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 www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 3 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 7 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 10 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 11 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 12 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. P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 13 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 14 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: P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 15 - 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 16 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 17 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia & Burkholderia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 18 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 19 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 20 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 21 1. 2. Grade Distribution (FAST, Clinical, M1M2D1D2, Scientific Subjects) Grading System P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 22 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 23 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) P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 24 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. P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 25 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. P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 26 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. P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 27 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: P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 28 www.bmc.edu.sa 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. P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 29 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 P. O. Box 6231, Jeddah 21442 Saudi Arabia www.bmc.edu.sa Tel.: 009662-656-1111 Fax: 009662-656-2415 Revised November 20, 2012 30