Immunology And Infection

Question 1

What are viruses?

Answer 1

They are not cells in their own right. They are obligate parasites that show host specificity, but can infect almost all other forms of life, including bacteria.

Question 2

How do viruses replicate?

Answer 2

Contain RNA or DNA as genetic material, allowing them to replicate using host-cell nuclear synthetic machinery. They then divide by budding out of host cell (cytolysis).

Question 3

What are the 4 routes of infection for viruses?

Answer 3

1) Faecal-oral (e.g. polio virus)
2) Airborne (e.g. small pox/ variola virus)
3) Insect vectors
4) Blood borne (e.g. HIV/AIDS, Hepatitis B/C)

Question 4

Outline the differences between prokaryotes and eukaryotes

Answer 4

Prokaryotes do not have internal membranes (photosynthetic bacteria are an exception), whereas eukaryotes have internal membranes that define organelles (e.g. nucleus, ER, mitochondria). Prokaryotes have a single copy of a chromosome (haploid), but eukaryotes can be haploid or diploid.
The cytoskeleton of prokaryotes is poorly defined, but that of eukaryotes is developed. Prokaryote cell wall contains peptidoglycan and they divide by binary fission exclusively.

Question 5

Outline bacterial motility/structure

Answer 5

A bacterial cell contains:

1) Pili
2) Capsule
3) Peptidoglycan cell wall
4) Plasma membrane
5) Nucleoid (DNA)
6) Cytoplasm
7) Ribosomes
8) Flagellum

Question 6

What is Shigella?

Answer 6

The Shigella species has an infectious dose of 10-100 bacteria. Its route of infection is faecal-oral, and spreads cell to cell using the host’s actin.

Question 7

What is Neisseria meningitidis?

Answer 7

This is a community acquired bacteria with multiple serotypes (distinct variations). Its colonisation rate is high, having infected 20% of the human population. It is the common cause of meningitis in adults and children (Streptococcus agalactiae is the most common cause in baby’s >3 months) Common serotypes include:

1) Septicaemia: a 10% case fatality due to its rapid progression, causing septic shock and severe inflammatory response.
2) Meningitis which causes cerebrospinal fluid leakage.

Question 8

What are hospital acquired (nosocomial) infections?

Answer 8

These are infections originating in a hospital. Common bacteria include: Clostridium difficile and Staphylococcus aureus, which is methicillin resistant.

Question 9

How is Mycobacterium tuberculosis detected?

Answer 9

1) Conventional chest X ray scan

2) High resolution PET-CT scan using 18F - fluorodeoxyglucose (FDG)

Question 10

What resources are needed to better treat infectious disease?

Answer 10

Effective treatment requires knowledge of the causative agent, its source and means of transmission (problem of Zoonotic infections), how they cause damage and how the human body reacts. Therefore there is a need for:

1) New drugs to combat anti-microbial resistance and shorten treatment
2) Better vaccines for adult population in high burden countries
3) Better tools for early diagnosis

Question 11

How do bacteria and viruses evolve so quickly?

Answer 11

Although bacteria and viruses have similar point mutation rates to humans (~10-8 for bacteria and humans, ~10-4 for viruses), they accumulate more mutations due to their generation time being far quicker (a matter of hours or day for bacteria and viruses, 26 years for humans).

Question 12

What are fungi?

Answer 12

These are eukaryotic cells that cause cutaneous, mucosal and/or systemic mycoses. They exist as yeasts, filaments or both. Yeasts bud or divide; filaments (hyphae) have cross walls or septa. Candida albicans is a common fungal infection.

Question 13

What are Protozoa?

Answer 13

These are unicellular eukaryotic organisms, that include intestinal, blood and tissue parasites. They replicate in the host by binary fission or by formation of trophozoites inside a cell. ,any have a complicated life cycle involving two hosts. Infection is acquired by ingestion or through a vector (e.g. insect or invertebrate vector). Common diseases caused by Protozoa include Malaria and Leishmaniasis.

Question 14

What is malaria?

Answer 14

It is a family of Plasmodium species that infects via a mosquito vector. They are blood and tissue parasite that form trophozoites inside a cell.

Question 15

What is leishmaniasis?

Answer 15

It is a cutaneous and visceral disease that infects via a sandfly vector. The Leishmania species are blood and tissue parasites that form trophozoites inside a cell.

Question 16

What are helminth worms?

Answer 16

These are metazoa with eukaryotic cells. They multi-cellular, making them visible to the naked eye and have life cycles outside the human host. Common ones include roundworms (e.g. Ascaris), flatworms (flukes) and tapeworms. Infection is acquired via faecal-oral transmission.

Question 17

Why is the diagnosis of infections important?

Answer 17

Many microorganisms can cause the same type of infection (e.g pneumonia can be caused by viruses, bacteria and fungi). Therefore diagnosis is important for: improving the effectiveness of treatment, avoiding long term complications, identifying and preventing outbreaks and preventing the overuse or misuse of treatments

Question 18

What are the 3 types of bacteriological tests?

Answer 18

1) Microscopy (e.g. gram stain): what type of bacteria
2) Culture (e.g. Hemolysis test, Lactose test, Catalase test and Coagulase test)
3) Sensitivities (e.g. Disk diffusion, MICs and Break-points)

Question 19

What is gram staining?

Answer 19

Gram staining identifies two groups of bacteria based on the physical and chemical composition of their cell wall.
•Gram-Negative = 2 membranes (outer and cytoplasmic) and thin peptidoglycan cell wall
•Gram-Positive = 1 (cytoplasmic) membrane and a thick peptidoglycan cell wall

Question 20

Outline the steps of gram staining

Answer 20

1) Crystal violet is applied
2) Iodine (mordant) is applied
3) Alcohol wash (for decolorisation) is applied
4) Safranin (counterstain) is applied

Question 21

What is bacterial morphology?

Answer 21

Bacteria can also be classified based on their morphology. The
basic morphologies are:
•Spheres = coccus
•Round ended cylinders = bacillus

Question 22

What is hemolytic activity testing?

Answer 22

Growth on complex medium containing 5% sheep red blood cells, that tests capacity of microorganism to produce hemolysins (enzymes that damage red blood cells).
•Gamma-hemolysis = no hemolysis (no zone)
•Alpha-hemolysis = partial hemolysis (opaque zone)
•Beta-hemolysis = complete hemolysis (transparent zone)

Question 23

What is hemolytic activity testing useful for differentiation?

Answer 23

It is useful for differentiating: Staphylococcus, Streptococcus
and Enterococcus. It is also useful for the further classification of gram-positive bacterial species.

Question 24

Outline the steps of hemolytic activity testing

Answer 24

1) Pick a bacterial colony
2) Streak out the bacterial colony onto blood agar
3) Assess hemolysis after overnight incubation

Question 25

What is lactose fermentation testing?

Answer 25

Growth on MacConkey agar containing bile salts, crystal violet
and lactose, that tests the capacity of a microorganism to ferment lactose. It is also useful for differentiating gram-negative bacteria.
•No growth = bile salts inhibit growth of Gram-positives.
•Lactose fermenting = bacteria produce acid during lactose fermentation.
•Lactose non-fermenting = bacteria do not ferment lactose.

Question 26

Outline the steps of lactose fermentation testing

Answer 26

1) Pick a bacterial colony
2) Streak out the bacterial colony onto MacConkey agar
3) Assess lactose fermentation after overnight incubation

Question 27

What is catalase testing?

Answer 27

This test determines whether a bacteria produces catalase, an enzyme that catalyses breakdown of hydrogen peroxide (H2O2) into O2 and H20. It can discriminate staphylococci (produce catalase) and streptococci (do not produce catalase). It is also useful for differentiating gram-positive bacteria.
•Catalase + = O2 bubbles.
•Catalase - = no O2 bubbles.

Question 28

Outline the steps of catalase testing

Answer 28

1) Bacteria is applied onto a glass slide
2) 2H202 (hydrogen peroxide) is then applied
3) Generation of bubbles is then observed

Question 29

What is coagulase testing?

Answer 29

This test determines whether a bacteria produces coagulase, an enzyme that cross-links fibrinogen in plasma to form a clot on the bacterial surface. It can discriminate S. aureus (produce coagulase) and other staphylococci (do not produce coagulase).
•Coagulase + = clumps.
•Coagulase - = no clumps.

Question 30

Outline the steps of coagulase testing

Answer 30

1) Bacteria is applied onto a glass slide
2) Plasma is then also applied
3) The bacteria is incubated for 15 seconds and gently rotated
4) Generation of clumps is then observed

Question 31

What are hypersensitivity reactions?

Answer 31

These reactions require the immune system to have become pre-sensitized, and thus have existing adaptive immunological memory. They are however distinct in which elements of the adaptive immune response over- or inappropriately react. The “rate-limiting molecule” in all hypersensitivity reactions is antigen, as the amount of antigen and the rate at which the immune system can clear it, dictates the scale and length of time that a hypersensitivity reaction occurs for.

Question 32

What is Type 1 hypersensitivity?

Answer 32

This is sometimes called immediate or anaphylactic hypersensitivity, and is an allergic reaction provoked by re-exposure to a specific type of antigen referred to as an allergen (e.g. asthma, allergic rhinitis and atopic dermatitis). Due to the pre-synthesised nature of rapidly produced immune cells (e.g. mast cells, etc) these reactions require only a small amount of antigen to elicit a reaction.

Question 33

What mediates Type 1 hypersensitivity?

Answer 33

Mechanistically type 1 responses are mediated by antigen specific IgE antibodies. Non-allergic individuals predominantly only make IgE in response to parasitic infections or very potent venoms. Individuals with allergies however produce antibodies against common multivalent (antigen has multiple sites at which an antibody can attach or antigen can be produced) environmental antigens (allergens).

Question 34

What are skin prick tests?

Answer 34

These tests expose the skin to small amounts of allergen, and are often used to diagnosis allergy.

Question 35

What is “wheel-and-flare”?

Answer 35

This describes the inflamed, raised tissue often seen in allergic reactions.

Question 36

What is the result of the sensitization of the immune response to allergens?

Answer 36

The end result, is the generation of type 2 helper CD4 T cells and B cell helper follicular CD4 T cells which produce the type 2 cytokines IL-4 and IL-13; when these act on B cells they can promote B cell to switch to producing antigen specific IgE.

Question 37

How does IgE differ from other antibodies?

Answer 37

Unlike other antibodies IgE is very rarely found in the circulation, even in allergic individuals. This is because, once produced IgE is rapidly bound to the surface of innate immune cells, especially mast cells (released as progenitor from bone marrow and contain many granules) and basophils. These granulocytic cells express a high affinity IgE receptor, Fc epsilon receptor I (FcεRI).

Question 38

What happens if an allergen is encountered by cell bound IgE?

Answer 38

This results in rapid crosslinking and the degranulation/activation of the mast cell or basophil. It happens much faster, and across a much broader site, even a low antigen levels, than is seen during normal inflammation based activation of mast cell. Mast cells are widely distributed throughout the body, but most notably connective tissue (under the skin) and in association with epithelial mucosae (intestinal and respiratory epithelia). Mast cells contain several inflammatory mediators tor’s including histamines and leukotrienes. These act principally on blood vessels and smooth muscle, which express specific histamine receptors (GPCRs).

Question 39

What are the end products of type 1 hypersensitivity reactions?

