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Samenvatting Microbes And Infection
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Summary microbes and infectionLecture 1a: General introduction to infectious diseases
Antoni van Leeuwenhoek discovered the microscope and was able to see microorganisms.
Some were able to cause disease. Paul Ehrlich discovered a drug against spirochetes that
caused syphilis. John Enders cultured viruses and developed products for vaccines:
eradication of smallpox (see picture). AIDS was discovered by Françoise Barré-Sinoussi:
quickest discovery of origin at that time. Nowadays diseases are identified within 30 days:
e.g. COVID-19. Hard to prevent spreading because it not necessarily causes disease.
Vaccines were quickly developed.
Questions regarding infectious disease patient
- Is it an infection, or is it something else?
- Where is the infection?
- Which microbe is causing the infection and how does it cause disease?
- Should it be treated, and what is the best treatment?
Indications of an infection are fever, diarrhea, rash, chills, enlarged lymph nodes, etc.
Different microorganisms
There are a lot of different microorganisms, with their
own characteristics. The sizes are very diverse: viruses
can only be seen with electron microscopes, bacteria
are bigger, just like fungi and protozoa. Ectoparasites
and worms can become quite large.
Bacteria
Bacteria can have all kinds of shapes: spheres (cocci)
like diplococci, streptococci, tetrad, staphylococci,
and sarcina. They can be rods (bacilli), like chain of bacilli, flagellate rods, and spore formers, or spirals, like
vibrios, spirilla, and spirochaetes. Bacteria are unicellular prokaryotes, without nuclear membrane,
mitochondria, Golgi, and ER. It reproduces by asexual division. Thousands of bacterial species inhabit the
human body: human microbiome.
Bacteria can be gram negative: a plasma membrane and an outer
membrane (with LPS), with a layer of peptidoglycan in the middle.
Bacteria can be gram positive: a plasma membrane and a very thick
peptidoglycan layer.
Gram staining: samples are fixated on a glass and treated with crystal violet, then
iodine treatment, then decolorization, and a counter stain. The peptidoglycan layer
cannot be decolorized, and therefore gram positive bacteria color purple
(Actinomyces, Clostridium, Listeria, S. aureus, Coagulase negative Staphylococcus,
Streptococcus, Enterococcus), and gram negative bacteria color pink (H. influenzae,
E.coli, C. jejuni, Fusobacteria).
Bacteria are named based on their Genus (capital letter) and species, like Staphylococcus aureus.
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,Detection of bacteria is done using microscopy, cultures, susceptibility testing (antibiogram), MALDI-TOF,
serology (antigen-antibody) and nucleic acid amplification test (PCR).
Bacteria can cause disease by release of toxins, invasion of normally sterile tissues or fluids, virulence
factors that cause damage, or inflammation (immune response). A big problem based on bacteria is their
ability to become resistant: unfinished treatment, over prescribing, use in animals, poor infection control,
lack of hygiene and lack of new antibiotics.
Viruses
Viruses are quite simple: protein capsid with DNA or RNA in it. Sometimes there is
an envelope. To replicate, they need to infect cells and use the host cell
mechanisms to replicate and produce proteins. Viruses self-assemble from
preformed components. Examples of viruses are the coronavirus, bacteriophages,
the Ebola virus, influenza virus, smallpox, monkeypox, Orf virus, etc.
Viruses can be classified based on their genome: RNA or DNA, based on their capsid: helical or icosahedral,
and based on their envelope: present or not. There is a wide variety, also in the infection patterns they
cause: acute infection, chronic infection, latent infection, slow infection etc. Respiratory viruses were
seasonal before COVID pandemic.
Diagnostic tests of COVID-19 by viral RNA detection (PCR), viral antigen tests (self-test) or look at the
antibodies (this is based on immune response after infection or after vaccination).
Fungi
Fungi have a more complex structure compared with bacteria. They are
eukaryotes, so they contain a nucleus, mitochondria, Golgi system and ER.
We use fungi for bread, beer, wine, cheese, and mushrooms. They can be
unicellular (yeast) or multicellular (mold). Fungi are dimorphic: mold at
room temperature, spherical form in the body.
Parasites
Parasites are the most complex microorganisms and can use life cycles of different hosts. They are
eukaryotic as well and can be both unicellular and multicellular. They have a wide range in size. Protozoa
(one-celled) can be seen in the microscope and are present in the intestine (fecal-
oral route) or in the blood or tissue (arthropod vector like mosquito). Helminths
are larger and can be free-living or parasitic: flatworms, thorny-headed worms, or
roundworms. Ectoparasites (like lice) attach or burrow into the skin and remain
there for a longer time. They can be important vectors for different pathogens. Loa
Loa is transmitted by flies and form worms in the body, even in the eyes.
Epidemiology and defense
Epidemiology studies and analyses distribution, patterns and determinants of health and disease
conditions in defined population. It shapes policy decisions. Incubation times are different for all
microorganisms. Prevalence is all the patients present at a certain time, incidence describes the new cases.
R0 is the number of people a single infected person can transmit the disease to R0 > 1: virus survival.
The immune system removes infections. There are protection mechanisms at contact places: barriers in
eye, skin, urinary tract, respiratory tract, and GI tract. The immune system protects from pathogens but
can lead to immunopathology if it is out of balance: sometimes suppression increases survival. First the
innate response and then the adaptive response. Symptoms are caused by the microbe and immune
response.
