Infection, immune & Haem IIH

• Know the types of blood cells and their key role

• Understand haematopoiesis and how it is regulated

• Be familiar with why clinically we need to understand haematopoiesis

  • Use of growth factors

  • Haematological malignancies

• Red cells (erythrocytes) - Oxygen transport

• Platelets - Clotting

• White cells (leukocytes) - Immunity

• Lymphoid cells

  • T cells (directs), B cells (makes Abs) and NK cells (natural killer cells - directly kills)

• Myeloid cells may be either monocytes or granulocytes. The 3 types of granulocytes are:

  • Neutrophils, Eosinophils, Basophils (based in gut & Resp)

Innate immune response:

• Non-specific response, therefore no immunologic memory.

• Response is very fast, Inflammation tends to occur

• Also includes physical and chemical barriers e.g. lysozymes in tears and cilia in airways

• Monocytes, granulocytes (Neut, eosinophils, Basophils)

Adaptive immune response:

• Highly specific, can involve memory cells

• Slower as cells require priming

• Includes clonal expansion and clonal deletion

• Some cells survive as memory cells

• Lymphocytes ( T cells, B cells, NK cells)

• Produced in the bone marrow, regulated by GM-CSF

• Part of innate immune response

• Can migrate from blood > tissue > become macrophages

• Key roles in phagocytosis + cytokine production

  • Engulf and destroy dead host cells + pathogens

  • Produce IL-12 and IFN gamma which are important for intracellular immunity (pathogens within host cell)

Neutrophils (most no)- regulated by G-CSF

• Live in blood for few hrs > migrate to tissue and live 4-5 days. Engulf and destroy (phagocytes) bacteria

• Granules contain lysozyme and myeloperoxidase which are important for pathogen killing

Eosinophils - regulated by IL-5

• Response to parasite infection, not phagocytic, it release granules containing toxic substances.

Basophils - regulated by IL-3

• Associated with allergic diseases

Lymphocytes are part of adaptive immune response - small cells with low granularity.

1. T cells - Early progenitors from BM > circulation > thymus. Here they differentiate and selected to recognise antigen

2. B cells - Develop in BM > exit as antigen naive cells. Once recognise Ag, further differentiate into lymph nodes. Directed by T cells

3. NK cells - develop in BM

> Platelets contain granules that secrete substances to control clotting and break down of blood clot.

> Dont have nucleus!

> Lifespan of 8-12 days - removed by macrophages in the spleen and liver

> Low plt > easy bruising and bleed

Necessary for 2 processes to prevent blood loss post injury

1. Haemostasis - mechanism that leads to cessation of bleeding from a blood vessel.

2. Thrombosis - The formation of blood clots. which are then cleared after these processes.

• Have several progenitors - early one is known as megakaryoblast > megakaryocyte

• Megakaryocyte undergo endomitosis (DNA replication without cell division) - causes them to develop lobulated, polyploid nuclei and an expanded cytoplasm volume > more platelets to be produced. This gives distinct appearance.

• Platelets bud off from megakaryocytes

• Production is regulated by Thrombopoietin (TPO) - a peptide produced mainly by liver = liver dysfunction can cause thrombocytopenia due to lack of TPO

• Thrombopoietic GF is used to stimulate plt when low in pts

• Normal value - 150-450 x 10(9)/L

• RBCs are biconcave (to increase SA) Hbs, for gas exchange

• Originate from normoblasts which extrude their nuclei > reticulocytes.

• Reticulocytes have no mitochondria = sensitive to oxidative damage.

  • Retains their RNA = able to make Hb (not possible in erythrocytes).

  • Very flexible due to ankyrin & spectrin proteins

• RBC has lifespan of 120 days, 5x10(12)/L

Important in immune response, produced by haematopoiesis

• Dendritic cells - Professional antigen presenting cells found in tissues. Detect antigens in the tissues then present it to the innate and adaptive immune system

• Mast cells - Produced in the bone marrow but mature in tissues, these cells are very similar to basophils

• Haematopoiesis = process of blood cell production (10(12)

• Begins 17 days post fertilisation & continues throughout life in BM. Regulated by GF and cytokines

• Blood loss / infection > stress demand > haematopoietic tissues > rapid increase in cell production

Haematopoietic stem cells (HSC)

• These are either in quiescent (resting) or non-dividing state, have capacity to self-renew to maintain HSC no or give rise of specialised differentiated cells.

• HSC are multipotent = ability to differentiate into lineages of all blood cells. Commit to 2 pathways:

  • Myeloid precursor (common myeloid progenitor) > RBC, plt, basophil, eosinophils, Neut and monocytes

  • Lymphoid precursor (CLP) > T cells, B cells, NK cells

• Stem cells + multipotent progenitor cells identified by functional assay, while committed precursor cells & mature cells identified by routine marrow staining

The site of haematopoiesis differs depending on age:

• Foetus - yolk sack, moving to foetal liver

• Infants - Bone marrow (virtually all bones)

• Adults - Bone marrow of Axial skeleton (red marrow) i.e sternum, pelvis, vertebrae

• Erythropoiesis > erythrocytes (RBC)

• Begins in BM with HSC > differentiate > proerythroblasts > commit to erythrocyte lineage > forms smaller erythroblasts after division.

• Down the lineage, nucleus get smaller until extruded to form reticulocytes (still have RNA = can make Hb).

• Reticulocytes spends 1-2 days in BM, then 1-2 days in peripheral blood > mature into red cell (loss of RNA)

Note: reticulocyte (arrow) has no nucleus but stain pink due to increasing Hb as RNA is still present.

• Erythroblasts grow in islands (varying stages)

• Cluster of developing RBCs surrounds central macrophage forming erythroid island.

• Macrophage provides iron to the developing erythroblasts, removes nuclei from them to form reticulocyte then release it into blood stream.

• If the RBC are destroyed in the periphery, erythropoiesis is stimulated > high level of precursors e.g reticulocytes.

• It is regulated by erythropoitin (EPO) - O2 sensitive, produced by kidney + 10% by liver. EPO stimulates cells to divide

• Main stimulus is hypoxia > increase mRNA transcription by peritubular interstitial cells in the kidney > incr EPO secretion.

• EPO is low in renal impairment > unable to upregulate BM production of RBC.

Note: If RBCs are destroyed int he periphery > stimulates erythropoiesis > many precursors i.e Reticulocytes

Blood cancers are result of genetic abnormality - can also caused by viral infection e.g. Burkitt’s lymphoma post EBV

• Leukaemia = cancer of haematopoietic cells which arise from BM and spread to bone / LN / spleen

• Lymphoma = cancer of cells in LN / spleen which spead to BM and blood

Primary classification is by lineage - myeloid vs lymphoid

> Lymphoid cancers further classified as to T cell or B cell

> Leukaemias further classified as to whether it is acute or chronic. Acute leukaemia are rapid onset + more aggressive than chronic.

Leukaemia = cancer of haematopoietic cells. Classified into:

1. Acute - arise due to maturation arrest > block in haematopoiesis > over production of immature cells > crowding of BM

1. chronic - lack of maturation arrest > over production of dysfunctional mature cells = no -ve feedback on haematopoiesis > uncontrolled proliferation

• Blocks B cell development > inablity to make antibodies > rely on life long immunoglobulin replacement = highly susceptible to infection

• TFs are proteins that control gene expression > on / off gene transcription. If certain TFs are absent > blocks blood cell differentiation

In order to develop & differentiate, haematopoietic progenitor cells require:

• Intrinsic factors - i.e. lineage determining TFs and their epigenetic regulators

• Extrinsic regulators - both cellular & soluble GF found in the BM microenvironment. These factors can be up/down regulated according to certain stimuli.

