Course Objectives

• The content of this course includes many etiological agents responsible for global infectious diseases.
• It covers all biology of bacteria, viruses and other pathogens related with infectious diseases in humans.
• It will also provide opportunities for a student to develop diagnostic skills in microbiology, including the practical application and interpretation of laboratory tests for the diagnosis of infectious diseases.
• The content of this course includes isolation process of culturable microorganism from clinical samples like bacteria, fungus and other pathogens related with infectious diseases in humans.

Learning Outcomes

• Student will be able to explain the theoretical basis of the tools,technologies and methods common to microbiology.
• To demonstrate practical skills in the use of tools, technologies and methods common to microbiology, and apply the scientific method and hypothesis testing in the design and execution of experiments.
• To construct a summative project or paper that draws on current research, scholarship and/or techniques in microbiology.
• To demonstrate practical skills in the use of tools, technologies and methods common to microbiology, and apply the scientific method and hypothesis testing in the design and execution of experiments.

Course Syllabus

Module I

Medical Bacteriology: Anatomy and structure of prokaryotes ( Detail structure of gram positive and gram negative bacteria, Peptidoglycan synthesis etc). Classification of bacteria according both cell wall and shape. Nutritional requirement of bacteria, Biochemical test ( IMViC, Catalase, Coagulase etc). Sterilization technique, different staining procedures ( AFB, Flagella and Endospore staining etc), Culture media and its types. Pathogenesis and laboratory diagnosis of medically important gram positive and gram negative bacteria, Clinical significance of human pathogenic bacteria and their identification.

Practice

Demonstration of various parts of microscope its functioning. Preparation of media, cultivation of bacteria, Biochemical tests for identification of bacteria, Preservation of stock cultures of bacteria. Preparation of bacterial smear and staining – Gram’s, Acid-fast, Staining of bacterial spores flagella, capsule. Isolation, Characterization and identification of pathogens from various clinical specimens.  Study of antibiotic sensitivity of common pathogens.

Module II

Medical Virology: Morphology, general properties of viruses, detection of viruses and antigens in clinical specimens, laboratory diagnosis, Serological diagnosis of virus infections. Cultivation of viruses. Viral vaccines, their preparation and their immunization schedules. Viruses of importance to bacteria, bacteriophages, their structure, types, typing and application in bacterial genetics. Detail information about human pathogenic viruses.

Practice

Demonstration of various inoculation routes in fertilized hen egg ( Egg inoculation method). 

Module III

Medical Mycology: Morphology, general characteristic, taxonomy, classification of fungi, detection and recovery of fungi from clinical specimens. Dermatophytes and agents of superficial mycoses. Trichophyton. Epidermophyton and Microsporurn. Yeasts of medical importance, Candida, Cryptococcus Detail Information with lab diagnosis of human pathogenic Fungus.

Practice

To prepare culture media used routinely in mycology. To perform the staining techniques for identification of fungi. Isolation and identification fungus from clinical specimen.

Suggested Readings

1. Essentials of Medical Microbiology by  R. Bhatia and R. L. Lchhpujani. 4th Ed.

Ebook Link- https://www.pdfdrive.com/essentials-of-medical-microbiology-e33538815.html

2. Bailey & Scott’s Diagnostic Microbiology.

Ebook Link- https://www.pdfdrive.com/bailey-scotts-diagnostic-microbiology-e187863782.html

3. Textbook of Microbioogy by Ananthanereyan & Paniker. 7th Ed.

Ebook Link-https://www.pdfdrive.com/ananthanarayan-and-panikers-textbook-of-microbiology-e188138714.html

Online Tutorial Links

1. Demonstration of various parts of microscope.

Elink-https://vlab.amrita.edu/?sub=3&brch=187&sim=323&cnt=1

2. Antibiotic sensitivity Testing.

Elink- https://www.coursera.org/learn/antimicrobial-resistance

3. AFB staining.

Elink-https://vlab.amrita.edu/?sub=3&brch=73&sim=1338&cnt=5

Simulation Links For Lab

1. Egg Inoculation method.

Elink-https://vlab.amrita.edu/?sub=3&brch=76&sim=1223&cnt=2

2.To prepare culture media used routinely in mycology.

