Theme 4 : Infection and Immunity Flashcards
Describe using examples how bacteria are named
Scientific names written in italics or underlined
Genus first, then species
E.g pneumococcus = Streptococcus pneumoniae
Explain the difference between Eukaryotes and Prokaryotes in terms of their nucleus and organelles
Prokaryotes : No nucleus, no membrane bound organelles
Eukaryotes : Membrane - bound nucleus
Prokaryotes GENOME
Single, circular DNA
Haploid
Non-genomic DNA sometimes: e.g in plasmids
Eukaryotes GENOME
Chromosomes in nucleus
Diploid
Explain the difference between Eukaryotes and Prokaryotes in terms of their RIBOSOMES and it’s subunits
Prokaryotes: 70S
Subunits = 50S and 30S subunits
Eukaryotes: 80S
Sub units = 60S and 40S subunits
What is the cell wall of a prokaryote made out of?
Peptidoglycan
What does Gram stain depend primarily on?
The amount of peptidoglycans in bacterial cell wall
What are the steps of a Gram Stain?
- Fixation of Crystal violet stains the cell wall
- Iodine treatment is added
- Decolorisation using alcohol or acetone
- Counterstain with safranin (pink) if crystal violet colour is lost
What does the iodine treatment do?
To form a complex with crystal violet that is insoluble in water and deepens the colour
Ball-like spheric shapes of bacteria are called…
Cocci
Rodlike shapes of bacteria are called…
Bacilli
Banana-like / macaroni shaped bacteria are called…
Vibrio
What are the features of a Gram-positive bacteria?
Thick peptidoglycan layer
+ lipoteichoic and teichoic acid
Inner cytoplasmic membrane
What are the features of a Gram-negative bacteria?
Has an Outer membrane
Lipopolysaccharide
Protein channels = porins
Thin peptidoglycan
Inner cytoplasmic membrane
What does Bacterial envelope structure determine?
Determines Gram staining
Influences susceptibility to antibiotics
Determines pathogenicity
What is peptidoglycan?
3D polymer of N-acetylated sugars
and amino acid peptides that are cross-linked to make a rigid wall
What is a Cell membrane?
osmotic barrier between cell and environment made of protein and phospholipids, but not sterols
What are the N-acetylated sugars
found in peptidoglycans?
glucosamine (NAG) and muramic acid (NAM)
.
.
What are peptidoglycans cross-linked by?
Transpeptidase enzymes
What is endotoxin?
Lipopolysaccharide
What is a special feature that can only be found in Gram-negative bacteria and where?
Lipopolysaccharide in the outermembrane
What are the components LPS is made up of?
Lipid A = long-chain fatty acid anchor (active component)
Core polysaccharide chain
Variable CHO chain (= O antigen)
What is the function of LPS?
It is an endotoxin
Major structural component
Effective permeability barrier due to the porins (including to antimicrobials)
Modulates host immune response
What does Amphipathic mean?
really strong hydrophobic end and a really strong hydrophilic end
Why can’t you stain M. pneumoniae?
It doesn’t have a cell wall, and can’t be cultured because they need to be cultured intracellularly in a human cell
Why can’t you stain Mycobacteria?
It has a very thick lipid membrane made of mycolic acids which affect their Gram staining, and allow intracellular survival.
Use ZN stain instead.
What does facultative anaerobes mean?
Switch between aerobic and anaerobic metabolism
Difference between aerobes and anaerobes
aerobes use O2 as the final electron acceptor while anaerobes undergo fermentation (the final electron acceptor is an organic molecule)
Can you give me 3 examples of what bacteria can’t make and have to bring in?
Purines and pyrimidines
Amino acids
Vitamins
Name an example of an easy-to-grow bacteria and what they need
E.Coli needs glucose and inorganic salts only
Name an example of a hard bacteria to grow
Treponema pallidum (cause of syphilis)
What are the physical requirements for bacteria growth?
Temperature
pH
Salt content
What is a capsule?
Polysaccharide coat
‘hides’ immunogenic cell wall
Disadvantage of a capsule
Metabolic burden on the bacterium
What do bacterial ribosomes conatin?
RNA and proteins
What ifnluences bacteria move to move?
Chemotaxis – moving towards or away chemical stimuli
How do bacteria move? (3 ways)
Rotate a flagellum like a propeller
Use a pilus like a grappling hook: attach, and pull the cell forward
Corkscrew motility – if you are a spirochete
What are the 3 ways bacteria can stick?
Non-specific adherence “docking”
Specific adherence “anchoring”
Biofilm formation
What is tissue tropism?
Adhere to specific tissue
Describe the 2 different adherins
Pili = long, hairlike, 1 to 10, only in gram-negative bacteria
Fimbriae = short bristle-like fibres, 200 to 400 in a cell, G+ and G- bacteria
What is special about biofilm formation?
Resist host immune response; less susceptible to antibiotics
Name the 3 ways bacteria can reproduce
Transduction
Conjugation
Competence / transformation
Transduction
In a phage-infected bacterial cell, fragments of the host DNA are occasionally packaged into phage particles and can then be transferred to a recipient cell.
Conjugation
The transfer of DNA from a donor cell to a recipient that requires cell-to-cell contact.
Common Conjugation
Genes on conjugative plasmids, such as the F plasmid, encode products that are necessary for replication and transfer of the plasmid to the recipient.
Rare Conjugation
F plasmid becomes integrated into the host chromosome (Hfr), and conjugation results in a partial transfer of the donor chromosome.
Competence/transformation
Can take up free DNA from their environment.
How can the donor chromosomal DNA be permanently maintained and expressed in the recipient cell via competence/transformation?
If it is integrated into the recipient genome by physical recombination
What are Mobile genetic elements?
Plasmids and Transposons that code for toxins and antibiotic resistance genes
What are plasmids?
Circular ‘extra-chromosomal’ DNA
Independently replicating
Present in many bacteria
Can code for dozens of genes like viruses
Passed down to progeny (offspring)
Some transmitted between bacteria
What are Transposons?
DNA sequences that are able to move location in the genome.
Encode transposase plus other genes
Mobile between:
Genomic and plasmid DNA
Plasmids
Plasmid and genomic DNA
What happens to DNA processes (replication, translation, transcription) due to bacterial DNA is not enclosed within a membrane-bound nucleus?
Occurs adjacent to other cellular processes and DNA can be more readily transferred between the chromosomal DNA and mobile elements
What do spores allow bacteri to do?
Become dormant and stop multiplying to become more resistant
What are spores resistant to?
Drying
Resist very high and low temperatures
Disinfection
Digestion
Can last thousands of years
What helps maintain spore status?
The DNA, ribosomes and dipicolinic acid
What are spores important in? (in terms of lab research)
clinical disease pattern
infection control
The lag phase
No increase in cell numbers.
Adjustment to new environment
Gene regulation.
The exponential/log phase
Cell doubling.
Slope of the curve = growth rate of the organism in that environment.
The stationary phase
Nutrients become depleted
Metabolites build up
Division stops
Gene regulation
Death phase
Exhaustion of resources
Toxicity of environment
True or “professional” pathogens
cause disease in any susceptible host
“Opportunistic” pathogens
only cause disease in immunocompromised patients
Virulence
fundamental properties of the organism which determine how it causes the diseases it does
Symbiosis
mutual benefit
Colonisation
when an organism lies on us but is not causing infection
commensal
an organism which lives on us / in our gut but doesn’t cause infection
What kind of bacteria is Staphylococcus aureus and where is it found?
A normal commensal of anterior nares found in 20-60% of healthy adults at any one time
What are the 5 aspects
to consider with virulence?
Cell-wall factors
Secreted factors
Coagulase
Capsule
Regulation of gene expression
What are the the five main virulence mechanisms of S. aureus?
surface proteins which mainly function as adhesion molecules
A group of secreted proteins
A capsule around the organism
A cell wall-associated enzyme called Coagulase
A quorum sensing regulatory system that controls gene expression
What do Cell wall-associated adhesins of S. aureus do?