• Early acting ones - stem cell factor, Flt3 ligand, IL-3, TPO

• Late acting - G-CSF, GM-CSF, EPO, TPO

  • EPO is used for patients with anaemia in ESRF, cases of myelodysplasia, pre-autologous blood donation and Jehovah’s witness during blood loss

  • G-CSF - SC injection in neutropenia due to chemo or congenital issue. To mobilise stem cells into blood for harvest and transplant

  • TPO receptor agonists- used in thrombocytopenia due to ITP / myelodysplasia or post chemo or aplastic anaemia. E.g. Romiplostin (SC), Eltrombopag (PO)

Note: RBC transfusion lasts one month, platelet few days, stem cell transplant lasts life time

Cytopenia = reduction of mature blood cells. Caused by:

• Issue with production by BM centrally e.g apastic anaemia

• Destroyed rapidly in peripheral circulation e.g immune thrombocytopenia

• Haematopoiesis occuring in adult life again in liver and spleen

• Occurs in myelofibrosis or intreated thalassaemia where BM capacity is compromised or exceeded

• Measure of FBC

• By carrying out immunophenotyping - look at specific proteins or cell markers found on cell surface or inside. Done in bloods or BM

• Normally, peripheral blood contains only small no of HSC. It may be increased when BM is recovering from damage by cytotoxic drugs or post G-CSF to mobilise HSC into blood fot harvesting for transplants

• To evaluate haematopoiesis, BM cells accessed via needle biopsy from iliac crest. 2 types of assays:

  • Aspirate - semi liquid BM aspirate is extracted via thin needled and smeared onto a slide then looked under light microscope to see cell count + types. Can also do chromosome analysis

  • Trephine biopsy - Core of BM is taken with thick needle to look at cellularity, histology and architecture

• Define anaemia

• Signs / symptoms

• Causes of anaemia

  • Haemetenics deficiency

  • Bone marrow failures

  • Haemolysis / bleeding

> RBC have no nucleus, biconcave shape and contains Hb which binds to O2. The colour comes from iron-containing Hb.

> Hb consits of 4 polypeptie chains (globins) each with haem group > 4 binding sites for O2.

> Type of globin changes throughout human life.

• Fetal Hb (HbF) - made of 2α + 2γ globins, <1% of adult Hb

• HbA - Made of 2α + 2β globins (sickle cell > mutated β globins), most common form of Hb in adult (>95.5%).

• HbA2 - made of 2α and 2δ, less common varient

• HbS - a mutated variant in sickle cell anaemia, consisting of 2α and mutated 2βs > alternate shape of the RBC

  
  

  Note: Haem groups in Hb molecules are synthesised in mitochondria of developing erythrocyte

• pH - Low pH reduces oxygen affinity.

• Temperature - High temperature reduces oxygen affinity

• CO2 - High concentration reduces oxygen affinity

• 2,3 DPG - an enzyme that reduces oxygen affinity

These factors enable haemoglobin to release more oxygen at respiring tissues (Bohr effect).

Sideroblast anaemia

• Due to iron accumulation in the mitochondria of thses cells

• The erythroblasts are referred as sideroblasts

Reduction in the Hb concentration of the blood.

May be accompanied by reduced RBC count and reduced haematocrit (proportion of RBCs in blood)

Normal range varies depends on factors such as:

• Gender (loss in menstruation)

• Pregnancy (increased plasma volume) > apparent anaemia despite normal Hb values

• Extremes of age (reduced marrow)

• Different labs / testing platforms

• Altitude

• Plasma (55% of volume of which 91% is water)

  • Contains - plasma proteins, electrolytes, hormones, nutrients

• Buffy coat (45% of vol)

  • Platelets, WBC, RBC

Note: Variation in plasma vol may be misinterpreted:

• Reduced PV (dehydration) - mask anaemia by causing normal Hb concentration

• Increased PV (preg) - may cause apparent anaemia despite normal Hb levels.

Vary depends on type of anaemia (acute vs chronic), compensatory mechanisms, lung/heart function

• Symptoms - fatigue, SOB, palpitation, angina

• Signs - pallor, tachycardia, bounding pulse (to increase cardiac output), flow murmur, HF. O/E koilonychia, angular stomatitis, pale conjunctiva

Reduced production

• Iron deficiency - diet, malabsorption, chronic blood loss (menorrhagia, UGIB). > reduced serum ferritin+ transferrin sats , increased transferrin (TIBC), low he[cidin level

• B12 & folate - alcohol, diet (vegan), high cell turnover, pernicious anaemia (Ab against parietal cells > damage > loss of IF production needed for B12 absorption in ileum)

• Bone marrow pathology - impaired production e.g. aplastic anameia / myelodysplasia

• Displacement in BM - leukaemia, cancer, myelofibrosis

  • Pathology takes over BM > reduced BM > reduced production

• Chronic disease - Renal failure, myeloma (cancer of plasma cells), chronic inflammatory conditions (RA, TB, cancer)

GI causes

• Inflammation / dysfunction of stomach (gastritis), bowel (colitis), liver can > malabsorption

• Coeliac disease, gastrectomy, colectomy

• Folate is needed in DNA synthesis to turn uracil > thymidine - essential building block of DNA. B12 is also involved in this.

  • Deficiency > delayed nuclear development whilst cytoplasm grows > macrocytosis

• Foate is absorbed in duodenum & jejunum, >95% of folate in the body is in RBC

• B12 is absorbed in ileum - enabled by IF produced by parietal cells in stomach, stored in liver

• Excess RBC production (e.g in haemolysis) > folate deficiency

Aplastic anaemia

• BM doesn’t produce enough RBC

• Can be due to viruses (Hep B), radiation or drugs

• Rx by BM transplant or immunitherapy

Myelodysplasia

• Causes dysregulation of cell production > abnormal BM cells > mature into abnormal RBC.

• Can further develop into AML

• Rx by BM transplant or cytotoxic therapy, transfusion

• Haemolysis - immune or non-immune

  • can occur in blood (intravascular) or spleen (extravascular)

  • Lead to increase no of reticulocyte (precursor) > increased MCV / macrocytic anaemia

• Splenomegaly (increased haemolysis)

• Bleeding

• RBC membrane defect - Hereditary spherocytosis or elliptocytosis

• Hb defect (haemoglobinopathy) - sickle cell, thalassaemia

• RBC enzyme defect - G6PD or pyruvate kinase deficiency

Stimulus outside the RBC

• Auto-immune -Ab against RBC > haemolysis in spleen.

• Identified by +ve direct Coomb’s test

• Can occur due to lymphoma, RA / SLE, infection or idiopathic

Problem within RBC membrane

• Hereditary spherocytosis, elliptocytosis

Problem within RBC

• G6PD deficiency

• Defect in RBC cytoskeleton (associated with spectrin deficiency in RC membrane)

• Causes RBC to contract to sphere > increased surface tension & reduced flexibility > easily damanged

• Damaged cells removed by macrophages in the spleen

• Commonly an autosomal dominent inheritance

• Direct Coomb’s test - negative

• Causes normocytic anaemia, Rx by splenectomy / folic acid

Haemoglobinopathy = inherited blood disorders that affects Hb

1. Thalassaemia (defect in alpha / Beta globin gene)

   • autosomal recessive > ineffective erythropoiesis > haemolysis > microcytosis & hypochromic red cell

   • Sx: anaemia, dark urine, jaundice, splenomegaly

   • Rx by repeated transfusion

   • Different Hb proteins identified by electrophoresis

2. Sicke cell (defect in beta globin gene)

   • Autosomal recessive > Glutamic acid to valine > Hbs variant.