Elink-https://vlab.amrita.edu/?sub=3&brch=76&sim=693&cnt=2

All the practice components can be performed by simulation as well as virtual labs.

Online Source: Udemy, Coursera, article library, NCBI, Study.com, You tube, Frontier, Febs, unacademy, academia and Amrita Vlab etc.

Session Plan

Session 1

Lecture Topic- Medical Bacteriology- Anatomy and structure of prokaryotes ( Detail structure of gram positive and gram negative bacteria,Peptidoglycan synthesis etc).

Lecture Video- https://www.youtube.com/watch?v=ei6Z7orCpPk

https://www.youtube.com/watch?v=Didrc3wJ3E8

Lecture Notes- https://www.coursera.org/lecture/bacterial-infections/1-1-introduction-to-bacteria-by-bioinformatician-phd-peder-worning-HZ64m

Session 2

Lecture Topic- Classification of bacteria according cell wall.

Lecture Video- https://www.youtube.com/watch?v=8IJRzcPC9wg

Lecture Presentation- https://www.slideshare.net/shyrosh/classification-of-bacteria-49373508

Session 3

Lecture Topic- Classification of bacteria according on shape.

Lecture Video- https://www.youtube.com/watch?v=8IJRzcPC9wg

Lecture Presentation- https://www.slideshare.net/shyrosh/classification-of-bacteria-49373508

Session 4

Lecture Topic- Nutritional requirement of bacteria.

Lecture Video- https://www.youtube.com/watch?v=qxVVFFVHEoM

Lecture Presentation- https://www.slideshare.net/SuchittaU/nutritional-requirement-by-microorganisms

Session 5

Lecture Topic- Biochemical test ( IMViC)

Lecture Video- https://www.youtube.com/watch?v=az0dXYmXgAg

https://www.youtube.com/watch?v=WkGf-hq9QDE

Lecture Presentation-https://www.slideshare.net/Ankit9089343894/biochemical-testing

Session 6

Lecture Topic- Catalase Test

Lecture Video- https://www.youtube.com/watch?v=PGBf7Xehcns

Lecture Presentation- https://www.slideshare.net/RebikaRajbanshi/catalase-test

Session 7

Lecture Topic- Coagulase Test.

Lecture Video-https://www.youtube.com/watch?v=1p882Ey-Ri0

Lecture Presentation- https://vlab.amrita.edu/?sub=3&brch=73&sim=703&cnt=2

Session 8

Lecture Topic- Sterilization technique

Lecture Video- https://www.youtube.com/watch?v=E2110JMwTco

https://climb.pcc.edu/sterile-tech

Lecture Presentation- https://www.slideshare.net/SonamkzBhutia/sterilization-process

Session 9

Lecture Topic- Different staining procedures- AFB staining.

Lecture Video-https://vlab.amrita.edu/?sub=3&brch=73&sim=1338&cnt=2

https://www.youtube.com/watch?v=m76BRg-p7Sk

Lecture Presentation-https://www.slideshare.net/9925752690/ziehlneelsen-n-stain-acid-fast-stain

Session 10

Lecture Topic- Different staining procedures- Flagella staining

Lecture Video- https://vlab.amrita.edu/?sub=3&brch=73&sim=1338&cnt=1

Lecture Presentation- https://www.slideshare.net/DineshJain4/staining-of-microorganisms

Session 11

Lecture Topic-Different staining procedure- Endospore staining

Lecture Video- https://vlab.amrita.edu/?sub=3&brch=73&sim=1338&cnt=2

Lecture Presentation- https://www.slideshare.net/kaberinath123/spore-staining

Session 12

Lecture Topic- Culture media and its types.