Some bind host proteins like elastin and allow tissue adherence
They also can coat the bacterium in host proteins = Immune evasion
Describe Protein A
Binds the Fc portion of IgG
Ig molecules
held the wrong way round
A very specific version of this is protein A which binds immunoglobulin
Which proteins does S.aureus secrete?
exotoxins
Describe the exotoxins secreted by S.aureus
Cytotoxins
Pore-forming toxins, lyse host cells
Eg Panton-valentine leukocidin (PVL) – lyses polymorphs
Exfoliative toxins
Proteases which target epidermal structural proteins
Enterotoxins (superantigens)
Stimulate massive T cell activation, immune evasion
and more… complement inhibitors
What is S. aureus coagulase?
Cell wall-bound enzyme
Stimulates clotting
Plays a role in immune evasion
Also used as a test to distinguish S. aureus from other less virulent staphylococci in the laboratory
What does S. aureus polyssacharide capsule do?
Masks cell surface features from recognition by the immune system
Describe S.aureus’ capsule
Compared with other bacterial species the S. aureus capsule is typically thin - ”microcapsule” but helps avoid phagocytosis by neutrophils
What are the skin infections (3) caused by S.aureus?
Furunculosis
Staphylococcal abscess
Impetigo
The “glass test”
a way of showing that the rash is non-blanching ‘purpuric’ as this is characteristic of the rash seen in meningococcal disease
Consolidated lung
pus where there should be air
Haemoptysis
blood-stained sputum (phlegm)
Secretory IgA protease
Breaks down secreted immunoglobulin A, preventing mucosal clearance
Pneumococcal surface protein A (PspA)
ignore
Inhibits complement deposition and hence activation of cascade and clearance of bacteria
also neutralises lactoferrin’s bactericidal activity
Capsule immune invasion
Polysaccharide coat prevents complement-mediated phagocytosis.
Specific antibodies to capsule required (implications for immunisation)
> 100 different capsular types
What are autoinducers?
Signalling molecules that are produced in response to changes in cell-population density.
What are the signalling molecules for Gram-positive bacteria?
auto-inducing peptides (AIPs)
How do bacteria communicate?
Bacterial quorum sensing
What happens when autoinducer extracellular concentration is lower than intracellular concentration?
Cells continue to replicate
What happens when autoinducer extracellular concentration is equal to intracellular concentration?
Replicated cells begin to produce autoinducer too
What happens when autoinducer extracellular concentration is more than intracellular concentration?
Intracellular AI stops moving ou of the cell
How does higher AI concentration downregulate itself when extracellular concentration is much higher than intracellular concentration?
Inhibits its own transcription factor
How is AIP detected by bacteria?
2-component signal transduction circuit, activating a response regulator protein.
When AIP is detected and sends out a response regulator protein, what does this bind to and what happens?
This then binds to promoter DNA and regulates transcription of QS-regulated genes
What is the name if the gene cluster that encodes the peptide quorum-sensing system in S. aureus?
Accessory gene regulator (agr)
S. aureus is a common cause of infections for…
patients who need vascular access devices for e.g. cancer treatment
Where do S. aureus line infections commonly ‘seed’ in the blood to distant body sites? And what causes this?
Heart valves
Bones and joint
This is because of S. aureus adhesins
Which bacteria is a more common cause of line infection but why is it less severe than S. aureus?
S. epidermidis
However, these are much less severe and rarely seed in the blood
What is another illness caused by S.aureus but is not an infection? Which part of the bacteria causes this?
Food poisoning
Ingestion of Staphylococcal enterotoxins
In a gram test, Lipopolysaccharide (LPS) can only be found in?
Gram-negative
What is Lipid A?
long-chain fatty acid anchor (active component)
Name 3 properties of Lipopolysaccharide/endotoxin
Major structural component
Effective permeability barrier (including to antimicrobials)
Modulates host immune response
Name 3 components of Lipopolysaccharide/endotoxin
Lipid A = long-chain fatty acid anchor (active component)
Core polysaccharide chain
Variable CHO chain (= O antigen)
A breakdown in immunity leads to
immunodeficiency
A breakdown in tolerance leads to
autoimmune diseases and allergy
Why is Meningococcus difficult to study?
Extra-cellular pathogen; only effects humans – no good animal model for it
What prevents Meningococcus in the blood from entering Cerebrospinal fluid?
Nasopharyngeal epithelium, posterior to the nasal cavity
How does Meningococcus enter the Cerebrospinal fluid?
Primary adhesion is mediated by meningococcal type IV pilus to laminin receptors on brain endothelial cells.
What does primary adhesion cause?
Of meninges
Interaction of CD147 and Beta2-adrenoceptor stimulates changes within the cell that leads to the development of cortical plaques.
What does cortical plaques do after they developed?
protect bacteria from complement-mediated opsonisation and lysis
What happens to meningococcus after being in the coritcal plaques?
disrupt tight junctions between endothelial cells and so allows paracellular spread into CSF
What happens when N. meningitidis undergoes blabbing? (creating extra blebs)
shedding of lipopolysaccharide – distracts immune system
= very high levels of lipopolysaccharide in blood
= lethal
What is the most common form of pneumonia?
Streptococcus pneumoniae
Streptococcus pneumoniae can cause disseminated disease, what are the diseases Streptococcus pneumoniae cause? (6 places)
Upper Respiratory Tract Infections
Sinusitis
Otitis media
Bacteraemia
Meningitis
Endocarditis (Infection of heart valves)
What do specific adhesins give?
tropism
tissue tropism
Give an example of tissue tropism and explain why it is
Pneumococcal surface protein A (PspA) binds the laminin receptor on brain endothelial cells, triggering transcellular passage into the CSF
What is pneumolysin? What does it do when it is released?
Cytoplasmic enzyme
binds to cholesterol in host cell membrane; then oligomerises (collects up) to form pore
What does pneumolysin affect?
erythrocytes, platelets, innate and adaptive immune cells, cardiomyocytes, epithelial cells and endothelial cells.
What does pneumolysin cause?
Cytolysis activates complement proteins that alters the alveolar-capillary barrier
What does Secretory IgA protease from streptococcus pneumoniae do?
Breaks down secreted immunoglobulin A, preventing mucosal clearance
What does Pneumococcal surface protein A (PspA) from streptococcus pneumoniae do?
Inhibits complement deposition and hence activation of cascade and clearance of bacteria
Also neutralises lactoferrin’s bactericidal activity
What does the capsule of Streptococcus pneumoniae do?
Polysaccharide coat prevents complement-mediated phagocytosis.
Specific antibodies to capsule required (implications for immunisation)
> 100 different capsular types
Lipopolysaccharide’s blebbing off causes…
Triggering of many components and can cause rashes
What component of Neisseria meningitidis is targeted with this vaccine
Polysaccharide capsule
Why do HCAIs matter? (5)
Up to 10% of patients acquire infection in hospital in UK
Longer hospital stays – on average increased by 3 – 10 days
Costly - an extra £4000 - £10,000 to treat a patient with infection
Distressing for the patient, their family and the staff
More than 5000 deaths per annum
What is the resevoir?
where the infectious agent lives and lurks
– in or on humans; animals; the environment; food; things
What does ‘fomites’ mean?
inanimate objects that can carry and spread disease and infectious agents
What are the 3 routes of transmission of infections?
Contact
Droplet
Airborne
Contact transmission can be…
Direct or indirect (via fomites)
Transmission via fomites transmits to…
exposed mucosa, conjunctiva or the immediate environment
Which transmission of diseases can be artificially generated by some procedures?
Airborne transmission
What are natural orifices?
mouth, nose, eyes, vagina, anus etc – mucous membranes especially
What are iatrogenic?
wounds, catheters, IV cannula, endotracheal tube
What are the factors that cause people to be susceptible to HCAI?