   • When deoxygenated, the beta chains aggregate > RBC to sickle shape > chronic haemolysis + obstructed capillaries > painful crisis & organ damage

   • Also associated with spleen atrophy & degenration (hyposplenism)

• X-linked, > in male

• G6PD is important enzyme in pentose phosphate shunt - Maintains reduced NADPH - an only source of glutathione in RBC which mops up free radicals & protects against oxidative stress.

• RBC lacks mitochondria - glutathione is their only source of defence against oxidative damage

  • lack of it > oxidative stress > haemolysis

• Exacerbated by drugs, fava beans, infection

• Haemoglobin = Conc of Hb in blood

• Haematocrit = ratio of vol of RBC: total vol of blood

• RBC count = no of red cells

• MCV = average RBC size

• MCH = amount of Hb per RBC

• MCHC = amount of Hb relative to size of the cell

Learning objectives

• Sequence of events that occur post blood vessel injury

• Understand the role of plt in haemostasis

• Common inherited & acquired bleeding & clotting disorders

• Tests used to test coagulation system

• MOA of commonly used anticoagulants

• Overview of coagulation cascade incl how it is activated & key clotting factors that are activated to produce fibrin

Key players in blood clotting are - vessel wall, Von Willebrand’s factor, platelets and clotting proteins

• Coagulation factors - synthesised by liver using fat soluble Vit K. E.g Prothrombin, Factors VII, IX, X, XI, XII.

  • All these factors are present in circulation in inactive form > activated at site of injury

  • Vitamin K deficiency or liver failure > increase bleeding tendency

• vWF - produced by megakaryocytes & endothelial cells

• Plt are produced by megakaryocytes in BM

• Lifespan of 8-12 days

• Membrane contains glycoprotein receptors (GPIb / GPIIb/IIa) - essential for coagulation cascade

• Plt also possess actin and myosin fibrils > contracts > forms compact plt plug > haemostasis.

Primary haemostasis

• Forms the platelet plug (weaker) to quickly stop blood flow

• Uses collagen from vessel wall, vWF & platelets

Secondary haemostais

• Produce stronger fibrin plug, requires clotting proteins

• Blood vessel injury > endothelin release by injured endothelial cells > vasoconstriction > reduce blood loss

• Endothelial cells also release vWF + Thromboplastin (tissue factor) - vWF binds to endothelial collagen at A3 domain

• GPIb in plt membrane adheres to vWF at A1 domain > unwidnes to expost biding site to enalble plt binding to collagen which is found in sub-endothelial layer post damage > increase SA

• Plt/vWf complex adheres to collagen fibres at GPVI on plt membrane > ‘plt activation’ > release of granule contents (Ca2+, ADP, thrombospondin) from plt. Plt also synthesise thromboxane A2 (TxA2) & release factor X & fibrinogen

• TxA2 > vasoconstriction by binding to TP receptor & to TxA2 receptor on plt causing futher aggregation

  • Asprin inhibits TxA2 > reduced clotting

• ADP acts on P2Y12 receptor > aggregation

  • Clopidogrel targets P2Y12 receptor > inhibition

• GPIIb / IIIa receptors get exposed on plt > stronger binding to endothelial collagen > stronger plt aggregation by binding to vWF & fibrinogen (changes to fibrin through coagulation cascade)

  • Abciximab targets this pathway > prevents GPIIb/IIIa receptor binding > reduce aggregation

During primary haemostasis, plt synthesise factors such as TxA2, ADP which binds to P2Y12 receptor > plt aggregation > forms plt plug

• Asprin inhibits TxA2 > reduced clotting

• Clopidogrel targets P2Y12 receptor > inhibit ADP action on plt

• Eptifibatide targets and prevents GPIIb/IIIa receptor binding > reduce aggregation

There is not enough vWF or none or it is defective. Latex immunoassay can check vWF levels.

• Type 1 - Not enough vWF (heterozygous) = only one copy of the gene works > risk of bleeding

• Type 2 - dysfunctional vWF > no binding

  • Type 2A > absent / dysfunctional A3 domain (binding to collagen)

  • Type 2B > absent / dysfunctional A1 domain (binding to GPIb)

• Type 3 - no vWF (homozygous) > severe bleeding

• Collagen mutation > weaker defective collagen > issues in primary haemostasis > bleeding

• Sx: Hyperextension at joinds

• Scurvy > accquired form of collagen defect as Vit C is important for collagen synthesis.

• Dx with gene testing

• Bernard-Soulier syndrome:

  • Nonfunctioning GP1b, vWF cannot bind to platelet membrane

• Glanzmann's Thrombasthenia

  • GPIIB/IIIa dysfunctional, platelets cannot bind to one another, the plug won't hold

It is a series of proteins which activate one another to form clot.

> Most proteins are serine proteases with serine residues which are cleaved by another protein to activate it.

> Process begins with Extrinsic pathway (blue)

• Thromboplastin (TF) release by damaged vessel activates factor VII > activates factor X > activates factor II (thrombin) helped by factor V > cleaves fibrinogen forming fibrin (in small amounts)

> Extrinsic pathway initiates intrinsic pathway (yellow) which is activated by +ve feedback cycle

• Thrombin activates Factor XI > activates factor IX > activates more factor X (helped by factor VIII) > activates more factor II > +ve feedback cycle > cleaves more fibrinogen to form fibrin

• Fibrin associates with other fibrin to create a clot. Factor XIII is imp for cross-linkage to make clot stronger

• Process of haemostasis features +ve feedback cycle

• Anticoagulants in the blood plasma dampens the cycle:

  • Antithrombin - inhibits thrombin (Factor II) & factor X

  • Thrombin activates plasmin > breaks down fibrin strands that are already formed - removing clot once its not needed.

• Antithrombin deficiency is a prothrombotic disorder > excess clotting

Coagulation cascade involves series of proteins - mutations in these proteis > defect.

Mutations can occur in proteins such as - Thrombin, Factor X, XI, VIII, IX and fibrinogen

• Mutation in factor VIII > haemophilia A - an X-linked recessive condition

• Mutations in factor IX > haemophilia B

• Mutation in fibrinogen:

  • Afibrinogenaemia - absence of fibrinogen

    Hypofibrinogenaemia - less fibrinogen

    Dysfibrinogenaemia - dysfunctional fibrinogen

DIC = formation of lots of clotting > fibrinogen get used up

Haemophilia > intraarticular bleeding.

These drugs affect the cascade directly

• Apixaban/Rivaroxaban/Edoxaban

  • Good way to remember what these target is they all have an Xa in them, they target Factor X, blocking it from being activated (becoming factor Xa)

• Dabigatran

  • Tran = thrombin (factor II), it binds to thrombin and blocks clot formation

Don’t affect the cascade directly, insteads strengthens the effect of antithrombin. They are petasaccharides chains

• UFH - unfractionated heparin

  • Binds to a groove in antithrombin, changing its conformation, allowing it to bind to Factor Xa and stop it working. It also allows it to bind to thrombin and inhibit it too.

