| |
Introduction
Microbiology, the study of micro-organisms including bacteria,
fungi and viruses, is a vast subject with importance not only
for medicine but also in many other areas such as environmental
sciences, food technology and brewing. The vast majority of
micro-organisms are relatively benign, and most are beneficial
in performing an essential recycling role through the turnover
of organic materials in the environment. This
module is designed to introduce some of the concepts of microbiology,
with a clear emphasis on applications relevant to the pharmaceutical
sciences. The module will also provide an introduction to
later modules dealing further with antibiotics and biotechnology.
Micro-organisms can have significant effects within three
main areas of pharmaceutical sciences: |
|
 |
| |
• In causing diseased states, notably due to bacteria,
viruses and fungi.
• In generating pharmaceutical products, such as antibiotics
or vaccines
• In spoilage of pharmaceutical products, typically
by bacteria or fungi (yeast/moulds)
Who Should Do This Course?
This course is ideal for bioscience professionals (Academics,
Food Technologists, Research Scientists, Pharmacists, Biotechnologists,
etc.) and healthcare workers (Medical Practitioners, Nurses,
Medical Laboratory Scientists). Participants should have
at least diploma qualification or second year level achievement
in biomedical science undergraduate discipline.
Aims
This course will introduce
some of the basic concepts of microbiology, with particular
emphasis on pharmaceutical issues. The course will help
participants to understand the properties of some micro-organisms
and their role in pathogenicity and spoilage of pharmaceutical
preparations. A broad training in basic microbiological
issues for scientifically aware managers will be provided.
LEARNING
OUTCOMES
Knowledge
and Understanding:
After
completing this module you will be able to:
• Describe the structure and functions of bacterial
cell components and appreciate how antibiotics interact
with these components.
• Appreciate the different types of growth media and
their use in bacterial identification.
• Describe bacterial growth in open and closed environments.
• Appreciate causative organisms for several diseased
states.
• Understand the mechanisms whereby bacteria acquire
antibiotic resistance.
• Describe the basic principles of pathogenicity and
immunology
• Understand the role of fungi in common medical conditions
• Describe how viruses replicate and cause pathogenicity.
• Appreciate the various methods available for sterilisation
of pharmaceutical products.
Discipline
specific skills and you will also be able to:
• Safely handle potentially pathogenic organisms.
• Microscopically examine bacteria using a range of
stains and examine for motility
• Safely reconstitute penicillin and prepare Total
Parenteral Nutrition in an isolation unit.
• Perform aseptic manipulations.
READING LIST
There are numerous basic microbiology books in the library
and these will assist in your learning about basic bacterial
cell structure and function.
Recommended Texts
Prescott, LM, Harley, JP, Klien, DA. Microbiology 5th Edition
McGraw-Hill, Boston, 1999
ISBN 0-697-35439-3
For the more pharmaceutical aspects of the module, the
recommended text is:
"Pharmaceutical Microbiology" Edited by W.B.
Hugo and A.D. Russell (Blackwell Scientific Publications).
|
|
LECTURE CONTENT
Course Content
Lecture |
Topic |
| |
|
| |
Introduction
to Microbiology |
1 |
History
of Microbiology
Microbial Products
Microorganisms and disease
Thermolabile (Heat Sensitive) and Thermoresistant (Heat
tolerant) microbes.
Endospores and development of pure cultures |
| |
|
2 |
Microbial
Evolution: Phylogeny (Evolutionary relatedness)
The Protists: simple biological organisation at cellular
level.
Classification based on Morphological Characteristics:
2 types of cellular organism
1. Prokaryotes
2. Eukaryotes
Evolutionary Relatedness: Comparative sequencing of
rRNA
Biological World - 3 domains: BACTERIA, ARCHAEA, EUKARYA
Origins of Chloroplasts and Mitochondria: Endosymbiont
Theory |
| |
|
3 |
Structure
and Function of Prokaryotic Cells
Membranes
of Prokaryotic and Eukaryotic Cells
Cytoplasmic Membranes and Proteins in the cytoplasmic
membrane
Fluid Mosaic Model and Cytoplasmic Membranes
Eukaryotic membranes; Action of Sterols
Archaeal Membranes: Structure and Functions
Permeases; Group Translocation and Active Transport
(Proton motive force)
Sugar phosphotransferase system (PTS) and mechanisms
of glucose uptake
Types of transport protein: uniporters; symporters;
and antiporters |
| |
|
4 |
Bacterial
Cell Walls.
