Microbiology Syllabus BSc. 4th Year Tribhuvan University Nepal

Department of Microbiology

Institute of Science and Technology

Tribhuvan University, Kathmandu Nepal

Microbiology Syllabus BSc. 4th year

Environment and Public Health Microbiology (Theory)

Description of the Course

Course Title: Environment and Public Health             Full mark: 100

Course No: Microbiology (MB 401)                         Pass Marks: 35

Nature of the Course: Theory                                Year:  IV

Course Objectives

The main objective of the course is to provide knowledge on microbial ecology, basic epidemiological concepts and public health of infectious diseases. After completion of the course, the students will be able to:

1. Understand microbial ecology and their role in environment
2. Understand basics of epidemiology and health and disease measurements
3. Understand public health of infectious diseases

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Course Contents

Microbial ecology: 8 hrs

Microbial association in soil, water and air, components of microbial ecology, ecosystem and energy, tools and techniques of experimental microbial ecology

Microbiology of extreme environments: 10hrs

Growth and survival of microorganisms in extreme temperature, pH, humidity, salinity, and applications of extremophiles

Bioactive compounds of microorganisms: 8 hrs.

Bio pesticides, bacterial, viral and fungal pesticides, mechanism of action and applications of bio pesticides

Bioremediation: 8hrs

Principles of bioremediation, in situ and ex situ bioremediation of soil, water and air pollution, steps and approaches in bioremediation, removal of xenobiotic, bioleaching, petroleum degradation

Health and disease and epidemiological measurements: 10hrs

Definitions of epidemiology, applications of epidemiology, definitions of health and disease, indicators of health and disease, disease frequency measures (mortality, morbidity, incidence, prevalence, incidence density), measures of effect

Methods of transmission of diseases: 8hrs

Epidemic, endemic, pandemic, sporadic, outbreak, investigation of disease outbreaks, mode of transmission of diseases, chain of infection, cases, carriers, hosts

Management of diseases: 8hrs

Disease prevention, control, elimination and eradication

Drinking water microbiology: 15 hrs

Types of water, safe drinking water, physic-chemical and microbiological parameters of water quality, biological indicators of water pollution, national and WHO guidelines for drinking water quality standards, principle and procedures of drinking water treatment for large water supply system, methods for monitoring water quality

Waste management: 15 hrs.

Introduction, solid waste and its types, solid waste management, sewage and industrial effluents, composition and microbiology of sewage, methods for the treatment of waste water

Microbial air pollution: 10hrs

Introduction, methods of enumeration and identification of microorganisms in air (indoor and outdoor), indicator microorganisms of air pollution, air-borne diseases, air-pollution control

Water borne infections: 10hrs

Overview on common water-borne diseases, microbiology of causative agents, epidemiology, laboratory diagnosis, prevention and control of hepatitis A, cholera, typhoid, poliomyelitis

Air borne infections: 10hrs

Overview on common air-borne diseases, microbiology of causative agents, epidemiology, laboratory diagnosis, prevention and control of pneumonia, tuberculosis, influenza, measles

Food borne diseases: 10hrs

Concept on food borne infections and food intoxication, microbiology of causative microorganisms, epidemiology, laboratory diagnosis, prevention and control of Staphylococcal, Clostridia food poisoning and intoxication, Salmonellosis

Vector borne diseases: 10hrs

Overview on common vector-borne diseases and their vectors, microbiology of causative organisms, epidemiology, laboratory diagnosis and prevention and control of visceral leishmaniasis, malaria, filariasis, Japanese encephalitis, dengue

Sexually transmitted infections (STIs): 10hrs

Overview on common STIs, microbiology of causative agents, epidemiology, laboratory diagnosis and prevention and controls of syphilis, HIV/AIDS, hepatitis B

Recommended Readings

Text books

1. Park K (2008). Park's Textbook of Social and Preventive Medicine. 18th Edition.
2. Gordis L (2004). Epidemiology, 3rd Edition, Elsevier Saunders.
3. Atlas RM and Bartha R (1998). Microbial Ecology: Fundamentals and Applications. The Benjamin Cummins Publication Co. Inc.
4. Maier RM, Pepper IL and Gerba CP (2006). Environmental Microbiology. Academic Press, Elsevier Publication.