Length of Hospital Stay
Conditions
Invasive Procedures
Antibiotic Use
Age
Poor Hand Hygiene
Disinfection
High Patient Density
Members carrying infections
Vaccination
Immunosuppression
Multi-Drug Resistant Infections
Late Treatment
Invasive Infections
Infection Location
Infections in critical areas
Organ Dysfunction
Surgical Site Infections
What are the 2 categories of microbial flora that colonises our hands?
Resident
Transient
Resident flora
found on the surface, and are generally of low pathogenicity
Transient flora
made up of microorganisms acquired by touching contaminated surfaces and are readily transferred to the next person or object touched.
How do healthworkers reduce contamination?
removing all wrist and hand jewellery
wearing short-sleeved clothing when delivering patient care
making sure that fingernails are short, clean, and free from false nails and nail polish
covering cuts and abrasions with waterproof dressings.
Your patient needs intravenous fluids. You wash your hands before inserting the cannula. What part of the chain of transmission does this interrupt most?
The portal of exit – you wash your hands to reduce the bacterial load on your hands before touching the patient or performing an invasive procedure, acting on the portal of exit.
What does Selection of PPE (Personal Protective Equipment) depends on
risk of transmission of microorganisms to the patient or carer
risk of contamination of healthcare practitioners’ clothing and skin by patients’ blood or body fluids
be fit for purpose
What are the 2 types of gloves?
Non sterile (protects you) and Sterile (protect patients and you)
What are the 2 types of respiratory protection?PPE
Fluid resistant surgical masks - Risk of droplet transmission
Respirators -
Risk of airborne transmissions
What are the 2 types of clothing protection?
Apron (protects you) and Gown (protects you and (patient)
Your patient needs intravenous fluids. You put gloves on before inserting the cannula. What part of the chain of transmission does this interrupt most?
The portal of entry – gloves here are to help protect the clinician from exposure to the patient’s body fluids in case of a needle stick injury or any broken skin.
Negative pressure
sucking air into the room (not taking air out) protecting other patients
Positive pressure
air pushing outside of the room – protecting patient
What does MRSA screening do?
Reduce bacterial load preoperatively
Alter antibiotic prophylaxis
Source isolation
What are the 6 vaccinations Healthcare workers should be vaccinated against?
Influenza
MMR (Measles, Mumps, Rubella)
Chickenpox (VZV)
Hepatitis B
TB (BCG)
COVID-19 (SARS-CoV-2)
Leucocytes
white blood cells of the immune system
Where do all cellular elements of blood originate?
Bone marrow
Hematopoiesis
production of blood cells
Leucopoeisis
production of leucocytes
What are the two major leucocyte lineages?
Lymphoid (Lymphocytes) – small, bland-looking cells
Myeloid – larger cells; most have prominent cytoplasmic granules and are called granulocytes
What are mature cells called?
effector cells
What are Lymphoid tissues?
collections of leucocytes, and serve as meeting points for cells of the immune system
Describe B cells
produce antibodies
Antibodies are proteins that bind to antigens
Particularly important in dealing with extracelllular infections such as bacteria
Describe T cells
Precursors are produced in the bone marrow; complete maturation in the thymus during gestation
CD8 T cells are particularly important in dealing with intracellular infection (viral infection)
CD4 (helper) T cells are needed to direct the activity of the immune system
What are NK cells important in?
important in dealing with intracellular infection and tumours
What are the names of the cytokines that are named differently?
tumour necrosis factor (TNF) alpha or interferon (IFN) gamma
What do CXCL8 do?
attracts neutrophils to sites of infection
What are the Cardinal features of acute inflammation?
Pain (Dolor)
Heat (Calor)
Redness (Rubor)
Swelling (Tumor)
(Loss of function – added later)
How does inflammation happen?
For many infections, the first step is to breach a barrier such as the skin and enter the tissue
The first cell that will be met is a tissue macrophage
Tissue macrophages will engulf and kill organisms by a process called phagocytosis
Explain the process of phagocytosis
Organism phagocytosed into a phagosome, which then fuses with a lysosome containing digestive enzymes.
The organism is killed in this ‘phagolysosome’ by low pH, digestive enzymes, toxic free radicals and hydrogen-oxygen products
will also release soluble mediators
What are the soluble mediators released by phagocytes?
Cytokines:
Tumour necrosis factor alpha (TNF-alpha)
Interleukin-1 (IL-1)
Interleukin-6 (IL-6)
and Chemokines: CXCL8
How does Cytokines and chemokines promote local inflammation?
Attracting other cells, particularly neutrophils
Acting on blood vessels to cause:
Vasodilation
Increased permeability
Increased adhesion molecules
‘systemic’ inflammation
inflammation is not confined just to the local area
Outcomes of acute inflammation
Resolution: insult removed, tissue heals completely
Fibrosis: insult removed, but tissue is scarred
Chronic: insult cannot be removed
Abscess formation
bad things about inflammation
May damage healthy tissue = bystander damage
May be activated inappropriately (without infection)
May be activated in an uncontrolled manner: septic shock
good things about inflammation
Amplifies the immune response
Focuses the immune response
Activates the next stages of immunity (B cells/ T cells)
What does Antigen-specific mean?
The antibody binds to a particular antigen with high affinity, but not to other antigens
What region does the antigen bind to the antibody?
FAB region
What does the Fc region do?
interacts with other components of immunity
What is FAB made up of?
Light chains and heavy chains
Why is FAB known as the variable region?
Because this region needs to be able to bind any potential antigen, it is very VARIABLE between different antibodies
What is Fc region also known as and why?
Constant region - does not bind to anything
What can the variable region recognize on an antigen?
epitope - particular motifs on the surface of an antigen that can get together with the surface of the antibody
What is the constant region made up of?
heavy chains
How many types of antibodies can B lymphocyte cells produce and where are they on the cell?
one type, all on the surface
What happens to the antibodies that B lymphocytes make?
secreted into the bloodstream and circulated as free proteins
What is the other name for antibody?
immunoglobin (Ig)
What does antibody ‘isotypes’ mean?
Different heavy chain constant regions produce antibodies with different properties - constant region/heavy chain is swapped out
What are the 5 different antibody ‘isotypes’?
IgM, IgD, IgA, IgG, IgE - GAMED
What is the first antibody produced in an immune response?
IgM
IgM has a low affinity (doesn’t bind antigen very well) how is this counteracted to still be deemed useful?
Forming pentamers which are held together by a joining J chain to increase surface area which makes binding better. In circulation for 2 months
What is so special about IgA?
it is the only antibody that can pass through mucosal surfaces
IgA is found in secretions but specifically where and why?
In Colostrum (forerunner of breast milk) to protect infants bowel because they are not able to produce their own IgA
Describe the structure of IgA
Forms dimers (joining j chain) with 2 antibodies attached to each other by the constant (Fc) region protected from digestion by a secretory component (s chain) wrapped around
What other antibody is similar to IgM? But whats different about them?
IgD - but has no known function
What is IgG?
The main mature antibody form; circulates as a monomer
What is IgE? What is it believed to be important in?
Circulates as a monomer; exact function not known, but believed to be important in parasitic infection. Definitely important in allergic disease
How can antibodies help us?
By binding to things and directly affecting them
By binding to things then interacting with another element of the immune system
When bound to B cells: by acting as the B cell receptor
What is tetanus and how is it caused?
Muscle contraction - The bacteria Clostridium tetani releases a toxin
When is Tetanus immunoglobulin effective?
for prevention after high-risk injuries and for treatment
Describe ‘Receptor blocking by antibody’
Virus uses receptor to attach to host cell and gain entry - Antibody blocks receptor
What kind of receptors do phagocytic cells have and how does it effect phagocytosis?
receptors for the Fc portion of the antibody which enhances phagocytosis by reducing the repulsion between two negatively charged membranes
Describe the process of opsonisation
Process of coating bacteria to enhance phagocytosis
What is found on the surface of mast cells?