Answer 39

The end products are:

1) The release of histamine - cause dilatation of vessels in connective tissues, with increased blood flow to the surface of the skin and increased movement of fluid out of the blood stream (oedema). Also causes constriction of the bronchi, resulting in breathing difficulties. Can be treated with anti-histamines, corticosteroids or bronchodilators.
2) A host of cytokines that can recruit other cells and promote further Th2 differentiation
3) Highly active smooth muscle contracting molecules such as leukotrienes (produced by mast cells) and prostaglandins, these narrow the airways of asthmatics.

Question 40

Outline the type 1 sensitivity phases of response

Answer 40

The phases of response is caused by the variety of molecules released during type 1 responses:

1) The early phase::a result of bioactive small molecules produced directly by mast cells, occurs within minutes of allergen exposure.
2) A later response: often seen within a few hours is the result of the recruitment of early inflammatory cells such as neutrophils.
3) :A third phase (late response): often peaks 3-4 days after exposure where high frequencies of eosinophils are recruited and Th2 cells are present.

Patients with moderate respiratory or cardiovascular compromise should be observed for 8-10 hours hours before discharge. This is due to biphasic anaphylaxis, as occasionally symptoms return with a few hours of the initial reaction

Question 41

What is type 2 hypersensitivity?

Answer 41

It is otherwise known as antibody-mediated cytotoxic hypersensitivity, and involves the destruction of cells by IgG or IgM antibody bound to antigens present on the surface of the cells.

Question 42

What are examples of type 2 hypersensitivity?

Answer 42

1) Mismatched blood transfusion
2) Haemolytic disease of newborns
3) Immune thrombocytopenia
4) Graves disease

Question 43

Outline both ways that type 2 hypersensitivity is sensitised

Answer 43

1) Exposure to a foreign antigen

2) The aberrant response to a self-antigen resulting in IgGs or IgMs that recognise cell surface structures.

Question 44

Outline the mechanisms by which IgGs or IgMs can lead to disease

Answer 44

1) Anti-receptor activity – blocking or activating its function
2) Antibody dependent cell-mediated cytotoxicity (abbreviated to ADCC)
3) Classical activation of the complement cascade

Question 45

What is the complement cascade in type 2 hypersensitivity?

Answer 45

The complement cascade, is a complex process by which antibody on the surface of cells is recognised by the complement components, ultimately leading to the formation of the membrane attack complex (MAC) in the surface of the cell, and cell death due to loss of osmotic integrity. Activation of the classical complement pathway also however results in inflammation, opsonisation and recruitment and activation of immune cells.

Question 46

What is Antibody dependent cell-mediated cytotoxicity (ADCC)

Answer 46

Antibody-antigen complexes on the surface of cells are bound by Fc receptors (which bind the constant, not antigen specific, tail regions of IgM and IgG antibodies) expressed by cells such as granulocytes and NK cells lead to directed lysis of the target cell, but also the release of inflammatory mediators, chemokines and cytokines.

Question 47

What is type 3 hypersensitivity?

Answer 47

It is sometimes known as immune complex driven disease. Immune complexes are non-cell bound antigen-antibody complexes which are normally cleared through the activity of the immune system. If, however, the immune complexes cannot be efficiently cleared – for example if they are the result of antibodies reacting against self-antigens such as nuclear DNA– the immune complexes end up being deposited in the blood vessel walls and tissues, promoting inflammation and tissue damage. These reactions require chronic antigen presence, which prevents the natural clearance of immune complexes and leads these to build up and cause inflammation. The inflammatory response is mediated by massive infiltration of neutrophils.

Question 48

What are the symptoms of type 3 hypersensitivity?

Answer 48

1) Fever,
2) Rashes,
3) Joint pain and protein in the urine

Question 49

What 3 main autoimmune diseases are involve type 3 hypersensitivity reactions

Answer 49

1) Rheumatoid arthritis: caused by low doses of self-antigen and anti-IgG antibodies forming immune complexes within the joints.
2) Multiple sclerosis
3) Systemic lupus erythematosus (SLE)
4) Vasculitis
5) Glomerulonephritis: results from the deposition of free floating immune complexes in the basement membrane of kidneys, and the generation of,oval inflammation. This is an uneven process, partly due to the cellular makeup of the basement membrane, partly because immune complexes drive local sit3s of inflammation and partly due to availability of antigen.

Question 50

Are all diseases associated with type 3 hypersensitivity autoimmune in origin?

Answer 50

While many diseases associated with type III hypersensitivity are auto-immune in origin, as with all antibody mediated diseases, they can also result from encounters with foreign antigens. For instance persistent infections such as hepatitis virus infections can result in immune complex deposition, as can exposure to freely circulating foreign antigens such as drugs.

Question 51

What is serum sickness?

Answer 51

A person may be given anti-serum (antibodies specific to proteins) to neutralise venom. These are foreign proteins, and while they neutralize the venom, human bodies will react against them to produce antibodies that recognise the anti-venom antibodies. This process may take several weeks, and does not represent a problem as the anti-serum and venom will be long cleared. If the person needs that same anti-serum again, these antibodies will rapidly recognise the anti-serum and drive rapid inflammation.

Question 52

What is type 4 hypersensitivity?

Answer 52

This is also known as delayed-type or T cell mediated hypersensitivity, is primarily initiated by T cells. This is achieved when a sensitization phase occurs where antigen is presented to naïve T cells by antigen presenting dendritic cells, resulting in the generation of antigen specific memory T cells, a process that takes several weeks. On subsequent exposure these memory T cells respond by promoting inflammation at the site of exposure. However because the memory T cell response (which requires recruitment and expansion) is slightly slower than antibody mediated memory there is often a delay between exposure and response, with peak responses often seen 2-3 days after inflammation. The sensitise T cells also release cytokines that activate macrophages or cytotoxic T cells, which mediate direct cellular damage.

Question 53

What is the most common example of type 4 hypersensitivity?

Answer 53

This is contact dermatitis , caused by exposure to poison ivy, where a small molecule called urushiol acts as a hapten (and binds to proteins in the skin), drives a T helper 1 response (but due to its small nature rarely results in antibody production). On re-exposure these memory cells produce cytokines such as IFN-gamma which promote the pro-inflammatory activation of macrophages resulting in swelling and oedema, and the formation of blister like lesions.

Question 54

What are other examples of type 4 hypersensitivity?

Answer 54

Other contact antigens such as nickel salts or hair dyes can also drive Th1 based inflammation, as can many intracellular pathogens such measles virus and Mycobacterium tuberculosis.

Question 55

Is type 4 hypersensitivity limited to memory Th1 cell responses?

Answer 55

Type IV reactions are not limited to memory Th1 cell responses, as any memory T cell capable of driving an immune overreaction. For instance in asthma, allergens can cause overreaction of T helper 2 cells which produce soluble mediators that that promote bronchoconstriction. While CD8 T cells can lead to inflammation and rejection of a tissue graft by directly killing transplanted cells.

Question 56

What are haptens?

Answer 56

These are small molecules that on their own don’t form antigens, but do when bound to hosts. Examples include penicillin and urushiol (the causative molecule in poison ivy).

Question 57

What is Prontosil?

Answer 57

It was the first example of a sulphonamide antibiotic. It was bacteriostatic (stops bacteria from reproducing) and synthetic. Examples include sulpha-methoxazole and it is sometimes used together with Trimethoprim (co-trimoxazole). Prontosil is used to treat UTIs, RTIs, bacteraemia and prophylaxis for HIV+ individuals, and has become more common due to resistance to other antimicrobials, despite some host toxicity. Prontosil was also found to be effective against puerperal sepsis (childbed fever), caused primarily by S. pyogenes. However, Prontosil was only effective against Gram-positive bacteria.

Question 58

What are antibiotics?

Answer 58

An antibiotic is an antimicrobial agent produced by a microorganism that kills or inhibits other microorganisms. Most antibiotics in use today are produced by soil-dwelling fungi (Penicillium and Cephalosporium) or bacteria (Streptomyces and Bacillus). However, antibiotics commonly used today encompass a range of natural, semi-synthetic and synthetic chemicals with antimicrobial activity. After the discovery of Penicillin, ,any other antibiotics were identified, which enabled advances in surgery, cancer chemotherapy, survival of pre-term infants, survival of trauma, survival of those with compromised immune function (e.g. those receiving an organ transplantation). Unfortunately progress in antibiotic discovery has slowed dramatically in recent years.

Question 59

What are the 4 types of antibiotics?

Answer 59

1) Antimicrobial – chemical that selectively kills or inhibits microbes (bacteria, fungi, viruses).
2) Bactericidal – kills bacteria.
3) Bacteriostatic – stops bacteria growing.
5) Antiseptic – chemical that kills or inhibits microbes that is usually used topically to prevent infection.

Question 60

What are the effects of antibiotic resistance?

Answer 60

The emergence and dissemination of antibiotic resistant bacteria threatens many advances in medicine, due to:

1) Increased mortality
2) Increased morbidity
3) Increased cost (use of expensive therapy - newer drugs)
4) Increased time to gain access to effective therapy
5) Requirement for additional approaches (e.g. surgery)
6) Use of more toxic drugs (e.g. vancomycin)
7) Use of less effective ‘second choice’ antibiotics

Question 61

What are Aminoglycosides?

Answer 61

These bactericidal antibiotics include Gentamicin and Streptomycin. They target protein synthesis (30S ribosomaml subunit), RNA proofreading and cause damage to cell membrane. Their toxicity has limited use, but resistance to other antibiotics has led to increasing use.

Question 62

What is Rifampcin?

Answer 62

This is a bactericidal antibiotic that targets RpoB subunit of RNA polymerase. However, spontaneous resistance of bacteria is frequent. The antibiotic makes secretions go orange/red, by affecting compliance.

Question 63

What is Vancomycin?

Answer 63

This is a bactericidal antibiotic that targets the Lipid II component of cell wall biosynthesis, as well as wall crosslinking via D-ala residues. Its toxicity has limited use, but bacterial resistance to other antibiotics has led to increasing use (e.g. against MRSA).

Question 64

What is Linezolid?

Answer 64

This is a bacteriostatic antibiotics that inhibits the initiation of protein synthesis by binding to the 50S rRNA subunit. It has a Gram-positive spectrum of activity.

Question 65

What is Daptomycin?

Answer 65

This is a bactericidal that targets bacterial cell membrane. However, its toxicity limits its dose. It has a Gram-positive spectrum of activity.

Question 66

What are Beta-lactams?

Answer 66

Examples of these antibiotics include penicillin and methicillin. They function by interfering with the synthesis of the peptidoglycan component of the bacterial cell wall. They do this by binding to penicillin-binding proteins, which catalyse a number of steps in the synthesis of peptidoglycan.

Question 67

What is selective toxicity?

Answer 67

This describes the fact that antibiotics can target many different bacterial processes, without affecting host processes. This is due to the large number of differences between mammals and bacteria, which result in multiple targets for antibiotic therapy:

1) Inhibition of cell wall synthesis: Penicillins, cephalosporins, bacitracin and vancomycin.
2) Inhibition of protein synthesis: Chloramphenicol, erythromycin, tetracyclines and streptomycin.
3) Inhibition of nucleic acid replication and transcription: Quinolones and rifampin.
4) Injury to plasma membrane: Polymyxin B.
5) Inhibition of synthesis of essential metabolites: Sulphanilamide and trimethoprim.

Question 68

What are Macrolides?

Answer 68

These antibiotics include erythromycin and azithromycin. They function by targeting 50S ribosomal subunit, preventing amino-acyl transfer and thus truncation of polypeptides. They target Gram-positive and some Gram-negative infections.

