South Asian Institute

of
Technology and Medicine
Malabe
Sri Lanka

Faculty of Medicine
HANDBOOK
FOR STUDENTS
IN
MEDICAL MICROBIOLOGY
and
IMMUNOLOGY

2014

CONTENTS
1. Introduction
2. The staff in the department
3. The time table
4. The course content and topics
5. General objectives of the course
6. Specific objectives in
6.1 General microbiology
6.2 immunology
6.3 systematic bacteriology
6.4 virology
6.5 mycology
6.6 antibiotics
7. The teaching learning methods
7.1 Lectures
7.2 Practical sessions and demonstrations
7.3 Small group discussions
7.4 Tutorials
8. Assessments
8.1 Continuous summative and formative assessments
8.1.1 Control tests
8.1.2 Credit tests
8.2 Final assessment in microbiology and immunology

9. Recommended reading
APPENDICES
1. Gram Stain
2. Acid Fast stain
3. Gram stain assessment

1. Introduction
Welcome to the Department of Microbiology and to the course in
Microbiology.
Microbiology is the study of microscopic organisms. This course deals with
all aspects of microorganisms (bacteria, viruses and fungi), that cause
disease in humans, and those that have the potential to cause disease.
The learning of Microbiology should go hand in hand with your clinical
work in the wards. You should be able to relate the knowledge you learn in
the subject to cases of infectious diseases that you see and discuss in the
wards. In this way the subject becomes more interesting and relevant to
your ward work and also when you complete this course and move on to
become a medical doctor.
2. The staff in the department
Academic staff
Professors/ Senior Lecturers:
Nelun de Silva MBBS (Patna), Dip Micro(Col), MD Micro (Col)
Anura Weerasinghe -MBBS, MD, FRCP, DCH, DTM&H, FCCP, PhD
Nalaka Kanakaratne MD (Rus) MSc. (Kelaniya) PhD (Pera)
Lecturers:
Dr. Vindya Perera BVSc (Peradeniya)
Ms. J. Lohitharajah -BSc (Human Biology)(Hon) on study leave

3.

The time table

You will be with us learning Microbiology during semesters IV and V in
the medical curriculum. Each of you will have about 8 hours of contact time
per week with the staff in our department during the semester 1V and 4
hours in semester V, learning Microbiology. These are distributed among
the various teaching learning activities, which are described in detail below.
This should not mean that you have to limit yourself to learning
Microbiology during these hours. The contact time you have with us is for
the purpose of directing your learning and to facilitate your learning
process. Therefore you will need to devote many more hours where you
will learn on your own or in small groups.

At a glance the hours that are set aside for Microbiology in a week are as
follows:
SEMESTER 1V
6hours
Lectures in Microbiology and Immunology
2 hours
Small group discussions
Hands on Practical sessions
Practical demonstrations
Tutorials, Case studies
SEMESTER V
2 hours
Lectures in Microbiology - on line and face
to face
2 hours
Small group discussions
Practical demonstrations
Tutorials, Case studies

4.

The course content and topics

Introduction to bacteriology.
Classification & Structure of bacteria.
Disinfection & Sterilization.
Pathogenesis & virulence of bacteria.
Detection, Culture & identification of Bacteria.
Bacterial genetics & bacteriophages, Molecular Biology &
genetic engineering.
Normal flora
Introduction to Immunology, Immune system,
Innate (non-specific) Immunity, Acquired (adaptive,
specific) immunity, Cells & tissues involved in the immune
system, Antigens, Innate immunity- Mechanical barriers,
Cells involved in innate immunity.
Innate immunity - Humoral aspects including Complement.
Adaptive immunity, Immunoglobulins & Humoral immunity.
Cell mediated immunity & Hypersensitivity.
Methods of acquiring Specific immunity.
Auto immunity & Immune tolerance.
Immuno deficiency & Transplantation.
Immunity to bacterial, viral & fungal infections.
Immunization.
Staphylococci/ Streptococci / enterococci.

Gram +ve bacilli ( Corynebacteria & Bacillus sp.).

