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Summary Exam Infectious Diseases: All Lectures + book "Microbiology: A Clinical Approach, ISBN: 9780815345138" (AB_471024)

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  • Course
  • Infectious Diseases (AB_471024)
  • Institution
  • Vrije Universiteit Amsterdam (VU)
  • Book
  • Microbiology

This document contains a very comprehensive summary for the exam of Infectious Diseases/pathogeen-gastheer interacties. It includes the lectures and all the self-study chapters from the book "Microbiology, a clinical approach". The summary is written in English, since the exam will contain open qu...

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  • Chapters 4-9, 11-16, 19,20 & partly 21,22,24,25,26 (see document first page)
  • June 25, 2022
  • 107
  • 2021/2022
  • Summary

Subjects

  • biomedical sciences
  • gezondheid en leven
  • bacteria
  • viruses
  • immune system
  • vaccines
  • antibiotics
  • course second and third year
  • infectious diseases and gastheer pathogeen interacties

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  • Biomedical Sciences
  • Infectious Diseases (AB_471024)
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Infectious Diseases Exam
The lectures + the book “Microbiology a clinical approach”
Chapter 4-9, 11-16, 19, 20 completely
Part of the chapters: 21 M. tuberculosis, Influenza viruses & 22: Shigella, Salmonella, V. cholerae & 24: C.
tetani, C. botulism & 25: Epstein-Barr virus & 26: Chickenpox, Herpes Simplex virus type 1




Inhoud
Lecture 1 – Introduction infectious diseases & Chapter 4,5,7 .......................................................................................... 2
Lecture 2 – Bacterial Anatomy & Chapter 5,9 .................................................................................................................. 8
Lecture 3 – Requirement of infection & Chapter 4,5,6................................................................................................... 13
Lecture 4 – Bacterial invasion & Chapter 4,5 (and partly 22) & article Sansonetti ........................................................ 18
Lecture 5 – Toxins and tissue damage & Chapter 5 (and partly 24) ............................................................................... 24
Lecture 6 – Viruses and Viral Infections & Chapters 12,13 ............................................................................................. 31
Lecture 7 –Immunology & Microbial Diagnostics & Chapter 6,15,16............................................................................. 40
Lecture 8 – Microbial Genetics in Infections & Chapter 11 ............................................................................................ 47
Flip-the-classroom Antibiotics & Chapter 19 and 20 ...................................................................................................... 55
Lecture 9 – Emerging and re-emerging diseases: Antigenic variation & Chapter 8, 15,16 ............................................ 67
Lecture 10 – Eukaryotic parasites and pathology & Chapter 14..................................................................................... 76
Lecture 11 – Fungal Biology & Chapter 14 ...................................................................................................................... 83
Lecture 12 – Vaccines & Chapter 5,6,9,12,13 ................................................................................................................. 88
Chapter 21 – M. tuberculosis & Influenza viruses .......................................................................................................... 93
Chapter 25 – Epstein-Barr virus ...................................................................................................................................... 94
Chapter 26 – Chickenpox & Herpes Simplex virus type 1 ............................................................................................... 95
Chapter 15 & 16 – Prior knowledge immune system ..................................................................................................... 96
The innate immune system – Chapter 15 ................................................................................................................... 96
The adaptive immune system – Chapter 16 ............................................................................................................. 101



1

,Lecture 1 – Introduction infectious diseases & Chapter 4,5,7
The commensals are bacteria which give a health benefit, these have positive effects. They are primarily occurring in
the intestine and on the skin, where they provide for vitamins, help protect us from pathogens and to digest food.
These microorganisms are classified as mutualistic, meaning that they depend on us and we depend on them. The
cause of a disease is referred to as its etiology. The disease chance is defined as the (load of infection x the
pathogenicity)/the strength of the immune system.

Introduction to the different classes of pathogens
Pathogens listed by size:
Parasites: can be seen by eye
- Worms
Microorganisms:
- Protozoa: unicellular version
- Fungi: unicellular
- Bacteria
- Viruses: DNA or RNA or proteins: are not able to
divide/replicate without a host, therefore they are
not considered as microorganism.
➔ The light microscope is used for eukaryotic microorganisms and bacteria. Viruses cannot be seen with this
microscope; these can only be seen with electron microscopes.

