Learning Objective Notes for Microbiology

Lecture 1: Infections and their Causative Agents:

1) What is microbiology and why is it significant in relation to human disease?
a) Microbiology: the study of organisms which require assisted vision (microscope) to view
b) Infectious diseases are the second and fourth most common causes of death worldwide and the
leading cause of Infant mortality globally.
c) In addition, resistant strains of pathogens termed ‘Superbugs’ are becoming more prevalent in
developed countries.
d) Infectious agents also contribute to other diseases indirectly (the most famous example being
Helicobacter pylori and its involvement in peptic ulcers and gastric cancer)
2) What are ‘emerging infectious diseases’?
a) New infection diseases which emerge due to natural/ artificial selection causing the evolution of
existing strains of pathogens, zoonosis of pathogen from animal to human and the re-emergence
of historical pathogens.
b) Increased since the 1940s due to the following socioeconomic factors:
i) Increasing population density and mobility
ii) Antibiotic use leading to selection of resistant strains
iii) Agricultural practices (exposure when clearing land)
iv) Failure in public health (inadequate funding for programs such as vaccination)
c) Also increases in a well distributed manner due to biodiversity
3) Why is microbiology important to preventing disease?
a) Understanding of the relationship between host and microbial pathogens can lead to:
i) Improved sanitation practices
ii) Surveillance and monitoring of outbreaks
iii) Drug Therapy: particularly in better antimicrobials
iv) Vaccine development
Lecture 2: Introduction to Bacteria
1) How do we classify bacteria? What do we use to do this?
a) Generally, less compartmentalised than eukaryotes and simpler
 b)
c)
2) What distinguishes the bacterial genome from other organisms and how is this information
used for classification?
a) Bacterial genomes are usually contained in a ‘bacterial nucleoid’, which is a mass of genetic
material (DNA), RNA and proteins which is not membrane bound. The genome normally
consists of a single closed chromosome that is looped and supercoiled, meaning that it is much
smaller than in eukaryotes. Also contains plasmids (horizontal gene transfer)
b) The less dependent on host cells for reproduction a bacterium is (i.e. the less pathogenic it is), the
greater the genome size. However, bacteria genomes are generally functional genes, so relatively
few pseudogenes and no introns (junk DNA).
c) Genomic diversity within strains can be very high, so classification is based on the ‘core genome’,
conserved genes within a strain, and the ‘pan-genome’, other accessory genes providing features
that diversify the strain. //
d) Bacteria can be classified based on gene sequencing of the 16S ribosomal RNA. The 16S rRNA
is a protein that scaffolds the ribosomal protein, interacting with 23S to assist in the binding of
50S and 30S subunits of the ribosome. 16S consists of highly conserved and hypervariable
regions (V1-V9).
e) Since the conserved regions are always in the same place, variation in the V regions allow for
comparison across species and genera. This is known as ‘pattern-based sequencing’.
f) Limited by the infinite diversity that can be produced by bacteria, so most strains of bacteria
present are currently not known.
3) What are the physical properties of bacteria and how are these characteristics used to identify
them?
a) Cell wall and Gram stain: Bacteria have a characteristic cell wall that allows them to form five
basic shapes:

b) The cell wall is fixed in shape due to peptidoglycan, which can be used to classify bacteria
through Gram Staining. This staining works by exploiting the fact that cell walls that are Gram-
positive have more peptidoglycan than Gram-negative, so will retain the crystal violet stain when
 washed and countered stain, whilst Gram-negative bacteria will lose the stain and be coloured

pink by the safranin.