Gram - ve cocci -- Neisseria.
Small Gram -ve bacilli(Haemophilus etc.)
Salmonella/ Shigella/ E.coli.
Pseudomonas/ vibrio / Aeromonas / Plesiomonas
Anaerobes -- Clostridia / Bacteroides.
Campylobacter/ Helicobacter.
Mycoplasma/ Rickettsiae/Chlamydiae.
Mycobacteria / Norcardia / Actinomycetes.
Spirochaetes.
Antibiotics / Antimicrobial therapy.
Introduction to Virology.
Viruses of the Respiratory tract
Hepatitis.
Herpes group of viruses.
pox viruses/ parvovirus/ papilloma viruses.
Mumps / Measles/ Rubella.
Rabies.
HIV .
Diarrhoeagenic viruses.
Entero & Arboviruses.
Mycology.
Collection & transport of specimens
UTI.
Upper respiratory infections.
Bone & joint infections.
PUO / Sepsis / Septic shock.
Congenital, perinatal infections & blood borne infections.
Infections of CNS & lower respiratory tract infections.
Abdominal infections, Gastroenteritis & food poisoning.
Hospital acquired infections and infection control.
Eye & Ear Infections.
Bone and joint infections.
Sexually Transmitted Diseases.
Skin Infections.

5. General objectives of the course

At the end of the teaching-learning course in Medical Microbiology the
student should be able to:
List the generic names of common microorganisms (bacteria,
viruses & fungi), which cause disease in humans.
Select the ones that are frequently encountered and prioritise
them in order of importance
Describe their habitat and routes of transmission and explain the
pathogenesis of infections caused by them
Relate the clinical signs and symptoms of these diseases to the
underlying pathogenesis
Explain the mechanism of action, identify the spectrum of activity
of anti microbial agents and describe the resistance mechanisms
of microorganisms against antimicrobials.
Select appropriate antimicrobial agents that can be used in
treatment and prophylaxis, being aware of on guidelines for
empiric therapy, culture and antibiotic susceptibility test (ABST)
reports, limitations (cost, availability, patient factors, etc..)
Explain measures for the prevention and control of these diseases.
Advice on immunisation procedures for bacterial & viral diseases
Recognise the basic microscopic features of the common bacterial
pathogens and fungi and identify them in direct mounts, Gram
and acid fast stained smears.
Assist in the diagnosis of infectious diseases by
o Identifying the microbiological tests available for the
diagnosis of these infections
o Selecting the appropriate test according to the duration
of the illness
o Advising on collection and transport of relevant
microbiological specimens
Define and list the antiseptics, disinfectants and sterilising agents,
explain their mode of action and select the appropriate ones for
use in patient care and in the laboratory
Describe the immunological mechanisms that come into play
when a human host is exposed to a pathogen
Interpret these mechanisms when selecting tests for
immunological diagnosis in the context of available tests in the
country
- Perform Gram stains of prepared smears of cultures or clinical
specimens and identify as far as possible the microorganisms
there in by their microscopic morphology and staining
characteristics.

6.

Specific objectives
6.1 SPECIFIC OBJECTIVES IN GENERAL MICROBIOLOGY
At the end of each session of teaching learning on general
microbiology, the students should be able to:
1. List the generic names of common microorganisms (Bacteria,
Viruses & Fungi), which cause disease in humans.
2. Recognize the basic microscopic features of the common
bacterial pathogens and Fungi and identify them in direct mounts,
Gram and acid fast smears.
3. Select the microbes that are encountered in this country and
prioritize them in order of importance.
3.1 Describe the habitat and routes of transmission and explain
the pathogenesis of infections caused by these.
3.2 Relate the clinical signs and symptoms of these diseases to
the underlying pathogenesis.
3.3 List microbiological tests available for the diagnosis of these
infectious diseases.
3.4 Select appropriate tests according to the duration of the
illness.
3.5 Advise on and be able to collect and transport relevant
microbiological specimens.
3.6 Select appropriate antimicrobial agents that can be used in
treatment and prophylaxis, being aware of
the guidelines for empiric therapy, culture and antibiotic
susceptibility test (ABST) reports and limitations( cost, availability,
patient factors, etc..)
3.7 Explain the measures for the prevention and control of
these diseases.
4. Explain the mechanism of action, identify the spectrum of
activity of antimicrobial agents and describe the resistance
mechanisms of microorganisms against antimicrobials.
5. Advise on appropriate immunization procedures for the bacterial
and viral diseases.
6. Define and list the antiseptics, disinfectants and sterilizing
agents, explain their mode of action and select the appropriate
ones for patient care and in the laboratory.
7. Describe the normal and exaggerated immunological responses
of a human host when exposed to a pathogen / foreign antigen/
self antigens.