Question 69

What are Quinolones?

Answer 69

These are synthetic, bactericidal antibiotics, that target a broad spectrum of bacterial processes. They target DNA gyrase in Gram negative and topoisomerase IV in Gram positive bacteria.

Question 70

What misconceptions were there at the dawn of the antibiotic era?

Answer 70

1) Resistance against more than one class of antibiotics at the same time would not occur.
2) Horizontal gene transfer would not occur.
3) Resistant organisms would be significantly less ‘fit’ (sometimes true, sometimes not).

Question 71

At what point is bacterial resistance reached?

Answer 71

Bacteria resistance is achieved when breakpoint has been reached. This is the clinically achievable antibiotic concentration at which growth is no longer inhibited. The Minimal inhibitory concentration (MIC), is the lowest concentration of antibiotic required to inhibit growth.

Question 72

Outline the evolution of antibiotic resistance by natural selection

Answer 72

1) Bacterial population contains cells with antibiotic resistance to mutations/acquired DNA - possibly with a fitness cost (e.g. slow growth).
2) In the absence of resistance pressure (e.g. antibiotics) antibiotic resistant bacteria have no advantage, and may in fact be at a disadvantage.
—> This leads to low population of antibiotic resistant strains in the patient population.
3) In the presence of selection pressure (e.g. antibiotics) resistance mutants outcompete other bacteria.
—> This leads to high prevalence of antibiotic resistant strains in the patient population.

Question 73

Outline the 4 mechanisms by which antibiotic resistance occurs

Answer 73

1) Altered target site: Can arise via acquisition of alternative gene or a gene that encodes a target-modifying enzyme. Methicillin-resistant Staphylococcus aureus (MRSA) encodes an alternative PBP (PBP2a) with low affinity for beta-lactams. Streptococcus pneumoniae resistance to erythromycin occurs via the acquisition of the erm gene, which encodes an enzyme that methylates the AB target site in the 50S ribosomal subunit.
2) Inactivation of antibiotic: Enzymatic degradation or alteration, rendering antibiotic ineffective. Examples include beta-lactamase (bla) and chloramphenicol acetyl-transferase (cat). ESBL and NDM-1 are examples of broad-spectrum beta-lactamases (can degrade a wide range of beta-lactams, including newest).
3) Altered metabolism: Increased production of enzyme substrate can out-compete antibiotic inhibitor (e.g. increased production of PABA confers resistance to sulfonamides). Alternatively, bacteria switch to other metabolic pathways, reducing requirement for PABA.
4) Decreased drug accumulation: Reduced penetration of antibiotics into bacterial cell (permeability) and/or increased efflux of antibiotics out of the cell using pumps – drug does not reach concentration required to be effective.

Question 74

What are the 3 sources of antibiotic resistant genes?

Answer 74

1) Plasmids: extra-chromosomal circular DNA, often multiple copy. They often carry mutliple antibiotic resistant genes – selection for one maintains resistance to all.
2) Transposons: they integrate into chromosomal DNA, allowing the transfer of genes from plasmid to chromosome and vice versa.
3) Naked DNA: DNA from dead bacteria released into environment.

Question 75

How are antibiotic resistant genes spread?

Answer 75

Genes responsible for conferring antibiotic resistance can be shared between bacteria via several different mechanisms:

1) Transformation: the uptake of extracellular DNA
2) Conjugation: pilus-mediated DNA transfer
3) Transduction: phage-mediated DNA transfer

Question 76

What are the 5 non-genetic mechanisms of resistance/treatment failure?

Answer 76

1) Biofilm
2) Intracellular location
3) Slow growth
4) Spores
5) Persisters

Question 77

What are some reasons for treatment failure?

Answer 77

1) Inappropriate choice for organism
2) Poor penetration of antibiotic into target site
3) Inappropriate dose (half life)
4) Inappropriate administration (oral vs IV)
5) Presence of AB resistance within commensal flora e.g. secretion of beta-lactamase

Question 78

How do hospitals aid antibiotic resistance?

Answer 78

Large numbers of infected people receiving high doses of antibiotics - strong selective pressure for emergence/maintenance of antibiotic resistance.

Question 79

What are the risk factors of healthcare associated infections?

Answer 79

1) High number of ill people (immunosuppression)
2) Crowded wards
3) Presence of pathogens
4) Broken skin – surgical wound/IV catheter
5) Indwelling devices - intubation
6) Antibiotic therapy may suppress normal flora
8) Transmission by staff – contact with multiple patients

Question 80

How does antibiotic therapy impair commensal flora (microbiota)?

Answer 80

In healthy individual, commensal organisms can out-compete pathogen adhesion, metabolism and growth. Therefore, the pathogen cannot colonise at levels sufficient for infection. However, antibiotic therapy inadvertently destroys the commensal flora, allowing the overgrowth of the pathogen, due to a lack of competition. The pathogen can then produce toxins and damage host cells, leading to symptomatic infection that can be spread to other people.

Question 81

How can antibiotic resistance be overcome?

Answer 81

1) Modification of existing medications to e.g. Prevent cleavage (beta-lactams) or enhance efficacy. E.g. Methicillin.
2) Combinations of antibiotic + inhibitor, such as Co-amoxiclav (amoxicillin and clavulanic acid) for the Beta-lactamase pathway.

Question 82

What are fungi?

Answer 82

Fungi are eukaryote organisms that digest their food outside of the cell by secreting hydrolytic enzymes which can break down biopolymers to be absorbed for nutrition.

Question 83

What are the 3 main classes of condition in humans, caused by fungi?

Answer 83

1) Allergy – allergic reactions to fungal products e.g. allergic bronchopulmonary aspergillosis (ABPA)
2) Mycotoxicoses – ingestion of fungi and their toxic products e. g. aflatoxin
3) Mycoses – superficial, subcutaneous or systemic colonisation, invasion and destruction of human tissue. See image for their classification in releation to tissue location.

Question 84

How are mycoses classified?

Answer 84

They are classified by the level of tissue affected (e.g. deep mycoses = brain, heart, lungs, liver, spleen and kidneys).

Question 85

What are the target for antifungal therapy?

Answer 85

1) Cell membrane: fungi use principally ergosterol, instead of cholesterol
2) DNA synthesis: some compounds may be selectively activated by fungi, arresting DNA synthesis
3) Cell wall: unlike mammalian cells, fungi have a cell wall

Question 86

What are viruses?

Answer 86

Viruses are infectious obligate intracellular parasites, with a genome that comprises DNA or RNA. Within an appropriate host cell, the viral genome is replicated and directs the synthesis, by cellular systems, of more viral components and genomes. The components effect the transport of replicated viral genomes through the environment to new host cells.

Question 87

Outline the structure of viruses

Answer 87

All virus particles (virions) are small, between 10nm-1μm. Some variometer may have a symmetrical protein capsid (e.g. Adenovirus, Picornavirus and Calicivirus), some are non-enveloped, and some have lipid envelope derived from the host cell membrane. Some viruses, such as measles, are pleiomorphic, meaning that the have a variability of their size, shape and staining. However, the Ebola virus is a very typical shape of a virus.

Question 88

How are viruses named?

Answer 88

Viruses can be named in 5 different ways:

1) The disease: Poliovirus, Rabies
2) The person who discovered it: Epstein Barr virus
3) The place it was discovered: Coxsackievirus, Spanish Flu
4) The part of the body affected: Rhinovirus, Hepatitis virus
5) The way it was spread: Dengue, Influenza

Question 89

What are the differences between RNA and DNA viruses?

Answer 89

RNA viruses and retroviruses use their own polymerase to replicate, which lack proof reading capacity leading to high mutation rate. RNA viral genomes are limited in size due to inherent instability to RNA vs DNA. The largest RNA viruses are coronaviruses genome size around 30kb, whereas DNA viruses have genomes up to 100s kb. RNA viruses often use complex coding strategies to make more proteins than expected from a small RNA genome. In DNA viruses, there is plenty of room for accessory genes that can modify the host immune response. These genes are often lost in passage in culture.

Question 90

What is the function of segmented genomes in viruses?

Answer 90

Segmented genomes allow an additional easy form of recombination known as reassortment, but also impose more difficult packaging strategies. Influenza has 8 different RNA segments, rotavirus has 11.

Question 91

Outline the replication cycle of HIV-1

Answer 91

1) Fusion of HIV to the host cell surface.
2) HIV RNA, reverse transcriptase, integrase and other viral proteins enter the cell.
3) Viral DNA is formed by reverse transcription.
4) Viral DNA is transported across the nucleus and integrates into the host DNA.
5) The newly produced viral DNA is used as genomic RNA to make viral proteins.
6) New viral RNA and proteins move to the cell surface, and a new, immature HIV forms.
7) The virus matures by protease, releasing individual HIV proteins.

Question 92

How are viruses investigated in the laboratory?

Answer 92

The Cytopathic effect could be investigated. It is usually a result of the virus lysing the cell and could be due to shut down of host protein synthesis or accumulation of viral proteins. As a result of this, the viruses also form plaques in monocytes. A plaque assay can then be used to quantify how many virus particles are in a particular preparation of virus, by making dilutions and putting them onto mono layers of cells and after 2-3 days, counting the number of plaques formed.

Question 93

What is syncytia?

Answer 93

Some viruses don’t form plaques (e.g. HIV) but instead fuse all of the cells around them together, forming syncytium assay. The number of syncytia is also a measure of how many virus particles were in the sample of virus.

Question 94

How are viruses diagnosed?

Answer 94

1) Detecting viral genome PCR, RT-PCR (used to confirm aetiologic agent)
2) Detecting viral antigen IFA, ELISA
3) Detecting virus particles EM, HA
4) Detecting virus cytopathic effect in cultured cells: Virus isolation
5) Detecting antibodies to virus: Serology

Question 95

How can viruses be engineered?

Answer 95

Virus genomes are so small they can be synthesized. When introduced into permissive cells they direct synthesis of all their components, so new viruses are made de novo. This allows reverse genetics, the creation of viruses at will with engineered mutations in their genomes.

Question 96

Why are there only a few effective antivirals?

Answer 96

Selectivity and specificity are the problems, it is also difficult to distinguish between virus replicative mechanisms and host replicative processes. An acceptable therapeutic index is required.

Question 97

What do Anti-viral drugs target?

Answer 97

Many antiviral drugs target viral enzymes. Others act as nucleoside analogues (e.g. Acyclovir, Zidovudine, Remdesivir, Favipiravir), to inhibit or interfere with nucleic acid replication, but need to achieve some element of specificity for the viral polymerase.
Directly Acting Antivirals target specific viral factors. These are usually specific fog a particular virus and so their use must be coupled with appropriate diagnostics.

Question 98

What is Aclovir?

Answer 98

Aclovir is a modified nucleoside incorporated into DNA. Its lack of 3’ -OH prevents phosphodiester bond formation, causing chain termination.

Question 99

Outline the specificity of Aclovir

Answer 99

1) It is only activated inside virus infected cells.
2) Its specificity is largely due to phosphorylation of ACV to ACVMP by virus-encoded thymidine kinase.
3) It is subsequently phosphorylated to ACVTP by cellular enzymes.
4) It’s has a higher affinity for viral DNA polymerase than for host cell polymerase.
5) Resistance is rare but maps to thymidine kinase.

Question 100

What is Remdesivir?

