Dear student,
This document contains a summary of the book ‘Microbiology: a clinical
approach’ 1st edition by Anthony Strelkauskas. The book is learning material for
the course ‘Infectious Diseases’ (AB_471024) of the study Gezondheid en Leven
(2nd & 3rd year) / Biomedical Sciences (3rd year) given at VU Amsterdam. The
document is written in June 2022. The syllabus said that the corresponding book
had to be 2nd edition, but the coordinator said that the 1st edition is also sufficient!
The chapters included are:
• Chapter 4 (page 1): An introduction to cell structure and host-pathogen
relationships
• Chapter 5 (page 9): Requirements for infection
• Chapter 6 (page 13): Transmission of infection, the compromised host, and
Epidemiology
• Chapter 7 (page 17): Principles of disease
• Chapter 8 (page 20): Emerging and Re-emerging infectious diseases
• Chapter 9 (page 23): The clinical significance of bacterial anatomy
• Chapter 11 (page 30): Microbial genetics and infectious disease
• Chapter 12 (page 35): The structure and infection cycle of viruses
• Chapter 13 (page 41): Viral pathogenesis
• Chapter 14 (page 45): Parasitic and Fungal infections
• Chapter 15 (page 55): The innate immune response
• Chapter 16 (page 61): The adaptive immune response
• Chapter 19 (page 64): Antibiotics
• Chapter 20 (page 67): Antibiotic Resistance
• Chapter 21 (page 69): ONLY parts discussing Tuberculosis & Influenza
• Chapter 22 (page 71): ONLY parts discussing Shigella, Salmonella,
Cholera
• Chapter 24 (page 72): ONLY parts discussing Tetanus & Botulism
• Chapter 25 (page 73): ONLY part discussing Epstein-Barr Virus
• Chapter 26 (page 74): ONLY parts discussing Chickenpox & HSV-1
While making the summary, I noticed that chapter 11, 15 & 16 discussed a lot of
information that was dealt with in previous courses. So be aware that these
chapters are not fully summarized, but only the parts that were new or still
unclear to me!
Good luck with studying
P.S. Check out my bundle for this course including my lecture notes to be
completely prepared for the exam!
, Study: Biomedical Sciences / Gezondheid en Leven
Bacteria
Size, shape, and multicell arrangement
The major bacterial shapes are speres, ovoids, straight rods, curved
rods, and spirals.
- Spherical and ovoid bacteria are called cocci
- Both types of rod are called bacilli
- Very short rods, can be mistaken for cocci, and are therefore
referred to as coccobacilli
- Rod-shaped bacteria that have tapered ends are called fusiform
bacilli.
- Spiral bacteria are called spirilla if the cell is rigid and spirochetes if
it is flexible and undulating.
In addition to their distinctive shapes, bacteria can form distinctive
multicell arrangements that are easily identified.
- Cocci can form two-cell arrangements called diplococci.
o This is seen in bacteria like Streptococcus
pneumoniae, which causes respiratory infections
and Neisseria gonorrhoeae, which is an STI
(gonorrhoea).
- Cocci can also form chains and clusters.
For an additional degree of classification, we use staining.
Staining
Basic dyes are the most commonly used stains and are composed of positively charged
molecules. These molecules are attracted to bacterial cells, which have an overall negative
charge on their surface.
- Simple stains consist of only one dye, and these stains are used to identify the shape and
multicell arrangement of bacteria.
o Safranin
o Crystal violet
o Methylene blue
o Carbolfuchsin
- Differential stains use two or more dyes to distinguish either between two or more
organisms or between different parts of the same organism. The format of a typical
differential stain is first the addition of the primary stain, followed by the decolorizing
agent, and last the counterstain.
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, o Gram
o Negative (capsule)
o Flagella
o Ziehl-Neelsen acid fast, and endospore.
Gram stain
Can be used to separate most bacteria into four major groups:
- Gram-positive (Gram+)
- Gram-negative (Gram-)
- Gram-variable
- Gram-nonreactive.
The gram stain takes advantage of the differences in the cell walls of these groups of bacteria
(chapter 9!)
The picture shown above shows the procedure of gram staining
Procedure: Initially the gram staining uses the dye crystal violet, which is taken up by all bacteria. The cells are then
treated with iodine as a mordant (a substance that sets the colour and makes it permanent), which helps the Gram-
positive cells retain the crystal violet. When alcohol is added in the next step, the Gram-negative cells lose their colour
but the Gram-positive cells retain the violet dye. Because the now-colour-less Gram-negative cells would be invisible
under a microscope at this point, they are counterstained with the red dye safranin. Any Gram-variable bacteria in the
mix are recognizable by the way in which they stain unevenly. Gram-nonreactive bacteria do not stain and must be
stained with a simple stain to be seen.
Negative (capsule) stain
This stain can be used to identify bacterial shapes, and in particular
spirochetes. It can also be used to identify the presence of a capsule, which
is a structure that surrounds certain bacterial cells.