Prokaryote: bacteria Eukaryote: worms, protozoa, fungi




No nucleus DNA in nucleus as multiple chromosomes which
contain histones
DNA is one circular chromosome Extrachromosomal DNA present in chromosomes
and/or plasmids
Additional DNA as plasmids Nuclear membrane and membraned organelles
Transcription & translation simultaneously in Transcription in nucleus & Translation in cytoplasm
cytoplasm
Rigid cell wall, which contains peptidoglycan, Cell wall only in fungi and plants, sometimes
lipopolysacharides and teichoic acids. contains cilia or flagella
Contains external layer: capsule or slime Does not contain an external layer
Reproduces via binary fission Reproduces via mitosis or meiosis


Definitions in infectious diseases
Pathogenicity: the ability of a microorganism to inflict damage on its host, this is often referring to genetic
components of the pathogen and this is host-independent, it does not depend on host specific traits.
Virulence: the extent of damage that a pathogen is able to inflict on its host, this is divined by the host-pathogen
interactions and this is host-dependent. This mostly depends on genetically encoded factors of the pathogen
(virulence factors, of which later more).
Infection: colonization and growth of a microorganism within a host. Does not always cause symptoms and disease.
Disease: damage to the host, that interferes with normal functions of the host cells; this gives symptoms which can
be mild or severe.
➔ Some common terms used when describing infections are:



2

,The relationship between the human host and microorganisms
- Microbiota: the normal flora of bacteria on our body. This is different for every individual and the biome can
change over time and it is different in every part of our body. The microbiota can also change due to dietary,
seasons, hormonal change an exposure to antibiotics. In definition, a healthy microbiome is ecologically
stable and functional. This means there is very little change to its composition under stress or it quickly
returns to its normal state. There is also evidence that the microbiome composition could contribute to
obesity, diabetes, atherosclerosis, autism, allergies, asthma, chronic gastrointestinal diseases, bowel
syndromes and celiac disease.
- Superorganism: humans are two-legged ecosystems: consisting of the microbes and their genetic
information (called the metagenome) and the environment in which they all interact.
There are three types of relationships between a host and bacteria living on that host:
- Commensalism: in which one partner is benefited but the other is unaffected. The relationship between
humans and the microbial flora is one form of commensalism.
- Mutualism: in which the host offers benefits to the bacteria and the bacteria offers benefits to the host.
Examples are, bacteria which provide us with vitamin K and B, and we on the other hand offer them
nutrients and a place to stay.
- Parasitism: one partner benefits at the expense of the other. These are the pathogens which make us ill.
Host-bacteria relationships:
- Microbial antagonism: microbial flora can protect us from disease caused by other bacteria. Bacteria that
reside in our body will fight to prevent outsiders from taking up residence. In fact, many bacteria can
produce bacteriocins, which are essentially localized bacterial antibiotics. These can kill invading organisms
but do not affect the bacteria that produce them.
- Opportunistic pathogens: these are pathogens that are harmless in the normal location, but can cause
disease when they move to an area where it is normally not found or
where the host’s immune responses are weakened.

Viruses in different shapes and kinds
- Cylinder shaped or round shaped
- Consisting of double stranded/single stranded DNA/RNA
- Sometimes contains a membrane
➔ Bacteriophage: infects bacteria

Bacteria in different shapes: only the common shapes are discussed
- Spherical = cocci
- Rod-shaped = bacilli
➔ Very short rods are called coccobacilli and rod-shaped bacteria with
tapered ends are called fusiform bacilli.
- Spiral = spirillum when the cell is rigid and spirochetes when the cell is
flexible and undulating.
- Ovoid = are egg-shaped


3

,The shape predicts the kind of bacteria and the way they cluster: different pathogens cluster differently:
- Diplococci: appear in pairs. This is seen by Streptococcus pneumoniae.
- Tetrad: appear in a cluster of 4
- Streptococci: form chains. This is seen by Streptococcus pyogenes.
- Staphylococci: forms clusters of bacteria, this is less organized. The most known member is Staphylococcus
aureus.

Staining bacteria to visualize
Most stains contain positively charged molecules which are attracted to bacterial cells because they have an overall
negative charge. Simple stains consist of only one dye, and these stains are used to identify the shape and multicell
arrangement of bacteria. 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 stain is first the addition of the
primary stain, followed by the decolorizing agent and least the counterstain.

The gram stains
The most used stain is the Gram staining:
distinguishes between the gram positive and
negative bacteria. This has to do with the
buildup of the cell wall. The staining uses
different solutions: starting with Crystal violet
this stains all bacteria purple, iodine as a mordant (a substance that sets the color inside the cell and makes it
permanent) forms complexes with the bacteria and the latter staining, alcohol makes sure that the Crystal violet
iodine complex is washed away in the gram-negative bacteria. (Therefore, only the positive bacteria will stay purple).
Then a counter stain is done with Safranin in order to color the negative bacteria pink.
➔ Negative: pink, positive: purple
What is the difference in the cell wall:
The main different is that gram-positive bacteria have a very thick peptidoglycan layer, while the gram-negative
bacteria have a thin peptidoglycan layer combined with an outer membrane. The thickness of the peptidoglycan will
cause the hold of the color; the positive bacteria have a very thick wall and therefore the color will stay.

