be given for courses taught
for the entire year (two semesters).
Quizzes are to be conducted for 15 minutes and
incorporated into a lecture period.
Quizzes will be paper based unless exceptions made by
the Vice Dean of Academic Affairs.
Quiz results must be announced to the students within
3 days.
Students have the right to approach their Head of
Program with any concerns regarding quiz results.
3.2. Exam Rules for Students
3.2.1. All forbidden items must be left home or outside the
exam area. BMC is not responsible for them.
3.2.2. Students must present their BMC ID to the Exam
Supervisor at the door for entrance to the exam.
3.2.3. Deprived students will not be allowed to enter the exam
hall.
3.2.4. Students will begin checking in fifteen minutes prior to
the exam time and may not be later than 20 minutes or
he/she will not be allowed to take the exam. The Exam
Supervisor may receive permission from the Vice Dean
of Academic Affairs to make an exception in extreme
cases.
3.2.5. Students may not leave until half of the exam time has
passed and it is approved by the exam supervisor after
the complete attendance has been taken.
3.2.6. Students are to fill out the provided Answer Sheet for
the MCQ section of the exam according to the following
instructions:
Use a #2 pencil to fill in the bubbles. Do not use ink pens.
If more than one bubble for the same question is filled in, it will be exempted (not count)
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



Write the student ID in appropriate columns & fill in the bubbles accordingly
Make heavy black marks for the final answer that fill in the bubble completely
Erase any unwanted answers completely or the checking machine will recognize more than
one answer and exempt the answer
Only one answer per question
3.2.7.
3.2.8.
Students are not allowed to leave and return while the
exam is in process for any reason.
If a student is caught with a mobile phone or other
devices, papers, answers written on their person, or any
other obvious cheating material, the invigilator will
terminate the exam and fill out an Exam Misconduct Form
which will be signed by the invigilator and the supervisor.
The exam will not be valid and a resit exam must be
taken.
3.2.9.
If a student is caught verbally cheating or looking on
another student’s paper, he will receive one warning by
the supervisor. If caught again, the paper will be marked
‘cheating’ and the invigilator will terminate the exam and
fill out an Exam Misconduct Form which will be signed by
the invigilator and the supervisor. The exam will not be
valid and a resit exam must be taken.
3.2.10. It is absolutely forbidden for any student to disobey or
disrespect either verbally or physically, any BMC staff
associated with the exam process including Academic,
Student Affairs, or Security staff. An Exam Misconduct
Form will be filled. Disciplinary action will be taken
according to BMC policy.
3.2.11. It is absolutely forbidden for another person to take the
exam for a BMC student. This will result in instant
expulsion from BMC.
3.2.12. Students may request a Student Exam Complaint Form
from the exam supervisor to be filled out immediately
following the exam regarding any concerns or complaints
about the exam, exam procedure or the exam staff. The
student will submit it directly to the exam supervisor who
will give it to the supervisor of the Control Room. The
student may seek a written response within two days of
the exam from the Control Room Supervisor. The student
has the right to request a formal meeting of the
Grievance Committee to resolve the concern according to
policy.
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3.2.13. Students must turn in to the invigilators any scrap paper
given during the exam before leaving.
All students must bring to the exam:
1. Official BMC ID with picture
2. Calculator if specified by professor as necessary. Mobile phones will not be
allowed to be used as a calculator. Borrowing will not be allowed.
Forbidden items (Do NOT BRING):
1. purses
2. mobile phones, I Pads, All Devices
3. papers, books, any study materials
4. sunglasses, caps
5. food & drink
4. Attendance; Classes/Exams:
4.1. Attendance
4.1.1.
The student is given the first warning if his absence is more than 10% in
lectures, labs or clinical classes whether with excuse or not.
4.1.2.
