Molecular Infection Biology
DETAILED VERSION
AM_470657
P2 2021
AM_470657
MOLECULAR INFECTION BIOLOGY SHORT VERSION
,Molecular Infection Biology
Inhoud
1.What is a pathogen? Symbiosis versus pathogenesis ...................................................................... 2
2.Which pathogen strain to use? ........................................................................................................ 7
3.What infection disease models? .................................................................................................... 14
4.How to identify virulence factors? ................................................................................................. 21
5.Virulence factors: Immune system interplay & Red queen hypothesis ......................................... 28
6.Virulence factors: Adaptation in metabolism ................................................................................ 35
7.Virulence factors: Intracellular trafficking & Survival .................................................................... 43
8.Regulation of virulence factors ...................................................................................................... 49
9.Pathogens in the gut microflora: Clostridium difficile ................................................................... 58
10.Molecular detection of novel viruses & Coronaviruses and coronavirus reinfections ................ 64
11.Bacterial Vaccine Design .............................................................................................................. 69
1
,Molecular Infection Biology
1.What is a pathogen? Symbiosis versus pathogenesis
A pathogen is a microbiological agent that causes disease or illness to its host. The term pathogen is
derived from the Greek That which produces pain or suffering. The lecture is about the definition of a
pathogen, because this definition is not quite right.
The problem is that there are pathogens and there is our microflora, but can we make this distinction?
If you look at the normal microflora, the gut has the largest number of microflora. Other places that
include microflora are: the skin, the mouth and respiratory tract, the vagina, the stomach and
esophagus. The composition of bacteria in every niche is very different.
The gut microflora alone consists of more than 500 species, mainly
the Firmicutes and Bacteroidetes. What you can do to analyze the
effects of the gut microflora is using gnotobiotic animals (germ-
free):
Mice are taken out via cesarean section and treated with
antibiotics (inside whom sterile, but impossible to take out sterile).
After they are raised in a germ-free environment, which is very
difficult, they are treated with antibiotics. The effects on the host
are:
o They need 30% more calories (microflora break down
complex polymers) gut anaerobes degrade and ferment
indigestible plant material and release small simplified
carbohydrates (butyric acid).
o have less vascularization and poor
development villi.
o have underdeveloped mucosal immune
response. Gut microflora induce immune
response, including production of
antimicrobial peptides.
Despite the fact that our gut microbiome is very
important to us, we can get problems in the
microflora. This has to do with a number of reasons:
normal microflora at the wrong place and
abnormalities in host defense. The normal microflora
can be at the wrong place by several reasons:
1. Damage to the epithelium: Damage to the colon epithelium (spontaneous or after surgery)
results in the infiltration of gut microflora in peritoneum. Coinfection of E.coli and B.fragilis
has an synergistic effect, which result in abscess formation. This results in an high morbidity
and mortality rate.
2. New sites for normal microflora: an example are the urinary tract infections which are caused
by E.coli. urinary tract infections can result in bladder infections (cystitis) and kidney infections
(pyelonephritis). It is mainly caused in women, because of the close proximity of the urethra
and the anus.
3. Foreign bodies (surgical implants): Infections due to foreign bodies cause septic shock in 1-5%
of patients. S.aureus and S.epidermidis are the common pathogens.
4. Wrong host: Different mammals have similar composition of gut flora, however, with strain-
specific bacteria.
- An outbreak occurred in western United States, in the fall of 1996. The outbreak was
traced to unpasteurized apple juice. The strain that was already identified. The factory was
2
, Molecular Infection Biology
clean an hygienic, and there was no putative source of contamination. The apples packing
houses, were not ideal. The water for the apples changes only once a day, E.coli was
present, but no O157:H7 strain. Specific lot of apples traced to tree farms: turkey manure
tested, no E. coli O157:H7. However, one of the farms was hosted by a deer population.
- Another example: Over 50 children in the US have been taken to hospital after a Disney
film was released in December, showing the beautiful Princess kissing a frog. Most of the
children infected with salmonella in the States were girls under the age of 10, which were
kissing frogs. Salmonella is part of the normal skin flora of frogs.
- Humans sometimes get infected when bitten by dogs/cats. 5-10% of bites become
infected. Capnocytophaga canimorsus belongs to the normal oral flora (of dogs and cats).
The infection can cause sepsis.