7.1 Interpret these responses when selecting tests for

immunological diagnosis of infectious diseases, being aware of the
tests available in the country.
8. Perform the Gram stain in clinical specimens and identify
bacteria by their staining character and microscopic morphology.
6.2 SPECIFIC OBJECTIVES IN SYSTEMATIC BACTERIOLOGY
At the end of each session of teaching learning on Systematic
Bacteriology, the students should be able to:
1. List the bacterial species that cause important and
common infective diseases.
2. Define the characteristics of the genera to which these
bacteria belong.
3. Identify their natural source, habitat and growth
requirements for artificial culture in the laboratory
4. Identify them by their microscopic morphology, and
colony appearance
5. List the infections or clinical syndromes they cause in
humans.
6. Explain the pathogenesis of infections they cause.
7. Advise staff and patients regarding collection and
transport of clinical specimens for the microbiological
diagnosis of infective diseases.
8. Interpret reports of microbiological investigations done
in these infective diseases
9. List front line and second line antibiotics effective against
major pathogenic bacteria and select appropriate
antibacterial agents for the treatment of infections
caused by them.
10. Explain the epidemiology of such infections and update
themselves on the prevalence of infective diseases in the
community.
11. Formulate methods to prevent and control infections in
the community and in the hospital, caused by the
bacteria based on their habitat and modes of spread.
12. Perform direct smears of clinical specimens / broth or
solid cultures, stain appropriately and identify the
bacteria as far as possible.

6.3 SPECIFIC OBJECTIVES FOR SYSTEMATIC VIROLOGY.

At the end of each session of teaching learning on
systematic virology, the students should be able to:
1. State some historical facts regarding the virus or the group of
viruses or the discovery of it.
2. Identify the common characteristics of the family and the
genus to which the virus belongs.
3. Identify the important and pathogenic serotypes /strains /
variants of the genus.
4. Explain the morphology and common characteristics of the
virus.
5. Explain the methods of transmission of the virus to the
human host, and the natural hosts and vectors (if any).
6. List the common diseases and syndromes caused by the virus.
7. Recognize and describe briefly the clinical features of
common diseases and syndromes caused by the virus.
8. Explain the pathogenesis and outcome of such viral
infections.
9. Choose the appropriate laboratory diagnostic methods
available for detection of the viral infection.
10. Instruct how the appropriate clinical specimens are collected
and transported for laboratory diagnosis of viral infection.
11. Interpret laboratory reports for viral infections.
12. Prescribe appropriate anti viral drugs (if any) for such viral
infections.
13. Describe briefly the epidemiology (i.e. the prevalence,
distribution, at risk population etc) of such infections.
14. Explain the appropriate methods of prevention and control of
viral infections in the community.
6.4 SPECIFIC OBJECTIVES FOR MYCOLOGY
At the end of each session of teaching learning on Mycology,
the students should be able to:
1. List the aetiological agents and identify the clinical features
and recognize common superficial, subcutaneous and
systemic fungal infections. Eg. Taenia, kerion, pityriasis
versicolor,
piedra,
onychomycosis,
candidasis,
chromomycosis,
mycetoma
and
rhinosporidiosis,
aspergillosis and cryptoccosis.

2. Describe their pathogenesis.

3. Advise on collection and transport of specimens for their
laboratory diagnosis.
4. Treat and advise on prevention (if any) of superficial fungal
infections.
6.5 SPECIFIC OBJECTIVES FOR ANTIMICROBIAL AGENTS
At the end of each session of teaching learning on Antibiotics,
the students should be able to:
1. Recall some interesting facts in the history of development of
antimicrobials.
2. Explain the mechanisms of action of antimicrobials.
3. Describe the origin and types of drug resistance by microbes.
4. Identify the clinical settings where antimicrobial agents are used
for empiric and definitive therapy.
5. Identify the clinical conditions where antimicrobials are used for
prophylaxis.
6. Outline the tests that are done in the laboratory, to guide
clinicians on antimicrobial therapy.
7. Describe the development of antimicrobial drug resistance by
microbes and its clinical implications.
8. List the generic names, describe the mechanism of action,
spectrum of activity, adverse effects of commonly used
antimicrobials in each group e.g. penicillins, aminoglycosides,
cephalosporins, azoles etc.
9. Identify the drug/s of choice and schedules in the treatment of
common infective diseases such as Tuberculosis, Leprosy,
Typhoid, Infective endocarditis, UTI, pneumonia, gastroenteritis, meningitis & encephalitis, taenia infections, herpes
infections etc.
10. Interpret antibiotic susceptibility test reports issued by the
laboratory.
11. Select an appropriate antimicrobial to treat common infective
diseases.

10

1.