Answer 100

It is an analogue of adenosine, that causes chain termination 3 nucleotides downstream of incorporation. It was Developed by Gilead for Hepatitis C and tested against Ebola, but didn’t meet the endpoint.

Question 101

What would be the qualities of the perfect antiviral against influenza?

Answer 101

It would target a unique and essential gene or function of the virus. It would also be both e effective against a range of influenza types and strains and easy to administer even to very sick patients. It would have few side effects for compliancy.

Question 102

What are Adamantes?

Answer 102

Either Amantidine or Rimantadine, they are cyclic amines with bulky, cagelike structures. They are formed as byproducts of petroleum refinement and are active against influenza A virus only. The M2 ion channel is the target for amantadine.

Question 103

Outline the resistance of viruses to amantadine

Answer 103

The resistance is caused by single point mutations (e.g. S31N). There is little cost to fitness, resistant virus virulent and transmissible. Most H3N2 circulating viruses are amantadine resistant. Many H5N1 strains are resistant due to overuse in poultry industry. Swine flu pH1N1 2009 emerged already carrying S31N.

Question 104

Why are mice with humanized immune systems creating new biological antiviral agents?

Answer 104

Because the antibodies these mice generate can be given to humans without inducing a species specific immune response against the therapy

Question 105

What are 3 major neuraminidase inhibitors?

Answer 105

1) Sialic acid
2) Relenza: Not as successful as Tamiflu because its chemistry means that the virus more readily acquires resistance.
3) Tamiflu

Question 106

Outline the mechanism of neuraminidase inhibitors

Answer 106

The crystal structure of the neuraminidase protein that allows rational antiviral drug designs. In normal neuraminidase function, the protein cleaves the receptor bound to the virion, allowing the virion to detach and continue viral replication. Neuraminidase inhibitors prevent this, thereby halting viral replication. All of the Influenza Viruses circulating in humans today are susceptible to NAIs.

Question 107

What is Baloxavir?

Answer 107

This is a new anti-influenza antiviral drug targeting polymerase, by inhibiting the PA endonuclease. It decreases virus shedding, allowing it to interrupt transmission. Resistance is conferred by single point mutations PA I38T. Mutation has been observed in H3N2 after treatment often in children

Question 108

What is Hepatitis C?

Answer 108

HCV is a hepatotropic flavivirus that was spread widely in the 1970s in blood products before screening was put in place. 170 million people are chronically infected and 4% will proceed to hepatocellular carcinoma. For more than 20 years therapy relied on interferon treatment with ribavirin, which was only effective in 50% of patients infected with the most common genotype 1 of the virus, and carried unpleasant side effects.

Question 109

What is passive immunotherapy?

Answer 109

Antibodies are taken from recovered individuals, or produced from immortalized B cells.

Question 110

What is Palivizumab?

Answer 110

It is a humanized monoclonal antibody against the F protein, used to treat Respiratory Syncytial Virus (RSV), in infants. It has reduced the RSV hospitalization by 55% and has improved monoclonal antibodies against the Pre-fusion RSV F protein in trials.

Question 111

What is adaptive immunity?

Answer 111

The absence of adaptive immunity results in inability to clear infections. It protects individuals from repeat infections with the same pathogen. However, it is not without costs, as evidenced by autoimmunity.

Question 112

What is immunological memory?

Answer 112

This is the basis for vaccines, as it occurs once the immune system has recognised and responded to an antigen. Memory responses are characterised by a more rapid and heightened immune reaction that serves to eliminate pathogens fast and prevent diseases, allowing a reduction in severity on re-exposure. Antigen-specific lymphocytes (B + T) are the cellular basis for the immunological response.

Question 113

What are the 2 types of adaptive immune response?

Answer 113

1) The ‘cell-mediated’ response (T cells) plays two roles, producing cytokines to help shape immune response (CD4) and killing infected cells (CD8).
2) The ‘humoral’ response (B cells): produces antibodies.

Both the cell mediated and humeral response lead to the production of “memory” cells.

Question 114

Define antigen

Answer 114

Molecules that act induce an adaptive immune response (mostly protein). They are effectively how the adaptive immune system sees pathogens.

Question 115

Define epitope

Answer 115

This is the region of an antigen which the receptor binds to. T cells recognise linear epitopes, in the context of major histocompatibility complex (MHC) and antibodies recognise structural epitopes.

Question 116

Outline antibody specificity

Answer 116

Humans can make billions of different antibody molecules, each with a distinct antigen binding site. Each antibody recognises its antigen with great specificity.

Question 117

Outline the clonal expansion of antibodies

Answer 117

Each lymphocyte bears a single, unique receptor. Interaction between a foreign molecule and that receptor leads to activation and clonal expansion. Differentiated effector cells of that lineage will bear the same receptor.

Question 118

Why is antigenic variability an issue?

Answer 118

Humans are exposed to an incredibly large amount of different microbes and other antigenic determinants, and the immune system must be able to respond to them all. However, as the adaptive immune system is exquisitely specific, a very large pool of cells with specific receptors are needed that can recognise the huge array of antigens.

Question 119

How does the adaptive immune system deal with antigenic variability?

Answer 119

To deal with antigenic diversity, the adaptive immune system encodes a massive repertoire of lymphocytes receptors. 1015 different antibody molecules alone can be generated. Each antibody is produced by a specific B lymphocyte expressing a specific BCR, this requires 1015 different genes. This would be impossible if 1 gene per antibody, as humans only have 25,000 genes total for all functions.

Question 120

How is antigen receptor variability generated?

Answer 120

Antigenic variability is generated by immunoglobulin gene rearrangement. Functional genes for antigen receptors do not exist until they are generated during lymphocyte development. Each BCR receptor chain (kappa, lambda and heavy chain genes) is encoded by separate multigene families on different chromosomes. During B cell maturation these gene segments are rearranged and brought together. In this way, immunoglobulin gene rearrangement generates the diversity of the lymphocyte repertoire

Question 121

What is the T cell receptor?

Answer 121

The T cell receptor is part of a complex of proteins on the cell surface. The variable region of the receptor is made by gene reassortment (1015 – 1020) and recognises antigen fragments presented by other cells in the context of MHC.

Question 122

What is the major histocompatibility complex (MHC)?

Answer 122

The Major Histocompatibility Complex (MHC) plays a central role in defining self and not self. It presents antigens to T cells and is critical in surgery and donor matching.

Question 123

What are the 2 types of MHC?

Answer 123

1) MHC class I: they are all nucleated cells, although at various levels, they have a single variable alpha chain plus a common beta-microglobulin.
2) MHC class II: normally only on “professional” antigen presenting cells, they have 2 chains - alpha and beta.

Question 124

How is the MHC gene expressed?

Answer 124

MHC is encoded by HLA genes in humans. The MHC is polygenic: 3 class I and class II loci. It’s expression is co-dominant (maternal and paternal genes both expressed), therefore each person can have up to 6 of each gene if completely heterozygous.

Question 125

Outline MHC and T Cell receptor (TCR) interactions

Answer 125

1) CD8 binds to the alpha-3 domain of MHC1, allowing it to bind to the antigen of an intracellular pathogen. This is processed in the cytosol.
2) CD4 binds to the beta-2 domain of MCH2, allowing it to bind to the antigen of an extracellular pathogen. This is processed in the endosomes.

Question 126

What are the differences between the 2 families of T cells?

Answer 126

CD4 (helper) and CD8 (cytotoxic killer) are defined by cell surface molecules CD4 (which binds MHCII) and CD8 (which binds MHCI). They are also functionally different

Question 127

What are the classes of CD4 Helper T Cells?

Answer 127

T Helper cells produce cytokines, a family of inflammatory mediators. Cytokines have diverse actions on a wide range of cells and influence the outcome of the immune response:
1) Tfh: Pro-Antibody; IL-21
2) Th17: Pro Inflammatory, control bacterial and fungal infection; IL-17, IL-23, IL-6
3) Th1: Pro-inflammatory, boost cellular immune response, interferon gamma, tumour necrosis factor; IL-12
4) Treg (Th0): Anti-Inflammatory, limit the immune response; IL-10, TGFβ
5) Th2: Pro-Allergic, boost multicellular response;
IL-4, IL-5, IL-13

Question 128

What is the function of CD8 Cytotoxic T Cells?

Answer 128

Cytotoxic T cells (CTL) kill their targets by programmed cell death, apoptosis. Apoptosis is characterized by the fragmentation of nuclear DNA. They also store perforin, granzymes, granulysin in cytotoxic granules released after target recognition. Perforin molecules polymerise and form pores.

Question 129

How do CD8 cells kill infected cells?

Answer 129

1) In uninfected cells, MHCI molecules show self peptides.
2) The CD8 cell scans cells, looking for non-self MHC. If none are found, it does nothing.
3) A virus infects the cell and releases its contents.
4) The cell now starts making viral proteins.
5) It displays these as non-self MHC.
6) The CD8 cells detects the non-self MHC and attacks.
7) The CD8 cell kills the virally infected cell.

Question 130

What is the function of antibodies?

Answer 130

Antibodies are extremely important in protection against reinfection. They have 3 core protective roles:

1) Neutralisation - preventing bacterial adherence
2) Opsonisation - promoting phagocytosis
3) Complement activation - activating complement which activates opsonisation and lyses some bacteria

Question 131

Outline the types and characteristics of antibodies

Answer 131

1) IgG: Has the highest opsonisation and neutralisation. It is classified into 4 subclasses: IgG1, IgG2, IgG3 and IgG4.
2) IgM: Produced first upon antigen invasion and increases transiently. It consists of a pentamer with 10 antigen binding sites.
3) IgA: It is expressed in mucosal tissues and forms dimers after excretion.
4) IgD: has an unknown function.
5) IgE: involved in allergy response.

Question 132

Where are B cells produced?

Answer 132

B cell generation and maturation occurs in bone marrow in the absence of antigen. They are derived from stem cells in the bone marrow. They migrate into the circulation (blood, lymphatic system) and into lymphoid tissues. Mature B cells are specific for a particular antigen, with the specificity residing in the B cell receptor (BCR) for antigen.

Question 133

Outline the function of the B cell receptor (BCR)

Answer 133

BCR have a unique binding site which bind to a portion of the antigen called antigenic determinant or epitope. It is made before the cell ever encounters antigen and is present in thousands of identical copies on the surface of the B lymphocyte. B cells bind soluble antigen.

Question 134

How are B cells activated?

Answer 134

Naïve antigen-specific lymphocytes (B or T) cannot be activated by antigen alone, naïve B cells require accessory signal. This can come neither directly from microbial constituents, or from a T helper cell.

Question 135

What are the 2 pathways by which antibody production is achieved?

Answer 135

1) T Helper Cell: this is Thymus-dependent. It produces immunoglobulins of all classes, as well as memory cells.
2) Microbial constituents: thus is Thymus-independent. It produces only IgM and does not produce memory cells.

Question 136

What are Thymus-independent antigens?

Answer 136

They directly activate B cells without the help of T cells. They are often polysaccharides, and need to have a repetitive structure (e.g. bacterial surface sugars). The second signal required is provided by a microbial PAMP (e.g. LPS).

Question 137

Outline B Cell activation by T cells

Answer 137

1) The membrane bound BCR recognises antigen.
2) The receptor-bound antigen is internalised and degraded into peptides
3) Peptides associate with “self” molecules (MHC class II) and is expressed at the cell surface
4) This complex is recognised by matched CD4 T helper cell
5) B cell activated.

Question 138

Which cellular receptor hind antibodies?