Reference books

1. StolpH (1988). Microbial Ecology: Organisms, Habitats, Activities. Cambridge

Environment and Public Health Microbiology (Practical)

Description of course

Course Title: Environment and Public Health Microbiology Practical  Full Marks: 50

Course No: 402(Major)                                                           Pass Marks: 20

Nature of the Course: Practical                                                 Year: IV

Course Objectives

After completion of the course, the students will be able to:

1. Conduct the analysis of environmental samples. 
2. Perform field level tests for the diagnosis of diseases.

Course Contents

1. To perform bacteriological examination of drinking water: Most Probable Number (MPN), membrane filter (MF) methods, physic-chemical parameters of water tests, DO, BOD, COD, residual chlorine, ammonia, nitrate/nitrite, sulfate, chloride, iron
2. To demonstrate water treatment station: Field visit to water treatment station and report submission
3. To assess air pollution: Air microbes in indoor and outdoor environments
4. To perform rapid diagnosis of viral diseases using test kits: HIV, hepatitis B, hepatitis C, rotavirus
5. To understand the disease reporting system of Nepal: Visit District Public/Health Office and report submission

By Chakra Web: www.chakrapanibhandari.com.np Email:

Medical Microbiology (Theory)

Description of Course

Course Title: Medical Microbiology                      Full Marks: 100

Course No: MB 403 (Major)                                Pass Marks: 35

Nature of the Course: Theory                             Year: IV

Course Objectives

After completion of the course, the students will be able to:

1. Understand the microbial world in the human body
2. Understand the immunity process in human body
3. Describe biology, pathogenesis and diagnostic methods of bacteria, virus, fungi and parasites

Course Contents

Historical background of medical microbiology: 5 hrs.

Historical aspects of medical microbiology, major contributors in medical microbiology

Normal flora of the human body: 10 hrs

Normal flora of human body (skin, gastrointestinal tract, respiratory tract, genito-urinary tract), opportunistic pathogens

Immunity process: 30 hrs

Types of immunity, immune globulins and their types, antigen antibody reactions, auto immune diseases, hypersensitivity

Safety measures in clinical laboratory: 8 hrs

Principles of laboratories safety, decontamination and safe disposal of contaminated materials, bio-safety level laboratories, risk and hazard group of microorganisms

Methods of specimen collection, transportation, processing and culture of clinical samples for detection of bacteria: 10 hrs

Cerebrospinal fluid, blood, sputum, urine, stool, other body fluids, pus and wound exudates, culture procedures, possible pathogens in different clinical specimens

Common pathogenic bacteria: 20hrs

Biology, infections and diagnostic methods of: Mycobacterium, Bacillus, Staphylococcus, Streptococcus, Escherichia coli, Salmonella, Shigella, Vibrio, Rickettsia, Mycoplasma, Treponema

Method of collection, transportation and processing of clinical samples for detection of virus: 10 hrs

Introduction, types of samples, maintenance of temperature and transportation, identification and interpretation, culture of virus in chick embryo and cell lines, cytopathic effects, detection of virus from culture, serological tests for the diagnosis of viruses

Common pathogenic viruses: 20 hrs

Biology, infections and diagnostic methods of: Small pox virus, Herpes viruses, hepatitis viruses, mumps virus, measles virus, influenza virus, HIV, rotavirus, polio virus, rabies virus

Sample collection and laboratory diagnosis of mycotic infections: 6 hrs

Samples for fungal infections, nasal swab, skin scraping, other samples

Medically important fungi: 10 hrs

Introduction, classification, and characteristics of medically important fungi and yeasts

Biology, infections and diagnostic methods of: Dermatophytes, Aspergillus, Histoplasma, Candida, Cryptococcus

Method of collections of samples and processing for detection of parasites: 6 hrs

Introduction, types of samples for parasite detection, sample processing and detection methods for blood, intestinal and tissue parasites

Common pathogenic parasites 15hrs

Biology, infections and diagnostic methods of: Entamoeba, Giardia, Plasmodium spp.,Leishmania spp., Taenia, Ascarislumbricoides, Ancylo stomaduodanale

Recommended Readings

Text books

1. Cheesbrough M (2007). Medical Laboratory Manual for Tropical Countries Vol. 2 ELBS London.
2. Tille P (2014). Bailey & Scott’s Diagnostic Microbiology (13th edition). Elsevier.
3. Collee JG, Fraser AG, Marmion BP and Simmons A (1996). Mackie &McCartney Practical Medical Microbiology (14th edition). Churchill Livingstone.