6.6 SPECIFIC OBJECTIVES FOR IMMUNOLOGY

Basic Immune mechanism
a. Innate Immunity
1. define the term "innate immunity"
2. describe the innate immune mechanisms found in the body:
cells and molecules
3. define the term "acquired immunity" and describe how it
differs from innate immunity
b. Acquired immunity
1. list the types of acquired immunity
2. define the term "antigen'
3. list the antigen-presenting cells (APCs) and explain how APCs
present the antigens on their cell surfaces
4. state the sites of location of lymphocytes
5. define the terms "cell-mediated immunity" and "humoral
immunity" and state the type of lymphocyte that promotes
each of them
6. give the sites of pre-processing of the T and B lymphocytes
7. explain the mechanism of activation of lymphocytes by
specific antigens to form clones
8. explain the mechanism of specificity of the T and B
lymphocyte clones
9. explain how antigens are presented to the T and B
lymphocytes
a. Humoral immunity
1. describe the series of events which take place from the time
a B lymphocyte encounters an antigen up to the formation of
antibodies
2. explain the difference between the primary and the
secondary antibody response
3. recognise that antibodies are gamma globulins which are
called immunoglobulins
4. state the different types of immunoglobulins and describe
their functions
b. Cell-mediated immunity
1. describe the events taking place when a T lymphocyte is
exposed to an appropriate antigen
2. recognise that T cell markers (surface receptor proteins) are
firmly bound to the cell surface
3. list the types of T cells and describe the functions of each of
them
c. Introduction to applied immunology
1. Hypersensitivity
2. Autoimmunity
3. Immunodeficiency

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7 The teaching learning activities (TLA)

7.1
Lectures
The permanent academic staff of the department will conduct the
lectures. This is the main TLA in this course where the core
knowledge in Microbiology will be learnt. The schedule of lectures
together with the dates will be displayed on the notice board at the
beginning of semester 1V and V. It would be good if you can come
prepared for these lectures in which case you will be able to follow
the lecture very clearly and make this TLA a productive learning
process.
The teachers will use power point presentations to facilitate
learning during the lecture. Handouts of the slides will be provided
most of the time before the lectures. Some clinical Microbiology
lectures will be available on line on EDU 2.0 in semester V. Students
need to register to access these online lectures.
The topics are as follows:
SEMESTER 1V
Basic concepts in immunology , Antigens.
Antibodies/ Immunoglobulins (part 1).
Antibodies/ immunoglobulins (part 2).CD-antigens. Antigenrecognizing receptors of B- and T-lymphocytes
Major Histocompatibility Complex (MHC/ HLA).
MHC-dependent restriction and regulation of immune response
Cytokines. Functional variants of CD4 T-cells.
Induction of immune response immunogenesis
Effector stage of immune response: humoral immunity.
Effector stage of immune response: cellular immunity
Antiviral immunity
Structure of bacteria, bacterial genetics
Introduction to Bacteria , pathogenecity and virulence of
microorganisms: general conceptions & toxins
Introduction to viruses/ Antiviral agents, Sterilization & disinfection
Systematic bacteriology, mycology & antifungal agents
Antimicrobials and antimicrobial chemotherapy
SEMSTER V
Systematic virology and Clinical microbiology

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7.2 Practical sessions

The practical sessions in the semester 1V will train you to be
competent in performing the Gram stain (appendix 1).
You will be working in pairs or threes doing the staining
procedure, after which you will individually focus the stained
smear under the microscope and observe the microscopic
morphology and staining character of the bacteria in the smear.
The acid fast stain (Ziehl Neelson) procedure will be demonstrated
to you in this semester. (appendix 2)
7.3 Small group discussions
The students are exposed to this type of teaching learning activity
during the scheduled time for practical or lectures in Microbiology.
The batch will be divided into small groups of 10-12 students in
each group and the topic to be discussed will be given as questions
or clinical scenarios. At the end of the allocated time
lecturer/tutor will facilitate the discussion.
7.4
Tutorials
Some scheduled practical hours in Microbiology are utilized for
tutorials. Students are given the topic or questions a few days
before and active discussion carried out during the tutorial.
8. Assessments in Microbiology and Immunology
8.1. Continuous summative and formative assessments
8.1.1 Control Tests
These are purely formative assessments to ensure that students
are up-to-date with their course work These will be conducted on
different topics as scheduled tests or at the beginning of a lecture
on previous lecture topics. The objective of these tests is to give
feedback to students on how well they are progressing in their
course work in Immunology and Microbiology.
The format of these tests will be true false type of MCQ's,
Objective structured Practical examination (OSPE)or short answer
questions.