• LMWH - low molecular weight heparin

  • Used more commonly, also binds to that groove, however cannot also bind to Factor Xa

Inhibitor of Vitamin K epoxide reductase

• Vit K is involved in reduction of pre-pro factors 2, 7, 9 and 10, to form FII, FVII, FIX, FX

• In this process vitamin K is oxidised to Vit K-OH

• Vitamin K epoxide reductase resynthesises vitamin K from its oxidised form to make more clotting factors

• Inhibiting this enzyme inhibits the synthesis of these 4 coagulation factors > inhibiting coagulation

• This does not have an immediate effect

• Drug that Mimic the effects of plasmin

• Stimulate plasmin - such as TPA (Tissue plasminogen activator)

All clotting factors are tested for the same way:

1. Plasma (contains all clotting factors) is separated from blood sample using centrifuge

2. A substance is added to stimulates the clotting cascade at a certain point.

3. Time is measured for clot to form

There are 2 main ones we use:

• Stimulating at Factor XII, this tests the intrinsic pathway, where activated partial thromboplastin and silica are added to the plasma, and the Partial Thromboplastin Time (PTT) is measured

• Stimulating at Factor VII, this tests the extrinsic pathway, where the patient’s thromboplastin (tissue factor) is added to the plasma, and the Prothrombin time (PT) is measured

If the activated PTT and PT take too long to form a clot, it means there is an issue in a protein of the common pathway

• Hx of microbiology & its impact on science / medicine

• Describe the diversity of microbes - Prions > fungi

• How virus infect & replicate within host cell

• Identify major structures of bacterial cells & their functions

• Important E.g of viral, bacterial & fungal species

• Compare the key features of different microb

The four biosafety containment levels (BSL)

• BSL-1 – unlikely to cause diseases

• BSL-2 – can cause diseases but unlikely to spread in the community 

• BSL-3 – can cause disease AND spread but treatments are available.

• BSL-4 – the deadliest. Will cause serious disease, will spread and generally no treatments

• 1676 - Leeuwenhoek observed ‘anumalcules’

• 1796 - Edward Jenner found small pox vaccine

• 1882 - Robert Koch, 1st to isolate bacteria in a lab & grow on a media. Demostrated role of bacteria in causing disease - ‘Koch’s postulates’

• 1929 - Alexander flemming discovered 1st Abx penicillin

Infectious agents come in various shapes and sizes, from smallest to largest they are:

• Prions - misfolded proteins

• Viruses - require a host to replicate

• Prokaryotes - bacteria

• Eukaryotes - fungi, parasites, trypanosomes

Prions are misfold proteins due to mutation (proteinaceous infectious particle) - highly stable.

• Able to transmit their misfolding into a normal varient of same protein > creating self-replicating chain.

• Can cause e.g. CJD (spongiform encephalopathy), mad cow disease or scapie

• Resistance to disinfectants & heat Rx - difficult to remove

Mechanism of action:

• Begins with mutant protein (no DNA or RNA involvement) > induces misfolding of normal host protein > large chain reaction > aggregation of abnormal protein > deposits in brain > progressive degeneration

• Endogenous normal prion protein (PrPc - found in neural tissues & tonsil) get converted to disease causing form (PrPsc) > form amyloid fibres > aggregate & deposite

Plasmodium falciparum (malaria)

• Parasites are eukaryote that gains nutrients at host’s expense

• Range from single cell (protozoa, malaria) to large multicellular worms (helminths)

• Has complex life cycle

• Ubiquitous (found everywhre)

• Not a cell - contained within a shell of protein (capsid), consits of nucleic acid (DNA / RNA), may or may not be enveloped by lipid.

• They are obligate intracellular organisms = can only reproduce within a host cell.

• E.g Covid - RNA virus, zoonotic, spherical

• E.g Varicella - chickenpox / shingles, dsDNA, MMR vaccine

Classified using Baltimore classification based on how they synthesie their mRNA - help to predict behaviour of members of same group. Despite these classification, they all share features:

• All have basic viral lifecycle

• Have alternative splicing to increase the coding capacity of viral genomes

• Genome segmentation = genome is split across multiple DNA/RNA strands > evolutionary advantage

• Host range - some restricted to one host, others can jump between species (zoonotic)

Note: see lecture note for more on these viruses

1. Attachment to host cell - their outer proteins interact with host receptor

2. Entry into host cell & merge

3. Release of viral genome from capsid

4. Replication of viral genome

5. Assembly of new virions

6. Egress of new virions from cell

Bacteriophages - viruses that infect bacteria

• Depends on each specific virus, effects range from innocuous (harmless) to lethal.

• May integrate into host genome e.g. HIV

• Cause cell death due to mass production of virions

• Cause cell fusion, increased cell proliferation (papilloma) and latent infection (herpes)

• Most microbes are never pathogenic

• Opportunistic pathogens = can be pathogenic given a compromised immune system or a wound. Examples are

  • Pseudomonas - will infect most body sites. Anaerobes e.g Bacteroides fragilis can infect wounds if deep

• Obligate pathogenic bacteria are always pathogenic - require a human host cell as part of their life cycle. E.g Salmonella Typhi, it has no reservoir outside of humans.

Comes in many shapes & size buts are some features:

• They are prokaryotes (unicellular)

• Lack membrane bound organelles -No nuclei & mitochondria. DNA is suspended in the cytoplasm

• Have cell wall made of peptidoglycan (stains purple)

• Have appendages like flagella & fimbriae

• Plasma membrane performs many functions carried out my organelles in eukaryotes

• 10x smaller than eukaryotic cells > rapid metabolism & diffusion of nutrients = grow & divide rapidly

• Have membrane protein - important for transport in/out

• Cell defence, permeability barrier and cell communication.

• Important for antibiotics resistance

• have charge separation (proton motive force)

Based on nucleic acid sequences - divided largely into 2 groups:

• Gram neg - stains pink, have double membrane, thin peptidolycan (1-2 layers), labelled with lipopolysaccharides (LPS).

  • E.g. E.coli, Klebsiella

• Gram +ve - stains purple, have single plasma membrane, thick cross-linked peptidoglycan (3-20 layers), penetrated by wall teichoic acid (WTA).

  • E.g staphyloccoci, streptoccoci

-> Peptidoglycan (cell wall) is unique to bacteria - synthesis & structure is a common target for antibiotics.

-> Genotypic classification looked at differences in DNA sequences > whole genome sequencing > new species classification.

• 16s rRNA sequencing > new ‘bacteria’ & ‘archaea’ (single celled organism with no nucleus)

• Bacterial cytoplasm is densely packed with 70S ribosomes

  • Transcription & translation are coupled

• Genetic material - single circular chromosome sits in cytoplasm

  • Plasmids are extrachromosomal genetic elements

Flagella

• Important in pathogensis - molecular motors used to allow bacterial mortility.