Answer 138

Fc receptors bund antibodies at their Fc region (tail), an interaction that activates the cell possessing the Fc receptor.

Question 139

Define immune regulation

Answer 139

It is control of the immune response to prevent inappropriate reactions.

Question 140

Outline the importance of immune regulation

Answer 140

An immune response is required to protect from infection by pathogenic microorganisms and for survival of the infected mammalian organism. But too much immune response is as bad as no response at all. Immune regulation is achieved by a complex interactive network of immune cells and is required to:
•Avoid excessive lymphocyte activation and tissue damage during normal protective responses against infections;
•Prevent inappropriate reactions against self antigens (“tolerance”).

Question 141

What is autoimmunity?

Answer 141

These disorders are often classified as “immune-mediated inflammatory diseases” and can be either systemic or organ-specific.

Question 142

Outline examples of autoimmune disease

Answer 142

These are often chronic diseases with prominent inflammation, often caused by failure of tolerance or regulation:
–Rheumatoid Arthritis, Irritable Bowel Disease, Multiple Sclerosis, psoriasis, many others. Autoimmune diseases affect 2-5% of people, with their incidence increasing.

Question 143

How does autoimmunity cause autoimmune diseases?

Answer 143

The fundamental problem of autoimmunity is the imbalance between immune activation and control. The failure of control mechanisms is the underlying cause of autoimmune diseases. Underlying causative factors are susceptibility genes + environmental influences. Autoimmune disease are more prevalent in women.

Question 144

Outline the immune mechanism of autoimmune diseases

Answer 144

1) May result from immune responses against self antigens (autoimmunity) or microbial antigens (Crohn’s disease);
2) Immune response is inappropriately directed or controlled; effector mechanisms of injury are the same as in normal responses to microbes;
3) May be caused by T cells and antibodies.

Many immunological diseases are chronic and self-perpetuating: because it is attacking self-antigen there is always more antigen to attack.

Question 145

How does auto,immunity cause allergic reactions?

Answer 145

Harmful immune responses to non-infectious antigens can cause tissue damage and disease. This can be mediated by:
•Antibody (IgE) and mast cells – acute anaphylactic shock
•Or T cells – delayed type hypersensitivity

Question 146

How does autoimmunity cause hypercytokinemia and sepsis?

Answer 146

These are caused by too much of an immune response, often in a positive feedback loop. They are triggered by pathogens entering the wrong compartment (sepsis) or failure to regulate response to correct level.

Question 147

Outline the phases of cell mediated immunity

Answer 147

1) The infected cell collects material
2) MHC:peptide-TCR interaction occurs
3) Naïve T cell becomes an effector
4) Effector cell sees MHC:peptide on cell and performs function.
5) The effector pool contracts to memory.

Question 148

What are self limiting responses?

Answer 148

These are the cardinal feature of all immune responses. They are manifested by decline of immune responses. Their principal mechanism is for the immune response eliminates antigen that initiated the response. The first signal for lymphocyte activation is eliminated

Question 149

What is the 3 signal model?

Answer 149

These are the 3 signals required that license the cell to respond:

1) Antigen Recognition
2) Co-stimulation
3) Cytokine Release

Question 150

Why does immunity require antigens?

Answer 150

Responses against pathogens decline as the infection is eliminated, leading to the apoptosis of lymphocytes that lose their survival signals (antigen, etc). Memory cells are the survivors. Active control mechanisms may function to limit responses to persistent antigens (self antigens, possibly tumors and some chronic infections). These are often grouped under “tolerance” and thus forms the basis of cancer immunotherapy.

Question 151

What are the 3 possible outcomes at the end of an immune response?

Answer 151

1) Resolution: no tissue damage, returns to normal. Phagocytosis of debris by macrophages.
2) Repair: healing with scar tissue and regeneration. Fibroblasts and collagen synthesis.
3) Chronic inflammation: active inflammation and attempts to repair damage ongoing.

Question 152

Define immunological tolerance

Answer 152

This is specific unresponsiveness to an antigen that is induced by exposure of lymphocytes to that antigen (tolerogen vs immunogen).

Question 153

What is the significance of immunological tolerance?

Answer 153

All individuals are tolerant of their own antigens (self-tolerance); breakdown of self-tolerance results in autoimmunity. There maybe be therapeutic potential in tolerance, as restoring tolerance may be exploited to prevent graft rejection, treat autoimmune and allergic diseases

Question 154

What are the 2 types of tolerance?

Answer 154

1) Central: Before the T or B cells ever enter the circulation
2) Peripheral: Or once in the circulation

Question 155

What is central tolerance?

Answer 155

Lymphocytes that recognise self antigens are eliminated (deletion) or made harmless in the generative organs as part of the maturation process, before they enter the circulation.

Question 156

Why are cells deleted before circulation in central tolerance?

Answer 156

Central tolerance and deletion of cells at source is a function of the way the immune repertoire is generated. There are approximately 1015 possible TCR and 1015 possible antibodies generated at random. Some of these will be self-reactive and therefore need to be removed.

Question 157

How are B cells selected in central tolerance?

Answer 157

B cell down-selection of self reactive in immature cells relatively simple. If immature B cells in bone marrow encounter antigen in a form which can crosslink their IgM, apoptosis is triggered.

Question 158

How are T cells selected in central tolerance?

Answer 158

T cell selection occurs in the thymus. It is more complex than B cells selection because of MHC:TCR interactions. T cell receptors which are capable of binding self MHC/ self peptide need to be selected.

1) A T cell is useless if it doesn’t bind to any self-MHC at all and undergoes apoptosis due to neglect.
2) A T cell is dangerous if it binds too strongly to self-MHC, so it undergoes apoptosis due to negative selection.
3) A T cell is useful if it binds weakly to self-MHC, it is signalled to survive by positive selection.

Question 159

What is AutoImmune REgulator (AIRE)?

Answer 159

A specialised transcription factor allows thymic expression of genes that are expressed in peripheral tissues. AIRE promotes self tolerance by allowing the thymic expression of genes from other tissues. Hence, a T cell developing in the thymus can encounter MHC bearing peptides expressed in other parts of the body. Mutations in AIRE result in multi-organ autoimmunity.

Question 160

What is peripheral tolerance?

Answer 160

This is the destruction (apoptosis) or control (anergy or suppression) of any self reactive T or B cells which enter/escape into the circulation, as well as things that change.

Question 161

Outline BCR selection for the development of antibodies

Answer 161

B Cell antigen specificity is determined by the BCR (B cell receptor) which is surface bound antibody. BCR has a light and a heavy chain. Each is encoded by an individual gene, which is made by recombination of building blocks. This occurs in the bone marrow before the B cell is released.

Question 162

How is tolerance broken

Answer 162

Unlike T cells, B cells can change specificity after leaving the bone marrow (somatic hypermutation). This is normally good – as it improves antibody quality. Exposure to environmental antigens or self antigens in the context of infections can alter the outcome.

Question 163

What is anergy in peripheral tolerance?

Answer 163

Naive T cells need co-stimulatory signals in order to become activated. Most cells lack co-stimulatory proteins and MHC class II. If a naive T cell sees its MHC/peptide ligand without appropriate costimulatory protein it becomes anergic, meaning that it is less likely to be stimulated in future even if co-stimulation is then present.

Question 164

What is ignorance in peripheral tolerance?

Answer 164

Antigen may be present in too low a concentration to reach the threshold for T cell receptor triggering. Immunologically privileged sites (e.g. eye, brain). Compartmentalisation of cells and antigen controls interactions

Question 165

What is antigen induced cell death (AICD) in peripheral tolerance?

Answer 165

Activation through the T-cell receptor can result in apoptosis, influenced by the nature of the initial T-cell activation events. In peripheral tolerance, T cell death is often caused by the induction of expression of the death ligand, Fas ligand (CD95 ligand, FasL).

Question 166

What inhibits T cells?

Answer 166

A subset of helper T cells known as Treg (T regulatory cells) inhibit other T cells and other cells.

Question 167

What is the function of Treg?

Answer 167

This is a CD4 regulatory T cell, with a high IL-2 receptor (CD25) and Frokhead box Protein 3 (Foxp3) transcription factor. It has multiple mechanisms of action:

1) Secretion of immune-suppressive cytokines (TGF-beta, IL-10, IL-35),
2) Inactivation of dendritic cells or responding lymphocytes

Question 168

Why is the transcription Foxp3 important?

Answer 168

A mutation in FoxP3 leads to severe and fatal autoimmune disorder - Immune dysregulation, Polyendocrinopathy, Enteropathy X-linked (IPEX) syndrome.

Question 169

What is the “master” regulatory cytokine?

Answer 169

IL-10 so the key anti-inflammatory cytokine as it:

1) Is Multi-functional (pleiotropic)
2) Acts on a range of cells
3) Blocks pro-inflammatory cytokine synthesis including TNF, IL-6, IL-8, IFNγ
4) Downregulates Macrophage functions
5) Viral mimics

Question 170

Why is regulation critical in pregnancy?

Answer 170

Tregs only exist in mammals. Exposure to new antigen. Expressed in the context of foreign MHCI.

Question 171

What are the different types of Treg?

Answer 171

1) Natural” regulatory T cells (nTreg):
> Development (in thymus) requires recognition of self antigen during T cell maturation
> Reside in peripheral tissues to prevent harmful reactions against self
2) Inducible regulatory T cells (iTreg)
> Develop from mature CD4 T cells that are exposed to antigen in the periphery; no role for thymus
> May be generated in all immune responses, to limit collateral damage

Tregs reflect the Th subsets seen in T effectors

Question 172

Outline the function of T Helper cells

Answer 172

T Helper cells shape the immune response, tailoring for different pathogens. They do this through Cytokines:

1) Tfh: Pro-Antibody
2) Th17: Control bacterial and fungal infection
3) Th2: Anti-multicellular organisms
4) Th1: Boost Cellular Immune Response
5) Treg (Th0): Anti-Inflammatory

Question 173

What is the function of cytokines?

Answer 173

Cytokines program the immune response, by focussing it for the right kind of response. They can be inflammatory (increase the response) or anti-inflammatory (decrease the response). T helper type is defined by transcription factors and cytokines shape transcription factor pathways by cross-regulation. Examples include: Interferon gamma, Interleukin 2 and IL-10.

Question 174

What is the function of chemokines?

Answer 174

Chemokines drive movement around the body. They act like address labels sending stuff to the right place. Chemokine receptor profiles change with activation state of the cells.

Question 175

How do CD4 cells shape the antibody response?

Answer 175

The constant region (the stem of the antibody) is important in the function. Different antibody classes have different constant regions. The differences in function reflect the different types of response required to clear pathogens. There are a number of gene cassettes that can be swapped in and out.

Question 176

What causes Ig class switch?

Answer 176

T cells drive Ig class switch sing cytokines. The cytokine depends on the type of Helper T Cell.

Question 177

What is Human T-cell Leukaemia Virus Type I (HTLV-1)?

Answer 177

This was the first virus associated with human malignancy and is also associated with adult T-cell leukaemia (ATL) cases. 15-20 Million People infected are infected worldwide, with some areas more prevalent (e.g. Japan, Caribbean, Iran, Romania), approximately 5% will also develop ATL. The virus is transmitted either mother to infant (breast feeding/during birth), blood transfusion or through sexual contact. HTLV-1 infects preferentially T-cells / T-helper cells. It is assumed that the number of T-cells containing HTLV-1 DNA correlates with disease severity and likelihood of transmitting the virus.