➔ Capsule is important in bacteria that infect humans because it limits
the access of antiseptics, disinfectants and even antibiotics, thereby
protecting the infecting bacteria. Capsules can also defeat a host’s
defence mechanisms.
Procedure: the stain uses dyes such as nigrosine and India ink to colour the background surrounding encapsulated
bacteria in a sample being tested, making the capsule very visible. The stain colours only the background and not the
capsule itself. This allows scientists to see the capsule.
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, Flagella stain
Some types of bacteria have flagella. This flagella is an important part of the
infectious process because it allows the invading organisms to move from the
initial site of the infection. Bacterial flagella are too thin to be seen under the
microscope, therefore a flagella stain is used to coat the surface of the flagella
either with layers of dye or with metals (silver).
Ziehl-Neelsen Acid-fast stain
The presence or absence of a cell wall containing mycolic acid is the
underlying principle of Ziehl-Neelsen acid-fast staining because only this
type of cell wall is acid-fast.
- The term acid-fast refers to whether or not a bacterium that is first
stained and then washed with acid retains the staining dye.
- The walls of some bacteria where these stains are used for, have
a cell wall that contains mycolic acid and lipids, and the presence
of the presence of these substances in the cell wall makes the
wall difficult to penetrate.
A sample is treated first with heated carbol-fuchsin, a red dye that can penetrate all cell walls, regardless of whether or
not they contain mycolic acid. The next step is the addition of an acid– alcohol solution that removes the red colour only
from those cells in the sample in which the cell wall does not contain mycolic acid — in other words, only from cells that
are not acid-fast. The acid washing does not disturb the red colour of carbolfuchsin in any acid-fast cells.
Endospore stain
An endospore is a small, tough, dormant structure that forms in bacterial
cell. Bacteria that undergo sporulation (the process in which endospores
are formed) are particularly difficult to neutralize because the endospores
are extremely resistant to antiseptics, disinfectants, and antibiotics.
The endospore stain is a differential stain in which a sample is colored by heating
with malachite green for 5 minutes. The endospore walls are so thick and resistant
that extensive heating is required to make them permeable to the stain. The
sample is then washed thoroughly with water for 30 seconds, and in this washing
the dye is removed from all of each cell except the endospore, which stays green.
A final step of counterstaining with safranin turns the non-spore part of each cell
red (Figure 4.11). If the cells were stained with safranin only, the endospores
would appear as colorless regions in the cell interior
Host-pathogen relationships
Definitions
Mutualistic: microorganisms that depend on us for their survival, and we live more comfotabl
with them than without them.
Opportunistic pathogens: organisms that cause disease by taking advantage of a host’s
increased susceptibility to infection
Primary pathogens: those that can cause disease in individuals who are healthy. They have
evolved mechanisms that allow them to overcome the defences of the host and, once inside a
host, to multiply greatly.
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,Infection by any pathogen, whether opportunistic or primary, requires that the pathogen
1. Be able to multiply in sufficient numbers to secure establishment in the host
2. Be transmissible to new hosts.
Bacterial pathogenicity and virulence
Pathogens must be able to accomplish the following:
- A potential pathogen must be able to adhere to, penetrate, and persist in the host cell
- It must be able to avoid, evade, or compromise the host defence mechanisms
- It must damage the host and permit the spread of the infection
- It must be able to exit from one host and infect another host
Virulence: refers to just how harmful a given pathogen is to a host. This depends on genetic
factors of the pathogens.
- Virulence genes are carried either on the chromosome or on mobile genetic elements
called plasmids
- Clusters of virulence genes are called pathogenicity islands
- Some virulence genes are regulated by quorum sensing (environment-sensing
mechanism)↓
Quorum sensing
Specialized proteins in a pathogen cell called sensing proteins relay information about the cell’s
environment to other proteins that regulate genes controlling the transcription of virulence
genes.
The reason some bacteria do quorum sensing, is because they do not want to tip their hand
before they are present in large enough numbers to make the host sick. This is because the
bacteria have evolved to delay the production of toxins as a means of hiding from the host
defences, which would have no trouble in dealing with small numbers of pathogens.
Biofilms
This is the term for when bacteria
adhere and grow as aggregated
assemblies of cells. A biofilm is
important for health care because it
can either impede or totally prevent
the entry of antimicrobial agents and
other molecules that are potentially
toxic to bacteria. At the same time, a
biofilm is able to capture and retain
nutrients, thereby allowing the
bacterial population to increase in
number.
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,The host cell
The table under here shows the most important differences between the two cell types.
Eukaryotic cells
Plasma membrane
This is the outer layer of the eukaryotic cell. It has significant differences with that of bacteria in
the amounts of lipid and certain other components.
The plasma membrane is made up of phospholipid bilayer.
Lipids are not soluble in water and for this reason they are
said to be hydrophobic. Lipids therefore provide a perfect
barrier between water on the outside of the cell and water on
the inside of the cell. To still interact with its environment, the
lipid is bound with phosphate ions, which are hydrophilic.