Mast cells have surface Fc receptors
and become coated wth IgE antibody from circulation
What happens when an antigen interacts with a mast cell?
antigen binds to the IgE antibodies and cross-links them, then ‘degranulates’, releasing histamine
.
.
What is Antibody-dependent cellular cytotoxicity?
When a natural killer cell recognises antibody-coated bacteria by Fc receptor then the target organism is then killed by non-phagocytic means.
What does the interaction with a complement do?
Activates complement system, Opsonisation, Inflammation
and/or Terminal attack pathway
Describe the principle of receptor generation by somatic recombination
Each DNA region contains multiple different gene segments for the variable region of an antibody. To generate a complete gene encoding an antibody, a segment from each region is required
How can you generate a variable region of the antibody?
Combining gene segments from different regions
What are the advantages of somatic recombination?
Huge diversity = recognise whatever is in our environment
A large number of receptors can be made from a smaller area of DNA
Everybody has a unique repertoire = resilient in different environments/ against emergent pathogens
Still inherit the gene segments = benefit from evolutionary experience
What are the Disadvantages of somatic recombination?
The receptors are generated at random = many combinations will not work out:
Some can’t fit together biochemically and others will bind to our own proteins (self antigens)
B cells with dysfunctional receptors are mostly destroyed = process is energy intensive
Deletion of B cells that can recognise self-antigens is not complete = potential for autoimmune disease
What is clonal selection?
We all start with a unique set of B cells then During infection, B cells with the best response to the infection antigen are selected out and divided
What happens during Maturation of antibody response? (after IgM antibody release)
the B cells divide in the antigen-driven process then Class switch and
Somatic hypermutation occurs
What is Class switch?
IgM in the ‘primary response’ switches to IgG. The variable region of the antibody remains the same
What is Somatic hypermutation?
Random mutations are introduced into the variable region of the antibody, so the daughter cells produce a slightly different antibody.
Further rounds of clonal selection pick out the best receptors
What is the basis of the secondary immune response?
mature B cells become long-lived memory cells. When stimulated again, they respond vigorously
What causes Subsequent exposures to the same pathogen?
By high-affinity IgG antibodies in the secondary immune response
What does it mean when the immune system is tolerant?
B cells receptors (antibodies) are generated at random, so some will react to self antigens
Those that bind to self-antigens are either destroyed or kept under control
What is innate immunity?
the body’s first line of defense against germs entering the body
what is the fundamental feature of innate immunity?
recognition of antigen by non-specific pattern recognition receptors
Why is it called innate immunity?
receptors are ‘germline encoded’ - meaning built-in, a gene that encodes these receptors
What is the difference between cells in innate immunity and adaptive immunity?
B cells have receptors that are not germ line-encoded – produced by random somatic recombination
B cell receptors are antigen-specific
The system needs to ‘learn’ by clonal selection
B (and T) cell receptors are fundamentally different
What are the functions of innate immunity?
Prevents infection
Promotes acute inflammation
Responds rapidly
What is older in terms of evolutionary terms?
innate immunity is far older
What are the mechanical Innate barriers to infection for the skin and gut?
Epithelial cells joined by tight junctions
Longitudinal flow of air or fluid
What are the chemical Innate barriers to infection in the skin?
Fatty acids
Antibacterial peptides
What are the microbiological Innate barriers to infection in the skin?
Normal flora
What are the chemical Innate barriers to infection in the gut?
Low pH
Enzymes (pepsin)
Antibacterial peptides
What are the microbiological Innate barriers to infection in the gut?
Normal flora
Which are the areas that do not have a microbiological innate barrier?
Eyes/Nose and Lungs
What are the mechanical Innate barriers to infection in the lungs?
Epithelial cells joined by tight junctions
Movement of mucus by cilia
What are the chemical Innate barriers to infection in the lungs?
Antibacterial peptides
What are the mechanical Innate barriers to infection in the eyes/nose ?
Epithelial cells joined by tight junctions
What are the chemical Innate barriers to infection in the eyes/nose ?
Salivary enzymes (Lysozyme)
Why are antigen receptors of innate immunity used to detect antigens?
for ‘pathogen-associated molecular patterns’ (PAMPS)
What is PAMPS?
Pathogen-associated molecular patterns (PAMPs) that occur in lower organisms, but do not occur in humans
This can show the difference between higher and lower pathogens
This is an effective mechanism for distinguishing self from non-selfusing its molecular motifs
What is the name of the receptors that antigen receptors of innate immunity use for PAMPS to detect non-specific antigen?
pattern recognition receptors (PRRs)
Give an example of a PRR
Mannose binding lectin
What does Mannose binding lectin do?
The Globolous head recognizes the residues, They bind with high affinity to mannose and fucose residues with correct spacing
Then find the Difference between higher and lower organisms
What is an example of a pattern recognition receptor?
Toll-like receptors (TLRs)
Drosophila (fruit flies) are susceptible in fungal infections when…
with TLR mutations
Neutrophils and macrophages are highly phagocytic cells. What happens to the ingested material?
Ingested material killed by low pH, enzymes and respiratory burst that produces free radicals
What is the function of phagocytosis?
killing
activation of inflammation
antigen presentation (see T cell lecture)
What happenif mast cells meet parasite ?
Release histamine which causes
lots of gut contraction and diarrhoea to expel parasite
Describe how natural killer cells recognises bacteria and kill
The natural killer cells recognises antibody-coated bacteria by Fc receptor; the target organism is then killed by non-phagocytic means
What is the process called when natural killer cells recognise bacteria and killed by non-phagocytic means?
Process known as antibody-dependent cellular cytotoxicity (ADCC)
What do Eosinophils do? (causes)
Believed to be important in defence against parasites
Causes Local infiltration at sites of infection
Causes Numbers in blood increase during parasite infection
Can perform antibody-dependent cellular cytotoxicity
Where are Eosinophils found?
Found at sites of allergic inflammation
What makes up Eosinophils?
Pink is Granules that contain toxic enzymes
What does Phagocytosis activate the release of?
soluble mediators - cytokines and chemokines
What are the cytokines that are released during phagocytosis?
Tumour necrosis factor-alpha (TNF-alpha)
Interleukin-1 (IL-1)
Interleukin-6 (IL-6)
What is the chemokines that is released during phagocytosis?
CXCL8
How do chemokines and cytokines promote local inflammation?
Attracting other cells, particularly neutrophils
Acting on blood vessels to cause:
Vasodilation – more white blood cells, heat, more blood flow, redness
Increased permeability, allows fluid through - swelling
Increased adhesion molecules on blood vessel endothelium
What do Cytokines do to the liver during ‘systemic’ inflammation?
Causes the release of acute phase proteins (C-reactive protein, mannose-binding lectin)
Which causes activation of complement opsonisation
What do Cytokines do to the bone marrow endothelium during ‘systemic’ inflammation?
Causes neutrophils in bone marrow endothelium to be mobile which causes phagocytosis
What do Cytokines do to the hypothalamus during ‘systemic’ inflammation?
Causes an increase in body temperature
Which decreases viral and bacterial replication, increases antigen processing and specific immune response
What do Cytokines do to the fat/muscle during ‘systemic’ inflammation?
Protein and energy mobilization to allow an increase in body temperature
Which decreases viral and bacterial replication, increases antigen processing and specific immune response
What are Soluble mediators?
secreted substances that circulate and MEDIATE an effect
What is Complement in terms of immunity (specifically innate immunity)?
a series of enzymes that are produced in the liver and circulate in an inactive form in the bloodstream
What happens when the first enzyme of a complement is activated?
A triggered enzyme cascade occurs
What are the three ways that activates a complement system?
Classical (antibody-antigen complex)
Mannan-binding lectin
Alternative – complement directly on surface of bacteria
What happens when a complement system is activated?