The negative capsule stains
This can be used in order to identify shapes and in particular spirochetes. It can also be used to identify the presence
of a capsule. This can facilitate adherence and undermines the host’s defense mechanisms by inhibiting
phagocytosis. It uses dyes such as nigrosine and India ink to color the background surrounding encapsuled bacteria,
making the capsule visible. A second dye can be added to color the bacterium inside each capsule.

The flagella stain
A flagella gives a property which allows the bacteria to be motile. A flagella stain can be used to coat the surface of
the flagella either with layers of dye or with metals such as silver. This process is very hard to carry out.

The Ziehl-Neelsen acid-fast stain
This is used to detect Mycobacterium tuberculosis and Mycobacterium leprae. These bacteria have a cell wall that
contains mycolic acid and lipids, and the presence of these substances make the wall difficult to penetrate.
Therefore, heat is used to break down this acid and permit the entry of the stain. A sample is treated with heated
carbolfuchsin 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 color only from those cells in the sample which do
not contain the acids. The bacteria with the acids will remain colored.

The endospore stains
An endospore is a small, dormant structure that forms in bacterial cells and several types of bacteria can undergo
sporulation. These spores are resistant to antiseptics, disinfectants, radiation and antibiotics. The sample is colored
by heating with malachite green, the heat is needed to make the cells permeable to the stain. The sample is then
washed with water and in this washing the dye is removed from all of each cells except the endospore, which stays
green. Counterstaining with safranin turns the non-spore part of each cell red.

4

,General properties of pathogens
Robert Koch: First to show the link between microbes and disease, identified the causative agents of anthrax and
tuberculosis, developed techniques for obtaining pure cultures and established the Koch's postulates
Koch’s postulates:
1. The same pathogen must be present in every case of the disease, but not in healthy individuals.
2. The pathogen must be isolated from the sick host and grown in a pure culture.
3. The pure pathogen must cause the same disease when given to uninfected hosts.
4. The pathogen must be re-isolated from the newly infected hosts, and shown to be the same organisms as
isolated initially.
This can be applied for many bacterial infectious diseases that have caused epidemics like: Diphtheria
(Corynebacterium diphtheriae), Tuberculosis (Mycobacterium tuberculosis) & Cholera (Vibrio cholerae).
Nevertheless, the infectious diseases caused by viruses and infectious agents present in healthy people (problematic
because this happens a lot) cannot be used in these rules. This is the case, because there is no animal model
available, since bacteria do not grow in the lab and viruses need host cells to grow in the lab.

Primary pathogens: cause disease in healthy individuals, these pathogens follow the Koch’s postulates rules: they
are only present in ill individuals.
Opportunistic pathogens: cause disease in weakened individuals or when in unusual location; often belong to the
commensal microflora. These do not follow the Koch’s postulates rules. Examples are:
➔ Fungi: this group contains no primary pathogens and are often hospital related.
➔ Bacteria as: Staphylococcus aureus, in skin infections and Streptococcus pneumoniae, in lung infections
➔ Viruses as: Herpes simplex virus (HSV), in cold sores and Human papilloma virus, in warts
➔ Parasites as: Toxoplasma gondii, in systemic infections
Infection by any pathogen, whether opportunistic or primary, requires that the pathogen is able to multiply in
sufficient numbers to secure establishment in the host and be transmissible to new hosts. The pathogens benefit
from illness because it permits easer transmission (for example via coughing), but when a large number of hosts die
the spreading is no longer possible.

More over: what makes a bacterium pathogenic?
- 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 defense 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.
In order to regulate the expression of genes, which produce certain factors needed in the different stages of the
pathogen, the genes lay in clusters. Bacteria often contain only one chromosome and mobile genetic elements such
as plasmids. Certain clusters of virulence genes are called pathogenicity islands. Some virulence factors are regulated
by quorum sensing*.
*Next lecture

Virulence factors of the pathogen:
These are molecules of pathogenic microorganisms that increase the success of
infection: these factors are often specific to pathogenic microorganisms, frequently
interact with the host cells and are often present on the surface of the pathogen or
the pathogen excretes them. Overview of the kind of virulence factors: toxins,
capsules with protect the pathogen for the immune cells, surface molecules for the
attachment to the host cells and virulence plasmids containing genes encoding for
virulence factors.