Structure and function of bacterial cell capsule and
wall
Composition and Structure of Peptidoglycan
Cross linkages in peptidoglycan; Gram +ve and Gram –ve
bacteria
Lysozyme; Effect of penicillin
Function of Teichoic acids and lipopolysaccharides (LPS)
Cell walls of Archaea
Properties of some bacterial species: Staphylococcus;
Streptococcus; Bacillus; Clostridium; Listeria; Neisseria;
Pseudomonas; Vibrio; Yersinia; Bordetella; Escherichia;
Salmonella |
| |
|
5 |
Movement
and Attachment of Prokaryotes
Functional diversity in prokaryotes: spores, cysts
Bacterial Capsules, Slime, Layers and the Glycocalyx
Glycocalyx: Function; Phagocytosis; Adherence; Adherence
and disease
Applications of Bacterial Polysaccharides
Structure and Function: Pili; Fimbriae;
Bacterial Flagella and Chemotaxis
Spores; Cysts and Bacterial Endospores (structure; chemical
composition; formation, germination; sterilisation) |
| |
|
6 |
Genetic
Storage and Exchange in Prokarytes.
Prokaryotic Genome; Structure and function of Plasmids
DNA supercoiling and Topoisomerae
Initiation of DNA replication in Prokaryotes: Bi-directional
and Rolling Circle DNA replication
Gene exchange in Eukarya and Prokaryotes (Transformation;
Transduction; Conjugation)
Genetic basis of acquired antibiotic resistance in bacteria
Biochemical mechanisms of resistance and clinical problems
of bacterial resistance |
| |
|
7 |
Bacterial
Physiology & Biochemistry
Nutritional
Requirements.
Requirements and conditions for growth: Anabolic and
catabolic pathways: Glycolysis and TCA; Elemental requirements
of microbes: Essential major, minor and trace elements
Basic structural units: Heterotrophs and Autotrophs.
Organic requirements (Medium): C sources; steroids;
lipids; nucleosides; growth factors etc
Sources of Nitrogen and Oxygen; N fixation and ammonia
assimilation; Utilisation of minor and trace elements:
P, S, K, Mg, Fe, etc.; Development of media |
| |
|
8 |
Environmental
Requirements 1; Water, pH.
Water activity; Classes of solute (Electrolyte and Non-electrolytes);
Growth at extreme conditions (high and low Aw)
Compatible solutes: K ions and organic molecules (amino
acids. Polyols, etc)
Hypersaline environments: cell walls and osmotic pressure
effects |
| |
|
9 |
Environmental
Requirements 2; Temperature, pressure, Radiation
Effect of temperature: arrhenius equation; temperatures
for growth
Microbes in extreme environments: Psyhrophiles’
Mesophiles, Thermophiles etc.
pH environments and microbe adaptation to extreme pH:
acidophiles, Alkalinophiles
Pressure effects on microbes: Barophiles
Radiation effects on microbes: Ionizing (X rays, gamma
rays etc); UV to IR light
Responses to light: phototaxic and phototrophic microbes |
| |
|
10 |
Aerobic
Respiration
Revision of nutrition requirements and energy supply;
Electron acceptors and free energy production; Assimilative
and Dissimilative metabolism; Oxygen: Terminal electron
acceptor (Aerobes); Anaerobes: Fermentation and Anaerobic
respiration
Faculatative Anaerobes; Obligate Aerobes and Anaerobes;
Aerotolerant Anaerobes;
Microaerophiles; Anaerobic Respiration: Nitrate Fixation
and De-nitrification
Sulphate reduction; Carbonate as TEA; other electron
acceptors |
| |
|
11 |
Electron
Acceptors: Mechanisms of Energy Generation
Glycolysis (several glycolytic pathways); Krebs cycle
(TCA); Embden-Myerhof Pathway; Entner-Doudoroff pathway;
Substrate Level Phosphorylation; Oxidative phosphorylation:
Electron Transport Chains; classes of electron carrier;
H carriers; terminal electron carriers; ATP generation;
Sidedness of membranes; Protomotive Force PMF and ATP
generation
Chemiosmotic hypothesis and ATP synthesis |
| |
|
13 |
Autotrophs
Winogradsky’s definition; Facultative Autotrophs
and CO2 -Fixation pathways: Calvin cycle (Plants + many
bacteria); Green bacteria - reverse TCA Cycle; Archaea/acetogenic
bacteria - carbon monoxide – pathway; Energy Sources
for CO2-Fixation: Photolithotrophs and Chemlithotrophs;
Photosynthesis and Photosystem II; Generation of PMF;
Cyclic and Non Cyclic Photophosphorylation; Anoxygenic
Photosynthesis. |
| |
|
14 |
Photosynthetic