• Very immunogenic > inflammation

• Allow bacterium to exhibit chemotaxis - can move towards or away from attractants or repellents

Fimbriae (pili)

• Shorter & finer than flagella - Hair-like

• Help adhere to host cells, host cell invasion

• Conjugation > transfer of plasmid DNA between bacterial cells

• Capsule - thick outer polysaccharide gell

  • Act as ‘shield’ > hides from host & Abx resistance

• Endospores - tough, dormant structure formed when lacking nutrient > very resistance to Abx & stressors

• Slime - unorganised extracellular matrix to protects from environmental dangers

• Biofilm - organised matrix (‘house’), multicellular. Abx not able to penetrate it. infects devices e.g. catheter

• Extracellular polymeric substance (EPS) - made from polysaccharides, proteins & lipids

Mechanisms vary greatly - can invade the cell or act outside. Pathology depends on:

• Bacterial activity - toxin production / direct tissue damage

• Host response - immune sensitivity to bacterial Ag > stimulation of inflammation

-> Ways they cause disease

• Through exotoxins - proteins secreted by bacteria to destroly host cell / to release cellular contents / to invade

  • E.g Clostridium botulinum > food poisoning & paralysis by neurotoxin

• Lipopolysaccharide (LPS) - found on gram -ve bacteria

• Major immune stimulator > sepsis

• Only lipid A part is toxic

• Many types - terminal repeat regions determines specificity

• Gram -ve, rod shaped (bacillus)

• Can be non-pathogen (gut microbe) or pathogenic (shigella toxin)

• Mortile via fagella, forms biofilm

• Grame +ve, facultative anaerobe

• Commensal & pathogen

• 20-30 min doubling time

• MRSA - methicillin resistance gene acquired throguh horizontal gene transfer and is carried on mobilie genetic element

• It is gram +ve but dont stain with gram stain due to waxy cell wall (mycolic acid)

  • Requires acid-fast staining

• Non-motile, has no pili or fibrae - have unique adhesion molecule

• Doesnt form spore but can become dormant in host

• Can be single or multicellular

• Eukaryotic (similar to human cells) - hard to Rx as med may also affect human cell

• Unique feature - Have cell wall that contains chitin

• Can act as parasite or pathogen - causing simple infections (athlets foot) to serious ones in immunocompromised patients

  • Thrush by candida (yeast) is most common fungal inf

  • Aspergillus infection common patients with underlying TB / COPD

• May grow as hyphae - cylindrical tues which interconnects to form ‘mycelium’. It can be very large

• Can produe fruting bodies / spores when reporoducing > carried by wind

  • E.g Aspergillus fumigat - lives in soil, formes >100 spores / day > lung disease. limited Rx

Candida albicans (yeast) > oral thrush

• Member of human microbiome - can be oppportunistic in immunocompromised e.g. HIV

• Cause superficial & invasive infections

• Major biofilm former > problem for implanted devices

• No effective vaccine

• Shifts between oval yeast > elongated pesudohyphae > multicellular hypae

• Understand basic concepts of bacterial growth & the growth media

• Describe concept of gram-stain

• Different approaches used in bacterial Dx - Microscopy, biochem, mass-spectrometry, immunoassays, DNA methods

1. Liquid culture - bacteria gown in liquid media to quantify growth rate or to study physiology.

2. Solid media (agar) - used to identify bacteria, to quantify number of live bacteria or to isolate pure culture. Used for clinical situation.

Selective media

• Isolate specific bacteria by inhibiting growth of other species. E.g using bile salts & crystal violet

• Only specific group of bacteria will be able to grow

Differential media

• To differentiate between 2 different bacterial cultures.

• E.g by adding lactose to medium, some bacteria can ferment it while other’s cant. Fermentation > pH drop (<6.8 = pink, neural pH = colourless) - can differentiate colonies using coloured pH indicator.

  • E.g E.coli can ferment it > low pH > turns pink

  • Salmonella cant > neural pH > no colour change

-> The medium is known as MacConkey agar which only allows growth of gram -ve bacterial colonies - both selective & differential

This can be provided in 2 different mediums:

• Defined medium - Consits of pure chemicals in specific amounts > very reproducible growth

• Complex medium - Made up of digests of microbial, plant and/or animal products.

  • Not defined, as exact compounds / amount unknown. They allow the growth of a wide range of microbes

pH

• Most exhibit optimal growth around pH 7.4.

• Some (H.pylori) grow in stomach at pH 3

  • It creates micro-environment with higher pH by producing ammonia & HCO3 using the urea in blood.

Oxygen

• Many are aerobic (respire) - use O2 to create ATP

• Others are anaerobic (can’t respire) - 2 forms:

  • Aerolerant anaerobes = can tolerate & grow in air

  • Obligate anaerobes = can’t tolerate air > O2 inhibit their growth & kills the cells. Most GI bacteria are this category. Upon excretion, some produce spores which are robust & can tolerate heat + O2 + UV > germinate when conditions are favourable.

• Lag phase - Not much growth are bacteria adapting to new environment. Metabolic process just begining > generates ATP & make new ribosomes

• Exponential phase - Rapid cell growth & metabolism increases. Nutrients rapidly used up and waste products are formed

• Stationary phase - Growth plateaus, > slow or absent. Little nutrients left > bacteria prepare for survival without nutrients > sporulate (form spores resistant to stresses)

  • Some produce antibiotics to kill neighbouring cells and grow on their nutrients

• Death phase - culture starts to die

Cell wall containing peptidoglycan is a key feature of bacteria - taget for some Abx which inhibit its synthesis e.g. Penicillin

Gram-stain is used for rapid identification by microscopy.

The process is as follows:

1. Cells are stained with crystal violet stain and iodine (purple colour).

2. Cells are washed with alcohol (decolorises)

3. Cells are counter-stained with safranin (pink-red)

Gram +ve = cells remained purple = able to retain the iodine & crystal violet dye

Gram -ve = cells not able to retain iodine & crystal violet dye > washed away > stains pink with safranin stain

• Gram +ve = have inner cell membrane & outer cell wall made of very thick peptidoglycan which retains iodine / crystal violet dye

• Gram -ve = have inner cell membrane & thin outer peptidoglycan cell wall + an outer membrane surrounding the entire cell.

  • Outer membrane possess many heavily modified sugars which produce lipopolysaccharides (endotoxin) > activates immune system > septic shock.

  • The extra outer membrane > more resistance to Abx = why G-stain is clinically important to identify the type

Direct Microscopy

• Cheap & fast - sample is cultured, stained & seen under microscope to identify bacteria

• Sample e.g. sputum, blood, skin, urine, stool, CSF

MALDI-TOF mass spectrometer

• 1st, sample grown on agar > then identify bacteria

• Sample added to plate & ionised (+ve) > then accelerated into a tube to separates fragments of colony material based on m/z ration > peak patterns (specific to each bacteria) - compared with database to indentify the bacteria.

Ab detection immunoassay

• Used for some bacteria that can’t be cultured e.g Treponema pallidum (syphilis)

• Detects Ab against the bacteria (produced by B-cells of the patient during infection)

Antigen detection assay (lateral flow)

• Tests for antigen = Fragments of bacteria that are immunogenic in clinical samples.

Antigen detection assay (latex agglutination)

• Another form that detects bacterial Ag - used to Dx CSF infection e.g. bacterial meningitis

DNA-based methods & PCR

• If no tests available based on Ab / Ag - uses rapid amplification of DNA by polymerase chain reaction (PCR).

• Utilised in bactrial identification by creating primers which are specific to DNA of particular bacterium = DNA replication can occur only if the corrent DNA is present

DNA sequencing

• Reads the entire DNA sequence of the pathogen

• Sample (CSF) > extraction of DNA (remove human DNA too) > sequencing > analysing.

• Used in research rather than daily diagnostics

1. The antigen for the antibody is bound to the testing well.

2. The sample is added to the well and then washed away. If the correct antibody is present, it will NOT get washed away and remain bound.

3. Anti-human antibody is added, this will bind to the remaining antibody if present.

4. Anti-human antibody is washed away, however it will remain if the correct antibody is present.

5. The anti-human antibody has an enzyme attached to it. The substrate is finally added, and the enzyme catalyses a reaction which causes a colour change. = +ve test = Ab for the infection are present

This is done on a strip, with 3 main components:

• Conjugate-labelled antibodies (CLA -coloured) - recognise and bind to antigen

• Control antibodies - recognise and bind to conjugate-labelled antibodies so should always be positive to indicate the test is working.