Besides the normal microflora which is present at the wrong place, the problem could also reside by
abnormalities in the host defense. This could be caused by several reasons:
i Genetic defect:
SCID (Severe Combined Immune Deficiency) is one reason. People always tend to think that Genetic
defects needs to be as severe as SCID, but there are also mild genetic defects.
An example is the presence of the alpha-herpesviridae. The herpes simplex virus is a mild infection
(dsDNA virus, 125-250 kb). An average of 50-100% of the population is chronically infected with one
or more herpesviruses (HSV, VZV, EBV). They stay with you for the rest of your life. Infections are often
asymptomatic. Reactivation can also be asymptomatic (but with discharge). The herpes simplex virus
type 1 are known as the herpes facialis/labialis (cold sore). The type 2 is known as the herpes
(pro)genitalis.
HSV type 1 infect the peripheral cells. It
resides in neuron cells in a special form
which does not produce proteins. This
way it is not detected by the immune
system. They can reside for the rest of
the time, and they can be reactivated and
infect the peripheral cells again. It
doesn’t affect the other neuron cells. This
would otherwise be worse. About 99% of
the population the Herpes virus gets
reactivated and infects epithelial cells.
One in million get the herpes simplex encephalitis infection: which can be necrotic in brain tissue. This
is the most common type of sporadic viral encephalitis. High mortality/morbidity rate: before the use
of acyclovir: 70% mortality and 3% of survivors with normal brain function. People thought that these
people were unlucky. It turned out that they indeed are unlucky, because of the TLR composition. TLRs
can recognize different parts of viruses and/or bacteria. Unspecific immune system is a wrong name,
they are quite specific and you should refer to them as innate immune system. The TLRs are very
important. 4 TLRs are specific for viruses, TLR7/8 can recognize ssRNA, TLR3 can recognize dsRNA,
which is usually not present in the endosome and TLR9 recognizes unmethylated CpGs on the DNA.
They are all present in the endosome. If TLR 3 is activated, it upregulates type 1 interferons, by which
neighboring cells gets activated. Type 1 interferons trigger some genes. If the cells are infected they
go into apoptosis. So the virus cannot replicate anymore.
In families it can occur that the TLR3 can be affected, which is called a deficiency. They looked at
mutations that affect the TLR3 pathway, these were often SNP that can affect the pathway. The
3
DETAILED VERSION
AM_470657
P2 2021
AM_470657
MOLECULAR INFECTION BIOLOGY SHORT VERSION
,Molecular Infection Biology
Inhoud
1.What is a pathogen? Symbiosis versus pathogenesis ...................................................................... 2
2.Which pathogen strain to use? ........................................................................................................ 7
3.What infection disease models? .................................................................................................... 14
4.How to identify virulence factors? ................................................................................................. 21
5.Virulence factors: Immune system interplay & Red queen hypothesis ......................................... 28
6.Virulence factors: Adaptation in metabolism ................................................................................ 35
7.Virulence factors: Intracellular trafficking & Survival .................................................................... 43
8.Regulation of virulence factors ...................................................................................................... 49
9.Pathogens in the gut microflora: Clostridium difficile ................................................................... 58
10.Molecular detection of novel viruses & Coronaviruses and coronavirus reinfections ................ 64
11.Bacterial Vaccine Design .............................................................................................................. 69
1
,Molecular Infection Biology
1.What is a pathogen? Symbiosis versus pathogenesis
A pathogen is a microbiological agent that causes disease or illness to its host. The term pathogen is
derived from the Greek That which produces pain or suffering. The lecture is about the definition of a
pathogen, because this definition is not quite right.
The problem is that there are pathogens and there is our microflora, but can we make this distinction?
If you look at the normal microflora, the gut has the largest number of microflora. Other places that
include microflora are: the skin, the mouth and respiratory tract, the vagina, the stomach and
esophagus. The composition of bacteria in every niche is very different.
The gut microflora alone consists of more than 500 species, mainly
the Firmicutes and Bacteroidetes. What you can do to analyze the
effects of the gut microflora is using gnotobiotic animals (germ-
free):
Mice are taken out via cesarean section and treated with
antibiotics (inside whom sterile, but impossible to take out sterile).
After they are raised in a germ-free environment, which is very
difficult, they are treated with antibiotics. The effects on the host
are:
o They need 30% more calories (microflora break down
complex polymers) gut anaerobes degrade and ferment
indigestible plant material and release small simplified
carbohydrates (butyric acid).
o have less vascularization and poor
development villi.
o have underdeveloped mucosal immune
response. Gut microflora induce immune
response, including production of
antimicrobial peptides.
