Clinical Microbiology I
PHTM 314
Credit hours: 3 (2+1)
Course coordinator: Dr. Syed Mohd Danish Rizvi
Objectives of the course
Knowledge of microbial groups with respect to classification,
morphology, ultra-structure, nutrition and growth conditions.
Knowledge of different antimicrobial agents, their mode of
action and assessment.
Comprehension bacterial genetics and its contribution to
resistance to anti-microbial agents.
Knowledge of different microbes causing human infections
with respect to their general characteristics, pathogenesis,
Laboratory diagnosis, epidemiology, and treatment.
CLOs Aligned PLOs
1 Knowledge and Understanding
1.1 K3
Discuss the morphology, characters, classification, physiology, genetics
and pathogenesis of bacterial pathogens.
1.2 K3
Summarize etiology, epidemiology, pathogenesis, virulence factors,
laboratory diagnosis and clinical features of different bacterial diseases,
and discuss different antimicrobial agents with their mechanism of actions.
2 Skills:
2.1 S5
Observe the identity of microorganism’s based upon their biochemical
activities and staining reactions for appropriate medication therapy
2.2 Apply techniques used in microbiological testing and recommend the best S5
antibiotic for the treatment of different infections based upon the
laboratory results.
2.3 S7
Discover different methods of infection control and apply biosafety
measures for preventing lab acquired infections.
3 Values:
3.1 Suggest various treatments, preventive methods of medically important V1
bacteria based upon their pathogenesis and mode of transmission.
Topics to be Covered Hours
Introduction to microbiology, Classification of microorganism 1
Bacteria; Structure, nutrition & growth 4
Bacterial genetics 2
Antimicrobial agents
-Introduction & Characters of antimicrobial agents 1
-Classification of antimicrobial agents & Mechanisms of action
of antimicrobial agents
3
-Antibiotic resistance (definition, origin, and mechanisms) 3
Host-parasite relationship and pathogenesis 2
Staphylococci, Streptococci, and Neisseria 2
Gram-positive Rods ( Bacillus, Clostridium, and Cornybacteria) 4
Mycobacteria tuberculosis 1
Gram-negative Bacteria (E. coli, Pseudomonas aeruginosa, 5
Salmonella, shigella, Vibrios, Helicobacter, Campylobacter,
Klebseilla, and Proteus)
Ricketsia,Chlamydia, and Spirochetes 2
Total 30
# *Assessment task Week Due Percentage of Total
Assessment Score
Quiz 4 10%
1
Midterm 8 % 30
2
Assignments/activities During all semester %5
3
Practical exam 14 15%
4
Final exam 16 40%
5
Total 100%
Objectives of this lecture:
At the end of this lecture the students should be able to:
Know the definition of microbiology and its classification.
Know the importance of studying microbiology for the
pharmacist.
Describe the difference between eukaryotes and
prokaryotes.
Describe some of infectious agents like viruses, viroids, and
prions.
Describe the different shapes and arrangement of bacteria.
Introduction
Definition
Broad term that study living organism
that are too small to be seen with naked
eye
The science that deals with the study of
microorganisms, their activities and their
influences on different aspects of life
• Microbiology is essential to pharmacist in
the studying of following aspects:
– Biology of microorganism
– Epidemiology of microbes and their relation to public
health
– Infectious microbes, their diseases and treatment
– Laboratory diagnosis of microorganisms
– Production of antibiotics & vaccines
– Production of proteins from genetically engineered
microorganisms
– Production of preparations free from microorganisms
(sterile products)
– Quality control and assurance in pharmaceutical
industry
Production of
medicines
Microbiology
Control of Understanding
microbes infection
Fields of microbiology’s importance for pharmacists
Disciplines of
microbiology
Taxonomic Functional
Bacteriology (Bacteria) Immunology
Mycology (Fungi) Medical microbiology
Virology (Viruses) Veterinary microbiology
Parasitology (Parasites) Pharmaceutical microbiology
Phycology (Algae) Biotechnology
Genetic engineering
Food microbiology
Microbial ecology
Agricultural microbiology
• Taxonomic bases of microbiology:
- Bacteriology: Study of bacteria
- Mycology: Study of fungi
- Phycology: Study of algae
- Protozoology or parasitology: Study of parasites
including protozoa, helimenths, and some parasitic
insects
- Virology: Study of viruses and virus-like particles
• Functional bases of microbiology:
Immunology: Study of host reactions to
microorganisms.
Medical microbiology: concerned with roles of
microorganisms in infectious diseases in humans.
Veterinary microbiology: study animal infectious
diseases caused by microorganisms.
Pharmaceutical microbiology: concerned with the
development of drugs, chemical and physical agents as well
as methods for control of microbial growth and spread.
• Functional bases of microbiology:
Biotechnology: concerned with applications of
microorganisms in various fields especially fermentation
industries.
Genetic engineering: manipulation of microorganisms
for the production of valuable human proteins by
microorganisms utilizing recombinant DNA technology.