• Test antibodies - also recognise and bind to antigen.

Steps:

1. Sample is added, the contents travel along the strip.

2. If the antigens are present, they bind to the CLA

3. The CLA binds to the control antibody line as they bind to the CLA, so 1 coloured line appears (control line).

4. The CLA-antigen complex binds to the test antibody line as they bind to the antigen > another coloured line appears (+ve test).

No antigens = no bindinh = no coloured lined

Its another form of Ag detection - uses different system, used for CSF infection. It involves:

1. Latex particles coated with Ab are suspended in a medium

2. Sample is added

3. If the antigens are present in the sample, they bind to multiple antibody-latex complexes at once, causing cross-linking and aggregation.

Not always easy to interpret, not better than gram-staining.

Rapid amplification of DNA by PCR invovles:

• Sample which may contain pathogen DNA, primers (complimentary to pathogen DNA), dNTPs (monomers) and taq polymerase (heat resistance) to synthesise DNA

1. First DNA template is denatured to single stranded

2. Primers anneal to DNA template

3. Taq polymerase and dNTPs form new strand (extension)

4. Cycle repeats - new double strands denature, new strands formed from the single strands

5. Every cycle the DNA is amplified exponentially (each DNA molecule gives rise to two new molecules in each cycle)

To test the final sample - need to know how much DNA is present. Options are:

• Standard agarose gell electrophoresis - separates DNA fragments by size > identify bacterium in target specimen

• Quantitative PCR - uses fluorescent tags to quantify DNA after each cycle. E.g SYBR green binds to dsDNA or taqman

Advantages:

• Rapid (4-6hrs) clinical sampling to results than growing on a plate (takes 24 hrs)

• Useful when culture is difficult or will take very long time

Disadvantage:

• Use of specific primer tests only for particular bacteria > Yes / No for 1 pathogen = limited

  • Solution to this is DNA sequencing - reads all DNA in a sample to rapidly identify all microbes present (but not RNA virus)

• Classification of viruses.

• Viral life cycles.

• Common viruses that cause disease (Acute, chronic, latent).

• Differences in acute, chronic and latent patterns of disease.

• Routes of viral transmission

• Identification of viruses in the laboratory

• Obligate, sub-microscopic (too small to see under light microscope, need electron microscope) intracellular parasites

• Non living = pose no metabolic activity alone

  • Depends on host cell for raw materials & energy

• Enters host cell, hijack host’s intracellular machinery to replicate using its genome

• Exists either as extracellular virion containing DNA or RNA virus genome or as nucleic acid inside the host cell

• Composed primarily of:

  • Genome - DNA or RNA (not both)

    Protein shell (capsid) - encloses the genome

• Capsid may have some enzymes required for viral activity inside the host

• Can be enveloped or non-enveloped

  • Enveloped ones pose further outer lipid membrane (acquired when budding off host cell)

  • Non-enveloped ones don’t pose an outer membrane - only have capsid enclosing the genome

• Very small (biggest one is ~400nm) - have huge variation

• Take one of 2 main shapes:

  • Icosahedral - 20 triangular shaped faces, spherical like. e.g all DNA viruses except poxvirus

  • Helical - coiled capsid surrounding the genome. E.g most RNA viruses (some have variable extra helix)

Classified into 7 categories - Baltimore classification

Note:

• Group 4 - Sense RNA viruses, sense copy meaning it can be used as mRNA & directly translated inside host cells

• Group 5 - Antisense RNA virus, antisense copy = it requires conversion to sense RNA by RNA polymerase inside the host cell before translation. This category also includes viruses with mix of sense & antisense (ambisense) e.g influenza, ebola, measles

• Group 6 - RNA reverse transcribing virus (retrovirus) = it posses reverse transcriptase - an enzyme when inside host cell can use RNA strand of the virus to synthesise complimentary DNA strand + dsDNA containing virus’s genetic information which it can then integrate into host genome

• Group 7 - DNA Reverse Transcribing Viruses (retrovirus) – Possess reverse transcriptase. Use a DNA genome to produce an RNA strand, and then use reverse transcriptase to synthesize a complementary double-stranded DNA molecule for integration into the host genome (e.g. HBV – Hepatitis B).

1. Adsorption

2. Entry

3. Capsid transport to nucleus

4. Transcription

5. Translation

6. Replication

7. Capsid assembly

8. Glycosylation

9. Glycoprotein export to cell surface

10. Endocytosis of glycoprotein containing plasma membrane

11. Envelopment

12. Virus release

Entry into cells:

• Surface protein on capsid / lipid membrane on the virus > attach to receptors on host cell membrane

• Susceptibility of host cell to virus depends on the presence of receptor > entry of the virus

• Some viruses are highly specific = only infect certain cells e.g. Polio only attacks human by biding to decay accelerating factor receptor on cetain cell memembrane

• Other can infect humans & animals e.g influenza

• Mechanism of entry depends on the nature of the virus:

  • Non-enveloped viruses enter cells by receptor mediated endocytosis

  • Enveloped viruses enter cells by membrane fusion of their outer membrane with that of the host cell

• Once it enters the host cell, nucleic acid contents are released into the nucleus

• DNA or RNA genome is processed to form valid RNA strand (transciption) for translation by ribosomes.

• The genome encodes synthesis of 3 components:

  • Non-strutural proteins - includes enzymes & replication factors for genome synthesis e.g DNA / RNA polymerase

  • Structural proteins - required to form new capsids

  • Copies of viral genome -one for each virus

• In enveloped viruses, a lipid vesicle is formed & internalised, possessing surface glycoprotein.

  • This vesicle envelops the virus before release

• Elipse phase = timeframe for viral replication within a cell

  • Viral infectivity & identity is lost in this time - pt is asymptomatic

• Productive phase = once new copies of virus is synthesised, it is released to go infect other cells > pt may start to see Sx

• Some viruses don’t replicate within the host cell immediately - they remain latent for long time e.g Humar herpes

Level of distruption to host cell depnds on the virus:

• Most non-enveloped viruses known as cytopathic = completely destroys host cell by lysis > virus copies shoot out of the cell membrane

  • E.g. lytic infection (polio) > large no of virus production + forms cystals within host cell cytoplasm

• Most enveloped viruses - released by budding (less disruptive). Small no of viruses released > chronic infection

  • E.g Released as vesicle (influenza) or directly (HIV) from cell membrane

ELISA test - enzyme linked immunosorbent assay

• Identify virus via their Ag or Ab

• Ab detection assays - tests for Ab against virus Ag

• Lateral flow Ag test - tests for presence of viral Ag

• These methods are cheap, fast, reliable & automated

PCR methodologies

• Uses specific primers to viral DNA

• Can be done befre Ab have been produced by the body, used to screen blood donation & can rapidly adapt for new pathogen.

• Enveloped virus, studded with viral glycoproteins

• Group 5 virus = ss antisense RNA virus

• Carries genetic materia in 8 segments - each code for seperate proteins. Importantly:

  • Segment 4 HA: encodes for Haemagglutinin (blue)

  • Segment 6 NA: encodes for Neuraminidase (orange)

  • Segment 7 M2: Ion Channel (green)

• Influenza A - infect humans, birds, pigs, horses etc > pandemics

• Influenza B only infect humans > seasonal epidemics.