Lecture Video- https://www.youtube.com/watch?v=Yl1EZi0qX1Q

Lecture Presentation- https://www.slideshare.net/SonamkzBhutia/culture-media-159154491

Session 13

Lecture Topic- Laboratory diagnosis of medically important gram positive bacteria.

Lecture Video- https://vlab.amrita.edu/?sub=3&brch=73&sim=208&cnt=2

Session 14

Lecture Topic- Laboratory diagnosis of medically important gram negative bacteria.

Lecture Video- https://vlab.amrita.edu/?sub=3&brch=76&sim=1109&cnt=5

Session 15

Lecture Topic- Clinical significance of human pathogenic bacteria and their identification.

Lecture Notes-https://www.slideshare.net/amanullah9803150/identification-of-pathogenic-bacteria-in-clinical-microbiology

https://www.slideshare.net/MMASSY/bacterial-pathogenesis

Session 16

Lecture Topic-Collection and isolation, identification of bacteria from clinical samples.

Lecture Video- https://www.youtube.com/watch?v=cIddzUYzUI4

Lecture Presentation- https://apps.who.int/iris/bitstream/10665/66348/1/WHO_CDS_CSR_EDC_2000.4.pdf?ua=1&ua=1

https://www.who.int/foodsafety/publications/foodborne_disease/Annex_9.pdf

Session 17

Practice Topic- Demonstration of various parts of microscope and its functioning.

Practice Video- https://vlab.amrita.edu/?sub=3&brch=187&sim=323&cnt=1

https://www.youtube.com/watch?v=ZqlJSEu0Eo4

Session 18

Practice Topic- Preparation of media and cultivation of bacteria.

Practice Video- https://www.youtube.com/watch?v=cneascR3OEc

https://www.youtube.com/watch?v=949qQtAnjIc

Session 19

Practice Topic- Biochemical Test

Practice Video- https://www.youtube.com/watch?v=67R3p5UzDUU

https://www.youtube.com/watch?v=az0dXYmXgAg

Session 20

Practice Topic- Preservation of stock culture of bacteria.

Practice Video- https://www.youtube.com/watch?v=rm_E8I8P9lo

https://www.youtube.com/watch?v=p4awvOVGZXA

Session 21

Lecture Topic- Morphology and general properties of virus.

Lecture Video- https://www.youtube.com/watch?v=F82vNtNjcsA

Lecture Presentation- https://www.slideshare.net/specialclass/virus-morphology-classification

Session 22

Lecture Topic- Detection of viruses and antigens in clinical specimens.

Lecture Video- https://www.coursera.org/learn/microscopy

https://www.coursera.org/directory/videos/?courseId=xC3tPBE9Eeamsw7MRtVHjQ

https://www.coursera.org/lecture/nanotechnology/scanning-electron-microscopy-basic-function-WE2fL

Session 23

Lecture Topic- Serological diagnosis of virus infections.

Lecture Video- https://www.youtube.com/watch?v=eiSAswuW6UI

https://www.youtube.com/watch?v=jMDfd28i7Is

https://www.youtube.com/watch?v=nwYlk4eB7yA

Session 24

Lecture Topic- Cultivation of viruses.

Lecture Video- https://vlab.amrita.edu/?sub=3&brch=76&sim=1223&cnt=2

https://www.youtube.com/watch?v=Yi13OAshhSk

Lecture Presentation- https://www.slideshare.net/RaNaMB1/cultivation-of-viruses-97803294

Session 25

Lecture Topic- Viral vaccines, their preparation and their immunization schedules.

Lecture Video- https://www.coursera.org/lecture/aids-fear-hope/05-07-the-drugs-dr-riddell-describes-antiretroviral-therapy-Zeb6F

Session 26

Lecture Topic- Viruses of importance to bacteria, bacteriophages, their structure.

Lecture Video- https://vlab.amrita.edu/?sub=3&brch=76&sim=719&cnt=1

Lecture Presentation- https://www.slideshare.net/doctorrao/bacteriophages

https://www.slideshare.net/astrokaveh/bacteriophages-64533678

Session 27

Lecture Topic- Bacteriophage types, typing and application in bacterial genetics.

