MOLECULAR INFECTION
BIOLOGY
By Maite Erguin
Main lecturer: Wilbert Bitter
Biomedical Sciences Master’s at Vrije Universiteit Amsterdam
2021/22
,Contents
1. WHAT IS A PATHOGEN .................................................................................................................... 2
2. WHICH PATHOGEN STRAIN TO USE? ............................................................................................ 11
3. WHICH INFECTION MODEL TO USE? ............................................................................................. 16
4. WHICH GENETIC TECHNIQUE TO USE TO IDENTIFY VIRULENCE FACTORS? ................................. 23
5. VIRULENCE AND IMMUNE SYSTEM (Alex Speer) .......................................................................... 31
6. VIRULENCE AND METABOLISM (Jurgen R. Haanstra) ................................................................... 37
7. VIRULENCE AND INTRACELLULAR ROUTING (C. Kuijl) ................................................................... 43
8. VIRULENCE AND GENE REGULATION ............................................................................................ 51
9. PATHOGENS & GUT MICROFLORA (Wiep Klaas Smits) ................................................................. 60
10. MOLECULAR DETECTION OF PATHOGENS (Lia van der Hoek) .................................................... 67
11. VACCINE DEVELOPMENT (Peter van der Ley) ............................................................................. 72
1
,1. WHAT IS A PATHOGEN
• Gut microflora
o Normal microflora at the wrong place
o Abnormalities in host defense
• Herpes virus
o Herpes simplex encephalitis (HSE)
• Abnormalities in host defense: antibiotics
• Tuberculosis
o Tuberculosis infection cycle
o Models for analysis
• Epstein-Barr virus (EBV)
A pathogen is a microbiological agent that causes disease or illness to its host. The term pathogen
is derived from the Greek παθογένεια, "that which produces pain/suffering“. Pathogens can be
viruses, bacteria, protozoa, yeasts/fungi and worms.
Difference between microflora and real pathogens: Normal microflora’s pathogens are endogenous
and beneficial for the host, while real pathogens are exogenous and pathogenic for the host. The
major part of the microflora is on the colon. In the skin there are a lot of bacteria with different
compositions.
GUT MICROFLORA
(=Microbiota) There are more than 500 species, such as Firmicutes sp. (Clostridium species) or
Bacteroidites sp. (Bacteroides fragilis, Bacteroides thetaiotaomicron). Gnotobiotic animals are germ-
free. But when you use these, a) you need to use 30% more calories, because microbiota is a source
of metabolites, such as short-chain fatty acids (SCFAs). The food uptake without microbiota is
decreased. B) Also, these animals have less vascularization and poor development of villi. c) They
also have underdeveloped mucosal immune system.
For example, gut anaerobes (Bacteroides thetaiotaomicron) degrade and ferment
indigestible plant material → release of small simplified carbohydrates (butyric acid), and these
smaller carbohydrates can be used. Also, Gut microflora induce immune response, including
production of antimicrobial peptides.
2
, Paneth cells: Highly specialized secretory epithelial cells located in the small intestinal crypts of
Lieberkühn.
DISEASES BY NORMAL MICROFLORA
A) Normal microflora at the wrong place
• Damage to epithelium: B. fragilis. Damage to colon epithelium (spontaneous, after surgery)
results in the infiltration of gut microflora in peritoneum (serosa membrane in the
abdominal cavity). Coinfection E. coli and B. fragilis synergistic abscess formation, high
morbidity and mortality
• New sites for normal microflora: E. coli. Urinary tract infections, which can result in bladder
and kidney infections (cystitis and pyelonephritis). Cystitis happens mainly in women
because close proximity of urethra and anus.
• Foreign bodies (due to surgical implants): Staphylococcus epidermidis
• Wrong host: E. coli O157 (Old nomenclature, based on antibodies). Different mammals have
different microbiota. Examples:
o Outbreak of E. coli O157:H7 Apple juice. The factory where they made it was
clean. Apple packing houses were not ideal, though, cause water for apple washing
changed only one a day. The fam was hosted by a deer population! So when they
took apples from the floor, these weren’t OK. This strain is not problematic in deer
but it is in humans
o Salmonella that lives in the frog’s skin. But that microorganism in humans is not
good. After “The princess and the frog” movie, 50 children (mainly <10 year old girls)
kissed frogs and had salmonella infections.
o When humans are infected with Capnocytophaga canimorsus when they are bite
by dogs/cats (it belongs to its normal oral flora). This infection causes sepsis.
B) Abnormalities in host defense
• Genetic defect: SCID (Severe Combined Immune Deficiency). Boy in the bubble: Not working
B and T cells. Now we can treat the disease. Of course if you have low good antibodies you
get infections of normal microflora.