Question 178

What are the diseases caused by HTLV-1?

Answer 178

1) Adult T-cell Leukaemia (ATL)
2) Adult T-cell leukaemia/lymphoma (ATLL)
3) HTLV-1-associated myelopathy (HAM)
4) Tropical spastic paraparesis (TSP)
5) HTLV-1-associated infectious dermatitis
6) HTLV-1-associated uveitis (HUS)

Question 179

What are the key structures of HTLV-1

Answer 179

1) Viral envelope (lipid bilayer)
2) ssRNA genome
3) p-24 Capsid
4) Reverse Transcriptase
5) Protease
6 Integrase

Question 180

Outline the key functions of HTLV-1

Answer 180

1) Virion assembly and maturation
2) Viral entry and transformation tropism
3) Viral resistance
4) Viral infectivity and resistance
5) Rex: Positive post-transcriptional regulation
Tax: Viral transcription and oncogenesis
6) Transcription and post-transitional regulation

Question 181

Outline the replication cycle of HTLV-1

Answer 181

1) HTLV-1 enters T-cell
2) ssRNA released into host cell cytosol
3) ssRNA reverse transcribed (RT-enzyme) to ssDNA
4) ssDNA converted to dsDNA
5) dsDNA enters nucleus and integrates into host genome
6) Viral genome can replicate as part of the host chromosome

Question 182

What is the Western-blot Method (WB)?

Answer 182

This is a serological diagnostic method used to assess if patients have antibodies specific to HTLV-1 proteins.

Question 183

Outline the steps of the Western-blot Method

Answer 183

1) Step 1: Separation
> Different viral proteins (often defined from in vitro propagated cultures) separated based on their on a polyacrylamide protein gel
> Smaller proteins will migrate faster
2) Step 2: Transfer
> Proteins transferred using an electric transfer system onto a PVDF membrane
> Viral proteins will stick to the membrane, creating an image of the gel
> Viral proteins will be distinct but invisible bands on the membrane
3) Step 3: Staining
> Incubate membrane with human serum (primary antibody)
> Wash membrane
> Incubate membrane with secondary antibody linked to enzyme
> Wash membrane
> Add substrate for enzyme linked to secondary antibody (generated a colour reaction, visible precipitate or a luminescent signal)
4) Step 4: Visualisation
> In a patient infected with HTLV-1, antibodies are produced to several different viral proteins.

Question 184

Which proteins are indicative a positive HLV-1 infection?

Answer 184

1) The synthetic peptide: MTA-1
2) Viral core proteins: p53, p24 and p19
3) Recombinant glycoprotein: gd21

Question 185

Outline the steps of Polymerase Chain Reaction (PCR)

Answer 185

PCR consists of 30-49 cycles of only 3 steps:
Step 1: Denaturation - 1 minute at 94°C
Step 2: Annealing - 45 seconds at 54°C (forward and reverse primers)
Step 3: Extension - 2 minutes at 72°C (only dNTPs)
> Region amplified: 300 bp region of the tax gene (dsDNA or ssDNA)

Question 186

What are the 5 components of PCR?

Answer 186

Typical PCRs are performed in 50.0 μl reaction volumes containing:

1) DNA template
2) Primers (forwards and reverse)
3) DNA polymerase (Taq polymerase)
4) dNTPs
5) Reaction Buffer

Question 187

How is a HTLV-1 patient’s sample prepared for PCR?

Answer 187

Step 1: Take blood
> Sample used: peripheral blood and peripheral blood mononuclear cells (PBMCs) are isolated. PBMCs are a mix of cells: monocytes, lymphocytes, T-cells, B-cells and NK-cells.
Step 2: Isolate PBMC
> Blood is layered on a separation medium with a specific density and the tube us subjected to centrifugation
> Blood can be separated into blood plasma and the PBMC fraction
Step 3: Isolate DNA
> Cell lysis/ protein degradation
> Capture and cleaning of DNA
> Elution of DNA

Question 188

Outline DNA gel electrophoresis

Answer 188

This separates DNA based on size. DNA is negatively charged and so will migrate towards the positive anode. DNA can then be visualised with the intercalating DNA stain, either: Ethidium bromide – UV light or Sybr Safe – blue light. The DNA loading dye increases the density/weight of the sample making them sink into the wells, allows the well containing a sample to be seen and indicates how far the DNA fragments have migrated during run. The DNA marker/ladder estimates the size of the PCR fragment.

Question 189

Why can a standard PCR be used for diagnosis of HTLV-1?

Answer 189

During virus replication, viral RNA is reverse transcribed to ssDNA and converted to dsDNA that integrates into the host-cell genome. Viral infection can thus be determined by standard PCR using host cell DNA as template.

Question 190

What is Quantitative Real Time PCR (qRT-PCR or qPCR)?

Answer 190

This is a diagnostic method that can be carried out 2 different ways:

1) Fluorescence dye-based method (SYBR Green dye method)
2) DNA probe-based (TaqMan method)

Question 191

Outline the DNA probe-based method (TaqMan method)

Answer 191

1) Polymerisation and strand displacement
> In addition to the 2 primers used in standard PCR, a 3rd (oligo) probe is added, which also binds go the specific gene to be amplified
> The oligo binds to a region between the DNA region and that is amplified by the forward and reverse primer
> The oligo contains a fouorophore and quencher molecule at 5’ and 3’ respectively, which are quite closely arranged in some when the oligo is intact
2) Probe cleavage (release of reporter dye)
> Fluorescence occurs when reporter dye and quencher dye are no longer in close proximity
3) Completion of polymerisation
Taq-MAN qRT-PCR data can therefore be used for the detection of the HTLV-1 tax gene.

Question 192

How can qRT-PCR data be interpreted on a graph?

Answer 192

A Norm-Fluoro by Cycle Time (CT) graph can be used to determine whether a patient has reached the threshold fluorescence. When the threshold is reached, this can be used to determine the cycle time of the HTLV-1. If the threshold is not reached, then the patient is negative. A cycle time by log10 tax gene input copy number graph can then be used to determine the approximate number of viral copies. A log10 tax gene input copy number of 6, for instance, would be equal to 10^6 copies of that gene.

Question 193

Disease caused by S. aureus are divided into which two groups?

Answer 193

1) Localised pyogenic or “pus-producing” diseases that are characterised by tissue destruction mediated by hydrolytic enzymes and cytotoxins.
2) Diseases mediated by toxins that function as superantigens producing systemic diseases.

Question 194

What properties do all S.aureus bacteria share?

Answer 194

1) Ability to grow aerobically and anaerobically, over a wide range of temperatures, and in the presence of a high concentration of salt; the latter is important because these bacteria are a common cause of food poisoning.
2) Polysaccharide capsule that protects the bacteria from phagocytosis.
3) Cell surface proteins (protein A , clumping factor proteins) that mediate adherence of the bacteria to host tissues.
4) Catalase that protects staphylococci from peroxides produced by neutrophils and macrophages.
5) Coagulase converts fibrinogen to insoluble fibrin that forms clots and can protect S. aureus from phagocytosis

Question 195

What are the unique properties of hydrolytic enzymes and cytotoxins producing S. aureus?

Answer 195

1) Lipases, nucleases, and hyaluronidase that causes tissue destruction.
2) Cytotoxins (alpha, beta, delta, gamma, leukocidin) that lyse erythrocytes, neutrophils, macrophages, and other host cells.

Question 196

What are the unique properties of toxins producing S. aureus?

Answer 196

1) Enterotoxins (many antigenically distinct) are the heat-stable and acid-resistant toxins responsible for food poisoning.
2) Exfoliative toxins A and B cause the superficial layers of skin to peel off (scalded skin syndrome)
3) Toxic shock syndrome toxin is a heat- and protease-resistant toxin that mediates multiorgan pathology.

Question 197

Outline the epidemiology (distribution) of S. aureus

Answer 197

1) It is the common cause of infections both in the community and in the hospital because the bacteria are easily spread person-to-person and through direct contact or exposure to contaminated bed linens, clothing, and other surfaces.
2) Antibiotic-resistant strains (e.g., MRSA) are widely distributed in both the hospital (HA-MRSA) and community (CA-MRSA).

Question 198

Outline the pyogenic diseases caused by S. aureus

Answer 198

1) Impetigo : localized skin infection characterized by pus-filled vesicles on a reddened or erythematous base; seen mostly in children on their face and limbs
2) Folliculitis : impetigo involving hair follicles, such as the beard area
Furuncles (boils) and carbuncles : large, pus-filled skin nodules; can progress to deeper layers of the skin and spread into the blood and other areas of the body
3) Wound infections : characterized by erythema and pus at the site of trauma or surgery; more difficult to treat if a foreign body is present (e.g., splinter, surgical suture); majority of infections both in the community and hospital are caused by MRSA; recurrent bouts of infections are common
4) Pneumonia : abscess formation in the lungs; observed primarily in the very young and old and frequently following viral infections of the respiratory tract
5) Endocarditis : infection of the endothelial lining of the heart; disease can progress rapidly and is associated with high mortality rate
6) Osteomyelitis : destruction of bones, particularly the highly vascularized areas of long bones in children
7) Septic arthritis —infection of joint spaces characterized by a swollen, reddened joint with accumulation of pus; the most common cause of septic arthritis in children

Question 199

Outline the mediated diseases caused by S. aureus

Answer 199

1) Food poisoning : after consumption of food contaminated with the heat-stable enterotoxin , the onset of severe vomiting, diarrhea, and stomach cramps is rapid (2 to 4 hours) but resolves within 24 hours. This is because the intoxication is caused by the preformed toxin present in the food rather than an infection where the bacteria would have to grow and produce toxin in the intestine
2) Scalded skin syndrome : bacteria in a localized infection produce the toxin that spreads through the blood and causes the outermost layer of the skin to blister and peel off; almost exclusively seen in very young children
3) Toxic shock syndrome : bacteria in a localized infection produce the toxin that affects multiple organs; characterized initially by fever, hypotension, and a diffuse, macular, erythematous rash. There is a very high mortality rate associated with this disease unless antibiotics are promptly administered and the local infection managed.

Question 200

How is S. aureus treated, prevented and controlled?

Answer 200

1) Localized infections managed by incision and drainage
2) Antibiotic therapy indicated for systemic infections; empiric therapy should include antibiotics active against MRSA
3) Oral therapy can include trimethoprim-sulfamethoxazole, clindamycin, or doxycycline
4) Vancomycin is the drug of choice for intravenous therapy
5) Treatment is symptomatic for patients with food poisoning although the source of infection should be identified so other individuals will not be exposed
5) Proper cleansing of wounds and use of disinfectant help prevent infections
6) Thorough hand washing and covering exposed skin helps medical personnel prevent infection or spread to other patients
7) No vaccine is currently available

Question 201

Which common features do bacteria often share?

Answer 201

1) LPS in Gram-negative bacteria
2) LTA in Gram-positive bacteria
3) Flagella on certain bacteria

Question 202

What are immune evasion mechanisms?

Answer 202

There are mechanisms that some microbes have evolved to enhance their survival in their host, thereby contributing to bacterial pathogenesis.

Question 203

Which cells comprise the innate immune response and what is its function?

Answer 203

The innate immune response is very efficient at detecting and killing invading microbes. It comprises of:

1) Neutrophils
2) Basophils
3) Eosinophils
4) Dendritic cells
5) Macrophages

Question 204

What are neutrophils?