c) Gram positive cell walls: consist predominantly of peptidoglycan, but also teichoic acid and
lipoteichoic acid (Cell shape) and contains only one cell membrane.
d) Gram negative cell walls: more complex than GP, with an outer cell membrane as well. Also
contains porins and carriers that bring in small and large molecules respectively. Contains the
endotoxin Lipopolysaccharide (LPS) which stabilises the outer membrane.
e) Acid Fast Stain: used to identify Mycobacterium tuberculosis by indicating the presence of
mycolic acids, long fatty chains found in the cell wall. Cells are stained with carbol fuschin, de
stained with acid alcohol and then counterstained with methylene blue. Acid-fast bacteria
(mycobacterium) remain red as they retain the carbol fuschin whilst non acid-fast bacteria turn
blue.
f) Spore and Negative stain: Both negative and endospore??? pending
g) Capsules and Negative Stain: Capsules are ‘polysaccharide-based material’ that extends from
the cell surface to its surrounds. It contributes to the virulence of pathogenic bacteria by
increasing adherence to cell surfaces, protects against phagocytosis/ immune detection and
prevents dehydration. Since it is difficult to penetrate the capsule, negative staining, where a
negatively charged dye, nigrosine, will bind to glass background, but not the bacterial capsule.
Assists with classification by subtyping the bacteria using capsule antigens (Streptococcus pneumoniae
has over 90 subtypes).
h) Flagella and Serotyping: the flagella is thin, long hollow tube made of helical filaments. That is
used for location of the bacterium. Consists of basal body (part embedded in the cell and cell
wall), hook (part that bends outside the membrane to point it away from the cell) and filament
 (flagellin protein that causes movement). Flagella is used for serotyping surface antigens to
differentiate types (e.g. E. coli O1:H1, O1: H2 etc.)
4) By what process do bacteria reproduce and produce energy, and how is this used for identification?
a) Bacteria reproduce by binary fission, asexual cell division in two identical daughter cells. They will
grow exponentially in the following stages:
i) Lag phase: when bacteria are remodelling their metabolism to adapt to the environment. No
division occurs.
ii) Log Phase: exponential growth where doubling occurs at constant rate.
iii) Stationary Phase: no division occurs as there may be a depletion of growth factor/ nutrient
or accumulation of waste product.
iv) Death phase: when bacteria die due to sever depletion of nutrients or other environmental
factors.

v)
b) Bacteria acquire nutrients by using passive diffusion for small uncharged particle and facilitated
diffusion for larger essential particles. Active transport is only used for nutrients needed that are
present in a low concentration
c) The ability of different bacteria to use certain nutrients allow us to classify them, particularly in
their relation to oxygen for metabolism:
i) Strict aerobes
ii) Strict Anaerobes
iii) Facultative anaerobes- grow with or without oxygen
iv) Aerotolerant anaerobes- can survive in O2 but not grow
v) Microaerophiles: grow in low O2 conditions.
d) Biochemical assays can also be used to classify bacteria:
i) Hydrogen peroxide: a metabolic waste product that can be used by bacteria to kill
competition. A H2O2 test can be used to determine if a bacterium is catalase positive (Staph
aureus) and can break down H2O2 or catalase negative (Strep pneumoniae).
ii)
5) How can pathogenicity be used to classify bacteria?
Lecture 3: Bacterial Pathogenesis
1) What are the key attributes of pathogens?
2) What happens during Colonisation?
3) What happens during the process of Invasion?
4) How do bacteria cause tissue damage?
5) How do pathogenic bacteria evade the innate immune system (complement, phagocytosis and
capsule) and adaptive immune system?

Lecture 4: Antibiotics
1) What are antibiotics and how are they classified?
2) How do antibiotics affect bacterial growth?
3) What determines effectiveness of antibiotics in vivo?
4) What is the mechanism of action cell wall targeting antibiotics (beta-lactams and glycopeptides)?
5) What is the mechanism of action of protein synthesis targeting antibiotics (Amino glycosides)?
6) How do bacteria develop resistance to antibiotics?
Lecture 5: Virus Structure and Replication
1) What is a virus and what are its structural features (capsid) compared to other pathogens?
2) How are they classified?
3) What are the stages of viral replication using polio as an example?
Lecture 6: Viral Pathogenesis
1) How are viruses transmitted?
2) How do viruses commonly enter the body (respiratory, alimentary, shedding)?
3) How do they spread within the body and what conditions allow this to happen?
4) Why do viruses cause illness?
5) What are the outcomes of viral infection?
6) How do viruses evolve to avoid immune responses?
7) Use polio to explain pathogenesis
Lecture 7: Control of Virus Infection
1) How does vaccination work to prevent viral infection?
a) What are the types of vaccine?
2) How do antiviral drugs stop infection?
Case Study of Polio