The student is deprived from completing the course and taking the
final exams if his absence exceeds 25% of lectures, labs or clinical
classes and is considered failed in this course. The student may take a
resit exam by the end of the academic year and the final grade of the
subject total grade will be out of 60% (quizzes, final practical and
clinical grade will not be included). If the student has excuses for his or
her absence from classes, practical and clinical sessions it must be
submitted to the Academic Office to be reviewed by the Student Excuse
Review Committee. Only extreme emergency cases will be accepted for
a continuous period of not more than two weeks or total of three weeks
separated over the academic semester.
4.1.3.
The Academic Office directly informs the student that he is deprived
and proposes a report to the concerned department head and then
clarifies the dates of absence according to the attendance records.
4.1.4.
Based on the report presented by the Student Excuse Review
Committee of the Academic Office and after communicating with the
concerned department, the College Council has the right to remove
deprivation in maximum cases under rules and conditions previously
approved by the Council, ONLY if the absence percentage is not more
than 35% of lectures, labs or clinical classes.
4.2 Absences from Exams
4.2.1.
If the student missed a final exam without an acceptable
excuse submitted and approved by the Student Excuse
Review Committee, he gets an “F” in his results record and
He may take the resit exam by the end of the academic year
BUT his final grade of the subject will be accounted from
60% after passing the exam.
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4.2.2.
If the student is not able to take the final exam either in
semester based or whole year subjects for a strong excuse,
his case should be presented to the Student Excuse Review
Committee to check and accept his excuse after two weeks
of his/her missed exam. The student may take a resit exam
by the end of the academic year AND the final exam grade
will be out of 100, which will include quizzes, practical and
clinical final exams.
4.2.3.
Students who miss any of the quizzes or final practical
exams for any unforeseen emergency case must fill out a
Student Excuse Form from the Academic Office and submit
it within two weeks after the missed exam.
4.2.4.
If the Student Excuse Review Committee approves the
Excuse related to the missed quizzes and final practical
exams, the department of the related course will be
informed and the student will retake the final practical exam
BUT the grades of the previous or the second quiz will be
counted for the missed quiz.
4.2.5.
If the Student Excuse Review Committee disapproves the
excuse, the student will lose the grade of the missed quiz or
the final practical exam.
4.3 Class Timing
4.3.1 Classes are fifty minutes long. Classes must begin
immediately on time (i.e. 8:00 a.m.) and end ten minutes
before the next hour (i.e. 8:50 a.m.). If the class is longer than
one hour, a break must be given.
4.4 Late Rule
4.4.1 Students must be encouraged to get to class on time at the
beginning of the hour. However, no students may enter class
later than 10 minutes after the lecture has started.
5. Plagiarism, Dishonesty:
5.1. Academic Integrity
5.1.1.
Being a member of Batterjee Medical College’s academic society,
students shall abide by the rules of conduct, both social and academic.
5.1.2.
These policies include professionalism, good manners, and right
conduct. It also discusses other matters involving transgressions of
academic integrity such as plagiarism and cheating on exams.
5.1.3.
Plagiarism is stealing another person’s idea or writing. It is a form of
cheating and is absolutely forbidden in the College. All academic work
must be the student’s own and will be assessed by the academic staff
upon submission. Students may be asked to discuss the sources of their
work and ideas and must be prepared to give an oral defense if
suspected of plagiarism.
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5.1.4.
Any form of non-academic behavior including cheating will be
punished according to BMC Policy.
5.1.5.
Students have rights which include fair and nonbiased treatment by the
faculty in all academic affairs.
5.1.6.
Students have the right of appealing a grievance.
6. Appealing a Questionable Grade:
6.1.
Exam Result Audit
6.1.1. Students who wish to have their final examination grade audited may do
so providing that they:
6.1.1.1.
Submit a request to Student Affairs within one week after the
announcement of the results. Exceptions are per the discretion
of the Vice Dean of Academic Affairs.
6.1.1.2.
Pay the Audit Fee per exam which is to be returned only if
mistakes are found.
6.1.1.3.
A committee, under the supervision of the Program Head and
consisting of an academic staff member teaching the subject of
the exam and a control room member, will audit the designated
exam. The committee will make sure that:
6.1.1.3.1.
If the student requests to be present during the
audit, he is allowed to do so.