Replicating and living place of the pathogens:
Extracellular: this way has more confrontation with the immune system. These pathogens therefore contain more
self-protection (in the way of capsules and cell wall components). These pathogens also contain more weapons as
enzymes and toxins and have antigenic variation to avoid the immune system.
Intracellular: is a way to hide from the immune system and causes invasion: deeper penetration in the tissue. There
are different versions of intracellular locations:

5

, ➔ Bacteria are sometimes present in phagocytes. Bacteria sometimes like to be present in these cells in order
to defend themselves. The phagosome fuses with the lysosome, when this fuses the bacteria are killed and
the remaining part is excreted again. However, many bacteria interfere with this pathway in order to block
the fusion with the lysosome or due to the fact that they do not stay in the vesicles for long but enter the
cytosol. M. Tuberculosis is one of the most occurring bacteria in this way; this blocks the fusion and escapes
the compartment and enters the cytosol.
➔ Invasion by ingestion by nonphagocytic cells like the epithelial cells: this happens via the manipulation of the
cytoskeleton.
➔ Strictly intracellular: viruses need host cells for replication, all proteins of the new virus particles are made
by the host cell and components of virus come from host structures; e.g., envelope is made of the host
plasma membrane. It is also dependent on (transcription) factors from the host cell in order to make new
DNA/RNA.

Infection strategies
- Acute infection: multiply as fast as possible and spread rapidly, this gives a lot of damage. This is the most
virulent version and has a high population density (a lot of virus particles/bacteria are produced in a short
period). This way has a low change for transmission because people are very sick and avoid contact with
other people.
- Chronic infection or persistent infection: staying in the host for a long time, while causing as little damage
as possible. This is less virulent and has a low population density (less virus particles/bacteria are produced).
In this way the pathogens can spread more easily; more individuals can be infected (because the host keep
seeing a lot of others, since they are not really sick).

Article: the two most general strategies used by pathogenic microbes in order to lead to disease, are:
Frontal assault strategies/acute infection: require that the infecting microbes rapidly replicate, induce disease
symptoms that overwhelm the innate defenses of the host and find a new host before engagement of the adaptive
immune system. General characteristics are: a short incubation period, acute clinical symptoms, engaging with the
innate immune system, requiring transmission to new susceptible hosts to maintain infection, has a rapid microbial
replication, carrier state is uncommon, transmission often requires intimate contact, reservoir is often a specific host
or the pathogens are opportunistic and it often induces sterilizing immunity (high population density).
V. cholera: the cholera toxin is encoded in the genome of a bacteriophage which integrated into the V. cholera
genome (this turned a harmless pathogen into a strain that could proliferate in the human host). The receptor used
by the phage to infect the cholera is encoded as a pathogenicity island (PAI). After the toxin, it is rapidly shed from
the body in the diarrhea output, which avoids a strong inflammatory response.

Stealth assault strategies/chronic infection: involve a slower infection process in which the microbes subvert the
host’s innate and adaptive immune systems to set up a chronic or persistent infection. General characteristics are:
the incubation period may be indeterminate, indolent or asymptomatic carriage, it engages with the innate immune
system, avoids or manipulates the adaptive immune system, rapid microbial replication may punctuate a requiring
or terminal event, the carrier state is common with periods of shedding, transmission happens via direct contact or
persistence in the environment, the reservoir is usually a specific host or a group of related host species and it rarely
induces sterilizing immunity (low population density).
Helicobacter pylori: resides in the stomach. The LPS and flagella of the helicobacter bacterium are different,
therefore they are less recognized by the immune system.
- This bacteria produces the enzyme urease, which catalysis the hydrolysis of urea to CO2 and ammonia, this
helps to maintain the bacterial metabolism and survival and it makes a higher pH.
- It does subvert the innate immune system via toll like receptors (mainly TLR-4 and TLR-5 which are used to
recognize lipopolysaccharides and flagellar proteins respectively),
- It also modulates the adaptive immune system by blocking the antigen-dependent proliferation of T-cells.
This is caused by the secretion of the virulence factors CagA and VacA. VacA inhibits T-cell proliferation by
blocking T-cell receptors, resulting in inhibition of cytokine production. CagA inhibits B-cell proliferation
through inhibition of the JAK-STAT signal transduction pathway and it inhibits B-cell apoptosis (may
contribute to cancer development).
- The bacterium can also hide inside host cells, while it normally is an extracellular bacterium.
- It has a high antigenic variation and it can change the virulence factors.
6

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