Answer 204

These are the most abundant leukocytes in the blood, ranging at 50-70% of all leukocytes. They are recruited to areas of infection and detect microbes, before performing effector functions (e.g. killing microbes). However, they are also considered “simple” immune cells.

Question 205

Why must neutrophil response remain balanced?

Answer 205

Neutrophil responses must be balanced to prevent infection, but to also prevent damage (inflammation) to the host.

Question 206

What is the function of neutrophils?

Answer 206

1) When microbes enter the body, they become opsonised within antibodies and complement, resulting in the gradient of C3a and C5a, as well as bacterial proteins and peptides.
2) C3a is able to bind to C3aR, C5a binds to C5aR on endothelial cells. The endothelial cells express ICAM and neutrophils roll along the surface to the site of infection.
3) Neutrophils adhere to the ICAM receptors and migrate across the endothelial layer.
4) Neutrophils then become primed by the gradient of C3a and C5a or by the bacterial proteins or peptides.
5) After priming, neutrophils migrate to towards the microbes by a process called chemotaxis. Either towards complement components or towards bacterial proteins and peptides.
6) The neutrophils then become activated and upon activation, they can begin to perform effector functions to kills the invading microbes:
> Phagocytosis - the ingestion or bacteria and killing within the phagosomes by antimicrobial molecules.
> Degranulation - the production and release of the reactive O2 species or the release of antimicrobial molecules.
> Inflammation - the recruitment of other immune cells, by neutrophils, playing a key role in the inflammatory process

Question 207

What is Staphylococcus aureus (S. aureus)?

Answer 207

This is a gram-positive bacterium, that is a commensal and lives harmlessly in the nose of 30% of human population. S. aureus is an opportunistic pathogen able to cause minor skin infections to severe and life-threatening diseases.

Question 208

What is antibody opsonisation?

Answer 208

Antibodies bind bacterial antigens, allowing:

1) The deposition of complement in the classical complement pathway.
2) Neutrophils and other phagocytes the ability to detect invading microbes.

Question 209

How do S. aureus and other bacteria evade antibody opsonisation?

Answer 209

1) Expressing polysaccharide capsule: This helps to hide antigenic structures that can be detected by innate and adaptive immune components, such as complement and antibodies.
2) S. aureus protein A (SpA) binding IgG Fc region: Spa surface protein binds antibodies via their Fc region, not their Fab region, this prevents normal opsonisation, and therefore neutrophils cannot detect S. aureus.
3) S. aureus SSL10 binding IgG to inhibit detection: this is a secreted protein that binds to the Fc region of IgG, preventing the Fc receptors on neutrophils from detecting IgG antibodies on the surface of S. aureus.

Question 210

What are other antibody evasion strategies?

Answer 210

1) The expression of proteases: cleave antibodies into non-functional forms (e.g, Group B streptococcus IdeS)
2) Antigenic variation: switching the expression of antigens

Question 211

What is complement opsonisation?

Answer 211

This is one of the first processes that occurs when a microbe enters the body, and results in the deposition of complement onto the surface of bacteria, resulting in either the directing killing of the bacteria or the enhanced detection or the bacteria via phagocytes. Complement system is composed of a large number of proteins that react with one-another to opsonise pathogens or to directly kill them by membrane attack complex (MAC) formation.

Question 212

What are the key steps of the complement cascade?

Answer 212

1) Initiation: classical pathway, the lectin/MBL pathway or the alternative pathway
2) Formation of C3 convertase: occurs in all 3 initiation pathways
3) Formation of C5 convertase
4) MAC formation

Question 213

How does S. aureus and other bacteria evade complement opsonisation?

Answer 213

1) S. aureus SCIN binding C3bBb and inhibiting convertases: inhibits the formation of C3 convertase and C5 convertase, which prevents:
> C3b deposition
> C3a formation
> C5a formation
2) S. aureus Efb binds C3d and inhibits fB binding C3: binds C3d in C3, which induces conformation change, preventing the binding of factor B to C3 and C3dg binding CR2
3) Expression or SSL7 protein: this binds to C5, preventing the C5 from being converted into C5a or C5b, thus inhibiting the formation of the membrane attack complex (MAC).

Question 214

What are other complement evasion strategies?

Answer 214

1) Expression of proteases: cleave complement components so that they’re no longer functional. S. pyogenes expresses the protease SpeB which degrades C3 into non-functional forms, leading to an ineffective complement cascade and the reduction of the amount of complement deposition on the bacterial surface.
2) Recruiting host derived complement regulators: can be split into 2 broad groups:
> Bacteria capable of recruiting factor H or the surface, which is able to inactivate C3b into iC3b.
> Bacteria capable of recruiting complement factor binding protein 4, to the surface, which degrades C2a from from C3 convertases.

Question 215

How do neutrophils sense and respond to their environment?

Answer 215

Neutrophils express hundreds of different immune receptors, at their surface or in their secretory vesicles (SVs) and granules. Immune receptors allow neutrophils to sense and respond to their environment. They detect microbes, microbial products or self proteins, then W,lowing the neutrophils to be primed/activated.

Question 216

What are examples of immune receptors on neutrophils?

Answer 216

1) Toll like receptors (TLRs): able to detect conserved microbial structures.
2) C type lectin (CLEC) receptors: detect microbial carbohydrates.
3) Formulated peptide receptors (FPRs) detect formulated peptides.

Question 217

How do neutrophil immune receptors indirectly detect bacteria?

Answer 217

When microbes become opsonised by antibodies or complement, neutrophils detect opsonised microbes through Fc receptors or complement receptors:

1) Fc receptors: able to detect antibody opsonised microbes. These often signal through activating motifs called ITAMs, in then cytoplasm tails.
2) Complement receptors: able to detect complement opsonised microbes.

Question 218

How do neutrophil immune receptors modulate function?

Answer 218

There is a diverse range of immune receptors involved in generating and modulating a balanced immune response. Activatory receptors enhance immune cell activity. Inhibitory receptors suppress immune cell activity. Examples include:

1) Cytokine receptors: detect a range of different cytokines and signal for the neutrophil to become more or less activated.
2) Chemoattractant receptors: used to perform chemotaxis and migration towards the site of infection.
3) Inhibitory receptors (LAIR and SIGLEC): prevent neutrophils from becoming activated at the wrong time, wrong place or to the wrong extent. They have inhibitory motifs in their cytoplasm tails that counteract the ITAM motifs found in activating receptors (e.g. Fc receptors).
4) Activitating and inhibiting receptors (LILR and CEACAM)

Question 219

How does S. aureus able to inhibit chemotaxis and neutrophil activation?

Answer 219

Neutrophils express 2 receptors important for chemotaxis, C5a which detects complement component C5a and FPR1 receptor which detects formulated peptides produced by microbes. S. aureus inhibits chemotaxis by a protein called CHIPS:
1) CHIPS binds to the C5a receptor (C5aR) and the FPR1 receptors, preventing the interaction with their normal agnostic ligands C5a and fMLPs. 2) This means that cannot migrate to sites of infection or become activated through C5aR or FPR1.

Question 220

How does S. aureus inhibit phagocytosis?

Answer 220

Neutrophils express a number of different phagocytes receptors, one family of which is Fc receptors. There are a number of different Fc receptors which detect IgG opsonised microbes and a receptor that detects IgA opsonised microbes. S. aureus is able to prevent Fc receptor mediated phagocytosis by expressing molecules that bund these Fc receptors:

1) FLIPr binds Fc gamma receptors, preventing the detection of IgG-opsonised bacteria.
2) This reduces antibody mediated phagocytosis and killing of S. aureus.

Question 221

How does S. aureus kill neutrophils?

Answer 221

S. aureus can express a number of different toxins which are able to bind to receptors at the surface of neutrophils and lead to their lysis. The PVL toxin can kill human neutrophils. S. aureus can also express molecules at the surface which bind and inhibit functions of activating receptor.

Question 222

Outline the immune evasion of other bacteria

Answer 222

1) Expression of proteins that are able to bind inhibitory receptors and activate them, inducting inhibitory signals that switch of neutrophil activity.
2) Neutrophil granules contain anti-microbial compounds which are released in degranulation or utilised within the phagolysosome. Bacteria can produce proteins able to inhibit the effect of these antimicrobials.
3) The manipulation of intercellular signalling, used particularly by intracellular bacterial pathogens.
4) The modification of bacterial surface which allows the bacteria to evade detection via neutrophils.

Question 223

What are interferons?

Answer 223

Virally infected cells produce and release small proteins called interferons, which play a role in immune protection against viruses.
Interferon (IFN) is induced by molecules made by viruses that are sensed by the cell as foreign or in the wrong cellular location. For example, double-stranded RNA, RNA that lacks a 5’ cap, or DNA in the cytoplasm.
Interferon is secreted from the infected cell and binds to interferon receptors. IFN initiates the antiviral state in the infected cells and in surrounding cells.
The Antiviral state involves transcription of hundreds of genes that block viral replication, for example 2’5’ oligoadenylate synthetase and protein kinase R.
Interferon activates Natural Killer cells and systemic antiviral responses.

Question 224

What are vaccines?

Answer 224

This is something that stimulates the immune system, without causing serious harm or side effects. The aim of immunisation is to provoke immunological memory to protect individual against a particular pathogen if they later encounter it. Vaccines are the single most cost-effective tool available have for improving health.

Question 225

How do vaccines stop infection?

Answer 225

Vaccination is the generation or an immune memory but in the absence if the harmful infection that normally causes the immune memory. The vaccine works on the immune response in 3 main areas:
1) Prevention of entry
> Mainly mediated through antibodies, which work by binding onto the virus and neutralising it and leading to to engulfment of the pathogen by opsonisation, this is driven by the constant region of the antibody. The opsonised pathogen is more attractive to macrophages or other phagocytes cells.
2) Boosting immune response
> Antigens in the vaccine will be recognised by the CD4 T cells in the context of the MHC2 molecules. These CD4 molecules are then programmed to boost other aspects of the immune response, by working with B cells to make better antibodies.
3) Killing infected cells
> The programmed CD4 cells can train CD8 T cells to kill infected cells.

Question 226

What is the basic reproduction number (R0)?

Answer 226

This number indicates the number of cases one case generates on average over the course of their infectious period. The R0 can change over time.

1) If R0 < 1 the infection will die out in the long run.
2) If R0 > 1 the infection will be able to spread in a population.

Question 227

How do vaccines affect the basic reproduction number?

Answer 227

The aim of any intervention is to reduce the R0 from >1 to <1. With vaccines, as people become immunised, there will be fewer people to become infected after the first wave, hence reducing the R0, and becomes a value called the Rt (altered R0 value). If R0 reaches <1, infection can be cut off overall, as if the infected people only meet immune people, then the infection cannot spread passed the cause.

Question 228

What is herd immunity?

Answer 228

In a sustained transmission, a transmitting case meets susceptible people who then become transmitting cases, allowing the pathogen to spread out of control. However, in herd immunity, the transmitting cases on,y meet immune people, allowing susceptible people to be shielded from the infection.

Question 229

What do vaccines contain?

Answer 229

1) An antigen (in one of these forms):
•Inactivated Protein (e.g. Tetanus toxoid)
•Recombinant protein (e.g. Hep B)
•Live Attenuated Pathogen (e.g. Polio/ BCG)
•Dead Pathogen (e.g. Split Flu vaccine)
•Carbohydrate (e.g. S. pneumoniae)
2) Adjuvant: normally alum, sometimes something proprietary
3) Stabilising substances (e.g. Buffers - PBS)
4) Water

Question 230

What are inactivated toxoid vaccines?