6.1.1.3.2.
All exam sections have been checked and all the
marks were added to the student's mark.
6.1.1.3.3.
The total of the marks is identical to the one which
is written on the cover sheet.
6.1.1.3.4.
The student's mark in the e-record is correct.
6.1.2. If mistakes are found, the Audit Fee will be refunded and the grade
record will be corrected.
X. REQUIRED TEXTBOOKS
Review of Medical Microbiology & Immunology, Eleventh Edition, 2010 by the
McGraw-Hill Companies, Inc.
XI. RECOMMENDED TEXTBOOKS & OTHER READING MATERIALS
Books:
1. Review of medical microbiology and immunology (LANGE Basic Science)
2. Medical Microbiology & Immunology: Examination & Board Review
3. Bergey's Manual of Systematic Bacteriology
4. Clinical Bacteriology, Mycology and Parisitology : An Illustrated Colour Text
5. Diagnostic Medical Parasitology
6. Cellular and Molecular Immunology
7. Principles and Practice of Clinical Virology
8. Principles of Virology (2 Volume Set)
9. Microbiology: A Laboratory Manual
Electronic Materials, Web Sites etc:
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www.cdc.org
X.
STUDENT RESPONSIBILITIES:
1. Expectations from students:
Students are expected to respect the instructor, fellow students and
themselves and follow the following rules:
 No one is allowed to enter the class 10 minutes after the start of the
lecture.
 Students are not allowed to leave the class before completion of the
lecture without the instructor’s permission.
 Chatting, drinking, or eating during lectures is forbidden.
 Cell phone use is not permitted. They must be turned off or in silent
mode during lectures.
 Students must sit in their seats and not on the stage, steps, or floors.
 Shouting, whistling, singing or other disruptive behavior is forbidden.
 Entering the class from the male section to the female and vice versa is
not permitted.
 In the case of damage to college property, by students, they will bear the
cost of replacement or repair.
 Use of the projector, computer mouse, microphone or electrical supplies
is not allowed.
 Fighting is absolutely forbidden in the classes and anywhere on campus.
 Sleeping or resting during lectures is forbidden.
 Students must leave the classroom clean.
2. Student responsibilities to course:
 The student is responsible for his/her own success in the learning
process. He/she should be actively involved in the learning process and
should behave appropriately for a learning environment.
 The student is responsible for bringing to class all necessary materials
(book, notebook, pen, pencil, calculator, etc.).
 The student is responsible for participating in class discussion, group
discussions, class demonstrations etc…
 The student is responsible for reading the assigned material prior to
class.
 The student is responsible for reviewing his course contents and being
prepared to discuss the topics.
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 The student is responsible for asking clarification if anything is unclear to
him/her during the lecture.
 The student is responsible for seeking out his instructor during office
hours for assistance.
 The student is responsible for evaluating his course.
3. Expectations for each assignment & project:
 The student is responsible for completing all assignments and projects
according to the guidelines set by the instructor.
 The student is expected to finish all assignments and projects within the
time allocated by the instructor.
 The student is expected to do his fair share of any group project.
 The student is responsible for making sure the work is his own.
4. Conduct Leading to Dismissal:
 Cases of physical aggression and use of foul language.
 Sexual harassment with all the meanings of this term that are
contradicting with the teachings of the Islamic religion.
 Possession of weapons of any kind
 Drug & alcohol use
 If the student gets three consecutive warnings for his/her low GPA which
is less than 2 out of 5 or 1 out of 4 as recommended by the college
committee to give the student a fourth chance to improve his/her GPA.
 If the student did not meet all graduation requirements after failing two
consecutive years added to the period of the whole program and the
college’s committee is entitled to give the student an exceptional chance
to finish graduation requirements in no more than 3 years.
 If the student acts in a way that contradicts the teaching of our Islam and
the college’s rules.
Note: This is a contract between the faculty and students. In case of changes, the
students must be properly informed.
______________________________
Dr. Hassan Sami Shaibah
Vice Dean of Academic Affairs
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