Bacteria
Purple Bacteria: Rhodospirillineae and Purple-S-Bacteria:
Chromatiaceae
Purple non-S-Bacteria: Rhodospirillaceae and Chromatiaceae;
Green S Bacteria: Chlorobiineae; Green Non-S Bacteria:
Cloroflexicaceae; Absorption spectra of photosynthetic
pigments Other Phototrophic Bacteria: Heliobacterium;
Halobacteria |
| |
|
15 |
Chemolithotrophs
Biogeochemical cycling
Nitrification and nitrifying bacteria; Sulphur oxidizing
bacteria; S-oxidation/ denitrification bacteria; Iron
Oxidizing Bacteria; Acidophilic iron and sulphur oxidizing
bacteria; Non-acidophilic Iron Bacteria; hydrogen bacteria;
Sulphate reducing bacteria (SRB); Methanogens; ATP Production
by Lithotrophs; Reverse Electron Flow |
| |
|
16 |
Types
of eukaryotic microorganisms
Classification of Eukaryotes; Phylogeny of Eukarya
The hydrogenosome; Protozoa: classification (locomotion
and Official 1980 system); Amoeba – pseudopod
former; Paramecium – ciliate; Giardia –
Flagellate
Slime moulds; Fungi: Classification; Cell wall and metabolism;
Filamentous fungi
Asexual reproduction and Sexual Reproduction
Yeasts; Sexual reproduction in yeast
Algae; Algae – Phylogeny; Medically important
fungi
Mycoses are subdivided into 3 categories: Superficial;
Subcutaneous; Systemic |
| |
|
17 |
Taxonomy
of Protists
Diplomonads: Giardia lambia; Trichomonas; 18S RNA Not
reliable for Protist Taxonomy;
Microsporidia: uses and life cycle; A fungus. Taxonomy
according to Proteins; Choanoflagellates; Sponges (Metazoa);
Cellular Slime Moulds; Dictyostelium Slugs; Plants:
Chlamydomonas (Green Algae); Euglenophyta; Alveolata
(ciliates etc); Pfiesteria; Chromista (Brown Algae);
Cryptomonads; Foraminifera & Radiolarians |
| |
|
18 |
Fungi
Filamentous fungi; fungal thallus; Fungal subdivisions;
Yeast Cell Cycle; Life cycle of basidiomycete; Mushroom;
Fungal Mycelium; Fungal hypha; Secretion from mycelium;
DNA and genes; Nuclei distribution in hypha; Fungal
groups; Industrial uses of fungi cellulases; Mycorrhizae;
Fungi: Biological control agent; |
| |
|
19 |
Industrial
Microbiology and Biotechnology
Examples of products and industrial microorganisms;
Gene prospecting; random mutagenesis and screening;
Tools for genetic engineering; Fermentation; Formation
of primary and secondary metabolites; Medium and inoculum
preparation; Ethanol fermentation; Enzymes Production;
Products made by genetic engineering; Biotrends |
| |
|
20 |
Acellular
Microorganisms
Viruses: structure, classification; reproduction
Nature of Viruses; Genome Diversity; Electron Micrographs
and Virus Structures; Assay and Detection of Viruses;
Virus Replication; Epidemiology of Virus Diseases Vaccines |
| |
|
21 |
Microbial
Growth
Microbial
population and community dynamics
Analysis of a Population; Parameters to Assess Population;
Biomass; Component Analysis; Power of population to
increase; Environments (open/closed); Bacterial Growth;
Basic growth equations; Specific Growth Rate; Exponential
Growth; Growth Rate Constant; Closed System growth ;
Growth phases; Industrial applications; Human digestive
system; |
| |
|
22 |
Growth
in limited environments
Assumption: basic growth equations; Growth Curve; Pearl
- Verhulst - Logistic Model
Phases of Growth; Monod Equation; Saturation Constant
(Ks); Growth Yield |
| |
|
23 |
Microbial
growth in open environments
Chemostats; The Dilution Rate and Biomass Concentration;
The dilution rate & growth limiting substrate concentration;
Steady State; Growth Yield and Maintenance Energy |
| |
|
24 |
Epidemiology
of infectious diseases
Epidemics; Vaccination effect; Immunisation; Elimination
of Smallpox; Disease origin; Pathogen adaptation; Myxomatosis;
SARS; Flu epidemics/pandemics; H5N1 Chicken Flu |
| |
|
25 |
Microbial
growth in food
Food hygiene; Bacterial Toxins: Clostridium, Bacillus,
Staphylococcal, etc.
Food-borne microbial illness: Salmonella, Campylobacter,
etc.
Viral Gastroenteritis; Fungal food poisoning; Food Spoilage;
Food Preservation |
| |
|
26 |
Pathogenicity
and immunology
Pathogens and virulence; Damage to host; Body defense
mechanisms; Specific body defense mechanisms (immune
system)
|
|