Long triggered enzyme cascade to cell lysis and debris is removed in the spleen
How do cells lyse in a complement system?
In a Terminal pathway where components assemble a ‘pore’ which inserts into pathogen membranes
Describe the role complement plays in opsonisation
Activated complement component C3b sticks to pathogens
Binds to phagocyte C3b receptors
What can Interferon alpha and beta can be produced by? How is it activated?
virtually any cell activated by a viral infection
What are the Antiviral effects of alpha-interferons?
Stop cells dividing
Stop cells synthesising new proteins - Turn off replication
Stimulate production of anti-viral proteins by host cell
Where do Alpha and Beta-interferons work?
They diffuse out to surrounding cells and work locally
In the lab what do we use to culture bacteria?
Agar plates - Polysaccharide derived from seaweed
Mix with water plus:
Blood
Potato starch
Sugars / Salts
Antibiotics
pH indicators
What are the 3 most common types of agar plates for culturing bacteria?
blood
lysed blood (“chocolate”)
CLED (cysteine-lactose-electrolyte-deficient)
In 24 hours of incubation, what do the yellow streaks on CLED agar indicate?
They indicate that the bacteria ferments lactose to produce acid
At 48 hours in the lab, the closer the bacteria to the antibiotic (regardless of concentration) the…
More resistant
How long does it take for any information from microbiology?
24 hours
How long does it take for definitive information from microbiology?
48 hours
What does Treating infection require?
A knowledge of what bacteria cause what syndromes of infection
Knowledge of resistance rates
What does Diagnostic microbiology
do?
Corrects your guesses
Allows you to focus your treatment
Informs the epidemiology
Give two examples of a patient who would require a sample to be sent to microscopy
Patient with:
UTI
suprapubic pain and dysuria
What does an unstained urine sample allow someone to observe?
Allows you to count white cells
What would a Gram-stained urine sample of A patient with suprapubic pain and dysuria show?
Gram negative rods ≈
Coliform (Enterobacteriaciae)
What are the symptoms of meningitis?
fever, headache, photophobia
For microscopy, how do we collect samples from a patient with meningitis?
Lumbar puncture obtaining cerebrospinal fluid
Why could cerebrospinal fluid be turbid/cloudy?
Due to the presence of white cells and protein
What would you observe in a Gram-stained CSF sample of a patient with meningitis?
Gram negative diplococci ≈ Neisseria meningitidis
Give a situation where microscopy can be useful
Can be useful from ‘sterile sites’ e.g.
Cerebrospinal fluid (CSF), joint fluid
Give a situation where microscopy cannot be useful
from ‘non-sterile’ sites
e.g. Sputum from a patient with chest infection
What would you use (in microscopy) on a patient with pneumonia and what would you observe?
alsohas HIV
Electron microscopy with Silver stain of lung biopsy of sputum showing Pneumocystis jiroveci
What would you use (in microscopy) on a patient with Vesicular rash and what would you observe?
herpes zoster virus (Herpes zoster) particles viewed under an electron microscope of vesicle fluid
What is sputum?
a thick type of mucus made in your lungs
What 2 stains would you use (in microscopy) on a patient with TB and what would you observe?
Ziehl Neelsen staining of sputum and Auramine fluorescence staining
to see the Acid-fast bacilli, then PCR after in contact tracing
What test would you use to identify if a patient has pinworm infection (Enterobius vermicularis)?
direct visualization of the pinworm through endoscopy and ‘Sellotape test’ of the ova (eggs) down a light microscope
When do we use Microscopy?
Gram staining for bacteria
Samples from a sterile site
A single pathogen expected
Special stains for
Other organisms eg TB
Electron microscopy for viruses
Direct visualisation of parasites and ova
What is the disadvantage of Bacterial culture?
Very slow and labour intensive
What are the advantages of Bacterial culture?
Good for detecting bacteria you can stain and grow
Reliable identification and resistance testing
Provides a lot of information
How do we test bacterial susceptibility in bacterial culture?
Disc testing
How do we identify bacteria in bacterial culture? (traditionally and new)
API strip testing - the basis of bacterial metabolism
MALDI-TOF (matrix-assisted laser desorption/ ionisation time of flight) is a method that uses mass spectrometry to identify it.
Describe the method of bacterial culture
Can quantify bacteria
Purification
Provisional identification
Antibiotic susceptibility testing
What are the 3 lab techniques used to identify Difficult-to-culture organisms?
Serological Techniques
Molecular Techniques (PCR)
Tissue culture
What are the organisms that stain poorly or you can’t culture? Give an example
Viruses
Cell wall deficient bacteria
For example:
Community-Acquired Pneumonia
Mycoplasma pneumoniae
Chlamydia pneumoniae
What is Serology?
Detection of antibodies using serum
IgM (acute infection)
IgG (long standing immune response)
Give examples of when can we use Serology
Patients with:
Chlamydia
Mycoplasma
Epstein Barr Virus (EBV)
Cytomegalovirus (CMV)
What is serum?
the fluid and solute component of blood which does not play a role in clotting
The GP sends serum to the laboratory for testing and the result comes back…
EBV
IgM negative
IgG negative
What does this mean?
They are EBV-susceptible
The GP repeats the blood tests one week later…
EBV
IgM positive
IgG negative
What does this mean?
They have an Acute EBV infection
The GP sends serum to the laboratory for testing and the result comes back, The GP repeats the blood tests one week later…
CMV
IgM negative
IgG positive
What does this mean?
They have CMV immunity
What is the disadvantage of serology?
Antibodies take time to develop (weeks)
What are Molecular diagnostic techniques?
Polymerase Chain Reaction (PCR)
Method to amplify DNA or RNA
and are Almost infinitely sensitive
What are the Significant Limitations of Molecular diagnostic techniques?
Inhibitors in biological samples
Sensitivity:
Laboratory contamination
Latent infections
But does not mean its positive this is causing it. Could be latent
What does latency mean?
ability of infection to remain dormant for long periods of time before reactivation - Genetic material present but not causing disease
Give examples of latent bacteria
Chicken pox reactivating as Herpes zoster (shingles)
Cold sores (HSV)
CMV & EBV (subclinical unless immune suppressed)
Tuberculosis
When is PCR useful? (patients)
Patients with:
Viral encephalitis
HIV
What is Viral encephalitis?
an inflammation of the brain caused by a virus that causes Fever, headache, confusion and fits
What are the causes of viral encephalitis?
Enteroviruses most common
Herpes viruses (HSV, VZV, CMZ, EBV)
What is the advantage of PCR when diagnosing someone with viral encephalitis?
Good negative predictive value
= the probability that a negative test result means that the patient does not have the disease
What is the disadvantage of PCR when diagnosing someone with viral encephalitis? But how is this counteracted?
Poor positive predictive value – the probability that a positive result means that the patient has the disease
backed up by brain imaging, cells in spinal fluid
Why do we use PCR in HIV patients?
To diagnosis in early HIV infection
To diagnose resistance
Monitoring response to treatment (‘viral load’)
Why do we use Whole-genome sequencing of bacteria in molecular techniques?
Compare strains to see how related they are/evolve
Interrogate for antibiotic resistance genes
Set to revolutionise the diagnosis of infection which is :
Rapid (hours)
Cheap (comparable to culture)
can use Desktop Platforms
When do we use tissue culture?
Intracellular organisms such as:
Viruses
Mycoplasma
Chlamydia
What are the 2 main ways of tissue culture?
Cytopathic effects on cells – create an environment
Expression of viral proteins detected at the cell surface
What do you mean by Virus-induced Cytopathic effects on cells?
Virus-induced cytopathic effect is the setting of cell changes or alterations resulting from a viral infection comparing cells grown artificially in a laboratory that are normal and cells that have been exposed to a virus
What do you mean by Expression of viral proteins detected at the cell surface?