These phosphate groups face outward and the lipid layers
inward.
Other molecules in the plasma membrane:
- Proteins involved in communication and transport
and structural roles.
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, o Some act as receptors for signals sent by other cells; they also can serve as a
site for virus attachment
- Important to remember is that the phospholipid bilayer structure is also seen on
membrane-enclosed structures inside the cell. This allows the plasma membrane to
interact with these internal structures during certain cellular functions.
Role of plasma membrane in infection
The plasma membrane must be breached if microorganisms are to gain entrance. This is
particularly true for viruses. They are able to infect host cells that have a specific receptor for
viral particles located on their plasma membrane.
➔ In many viral infections, the viral particle acquires a part of the host’s plasma membrane
as the particle leaves the infected host cell. This piece of plasma membrane wraps
around the virus and is referred to as the viral envelope.
Cytoplasm
The cytoplasm is all the volume of the cell that is inside the plasma membrane but outside the
nucleus. It is made up of
1. Semifluid material consisting mainly of water plus a variety of dissolved substances
(cytosol)
2. Membrane-enclosed structures called organelles
3. Structures that are not bound by a membrane.
It is found in both prokaryotic and eukaryotic cells, but membrane-enclosed organelles are found
only in eukaryotic cells.
Role of cytoplasm in infection
Particularly involved in viral infections. During a viral infection, the cytoplasm is the place where
all individual viral particles are manufactured and assembled.
Cytoplasmic structures not enclosed by a membrane
Cytoskeleton
This consists of
- Microfilaments
o Made up of actin (protein). Anchor the cytoskeleton to proteins in the plasma
membrane and give the cytoplasm a gel-like consistency
- Intermediate filaments
o Larger than microfilaments and are composed of a variety of different molecular
subunits belonging to the family of proteins called keratins. Provide additional
strength and stability to the cytoskeleton. Are also involved with positioning cells
alongside one another in tissues
- Microtubules
o Hollow tubes made up of tubulin (protein). Are involved in the movement of other
structures that reside in the cytoplasm in particular chromosomes during mitosis
and meiosis.
Role of cytoskeleton in infection
Some bacteria (f.e. shigella) destroy the lining of the intestinal tract when they infect the cells
forming that lining.
Cilia
Are only found in eukaryotic cells! They are made up of microtubules arrayed in an arrangement
in which nine groups of microtubules form a ring encircling two central microtubules. By moving
in unison, cilia move liquids and secretions across the surface of the membrane.
Role of cilia in infection
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, Ciliated cells work with mucus-secreting cells to remove foreign materials, including
microorganisms, from the respiratory tract, thereby preventing the ‘staying in’ requirement for
successful infection.
Flagella
Flagella are responsible for cell motility and are composed of the protein tubulin (like
microtubules). The only cells in humans that contain flagella are sperm cells.
Ribosomes
Found in both type of cells and is responsible for the production of proteins. Ribosomes are
either floating free in the cytosol or attached to the ER.
Role of eukaryotic ribosome in infection
Eukaryotic ribosomes are actively involved in viral infections, but not by choice. The ribosomes
make all of the new viral particles.
- The bacterial ribosome is one of the targets attacked by certain antibiotics.
Cytoplasmic structures enclosed by a membrane
These consists of the cells organelles. Remember that the membrane enclosing the organelle is
of the same type as the plasma membrane surrounding the whole cell – a phospholipid bilayer!
Mitochondria
Are the energy-producing elements of the eukaryotic cell. They are
the organelles where most ATP is produced. A mitochondrion has
two membranes enclosing it, and ATP is made on the folds.
- Mitochondria also contain their own ribosomes and their
own DNA, which replicates independently of the host cell.
The mitochondrial chromosome is single and circular, and
the ribosomes in mitochondria are different, they are the
same as those seen in bacteria. In fact, mitochondria share
a lot of similarities with bacteria. Therefore, they have
fostered the endosymbiotic theory, which describes a
process whereby early in evolution, bacteria and eukaryotic
organisms had a symbiotic relationship – a relationship in
which two organisms lived as one unit.
Endoplasmic reticulum and Golgi Apparatus
Both are systems of membranes that form numerous flattened sacs and platelike structures in
the cytoplasm of the eukaryotic cell. These structures are not found in prokaryotes.
- The ER is the site where various cellular components are synthesized. If ribosomes are
attached to the ER, it is referred to as rough endoplasmic reticulum (otherwise smooth
ER). In smooth ER lipids and other nonprotein components are produced. The ER moves
synthesized materials to the Golgi apparatus
- The Golgi apparatus has three functions:
o Modifying and packaging products that come from the ER
o Renewing the plasma membrane
o Producing lysosomes
The two organelles can interact with each other, because they have the same outer membrane.
This is also the mechanism that is used to move newly synthesized components from the ER to
the Golgi apparatus.
Role of ER in infection
In viral infections, the ER is the site of the biosynthesis and assembly of viruses. It is also
associated with the adaptive immune response, a major host defence against infection.
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