• Influenza C infect humans & pigs > mild respiratory illness

-> The virus can be classified as avian, swine, or other animal name + influenza

-> Divided into subtypes based on 2 viral proteins:

• Haemagglutinin (H1 – H18) (18 different types) e.g H5N1

• Neuraminidase (N1 – N11) (11 different types)

• Influenza targets epithelial cells of airways

• HA interacts with sialic acid residue (a-2,6 or a-2,3) on the cell surface receptors > induces receptor mediated endocytosis > virus enters the cell

• Upon replication, NA destroys sialic acid residues on infected cell so that a new virus can’t re-attach to same cell

• Ab will target either HA or NA

  • HA Ab prevents attachment of virus to cell by blocking the binding site to sialic acid > neutralise the protein.

• Infection by virus & the Ab production > immunity to futher infection but infection does occur repeatedly due to antigenic drift / shift of the virus

Host survival from acute infection > Ab > immunity - yet, acute infection by some virus happens repeatedly e.g infulenza & rhino

This is due to antigenic variation:

-> Antigenic drift

• As virus replicated, it continually collects small random genetic mutations in its genome - due to fast replication rate & lack of proof reading ability by RNA polymerase)

  • RNA virus have more mutation rate than DNA viruses as they use RNA polymerase to replicate the genome

• These mutations accumulate over time > eventually change the structure of the protein > no longer recognised by host immue system > same Ab can no longer binds

-> Antigenic shift

• Unique to influenza A as it is segmented virus which can swab between viruses affected different species.

• There is an abrupt & major change in the virus > completely new protein (HA/NA) to which host does not have immunity > high susceptibility > pandemic e.g Spanish, Asian, Hong kong flu

• Happens when virus jumps between species or it swaps fragments.

  
  

• Small enveloped virus, studded with Hep B surface Ag sized S, M, L.

• Group 7 virus = contains dsDNA

• Extremely infectious (100x more than HIV) - remains infectious outside the body for 7 days

• Perinatal transmission (mother to child at birth)

• Parenteral transmission (blood, blood products)

• Needlestick injury, tattooing, piercing

• Sexual

• Infected body fluids (saliva, menstrual, vaginal, seminal fluids)

• Medical/surgical/dental instruments

This puts certain groups at a higher risk:

• Health care workers, MSM/multiple partners/sex workers

• Blood transfusion recipients

• I.V. drug users

• Infants of HBV carrier mothers

• Recipients of solid organ transplants

• Long incubation perior of 30-180 days before onest of Sx - transmission can still occur in this stage

• Sx vary between ages in acute infection (mild - fatal)

  • 30-50% adults jaundice, hepatitis. Mild in children

• If acute infection doesn’t resolve > chronic infection

  • More likely in infants than adults - 80-90% in 1st yr of life > chronic hep.

  • In adults 20-30% > liver disease with chronic infection

Acute infection

• High Hep B E antigen (HBeAg) = virus replication

• After a delay, the body develops HBe Ab against Hep B surface antigens (HBsAg)

  • If this is effective > fall in HBV DNA, HBeAg & HBsAg

• HBe Ab will last lifetime

Chronic infection

• HBV DNA, HBsAg and HbeAg remain present in the serum due to continued viral infection

• Increase in ALT/AST level = liver disease

• Small enveloped virus, studded with 2 key glycoproteins: GP1 & GP2

• Group 4 virus = ss +ve sense RNA

• 95% cases cured with antiviral therapy

• Currently no vaccine

Transmission is purely through blood. By following ways:

• Injecting drug use/sharing injection equipment

• Reuse or inadequate sterilization of medical/surgical/dental equipment (esp. syringes/needles)

• Transfusion of unscreened blood and blood products

• Sexual practices that lead to exposure to blood

• Perinatal transmission (mother to child at birth) is less common

• Incubation period - 2 weeks to 6 months

• Acute infection

  • 80% asymptomatic, 20% with fever, fatique, poor appetite, N&V, abdo pain, dark urine, joint pain, jaundice

  • Asymptomatic to fulminant fatal

• Chronic infection

  • When acute infection doesn’t resolve > chronic

  • Likley in 50-60% infants, 50-90%adults.

  • 20-30% will develop cirrhosis & liver cancer

• May co-exist in HIV patients > liver disease > mortality

• Antibody testing - ? historic infection

  • If Ab +ve, will need viral nucleic acid test ?current infection

• HCV Ab neg = not infected

  HCV Ab +ve, HCV RNA -ve = no current infection

  HCV Ab +ve, HCV RNA +ve = active infection

• Check ALT - high = liver cirrhosis

• HCV is a +ve sense RNA virus = very high mutation rate > different genotypes acorss the world.

  • Due to this, there are 6 genotypes divided into Groups 1-6. Rx depends on the group

• In adults (18+) – Pan-genomic regimen such as sofosbuvir + velpatasvir, glecaprevir + pibrentasvir, or sofosbuvir + velpatasvir + voxilaprevir.

• In ages 12-17 – Depends on genotype:

  • Genotypes 1, 4, 5, 6 – Sofosbuvir + ledipasvir for 12 weeks

    Genotype 2 – Sofosbuvir + ribavirin for 12 weeks

    Genotype 3 – Sofosbuvir + ribavirin for 24 weeks

• Ages < 12 – Defer treatment until 12 years old.

• Enveloped, belongs to Group 1 = dsDNA, bigger than most viruses.

• There are 8 human herpes viruses:

  • Herpes simplex virus 1 (HSV-1)

    Herpes simplex virus 2 (HSV-2)

    Human cytomegalovirus (HCMV)

    Varicella zoster virus (VZV)

    Epstein Barr virus (EBV)

    Human herpesvirus 6A/6B (HHV-6A/6B)

    Human herpesvirus 7 (HHV-7)

    Kaposi’s sarcoma-associated herpesvirus (KSHV / HHV-8)

• HSV-1 and HSV-2 are highly prevalent > ~63% of world’s population under age of 50 are carrying HSV-1, 13% carring HSV-2

• HSV-1 - commonly associated with oral infection = transmit via oral-oral contact

• HSV-2 - tends to infect genital area = transmit via genital-genital contact

• Oral to genital contact can transmit either HSV-1 or HSV-2 from one site to another - highly contagious when symptomatic

Lytic cycle (activation)

• The virus is active > infection of mucoepithelial cells > replicate there & release infectious virus

• Leads to symptoms e.g. stomatitis

Latency

• Post lytic cycle.

• Virus is inactive within sensory cells in dorsal root ganglion supplying the affected area = immunologically silent

• HSV-1 tends to resides in trigeminal ganglion of the trigeminal nerve

  • HSV-2 resides in sacral ganglia in the scrum

• Once reactivate > new copies of virus travel along the sensory neurones > mucoepithelial cells of the skin > Sx of cold sores around the mouth

-> Depending on neurovirulence, the virus may proliferate within the CNS > meningitis or encephalitis

-> Due to this lytic/latency cycle, unable to completely get rid of HSV once infected

• Those with HIV / immunsuppressive Rx are more susceptible to frequent / severe presentation

• Lytic cycle

  • Virus DNA replication

  • New progeny of viruses made

  • Full range of virus proteins expressed

  • Highly immunogenic

• Latency

  • No virus protein expression, all activity downregulated

  • Episomal DNA replicated with host cell DNA

  • Immunologically silent

Varicella-Zoster virus

• Chicken pox is due to infection 1st time, shingles is due to reactivation post latent period (> in immunocompromised)

• VZV enters the system through saliva > latency in sensory dorsal root ganglion

• Sx - rash in a dermatomal distribution, commonly thoracic

Risks:

• Infants, adolescents, adults, preg women, HIV/AIDS, cancer

• Pt who had transplant, on chemo / immunosuppresion / LT steroids

Complications of chickenpox:

• Bacterial skin & soft tissue infection - e.g Group A strep (nec fasc)

• Pneumonia, encephaliits, cerebellar ataxia

• Haemorrhagic complications & sepsis

Cytomegalovirus

• Transmitted by body fluids such as urine, breast milk, sexual contact, blood products, organ donation & bone marrow transplants

• Primary infection - usually asymptomatic

  • 8% symptomatic with fever, mononucleosis & hepatitis.