Answer 230

An example of this type of vaccine would be the tetanus toxoid. This type of vaccine comprises of a chemically inactivated form of toxin, which induces antibody. The antibody then blocks the toxin from binding the nerves. The advantages of this type of vaccine are: it’s cheap, well characterised, safe and has been in use for many decades. The disadvantages of this type of vaccine are: it requires good understanding of biology of infection and not all organisms encode toxins.

Question 231

What are recombinant protein vaccines?

Answer 231

An example of this type of vaccine is the Hep B Surface Antigen (HbSAg). This type of vaccine comprises of a recombinant protein from pathogen, which induces classic neutralising antibodies. The advantages are: it’s pure and it’s safe. The disadvantages are: it’s relatively expensive, not immunogenic and it has not proved to be the answer to all pathogens.

Question 232

Why are bacterial coats a problem for vaccination?

Answer 232

Bacteria often have a capsule, made of polysaccharide. This is not very good at inducing a B cell response, as it is a T independent antigen. Therefore, alternative approaches are needed.

Question 233

What are conjugate vaccines?

Answer 233

An example of this type of vaccine is S. pneumoniae. This vaccine comprises of a polysaccharide coat component coupled to an immunogenic “carrier” protein. The protein enlists CD4 help to boost B cell response to the polysaccharide. The advantages of this type of vaccine are: it improves immunogenicity, and it is highly effective at controlling bacterial infection. The disadvantages at: its cost, carrier protein interference, the facts that it’s very strain specific and the polysaccharide alone is poorly immunogenic.

Question 234

What are dead pathogen vaccines?

Answer 234

An example of this type of vaccine is the Influenza split vaccine. It compromise of a chemically killed pathogen that Induces antibody and T cell responses. The advantages of this type of vaccine are: it Leaves antigenic components intact and in context of other antigen, it is immunogenic because of the inclusion of other components, it’s also cheap and quick. The disadvantages are: fixing/killing can alter chemical structure of antigen, it’s “dirty”, it requires the capacity to grow the pathogen (H5N1), there is a vaccine induced pathogenicity a risk, as well as a risk of contamination with live pathogen (Polio), not happened since 1953.

Question 235

What are live attenuated vaccines?

Answer 235

Examples of this type of vaccine BCG, LAIV and OPV. These vaccines comprise of pathogens attenuated by serial passage, leading to a loss of virulence factors. Because they replicate in situ they trigger the innate response and boost the immune response. The advantages of this type of vaccine are: they induce a strong immune response, and they can induce a local immune response in the site where infection might occur (e.g. LAIV). The disadvantages of this type of vaccine are: they can revert to virulence, they can infect immunocompromised individuals (BCG/HIV), attenuation may lose key antigens and can be outcompetes by other infections.

Question 236

Define adjuvants

Answer 236

These are substances used in combination with a specific antigen that produced a more robust immune response than the antigen alone. Adjuvants are becoming more fequentlu used in vaccines.

Question 237

What is the function of adjuvants?

Answer 237

Adjuvants induce ‘danger signals’ that activate dendritic cells to present antigen to T cells and are part of licensing the response. Adjuvants stimulate the DC, which uptakes antigen and moves to Lymph node. This upregulates stimulatory signalling and cytokines.

Question 238

Why are new vaccines needed?

Answer 238

1) Changing (aging) Demographics
2) Changing Environment (Dengue/ other arboviruses)
3) New Diseases (COVID-19)
4) Old Diseases we still can’t fix (HIV/ TB/ Malaria…)
5) Antibiotic Resistance (MRSA, all bacteria)

Question 239

What are the barriers to future vaccines?

Answer 239

1) Scientific Challenges
2) Injection Safety
3) Logistics/ Cold Chain
4) Development Issues:
> Time: 8 yrs in 1960s; 15 yrs now
> Cost of vaccine development high
> Cost of the product
5) Public expectation of risk-free vaccines

Question 240

How does high variation of the target organism affect vaccines?

Answer 240

There are many circulating viruses. Classic Immune memory will only recognise one of these strains. Therefore vaccine antigens need to cover all the variety.

Question 241

How are new vaccines introduced in the UK?

Answer 241

1) Recommendations for vaccine policy
> Joint Committee on Vaccination and Immunisation (JCVI)
2) Vaccine policy decisions
> Department of Health (DH)
3) Licensing of vaccine
> Medicines and Healthcare products Regulatory Agency (MHRA)
4) Purchase of vaccine
> Department of Health from pharmaceutical companies
5) Control of vaccine (including batch release)
> National Institute for Biological Standards and Control (NIBSC)
6) Post licensure assessment and changes
> PHE/ JCVI (Epidemiology, assessment, trials)

Question 242

What considerations are there when scheduling a vaccine?

Answer 242

– Aim
– Need
– Scheduling with other vaccines
– Availability
– Cost
– Population accessibility
– Cultural attitudes and practices
– Facilities available for delivery

Question 243

What are the 4 different pathogen niches during infection?

Answer 243

1) Extracellular (e.g. Staphylococcus, Streptococcus, Candida, microbiota, worms)
2) Intracellular vacuolar (e.g. Salmonella, Chlamydia, Legionella, Coxiella, Plasmodium)
3) Intracellular cytosolic (e.g. viruses, Listeria, Burkholderia, Mycobacterium)
4) Surface adherent (e.g. enteropathogenic & enterohaemorrhagic E. coli)

Question 244

How does an immune response to infection start?

Answer 244

1) Tissue damage (e.g. injury)
2) Molecular detection of microbes – wrong thing in the wrong place at the wrong time
3) Inter-cellular communication (e.g. interleukins)
4) Priming the adaptive immune response

Question 245

How does an immune response to infection end?

Answer 245

1) Clearing infection
2) Stopping inflammatory cytokine production
3) Repairing tissue damage
4) Remembering the infection – immune memory!

Question 246

Outline the function and components of innate immunity

Answer 246

This is the fast acting, first line of defence. It is specific for structures shared by classes of microbes - pathogen-associated molecular patterns (PAMPs), of which there are around 1000. It has less than 100 types of invariant pattern recognition receptors encoded in the germline, with limited diversity. The distribution of the receptors is non-clonal, so identical receptors are found on all cells of the same lineage. It composes of:
1) Physical barriers - Skin, mucous, epithelial cells
2) Humoral - Complement, lectins (e.g. collectins, ficolins), pentraxins, A
antimicrobial peptides
3) Cellular- Neutrophils, macrophages, dendritic cells, natural killer (NK) cells

Question 247

Outline the function and components of adaptive immunity

Answer 247

This is a lower but long-lasting type of immunity. It is specific for the antigens of around 10^7 microbial molecules, but may recognise the antigen of non-microbial molecules. It is encoded by genes produced by somatic recombination of gene segments, allowing greater diversity. However, it only has 2 types of receptor, Ig and TCR, with millions of variations between them. The distribution of the receptors is clonal, as clones of lymphocytes with distinct specificities express different receptors. It composes of:

1) Humoral- Antibodies (immunoglobulins of various types) and complement
2) Cellular: Cytotoxic T-cells, T helper cells, T regulatory cells, B lymphocytes and Plasma cells.

Question 248

Outline the sequence of molecular and cellular events following infection

Answer 248

1) Microbial molecules are detected by naive host cells
2) The gene expression of the naive host cell changes allowing it to release antimicrobial molecules and communication signals (e.g. interleukins, chemokines and interferons)
3) This leads to signal transduction and the “activation” of the host cells, from resting cells to specialised cells.

Question 249

Which cells are the “first responders” in immune response?

Answer 249

Neutrophils are the first to respond but are short-lived, lasting only around 6 hours. These are then followed by macrophages. “Naïve” cells become “activated” upon interaction with microbes. Phagocytes control infection and limit/repair tissue damage. Uncontrolled activities of phagocytes is not good, as it can lead to:
•Granulomas
•Excessive inflammation & inappropriate adaptive immunity
•Tissue damage

Question 250

Outline pathogen specific phagocyte responses

Answer 250

1) Bacteria:
> Immune response - inflammatory cytokines, antimicrobial genes, metabolic genes and immunomodulatory genes.
> No immune response - resolution of inflammation
2) Fungi:
> Proinflammatory cytokines, antimicrobial genes, metabolic genes and immunomodulatory genes
3) Viruses:
> Interferon production, proinflammatory cytokines, antiviral genes and immunomodulatory genes

Question 251

Outline phagocyte activation and pathogen killing

Answer 251

Macrophages are tissue resident or circulatory - recruited from the bone-marrow. Their “activation” entails the expression of new genes, which is induced by microbes & cytokines. Activated macrophages display enhanced:
•Phagocytosis & Migration
•Cytokine/chemokine production
•Expression of cell surface molecules
•Antimicrobial activity
•Antigen presentation & T cell activation

Question 252

What is the function of interferons?

Answer 252

Interferons are special cytokines, that have direct antiviral activities. Type I & III interferons promote antiviral responses and Type II interferon promotes immunity against intracellular bacteria. 
 1)Their antiviral genes include:
•Nucleases
•Inhibitors of virus entry & exit
•Inhibitors of viral uncoating and replication
•Inhibitors of protein translation
2) Immunomodulatory roles include 
•Enhanced T-cell responses
•Anti-inflammatory actions
•Tissue repair

Question 253

What is the function of cytotoxic T cells and natural killer cells?

Answer 253

The action of these cells kills virus-infected cells, as cell death removes viral replicative niches. CTLs and NK cells are contact dependent, as they kill infected cells directly. Host cells infected with intracellular bacterial pathogens also undergo forms of cell death (contact-independent).

Question 254

What are the 2 types of effector mechanism for humoral innate immunity?

Answer 254

1) Soluble effector mechanisms
> Complement mediated bacterial destruction
> Lectin-binding to neutralise cell attachment or entry
> Iron chelation (siderophores) to prevent replication
> Antibiotic-like peptides
2) Cellular effector mechanisms
> Reactive Oxygen and Nitrogen radicals
> Acidification and digestion within phagosomes

Question 255

How do dendritic cells and macrophages activate T cells?

Answer 255

Activated macrophages and DCs present antigens in combination with MHC-I or MHC-II to T cells. Cytokines produced by antigen-presenting cells produce a suitable milieu for T-cell activation, for instance, IL-12 promotes T-cell replication. T cells provide cytokines that activate phagocytes, allowing responses that are specific to general class of pathogens.

Question 256

How do T cells help B cells produce antibodies?

Answer 256

Antigen presenting cells (e.g. dendritic cells and macrophages) are activated by infection and cytokines. T cell are activated by cognate MHC + foreign peptide recognition. B cells become licensed for antibody production against antigen being presented on the BCR. The antibody-mediated enhanced antimicrobial response involves:
•Phagocytosis (opsonisation)
•Complement activation

Question 257

What are the cytokines and major immune reactions of effector T cells?

Answer 257

1) Th1: its defining cytokine is IFN-gamma, which targets macrophages to allow their activation. Its role in host defence is against intracellular pathogens.
2) Th2: its defining cytokines are IL-4, IL-5 and IL-13, which target eosinophils and mast cells to allow their activation. They can alternatively also activate macrophages. Its role in host defence is against Helminths.
3) Th17: its defining cytokines are IL-17 and IL-22, which target neutrophil, to both recruit and activate them. Its role in host defence is against extracellular bacteria and fungi.