Lecture Notes- https://www.slideshare.net/drakmane/bacteriophage-65365639

Session 28

Lecture Topic- Detail information about human pathogenic viruses.

Lecture Video- https://www.coursera.org/lecture/stories-of-infection/hepatitis-b-77bsj

https://www.coursera.org/learn/covid19clinicalupdate

Lecture Notes-http://apps.searo.who.int/pds_docs/B4416.pdf

Session 29

Practice Topic- Egg inoculation method.

Practice Video- https://www.youtube.com/watch?v=766QH_qaYN8

Session 30

Lecture Topic-  Morphology, general characteristic & classification of fungi.

Lecture Notes- https://courses.lumenlearning.com/biology2xmaster/chapter/classification-of-fungi/

https://www.coursera.org/lecture/antibiotic-stewardship/candidemia-63OUW

https://www.coursera.org/lecture/epidemic-pandemic-outbreak/week-2-video-1-what-causes-infection-what-is-an-infectious-disease-2385C

Session 31

Lecture Topic- Detection and recovery of fungi from clinical specimens.

Lecture Video- https://www.coursera.org/lecture/dermatology/fungal-infections-ZMX7J

Lecture Presentation-https://www.coursera.org/learn/epidemics

https://www.cdc.gov/fungal/features/fungal-infections.html

Session 32

Lecture Topic- Dermatophytes and agents of superficial mycoses.

Lecture Notes- https://www.coursera.org/lecture/dermatology/fungal-infections-ZMX7J

Session 33

Lecture Topic- Trichophyton.

Lecture Video- https://www.youtube.com/watch?v=GdgRPj7zmwA

Lecture Presentation- https://www.slideshare.net/rubaiyakabir/dermatophytes-69013431

Session 34

Lecture Topic- Epidermophyton.

Lecture Video- https://www.youtube.com/watch?v=Kh4eS1CX6gA

Lecture Presentation- https://www.slideshare.net/PrincessAlenAguilar/trichophyton-and-epidermophyton

Session 35

Lecture Topic- Microsporum.

Lecture Video- https://www.youtube.com/watch?v=OtsetpS_H0g

Lecture Presentation-http://www.authorstream.com/Presentation/Yugapanta-2082914-microsporum/

Session 36

Lecture Topic- Yeasts of medical importance.

Lecture Video- https://www.youtube.com/watch?v=XhfoIQzCECA

Lecture Presentation- https://www.slideshare.net/MdHasanChowdhury/yeast-77242952

Session 37

Lecture Topic- Candida.

Lecture Video- https://www.youtube.com/watch?v=CeOMzQ1CeMQ

Lecture Presentation- https://www.slideshare.net/mafambakhathu/candidiasis-46179900

Session 38

Lecture Topic- Cryptococcus.

Lecture Video- https://www.youtube.com/watch?v=PVpvPoMhmDg

Lecture Presentation-https://www.slideshare.net/MaryMwinga/cryptococcosis-97889849

Session 39

Lecture Topic- Detail Information with lab diagnosis of human pathogenic Fungus.

Lecture Video- https://vlab.amrita.edu/?sub=3&brch=76

Lecture Presentation-https://www.slideshare.net/HusseinAltameemi2/medical-microbiology-laboratory-introduction-to-medical-mycology

https://www.slideshare.net/Balamuruganr3/serological-tests-in-mycology

Session 40

Practice Topic- To prepare culture media used routinely in mycology.

Practice Video- https://www.youtube.com/watch?v=cneascR3OEc

https://www.youtube.com/watch?v=IAgf24XB7eY

Session 41

Practice Topic- Fungal staining.

Practice Video- https://www.youtube.com/watch?v=lhlSw1zsxgc

Session 42

Practice Topic- Isolation and identification of fungus from clinical specimen.

Practice Video- https://www.youtube.com/watch?v=FohwEA5byYM

https://www.youtube.com/watch?v=GV840R4Pyi4&t=161s

Case Studies

Case Studies