Reference books

1. Greenwood D, Slack RCB and Peutherer J (2001). Medical Microbiology ELBS, Dunclude Livingstone. Michael JP, Chan ECS and Kreig NR (1993). Microbiology. 5th edition McGraw Hill, Delhi.

Medical Microbiology (Practical)

Description of the Course

Course Title: Medical MicrobiologyPractical                Full Marks: 50

Course No: 404(Major)                                          Pass Marks: 20

Nature of the Course: Practical                                Year: IV

Course ObjectivesBy Chakra Web: www.chakrapanibhandari.com.np Email:

After completion of the course, the students will be able to:

1. collect, transport, and process the clinical samples for the diagnosis of microbial diseases.

Course Contents

1. To demonstrate safety precautions in microbiology laboratories: Demonstrate various safety measures and precautions to be taken in the laboratories
2. To collect and transport various clinical specimens: Blood, urine, stool, sputum, swabs
3. To perform different staining techniques: Gram's staining, capsule staining, spore staining, ZiehlNeelson, Albert stain, Giemsa stain
4. To prepare different culture media and monitoring their quality: Nutrient agar, blood agar, MacConkey agar, chocolate agar, SS agar, XLD agar, MSA, anaerobic culture medium
5. To prepare biochemical media and reagents for identification of bacteria: MR test, VP test, citrate test, urease test, SIM test, indole test, O/F test, TSI/KIA.
6. To differentiate different types of bacteria from biochemical tests: Carbohydrate utilization test, Nitrate reduction test, interpretation of the result
7. To perform an enzymatic test of the bacteria: Perform important enzymatic tests, coagulase test, catalase test, oxidase test, DNase test, Gelatin, Casein and lipid hydrolysis.
8. To demonstrate serological tests: Rapid diagnostic test kits, ELISA, hemagglutination test
9. To learn various sample collection techniques for diagnosis of mycotic infections: Skin scrapping, nails clipping, sputum collection, hair plucking
10. To prepare fungal culture media: Preparation of media; Sabouraud dextrose agar, potato dextrose agar, malt extract agar
11. To detect the fungi by direct microscopic methods: Detection of fungal elements: KOH preparation, iodine preparation, India ink preparation, lactophenol cotton blue staining
12. To examine the samples for intestinal and tissue parasites: Ascaris, Entamoebahistolytica, Giardia lamblia, Plasmodium spp., Leishmania spp.

Methods in Microbiology/Applied Microbiology (Theory)

Description of the Course

Course Title: Methods in Microbiology (Applied Microbiology)  Full Marks: 100

Course No: MB 405 (Applied Microbiology)                          Pass Marks: 35

Nature of the Course: Theory                                            Year: IV

Course Objectives

After completion of the course, the students will be able to:

1. Understand the principles, procedures and applications of methods used in the fields of microbiology

Course Contents

Safety measures in microbiology laboratory: 10 hrs

Principles of laboratories safety, biosafety level of laboratories and bio-hazards, risk group of microorganisms, decontamination and safe disposal of contaminated materials, sterilization and sterility techniques

Methods of specimen collection, transportation and processing of clinical samples for bacteria detection: 20 hrs

Cerebrospinal fluid, blood and other body fluids, sputum, urine, discharges and pus, stool, culture procedures, test algorithms for diagnosis of bacteria, antibiotic susceptibility tests (Kirby Bauer disc diffusion method, minimum inhibitory concentration determination)

Method of collection, transportation and processing of clinical samples for virus detection: 20 hrs

Introduction, types of samples, maintenance of temperature and transportation, identification and interpretation, culture of virus in chick embryo and cell lines, cytopathic effects, detection of virus from culture, serological tests for the diagnosis of viruses

Sample collection and laboratory diagnosis of mycotic infections: 10 hrs

Samples for fungal infections, sputum, nasal swab, skin scraping, hair and nails, CSF for fungal meningitis, microscopy, staining, culture

Method of collections of samples and processing for detection of parasites: 15 hrs

Introduction, types of samples for parasite detection, sample processing and detection methods for blood, stool and tissue parasites