13

8.1.2 Credit tests

Credit tests are conducted in each semester. These assessments
are formative as well as summative in nature. The total mark
obtained in credit tests will contribute to 20% of the total mark in
the final examination in Microbiology and Immunology.
The format of the credit tests will be any one of these methods
with a duration of approximately 30 to 60 mins. :
- A practical test to ascertain the capability of the student to
perform a Gram stain on a smear. They will be assessed on the
quality of the Gram stain. Focusing capability, observations and
interpretation.
- True false type of MCQ's, single best response (SBA) MCQs or
extended matching items (EMI)
- Short answer questions (SAQ)
- Objective structured Practical examination (OSPE)
8.2. Final assessment in microbiology and immunology at the end
th
of V semester.
The theory component will comprise of :
a.
Four Structured Essay Questions (SEQ) or 12 short answer
questions (SAQs) to be answered in 2 hours.
b. Twelve true false MCQs , two SBA MCQs and three EMIs to
be answered in one hour.
c.
Twenty Objective structured Practical examination (OSPE)
where power point projections are displayed with questions and
students are expected to answer in one hour.
d. Viva voce will be conducted by 4-5 panels of examiners.
Each panel will have two examiners and may include external
examiners as well. Each student will be examined by a single panel
for 8-10 mins.
Compilation of the final mark as a percentage main examination
SEQ/SAQ
MCQ
OSPE
viva voce
Credit tests at end of semester 1V & V
Total
Pass mark : 50%

14

30
20
20
10
20
100

 Students obtaining less than 50% in the total mark has to repeat
all components of the examination
To be eligible for distinction a student should obtain at least 75%
in the total mark and performed equally well in all components of
the examination.
Compilation of the final mark as a percentage Repeat examination
SEQ/SAQ
MCQ
OSPE
Viva voce
Total

40
25
25
10
100

9. Recommended Reading
1. Medical microbiology by D. Greenwood, R. Slack, J. Peutherer.-Churchill
Livingstone.
2. Medical Microbiology by Brooks G.F.
et al. Jawetz, Melnick,
st
Adelberg's . 21 ed. Appleton & Lange, 1998.
3. Medical Microbiology by Mims C. A., Playfair J. H. L., Roitt I., Wakelin
D., Williams R., Anderson R. M... Mosby. 1993.
th
4. Immunology by Roitt I., Brostoff J., Male D. 5 ed. Mosby. 1998.
5. Basic immunology by Sharon J.. Williams & Wilkins. 1998.
th
6. Immunology by Weir D. M., J. S. Churchill Livingston. 8 ed. 1997.
APPENDICES
APPENDIX 1: PRESTON & MORELL'S MODIFICATION OF GRAM'S STAIN
1. Apply Ammonium Oxalate-Crystal Violet stain for 1/2 minute.
2. Wash thoroughly with water.
3. Apply Lugol's Iodine solution for 1/2 minute.
4. Wash thoroughly with water.
5. Apply Iodine-Acetone solution for 1/2 minute.
6. Wash thoroughly with water.
7. Counter stain with dilute Carbol Fuchsin for 1/2 minute.
8. Wash thoroughly with water.
The whole smear must be flooded with each reagent and the previous
reagent must be completely washed at each stage. Care must also be taken
not to waste stains by over flooding the slide with the stain.

15

APPENDIX 2: ZIEHL-NEELSEN'S METHOD FOR ACID-FAST BACILLI

1. Flood the slide with Strong Carbol Fuchsin and heat, until steam rises.
(do not boil).
Allow the preparation to stain for 5 minutes, Heat being applied at
intervals to keep the stain hot. The stain must not be allowed to
evaporate and dry on the slide, if necessary pour more carbol fuchsin
to keep the whole slide covered with stain.
2. Wash the slide thoroughly under running water.
3. Decolourize in 3% acid alcohol by pouring the solution onto the smear.
Keep till the red colour of the smear is changed to light pink, Wash the
slide in water. The object of the washing is to remove the compound
acid with stain. The decolourization is finished when, after washing the
slide, the film is very faintly pink.
4. Wash the slide well in water.
5. Counterstain with methylene blue for 2 minutes
7. Wash the slide

APPENDIX 3: CHECK LIST FOR PERFORMANCE OF GRAM STAIN

1.
2.
3.
4.
5.
6.
7.
8.
9.
10
11
12

Observes the correct side of the slide on which the

smear has been made
Pours ammonium oxalate/crystal violet - just enough to
cover smear
Adjusts the rack if needed
Opens tap / adjusts water stream
Times each step
Washes adequately /Pours water on stain before
discarding
Pours Lugols iodine & times the procedure
Washes adequately
Pours iodine acetone & times precisely
Washes well
Counterstains with dilute carbol fuchshin & washes well
Dries on filter paper by pressing

16