3
BIOLOGY
By Maite Erguin
Main lecturer: Wilbert Bitter
Biomedical Sciences Master’s at Vrije Universiteit Amsterdam
2021/22
,Contents
1. WHAT IS A PATHOGEN .................................................................................................................... 2
2. WHICH PATHOGEN STRAIN TO USE? ............................................................................................ 11
3. WHICH INFECTION MODEL TO USE? ............................................................................................. 16
4. WHICH GENETIC TECHNIQUE TO USE TO IDENTIFY VIRULENCE FACTORS? ................................. 23
5. VIRULENCE AND IMMUNE SYSTEM (Alex Speer) .......................................................................... 31
6. VIRULENCE AND METABOLISM (Jurgen R. Haanstra) ................................................................... 37
7. VIRULENCE AND INTRACELLULAR ROUTING (C. Kuijl) ................................................................... 43
8. VIRULENCE AND GENE REGULATION ............................................................................................ 51
9. PATHOGENS & GUT MICROFLORA (Wiep Klaas Smits) ................................................................. 60
10. MOLECULAR DETECTION OF PATHOGENS (Lia van der Hoek) .................................................... 67
11. VACCINE DEVELOPMENT (Peter van der Ley) ............................................................................. 72
1
,1. WHAT IS A PATHOGEN
• Gut microflora
o Normal microflora at the wrong place
o Abnormalities in host defense
• Herpes virus
o Herpes simplex encephalitis (HSE)
• Abnormalities in host defense: antibiotics
• Tuberculosis
o Tuberculosis infection cycle
o Models for analysis
• Epstein-Barr virus (EBV)
A pathogen is a microbiological agent that causes disease or illness to its host. The term pathogen
is derived from the Greek παθογένεια, "that which produces pain/suffering“. Pathogens can be
viruses, bacteria, protozoa, yeasts/fungi and worms.
Difference between microflora and real pathogens: Normal microflora’s pathogens are endogenous
and beneficial for the host, while real pathogens are exogenous and pathogenic for the host. The
major part of the microflora is on the colon. In the skin there are a lot of bacteria with different
compositions.
GUT MICROFLORA
(=Microbiota) There are more than 500 species, such as Firmicutes sp. (Clostridium species) or
Bacteroidites sp. (Bacteroides fragilis, Bacteroides thetaiotaomicron). Gnotobiotic animals are germ-
free. But when you use these, a) you need to use 30% more calories, because microbiota is a source
of metabolites, such as short-chain fatty acids (SCFAs). The food uptake without microbiota is
decreased. B) Also, these animals have less vascularization and poor development of villi. c) They
also have underdeveloped mucosal immune system.
For example, gut anaerobes (Bacteroides thetaiotaomicron) degrade and ferment
indigestible plant material → release of small simplified carbohydrates (butyric acid), and these
smaller carbohydrates can be used. Also, Gut microflora induce immune response, including
production of antimicrobial peptides.
2
, Paneth cells: Highly specialized secretory epithelial cells located in the small intestinal crypts of
Lieberkühn.
DISEASES BY NORMAL MICROFLORA
A) Normal microflora at the wrong place
• Damage to epithelium: B. fragilis. Damage to colon epithelium (spontaneous, after surgery)
results in the infiltration of gut microflora in peritoneum (serosa membrane in the
abdominal cavity). Coinfection E. coli and B. fragilis synergistic abscess formation, high
morbidity and mortality
• New sites for normal microflora: E. coli. Urinary tract infections, which can result in bladder
and kidney infections (cystitis and pyelonephritis). Cystitis happens mainly in women
because close proximity of urethra and anus.
• Foreign bodies (due to surgical implants): Staphylococcus epidermidis
• Wrong host: E. coli O157 (Old nomenclature, based on antibodies). Different mammals have
different microbiota. Examples:
o Outbreak of E. coli O157:H7 Apple juice. The factory where they made it was
clean. Apple packing houses were not ideal, though, cause water for apple washing
changed only one a day. The fam was hosted by a deer population! So when they
took apples from the floor, these weren’t OK. This strain is not problematic in deer
but it is in humans
o Salmonella that lives in the frog’s skin. But that microorganism in humans is not
good. After “The princess and the frog” movie, 50 children (mainly <10 year old girls)
kissed frogs and had salmonella infections.
o When humans are infected with Capnocytophaga canimorsus when they are bite
by dogs/cats (it belongs to its normal oral flora). This infection causes sepsis.
B) Abnormalities in host defense
• Genetic defect: SCID (Severe Combined Immune Deficiency). Boy in the bubble: Not working
B and T cells. Now we can treat the disease. Of course if you have low good antibodies you
get infections of normal microflora.
3