Using Immunofluorescence - Detection of viral encoded protein expressed on cell surface
Antibodies labelled with fluorochrome
What is the benefit and disadvantage of serology?
For organisms you can’t grow
but it is Slow
What is the benefit and disadvantage of PCR?
Quick, sensitive
identifying latent infection
but Risk of contamination
What is the benefit and disadvantage of microscopy?
Quick, insensitive but non-specific
What is the benefit and disadvantage of bacterial culture?
specific, allows sensitivity testing
but Slow
What are healthcare-associated infections?
HCAIs are infections acquired in hospitals or as a result of healthcare interventions.
How are healthcare-associated infections caused?
They are caused by a wide variety of microorganisms, often by bacteria that normally live harmlessly in or on our body
Why do HCAIs matter?
Up to 10% of patients acquire infection in hospital in UK
Longer hospital stays – on average increased by 3 – 10 days
Costly - an extra £4000 - £10,000 to treat a patient with infection
More than 5000 deaths per annum
What is the chain of infection and what are its 6 components?
Transmission of infection is considered to be a cycle – AKA the “chain of infection”
Infection agents, resevoir, portal of exit, mode of transmission, portal of entry, susceptible host
What are the 3 routes of transmission?
- Contact:
Direct
Indirect (via fomites - Droplet:
>5-10µ in size (bigger)
fall with gravity within 1m
transmitted onto exposed mucosa, conjunctiva or the immediate environment - Airborne:
small airborne droplets and particles <5µ (smaller)
can remain in the air for long periods
can travel to fill the room
Can be artificially generated by some procedures
What are the 2 types of portals of entry?
natural orifices (mouth, nose, eyes, vagina, anus etc – mucous membranes especially)
or iatrogenic (wounds, catheters, IV cannula, endotracheal tube)
Who is susceptible to HCAI?
Patients with Underlying Medical Conditions: Patients with compromised immune systems, chronic illnesses, or other medical conditions are more vulnerable to infections.
Age: Infants, elderly individuals, and those with weaker immune systems are more susceptible.
Organ Dysfunction: Preexisting organ dysfunction can worsen with infection.
What increases HCAI susceptibility?
Length of Hospital Stay: Longer hospital stays increase the risk of exposure to infectious agents.
Invasive Procedures: Surgical interventions, catheterizations, and intubation increase the risk of introducing pathogens.
Antibiotic Use: Prolonged or inappropriate antibiotic use can lead to antibiotic-resistant infections.
Poor Hand Hygiene: Inadequate handwashing among healthcare workers can facilitate the spread of infections.
Inadequate Disinfection: Improper cleaning and disinfection of equipment and surfaces can harbor infectious agents.
High Patient Density: Overcrowded healthcare facilities can increase the risk of transmission.
Visitors and Family Members: Visitors carrying infections can introduce pathogens to patients.
Inadequate Vaccination: Lack of vaccination for preventable diseases can leave patients susceptible to infections.
Delay in Diagnosis and Treatment: Late identification and treatment can lead to complications.
Infection Location: Infections in critical areas, like the bloodstream or central nervous system, can be more severe.
How can we prevent HCAI via infection agent?
Targeted antimicrobial treatment
How can we prevent HCAI via resevoir?
Screening, source isolation, decolonisation
Mass DDT, vector control
How can we prevent HCAI via portal of exit?
Hand hygiene
Use of PPE
Waste disposal
Cough hygiene
How can we prevent HCAI via mode of transmission?
Use of PPE
Sharps disposal
How can we prevent HCAI via portal of entry?
Hand hygiene
Use of PPE
Aseptic technique
Risk assessment of inserted devices
How can we prevent HCAI via susceptible host?
Immunisations
Patient placement
What are the 2 types of microbial flora that the hands are colonised by?
The resident flora are found on the surface, just below the uppermost layer of skin, are adapted to survive in the local conditions and are generally of low pathogenicity, although some, such asStaphylococcus epidermidis,may cause infection if transferred on to a susceptible site such as an invasive device.
The transient flora are made up of microorganisms acquired by touching contaminated surfaces such as the environment, patients or other people, and are readily transferred to the next person or object touched. They may include a range of antimicrobial-resistant pathogens such as MRSA,Acinetobacteror other multi-resistant Gram-negative bacteria.If transferred into susceptible sites such as invasive devices or wounds, these microorganisms can cause life-threatening infections. Could lead to HCAI.
Explain bare below elbows in healthcare situations.
removing all wrist and hand jewellery;
wearing short-sleeved clothing when delivering patient care;
making sure that fingernails are short, clean, and free from false nails and nail polish;
covering cuts and abrasions with waterproof dressings.
When do we use alcohol gel?
excellent activity and the most rapid bactericidal action of all antiseptics
alcohols dry very rapidly, allowing for fast antisepsis at the point of care
less irritant to healthcare worker’s hands if contain appropriate emollients
When do we use soap and water?
Visibly soiled
Potentially contaminated with body fluids
When caring for patients with diarrhoea or vomiting, regardless of wearing gloves
Your patient needs intravenous fluids. You wash your hands before inserting the cannula. What part of the chain of transmission does this interrupt most?
The portal of exit – you wash your hands to reduce the bacterial load on your hands before touching the patient or performing an invasive procedure, acting on the portal of exit.
What does Selection of PPE depends on?
risk of transmission of microorganisms to the patient or carer
risk of contamination of healthcare practitioners’ clothing and skin by patients’ blood or body fluids
be fit for purpose
What are the 2 types of gloves?
Non-sterile - Dirty procedures,
Protect you
Sterile - Sterile procedures
Protect patient (and you)
When do we use gloves?
invasive procedures;
contact with sterile sites and nonintact skin or mucous membranes;
all activities that have been assessed as carrying a risk of exposure to blood or body fluids;
when handling sharps or contaminated devices.
What are the 2 Respiratory protection?
Fluid-resistant surgical masks
= Risk of droplet transmission
Respirators
= Risk of airborne transmissions (including AGP), FFP3, Must be fitted tested
What are the 2 types of Clothes protection?
Aprons – protect you
Gowns – protect patients (and you)
Your patient needs intravenous fluids. You put gloves on before inserting the cannula. What part of the chain of transmission does this interrupt most?
The portal of entry – gloves here are to help protect the clinician from exposure to the patient’s body fluids in case of a needle stick injury or any broken skin.
What is negative pressure?
sucking air into the room (not taking air out) protecting other patients
What is positive pressure?
air pushing outside of the room – protecting patient
When do we isolate patients?
Based on clinical diagnosis - don’t wait for lab results
Always isolate:
open tuberculosis
measles
infectious diarrhoea
fever in returning traveller (if risk of VHF)
Consider isolating resistant organisms
Describe screening for key organisms?
Search and destroy for Antibiotic-resistant organisms
Allows interventions to:
Optimise care for patient
Prevention spread to others
What does MRSA screening do?
Reduce bacterial load preoperatively
Alter antibiotic prophylxis
Source isolation
What happens when a patient’s MRSA screen comes back positive (before an operation)?
They start a decolonisation regime 5 days before admission, with regular hibiscrub wash and mupiricin up his nose.
At the time of his operation, the anesthetist alters their antibiotic prophylaxis to ensure cover for MRSA.
What happens when there is no swabbing for MRSA at his pre-op assessment?
They are given standard pre-op prophylaxis with flucloxacillin.
They develop an infected surgical site which develops into an MRSA sternal osteomyelitis, requiring weeks of antibiotics and multiple surgical debridement.
Healthcare workers should be vaccinated (or have proven immunity) against:
Influenza
MMR (Measles, Mumps, Rubella)
Chickenpox (VZV)
Hepatitis B
TB (BCG)
COVID-19 (SARS-CoV-2)
What is Monkeypox virus (MPXV)
ds-DNA virus - pox virus
From: Poxviridae family, Chordopoxvirinae subfamily, genus Orthopoxvirus
What is the size of MPXV?