2
,Lecture 1b: Bacteriology
The biological definition of life depends on an independent metabolism and independent replication. The
tree of life contains archaea, bacteria, and eukaryotes. They all have a common
ancestor cell. The human microbiota consists of 500-1000 species.
Prokaryotes have circular DNA, a cell wall, reproduce
asexually, have no nucleus, mitochondria, Golgi, or ER.
Eukaryotes have a nucleus, mitochondria, Golgi, ER, no
cell wall but only a membrane, etc.
Gram positive vs gram negative
- Gram positive bacteria have a plasma membrane with a thick layer of peptidoglycan. Some gram positive
bacteria can form spores in times of stress to let genetic material survive: a septum is formed at the edge
of the cell after which the spore is engulfed in the mother cell. When the mother cell dies, the spore is
released. Dipicolinic acid helps dehydration of the spore to preserve DNA by prevention of reactions
- Gram negative bacteria have two membranes: a plasma membrane and an outer membrane with a
peptidoglycan layer in between. Sometimes they have pili. Gram negative bacteria have LPS on the outer
membrane, which is an endotoxin that can lead to sepsis.
Gram staining: crystal violet (binds peptidoglycan), then iodine, decolorizer (removes purple stain from
gram negative bacteria by making holes), and safranin red (counter stain of the gram negatives). So, gram
positive bacteria become purple, gram negative bacteria become pink.
Peptidoglycan
Peptidoglycan consists of NAG and NAM, which contains a
pentapeptide of which the last two amino acids are d-alanine.
This can be used for crosslinking. Peptidoglycan is synthesized
by 3 steps: NAM/NAG synthesis, transfer over the membrane
and elongation (using bactoprenol) and peptide crosslinking
which is catalyzed by transpeptidases (PBP). Antibiotics use
these mechanisms: NAM/NAG synthesis can be inhibited by fosfomycin, D-ala D-ala
is a target of vancomycin, and transpeptidases are targeted by penicillin and other beta-lactams.
Bacterial cell division
Cell division requires growth and extension of cell wall components. A septum is produced to divide the
daughter cells. When there is incomplete cleavage, bacteria can remain linked, forming
chains (streptococci) or clusters (staphylococci).
Metabolism
Anabolism requires energy to build and catabolism releases energy. An example is
glycolysis, where glucose is turned into pyruvate, and in the case of oxygen, it is turned
into acetyl-CoA and follows the TCA cycle to generate ATP. NADH is also formed, leading to
ATP by going through the electron transport chain and pumping protons from cytoplasm to
periplasm. Without oxygen, fermentation occurs, leading to acid products and less ATP.
Evolution
Evolution in bacteria can occur through mutations and horizontal gene transfer: transformation (foreign
DNA in own DNA after lysis), conjugation (plasmid DNA or genomic DNA obtained through sex pilus),
transduction (bacteriophages with DNA infect cells), or transposition (jumping DNA pieces in genome).
Through these mechanisms, new genes and therefore new characteristics are obtained.
3
, Lecture 2: Innate and adaptive immune responses to bacteria and viruses
Before the immune response even must take place, there are
several barriers that prevent infection. If there is infection after all,
first the innate immune system reacts with a very broad response. If
this is not sufficient, the adaptive immunity helps through antigen
presentation, making it more specific. So, there are differences in
specificity, diversity, memory, secreted proteins, and used cells.
Responses to bacterial infections
Before the immune system can have an effect, there must be
recognition/sensing of the microorganism. After this, the innate immune system gets activated. When this
is not enough, the adaptive immune system comes to help.
Recognition
Bacteria contain certain patterns that makes them easy to
recognize by the immune system: PAMPs (pathogen-
associated molecular patterns). Examples are pilin,
proteins with N-formyl methionine, flagellin, DNA with
unmethylated CpG motives, and cell wall components.
These are sensed by receptors, for example signaling receptors (TLRs, NLRs, CDSs,
activating signaling cascades) or endocytotic receptors (C-type lectin-like receptors,
scavenger receptors, N-formyl receptors, lead to endocytosis)
Innate immunity
The main parts of the innate immunity are the complement system, inflammation, and the
phagocytes that migrate to the side of infection, ingest foreign particles, and present the
peptides to T cells.
• Phagocytosis is often done by macrophages. When microbes are taken up after
recognition with TLRs, they end up in a phagosome, which is fused with a lysosome to
a phagolysosome. Now the microbe can be broken down by ROS, NO and enzymes.
• The complement system has three different possibilities for initiation: classical
pathway (through microbe binding to antibodies), alternative pathway (binding other
proteins) or the lectin pathway (mannose on the microbe
binds to lectin). This leads to formation of complement
proteins: C3a and C5a cause inflammation. C3b causes
opsonization and phagocytosis. The membrane attack
complex is formed that leads to lysis.
• Inflammation occurs through secretion of inflammatory
cytokines, produced by macrophages, mast cells, endo- and
epithelial cells, and T cells. Examples are TNF, IL-1, and IL-6. They have local effects to increase
permeability and attract leukocytes. Systemic effects are fever, production of acute phase proteins,
and leukocyte production by the bone marrow.
Adaptive immunity
The main players of the adaptive immunity are the B cells that secrete
antibodies, the CD4 helper T cells, and the CD8 cytotoxic T cells.
• Antibody-mediated immunity mainly targets the components of
the cell wall or capsule. There is neutralization, opsonization, Fc
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