• Living organisms:
Organisms that contain all of the enzymes required for the replication
and possess the biologic equipment necessary for the production of
metabolic energy.
• Biota ( living cells): includes animals, plants and microorganisms.
The main differences between kingdoms of biota:
Microorganisms Animal Plant
Radiant or Organic Organic Radiant Energy
+ ve or - ve + ve - ve Movement
Eukaryotic and Prokaryotic Eukaryotic Eukaryotic Cell type
As seen from the table that microorganisms possess overlapping
characters and therefore they were classified separately in a separate
kingdom.
2- Kingdom system classification:
- Prokaryotes: the cell lacks a true nucleus structure
(primitive nucleus).
- Eukaryotes: the cell possess a membrane-enclosed
nucleus (true nucleus) and usually other organelles.
Prokaryotes and eukaryotes
- The classification into two groups- the prokaryotes and
eukaryotes- based primarily on their cellular structure and
mode of reproduction
- Prokaryotes are the bacteria and archaea, and eukaryotes are
all other cellular microorganisms, e.g. fungi, protozoa and
algae.
Prokaryotes and eukaryotes (continue)
- The crucial difference between these two types of cell is the
possession by the eukaryotes of a true cell nucleus in which
the chromosomes are separated from the cytoplasm by a
nuclear membrane.
- The prokaryotes have no true nucleus; they normally
possess just a single chromosome that is not separated from
the other cell contents by a membrane.
- Other major distinguishing features of the two groups are
that prokaryotes are normally haploid (possess only one
copy of the set of genes in the cell) and reproduce
asexually; eukaryotes, by contrast, are usually diploid
(possess two copies of their genes) and normally have the
potential to reproduce sexually
Differences between prokaryotes and eukaryotes
Eukaryotes Prokaryotes Characteristic
Present Absent Nuclear membrane, nucleolus and histones
> 1 (Linear) 1 (circular) Number of chromosomes and topology
80 S 70 S Ribosomes size
Present Absent Cell membrane sterols
Present Absent Organelles (mitochondria and chloroplasts)
Present Absent Meiosis and mitosis
A sexual & Sexual A sexual Reproduction
Present Absent Cytoplasmic streaming
Absent Present Transcription and translation couple
Absent Present Murein (peptidoglycan) in cell wall
• Viruses:
- Viruses are not considered as living organisms,
they do not have the attributes of cells, including the
ability to replicate and cell structure.
- Viruses are inert in the extracellular environment;
they replicate only in living cells (acquire the key
attribute of a living cell), being obligatory
intracellular parasites (depending upon host cells
for their necessary functions).
- Viruses are known to infect all cells, including
microbial cells with a high specific interaction.
- They are composed of nucleic acid (either DNA or
RNA) surrounded by proteins or capsid
Viroids (virusoids)
-They are even simpler than viruses, being
infectious particles comprising single-stranded
RNA without any associated protein. Those
that have been described are plant pathogens,
and so far, there are no known human
pathogens in this category.
Prions
- They are unique as infectious agents in that they contain no
nucleic acid.
- A prion is an atypical form of a mammalian protein that
can interact with a normal protein molecule and cause it to
undergo a conformational change so that it, in turn,
becomes a prion and ceases its normal function.
- Prions are the agents responsible for transmissible
spongiform encephalopathies, e.g. bovine spongiform
encephalopathy (BSE)
- They are the simplest and most recently recognized agents
of infectious disease, and are important in a pharmaceutical
context owing to their extreme resistance to conventional
sterilizing agents like steam, gamma radiation and
disinfectants
Nomenclature of microbes:
Linnaeous binomial system of nomenclature:
Each microorganism assigned with 2 names:
- Genus is the first name (Capitalized) and species
(not capitalized)
- Both names are underlined or written in italic
- Staphylococcus aureus or Staphylococcus aureus.
Morphology of Bacteria
• Two parts to Bacterial morphology:
– Shape
– Arrangement
Shape:
• Rod: bacillus
• Spheres: coccus
Bacillus Coccus Spirillum
• Spirals: spirillum
Arrangement
• Paired: diplo
• Grape-like clusters: staphylo
• Chains: strepto
Reading to support the course
Denyer, S. P., Hodges, N., Gorman, S. P. Gilmore, B. F
(2004) Hugo & Russell’s Pharmaceutical Microbiology, 7 th
edition, Wiley-Blackwell.
Hanlon, G. & Hodges, N. (2013) Essential Microbiology for
Pharmacy and Pharmaceutical Science, Wiley-Blackwell.
Harvey, R. A., Champe, P. C., Fisher, B. D. Lippincott’s
Illustrated Reviews: Microbiology, 2nd Edition.
Brooks, G. F., Butel, J. S., Carroll, K. C., Morse, S. A.,
Jawetz, Melnick, adelberg’s Medical Microbiology, 24 th
edition.
General microbiology texts will also contain supporting
information.