Orthopoxviruses size range: 140–450 nm
Describe the genome of MPXV
200-500 kbp that codes for over 200 genes
Describe the size of a virus, how they can be visualised, and their shapes
20 – 300 nm
visualized under electron microscopy
Shapes: icosahedral or helical
Viruses are Obligate intracellular parasites, what does that mean?
they use the host cellular machinery to replicate
Describe the envelope of a virus
Lipid bilayer that surrounds the capsid of some viruses (enveloped viruses)
It contains glycoproteins that forms projections, or spikes
What is the capsid?
A protein coat that encloses the genome and the core proteins
Describe the Genome of a virus (that it could be)
A virus contains either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) – the genetic material constitutes the viral core
Single stranded or double stranded
Circular or linear
Single molecule or fragmented
Positive or negative polarity
What is the difference between Hep B and Hep D (virus, type of DNA and size)
HBV:
Hepadnaviridae
ds DNA
42-47 nm
HDV:
Deltaviridae
ss circular RNA
~39 nm
What is the virus, type of DNA and size of CMV (Human cytomegalovirus)?
Herpesviridae
ds DNA (double-stranded)
150-200 nm
What is the virus, type of DNA of Influenza?
Orthomyxoviridae
Segmented (-) RNA strand
How is a virus transmitted to the human host? (if it originates from an animal with immunity to the disease)
Across the species barrier
Within the same species , what is vertical transmission?
One generation to the next - (mother to child transmission)
Within the same species, name person to person transmissions of disease
Horizontal route
Airborne
Fecal-oral
Sexual
Vector-borne
Blood
What counts as airborne transmission?
Droplets (>2 µm), aerosols (<2 µm)
Name examples of airborne transmitted diseases
Common cold (rhinoviruses)
Influenza (Orthomyxoviridae)
Measles (Paramyxoviridae)
Mumps (Paramyxoviridae)
Rubella (Togaviridae)
Chickenpox (Varicella Zoster Virus – VZV - Herpesviridae)
Name 2 diseases that where transmitted by Fecal-oral transmission
HAV – hepatitis A virus
HEV – hepatitis E virus
Name diseases spread via Sexual transmission
HIV – Human Immunodeficiency Virus (AIDS) – Acquired
Immunodeficiency Syndrome
HBV – Hepatitis B virus (hepatitis B) +/- HDV (hepatitis delta virus) – chronic viral hepatitis
HPV – Human papillomavirus (genital warts, cervical/anal cancer)
HHSV – Human Herpes Simples viruses (recurrent genital sores)
(HAV, hepatitis C virus [HCV])
What viruses are spread via Vector-borne infections?
Arboviruses
Aedes mosquitoes spread…
Dengue
Chikungunya
Zika
Culex mosquitoes spread…
West Nile viruses
Ticks spread…
Tick-borne encephalitis (TBE)
What is Parenteral transmission?
Contaminated blood products – needles:
Transfusions, needle pricks, tattoos, razor cuts …
Name 3 Blood-borne viruses (BBV)
HIV
HCV
HBV (+/- HDV)
Transmission of human monkeypox
In endemic countries, spillover events occur from zoonotic animal reservoirs into humans, potentially leading to limited outbreaks usually facilitated by close human contact.
Outbreaks can also occur in nonendemic regions through introduction of the virus via human travel or importation of animals harboring the virus.
Subsequent human-to-human transmission can then occur via household contacts and via other close contacts.
Where can Mother-to-child transmission occur?
In utero (during pregnancy)
Intra partum (at childbirth)
Breast feeding
Name viruses transmitted by Vertical transmission
HIV, HCV, HBV (BBV)
CMV, Zika virus, rubella virus
How can DNA viruses replicate?
Host DNA-dependent RNA polymerase
How can (-) RNA viruses
replicate?
Viral RNA-dependent RNA polymerase
Describe the seuqence of events of Clinical protocols and infection control during monkeypox outbreaks
- Presentation
- Surveilance, Case investigation, contact tracing
- infection control using PPE
- Treatment - antivirals and vaccines
What are the 7 ways we can Directy detect viruses?
Light microscopy (to visualize the specific cytopathic effect on the host cells)
Electron microscopy (to visualize the viruses)
Particle agglutination test (particles coated with virus-specific antibodies)
Immunofluorescence technique (IFT)
Serology (use of antibodies to detect viral antigen – HBsAg)
Quantitative real-time polymerase chain reaction (qPCR) and reverse-transcription PCR (RT-PCR)
Viral culture
What can qPCR and RT-PCR do?
Widely used in clinical practice to detect active infections (presence/absence of the virus)
It allows the quantification of the virus in a clinical sample
What are the Indirect detection texts we can use for viruses?
Complement fixation test
Hemagglutination inhibition test
Enzyme-linked immunosorbent assay (ELISA)
What is the difference between a patient with Acute Infection with recovery and someone with Chronic Infection for hepatitis B? (serology)
acute Infection with recovery - has anti-has
What are Outcomes of acute viral infections?
Complete resolution and recovery
= Clearance of the virus from the host
Chronic infection
= Persistence of the virus in the host
What is Continuous viral replication?
Continuous generation of infective virions (e.g., HBV, HCV, HIV)
What is Latency of a virus?
a unique transcription and translational status of a virus in which the productive replication cycle is silent but can reinitiate
Give examples of latent viruses
(e.g., Ebstein-Barr virus [EBV], HHSV-1, HHSV-2, VZV, CMV)
Long-lived cells like neurons (HHSV, VZV), hematopoietic stem cells (CMV), memory lymphocytes (EBV)
Give the antiviral treatment of SARS-CoV-2
Remdesivir – Inhibition of the RNA-dependent RNA polymerase
What are the Antiretrovirals of (HIV)
Attachment inhibitors
Fusion inhibitors
Nucleoside and non-nucleoside reverse transcriptase inhibitors
Integrase inhibitors
Protease inhibitors
How can we Prevent the viral infection of Airborne transmission?
Active immunization (vaccines)
Masks
Social distancing
Isolation and quarantine of infected individuals
Hand washing
How can we Prevent the viral infection of Fecal-oral transmission
Active immunization (Vaccines)
Ensure safe water supply
Ensure safe disposal excreta
Avoidance of raw/undercooked food
Hand washing
How can we Prevent the viral infection of HIV
Treatment as Prevention (TasP)
Pre-exposure Prophylaxis (PrEP)
Post-exposure Prophylaxis after Sexual Exposure (PEPSE)
Condoms
Male circumcision
Principles of viral replication
Attachment - binding between the virus and the target cell
- Interaction between the viral glycoproteins and the cell receptor(s)
Penetration of the virus into the host cell (often receptor-mediated endocytosis)
Uncoating – enzymatic removal of the protein coat and liberation of the viral nucleic acid and core proteins into the cytoplasm
Production of viral specific mRNA – host cell ribosomes will subsequently synthesize the viral proteins (core, capsid)
Morphogenesis and maturation of the new viruses
Release (bursting of infected cells or budding through the plasma membranes
What are the 2 ways + RNA can replicate?
Reverse transcription into cDNA -> integration into host DNA -> Host DNA-dependent RNA polymerase
Used directly as RNA template
Describe the replication cycle of HIV
- Attachment and Fusion into cell membrane
- Reverse transcription
- Integration (into nucleus)
- Transcription
- Translation
- Assembly of proteins then budding and maturation
What kind of virus is Poxviruses?
brick or oval-shaped viruses with large double-stranded DNA genomes
What kind of virus is HIV?
positive-sense single-stranded RNA
Pathogenesis
the study of the disease process
What are the Direct cytopathic effects caused by the virus replicating in the host cell?
Inhibition of cell transcription/translation
Changes in membrane permeability
Alterations of the cytoskeleton or trafficking pathways
Cell-cell fusion
Induction of apoptosis
What does Indirect immune-mediated cell death
mean?