Despite the fact that our gut microbiome is very
important to us, we can get problems in the
microflora. This has to do with a number of reasons:
normal microflora at the wrong place and
abnormalities in host defense. The normal microflora
can be at the wrong place by several reasons:
1. Damage to the epithelium: Damage to the colon epithelium (spontaneous or after surgery)
results in the infiltration of gut microflora in peritoneum. Coinfection of E.coli and B.fragilis
has an synergistic effect, which result in abscess formation. This results in an high morbidity
and mortality rate.
2. New sites for normal microflora: an example are the urinary tract infections which are caused
by E.coli. urinary tract infections can result in bladder infections (cystitis) and kidney infections
(pyelonephritis). It is mainly caused in women, because of the close proximity of the urethra
and the anus.
3. Foreign bodies (surgical implants): Infections due to foreign bodies cause septic shock in 1-5%
of patients. S.aureus and S.epidermidis are the common pathogens.
4. Wrong host: Different mammals have similar composition of gut flora, however, with strain-
specific bacteria.
- An outbreak occurred in western United States, in the fall of 1996. The outbreak was
traced to unpasteurized apple juice. The strain that was already identified. The factory was
2
, Molecular Infection Biology
clean an hygienic, and there was no putative source of contamination. The apples packing
houses, were not ideal. The water for the apples changes only once a day, E.coli was
present, but no O157:H7 strain. Specific lot of apples traced to tree farms: turkey manure
tested, no E. coli O157:H7. However, one of the farms was hosted by a deer population.
- Another example: Over 50 children in the US have been taken to hospital after a Disney
film was released in December, showing the beautiful Princess kissing a frog. Most of the
children infected with salmonella in the States were girls under the age of 10, which were
kissing frogs. Salmonella is part of the normal skin flora of frogs.
- Humans sometimes get infected when bitten by dogs/cats. 5-10% of bites become
infected. Capnocytophaga canimorsus belongs to the normal oral flora (of dogs and cats).
The infection can cause sepsis.
Besides the normal microflora which is present at the wrong place, the problem could also reside by
abnormalities in the host defense. This could be caused by several reasons:
i Genetic defect:
SCID (Severe Combined Immune Deficiency) is one reason. People always tend to think that Genetic
defects needs to be as severe as SCID, but there are also mild genetic defects.
An example is the presence of the alpha-herpesviridae. The herpes simplex virus is a mild infection
(dsDNA virus, 125-250 kb). An average of 50-100% of the population is chronically infected with one
or more herpesviruses (HSV, VZV, EBV). They stay with you for the rest of your life. Infections are often
asymptomatic. Reactivation can also be asymptomatic (but with discharge). The herpes simplex virus
type 1 are known as the herpes facialis/labialis (cold sore). The type 2 is known as the herpes
(pro)genitalis.
HSV type 1 infect the peripheral cells. It
resides in neuron cells in a special form
which does not produce proteins. This
way it is not detected by the immune
system. They can reside for the rest of
the time, and they can be reactivated and
infect the peripheral cells again. It
doesn’t affect the other neuron cells. This
would otherwise be worse. About 99% of
the population the Herpes virus gets
reactivated and infects epithelial cells.
One in million get the herpes simplex encephalitis infection: which can be necrotic in brain tissue. This
is the most common type of sporadic viral encephalitis. High mortality/morbidity rate: before the use
of acyclovir: 70% mortality and 3% of survivors with normal brain function. People thought that these
people were unlucky. It turned out that they indeed are unlucky, because of the TLR composition. TLRs
can recognize different parts of viruses and/or bacteria. Unspecific immune system is a wrong name,
they are quite specific and you should refer to them as innate immune system. The TLRs are very
important. 4 TLRs are specific for viruses, TLR7/8 can recognize ssRNA, TLR3 can recognize dsRNA,
which is usually not present in the endosome and TLR9 recognizes unmethylated CpGs on the DNA.
They are all present in the endosome. If TLR 3 is activated, it upregulates type 1 interferons, by which
neighboring cells gets activated. Type 1 interferons trigger some genes. If the cells are infected they
go into apoptosis. So the virus cannot replicate anymore.
In families it can occur that the TLR3 can be affected, which is called a deficiency. They looked at
mutations that affect the TLR3 pathway, these were often SNP that can affect the pathway. The
3