Immunological and serological tests: 15hrs

Principles, procedures, advantages and applications of precipitation, agglutination, complement fixation, ELISA, radio-immunoassay

Method of collections of water samples and microbiological analysis: 10 hrs

Introduction, types of water samples, water sample processing and detection methods, MPN, MF, BOD

Field level tests for disease diagnosis: 10 hrs

Principles, procedures and applications of rapid tests for malaria, kala-azar, lymphatic filariasis, dengue, HIV, HBV, HCV, rotavirus, JE, leptospirosis, typhoid

Molecular tests in microbiology laboratories: 15hrs

Samples for molecular diagnostic tests, DNA/RNA extraction, PCR, Real Time PCR, PCR-RFLP, sequencing, western blotting

Microbiological quality tests of foods: 15hrs

Quality test of milk and milk products, egg and egg products, meat and meat products, cereal and cereal products, HACCP, detection methods of carcinogens and toxins in food

Microbiology laboratory in agriculture: 10 hrs

Methods for preparation of bio-fertilizers, detection methods of pesticide, herbicide, insecticide, fungicide in soil, isolation and detection of pectinolytic, lignolytic, lipolytic, cellulolytic microorganisms from soil

Recommended Readings

Text books

1. Cheesbrough M (2007). Medical Laboratory Manual for Tropical Countries Vol. 2 ELBS London.
2. Brown AE (2012). Benson’s Microbiological Applications. Laboratory Manual in General Microbiology. (12th edition). McGraw-Hill Publisher.
3. Collee JG, Fraser AG, Marmion BP and Simmons A (1996). Mackie &McCartney Practical Medical Microbiology (14th edition). Churchill Livingstone.

Project Writing and Presentation

Description of the Course

Course Title: Project writing and Presentation                   Full Marks: 100

Course No: MB 406 (Major)                                          Pass Marks: 40

Nature of the Course: Project work                                Year: IV

Course Objectives

After completion of the course, the students will be able to:

1. carry out laboratory-based mini research
2. develop knowledge and skills in writing a scientific research report

Course Contents

Students in a group will be assigned relevant research topics related to their study by concerned department/campus. Students will perform laboratory experiments within the fourth academic year. The research will be supervised by the faculty member(s) of microbiology of concerned department/campus. After completion of laboratory work, the student should write the research report in the standard format on the basis of data/findings generated during the laboratory works. The student will submit the required number of copies of their research report to concerned department or campus for evaluation. The final evaluation of the project work will be made by a panel of external and internal examiners, head of the department and supervisor(s).

Instrumentation in Microbiology (Theory)

Description of the Course

Course Title: Instrumentation in Microbiology                     Full Marks: 50

Course No: MB 407                                                      Pass Marks: 18

Nature of the Course: Interdisciplinary subject                    Year: IV

Course Objectives

After completion of the course, the students will be able to:

1. Understand the working principles and procedures of instruments used in the microbiology laboratory

Course contents

General principle and approaches of biochemical investigations: 10hrs

Cell disruption techniques, protein extraction and purification

Working principle, instrumentation and application: 10hrs

Phase contrast, electron microscopy, fluorescence microscopy

Principle and applications: 15 hrs

Centrifugation techniques, Electrophoretic techniques: Agarose gel, Polyacrylamide gel electrophoresis

Types, instrumentation and uses of chromatographic techniques: 20hrs

Ion exchange chromatography, Affinity Chromatography, Paper and Thin layer chromatography, Gel Permeation chromatography, Gas Chromatography, High performance Liquid Chromatography (HPLC)

Principle, instrumentation and application: 10hrs

Ultra-violet and visible spectrometry, colorimeter

Principle, instrumentation and application of molecular techniques: 10hrs

Thermo cycler, Probes, Sequencer, Gel documentation system, Microarray

Recommended Readings

Text book

1. Skoog DA, Holler FJ and Nieman TA (2005), Principles of Instrumental Analysis, 5thEdition, Thomson Books/Cole
2. Wilson K and Walker J (Eds)(2005), Principles and Techniques of Biochemistry and Molecular Biology,6thEdition,Cambridge University Press Mendham J, Denny RC, Barnes JD and Thomas M (2008), Vogel's Text Book of Quantitative Chemical Analysis, 6th Edition, Pearson Education

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