Immune response (llike inflammation) to viral infections is responsible for systemic symptoms like fever
What are the first natural barriers viruses must overcome?
Intact skin
Mucosal surfaces (eye, respiratory tract, gastrointestinal tract, genitourinary tract)
Where does Primary replication occur?
At the initial site of infection
Describe the movement to secondary replication sites
Some remain localised
Other Spread to other organs:
Haematogenous spread (Blood)
Lymphatic spread
Neural spread
What is Invasiveness?
is the capacity of a virus to enter a tissue or an organ
What is Virulence?
The relative ability of a pathogen to cause disease
What is tropism and what are the types that you could find for viruses?
the ability of different viruses to infect different cell types:
specific receptors in the host cell
specific host enzymes for viral maturation
temperature
pH
What are the 2 example of viruses with a Direct cytopathic effect?
West Nile virus = neurons; it induces apoptosis; causes encephalitis and movement disorders
Ebola virus = vascular leakage; hypotension; hemorrhagic fever
Give an example of a Disease caused by antibodies-mediated immunity
Dengue fever
= massive release of cytokines after reinfection from a different serotype; vascular leakage and hemorrhage
Give an example of a Disease caused by virus-initiated autoimmunity
Guillain-Barré syndrome
Give examples of diseases that are caused by virus-induced tumorigeneses
HPV – cervical/anal cancer
HBV, HCV – hepatocellular carcinoma
What are CD4 T cells?
‘helper’ T cells with CD4 marker on its surface
What is CD8 T cells?
‘cytotoxic lymphocytes’ T cells with CD8 marker on its surface
How do T cells Direct the immune response?
Innate immunity and B cells may recognise antigen, but they don’t necessarily know how to respond.
Helper T cells (CD4 cells) orchestrate the response
How does T cells Kill virally infected cells?
Antibodies cannot cross cell membranes to kill cells that are infected with viruses.
Cytotoxic T cells (CD8 cells) can recognise infected cells and kill them
Where are T cell precursors (thymocytes) produced?
thymocytes are produced in the bone marrow
Where are T cells developed?
During gestation, they migrate from the bone marrow to the thymus
The thymus is specially adapted for the education of thymocytes
= Selection of cells that are likely to be useful
= Removal of cells that are likely to be self-reactive
What does the constant region of the T cell receptor interacts with?
lymphocyte
What does the variable region of the T cell receptor interacts with?
antigen
What produces the variable region?
by somatic recombination between T cell receptor gene segments
Describe T cell antigen recognition
The antigen recognised by T cells is peptide that has been processed from intact antigen
The peptide is presented to the T cell by major histocompatibility (MHC) molecules
What does CD8+ cytotoxic T cells do? and why
infected cells displays a ‘marker on its surface; this allows CD8 T cells to recognise it and kill it
The ‘marker’ is actually part of the virus causing the infection – the virus is processed into peptides by the infected cell, which are displayed on the surface
What happens to the antigen before they are assembled into virus particles?
Virally-infected cell is synthesising viral proteins
These pass through the ER and Golgi into the cytoplasm
What happens to the viral proteins in the cytoplasm?
A sample of the proteins in the cytoplasm of a cell (go backwards) are passed into the proteasome – a tubular organelle lined with enzymes
What happens to the viral proteins in the ER?
The proteins are degraded into peptides and transported back into the ER by the TAP transporter
In the ER, the peptides are loaded onto MHCI molecules
How does CD8 T cells recognize the cell is infected? (or has a foreign peptide)
CD8 T cells with the correct receptor can recognise the peptide as foreign and kill the target cell
In a healthy cell, the MHCI groove will contain a self-peptide on the surface and present to cytotoxic killer T cells and kill it
What makes CD4 different to CD8?
Only recognise The antigen is presented by MHC class II molecules
Antigen is only presented by specialised antigen presenting cells
The antigen is taken up from the extracellular space
How are antigens sampled in Class 2 pathway?
Macrophages and dendritic cells sample antigens from the extracellular space by endocytosis/ phagocytosis
Antigen is taken up into intracellular vesicles, inactive early endosomes of neutral pH endosomal proteases are activated to degrade antigen into peptide fragments
And vesicles containing peptides fuse with vesicle containing MHCII molecules
What are MCI and MCII?
MHCI or II = a classes of major histocompatibility complex (MHC) molecules normally found only on professional - a group of genes that encode proteins on the cell surface that have an important role in immune response
Describe how B cells present antigens
professional’ antigen presenting cells, but the antigen processing is slightly different; they can only present antigens that bind to their antibody receptor
Antigen internalised into intracellular vesicles and degraded to peptide fragments by lysozyme enzymes
Fragments bind to MHC class II and are transported to the cell surface = presents antigens
Describe the interaction of passing t cell recognition
Passing T cell with correct receptor can recognise peptide-MHCII complex
This interaction activates the T helper cell, allowing it to provide help to other cells of the immune system
How does CD4 T cells help B cell mature?
B cells recognise antigen by antibody receptors and internalise it to present fragment of antigen
This is Presented to T cells as peptide with MHCII
T cells provide signals to B cells via cytokines and juxtacrine signalling
This stimulates the T cell, which then stimulates the B cell appropriately
How does CD4 T cells help macrophages?
Macrophage infected (e.g. with mycobacterium tuberculosis) – unable to kill organism so…
TB peptides presented with MHCII on surface
TB-specific CD4 T cell recognises TB, and provides help to macrophage (cytokines and juxtacrine signalling)
What is granuloma?
Macrophages activated to improve ability to kill TB; fuse to form multi-nucleate giant cells, in order to contain infection
Describe how T cells undergo clonal selection
and how they are different to B cells
during infection, T cells with receptor of best fit will be selected for survival and their numbers will increase
After the infection, a few will remain as long-lived memory cells
However, T cells do not mutate their receptors like B cells
What do T cells do in primary infection?
Naive CD4 and CD8 response. Clonal selection of most responsive clones
What do T cells do in resolution of infection?
Most antigen-specific CD4 and CD8 cells die off, but some remain as memory cells
What do T cells do in secondary infection?
Pre-existing memory T cells respond more rapidly and robustly
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What kind of antigens do cells of adaptive immunity Recognise?
Each receptor is specific for a particular antigen
How are receptors in cells of Innate immunity Produced?
germline-encoded
How are receptors in cells of adaptive immunity Produced?
Receptors are produced by random somatic recombination
Which type of immunity does not learn?
Innate immunity
Which immunity takes longer to respond?
Adaptive immunity
What are the cells in innate immunity ?
Granulocytes, plus NK cells, barriers and various soluble mediators
What are the cells in adaptive immunity ?
T cells, B cells
How are the receptors on cells in innate immunity expressed like?
Receptors are the same on all cells that express them
How are the receptors on cells in adaptive immunity expressed like?
Receptors are clonally distributed (ie clones of cells with similar receptor derived from a single parent
What kind of antigen does B Cells recognise?
Recognise intact protein antigen
What kind of antigen does T Cells recognise?
Recognise peptides derived from processed antigen and presented to them by another cell
Where are the receptors of B cells found?
Receptor (antibody) is on the cell surface and secreted into the bloodstream
Where are the receptors found in T cells?
on the cell surface only
Which cell has major subsets do and what are the major subset differentiations on?
T cells
on the basis of two surface markers:
CD4 – helper T cells
CD8 – cytotoxic T cells
Which type of cell has their receptors mutate and when?
Mutate their receptor during affinity maturation
How does innate immunity distinguish self from non-self?
has pattern recognition receptors
What happens to receptors of adaptive immunity that recognise self-reactive T cells strongly?
The receptors of adaptive immunity that recognise self strongly are deleted in the thymus
Even if recognition does occur, they may not react because T cell help is required- this is how self tolerance is established