• Congenital CMV - passed on from mother to fetus in utero.

  • Can be asymptomatic but can > infection of multisystem > pneumonia, hepatitis, encephalitis

• Common in immunocompromised pt:

  • Transplant > penumonitis, gastritis, enterocolitis, hepatitis, retinitis, Graft-host disease

  • HIV/AIDS > similar to above

• Transmitted through saliva - referred as ‘kissing disease’

• Usually asymptomatic, occurs during childhood

• 4-7 week incubation period - replication in oropharyngeal epithelial cells & B cells

• Delayed primary infection in adult > infectious mononucleosis (glandular fever) > fever, pharyngitis, swollen LNs and hepatitis

• EBV can remain latent in B cells > exposes viral oncogenes & increase the risk of blood cancers:

  • B cell cancers - Burkitt lymphoma, Hodgkins lymphoma

  • Epithelial cell - nasopharyngeal Ca, gastric Ca

  • T & NK cell - extranodal NK/T cell lymphoma, NK leulaemia

• In immunocompromised, there is risk of other cancers:

  • Post transplant - lymphoproliferative disease, HL, encephalitis / myelitis, pneumonia, hepatitis

  • HIV related - Burkitt, large B cell or primary CNS lymphomas, HL, plasmablastic & primary effusion lymphomas

• Primary infection of HHV-8 > fatigue, diarrhoea, localised skin eruptions.

• In immunocompromised > fever, splenomegaly & lymphoid hyperplasia

• Can remain latent in B-cells & vascular endothelial cells

  • Reactivation > Kaposi Sarcoma (red/brown plaques & nodules on skin), primary effusion lymphoma (B cell) & muticentric casteman disease (B cell)

• What is antimicrobial resistance?

• How we measure it?

• How can we manage it ?

• Refers to the ability of a microbe to resist the effect of an antimicrobial that it was previously susceptible to

  • Can occur in bacteria, virus, fungi & protozoa

• Antimicrobial = both natural products like penicillin & chemically synthesised compounds like sulphonamides & trimethoprimes

  • They target enzymes & biological structures in pathogen that are not present in human

• AMR > global issue > increase LOS, morbidity, mortality, hospital acquired infections

Antibiotics = antimicrobials specific to bacteria. Classified based on their site of action of the bacterium:

• Bacterial cell wall and membrane

  • penicillin, cephalosporins, carbapenems, monobactams, glycopeptides and polymyxins

• Nucleic acid synthesis

  • olate antagonists, quinolones, Rifampicin

• Protein synthesis

  • These drugs will affect the ribosomes of bacteria

  • Macrolides, clindamycin. linezolid, chloramphenicol, tetracyclines, aminoglycosides

• Production of enzymes that degrade antimicrobials – eg Beta lactamases (antibiotics have beta lactam rings they need to function)

• Change in binding site by changing the protein the Abx binds to– eg MecA gene penicillin binding protein

• Membrane permeability – eg aminoglycosides

• Efflux pumps to pump out the Abx – eg Pseudomonas

The process of AMR is as follows:

• Some bacteria are resistant to an antimicrobial

• Antibiotic administered and it kills all the bacteria except the resistant population

• Resistant population grow and occupy the niche

Bacteria can acquire AMR in various ways:

• De novo - Due to a mutation in chromosomal DNA

• Inducible resistance - enzyme switches on when antibiotic present

• Transmitted - via plasmids transferred between bacteria species

E.g of resistant bacterias

• Methicillin-resistant Staphylococcus aureus (MRSA)

• Vancomycin-resistant Enterococci spp. (VRE)

• Extended-spectrum  β-lactamase producing Enterobacteriaceae spp. (ESBL)

Tuberculosis has 2 resistant types

• Multidrug-resistance TB (MDR-TB) - resistance to Rifampicin & isoniazide.

  • Requires 18 months Rx / surgical lung resection. Has 80% sruvival rate

• Extensively drug-resistant TB (XDR-TB) - resistant to Rifampicin, isoniazid, fluoroquinolones & injectable agent

  • Require 24 months Rx + surgery > 30-50% survival

Malaria

• Antimisinin-based combination therapies (ACT) were 1st line - in 2016 noted Plasmodium falciparum became resistant to all anti-malarial drugs

HIV

• Resistant antiretroviral drugs in 10-20% cases > drug resistant HIV

Influenza A

• Shown to have resistance to M2 receptors (amantidine & rimantadine)

Rate of AMR accelerated by:

• Drug prescribing - overprescribing > being taken in situations where they are not needed

• Drug access - in some areas antibiotics can be freely purchased without prescription

• Drug standards - Drug standards are not all to the same quality, lower quality drugs may not have a strong enough dose, therefore driving AMR

• Veterinary use - Antibiotics are used in food and livestock

• Global travel - Transport of AMR strains

  • 1:3 travelers acquire ESBL in stool, e.g to SE asia

• Environment - Strong correlation between AMR and socioeconomic and environmental factors. Untreated human sewage can be a breeding ground for all types of pathogens - some may be AMR

Phenotypic testing - mainly used in clinical practice

• Examines the growth of bacteria in the presence of known conc of Abx

• Done by preparing double dilutions of Abx with a broth that allows growth of testing bacteria > each tube is innoculated with bacterium

• Use it find the minimum inhibitory concentration (MIC) for the microbe against different Abx

  • MIC is the minimum in vitro conc of Abx needed to inhibit cartain amount of growth

  • Tube that fails to show growth (inhibited) is referred as MIC of that Abx for that individual bacterial strain

Genotypic resting - used in surveillance and research

• Identify genes associated with AMR using PCR / sequencing

  
  

1. Reducing exposure to antimicrobials - reduce burdern of infection by clean water, sanitation, food safety & minimise environmental spread

2. Optimising the use of Abx - by improved Dx, Abx stewardship programmes & monitoring data

3. Investing in innovation, supply & access - research to development of new therapeutics, diagnostics & vaccines

1. HIV background

2. HIV lifecycle

3. HIV entry

4. Therapeutic intervention

5. Clinical course of HIV

6. Mutations in HIV and drug resistance

7. Vaccine

• Men who have sex with men (21%)

• IV drug users (13%)

• Sex workers and their clients

• Mother to child (0.7%)

• Heterosexual contact (49%)

Above % represent new infections

• Moves along multiple stages, starting with incubation period of 2-4 weeks.

• Acute infection - most people are unaware but may have Sx of fever, headache, rash or sore throat

• Chronic infection - Asymptomatic / latent as HIV replicating at low levels

  • Can last for decades or longer - transmission can still occur

  • Eventually, viral load increases > low CD4 T cell count

• Acquired immunodeficiency syndrome (AIDS)

  • Established when CD4 Tcell count is <200 cells/mm

  • AIDS increase susceptibility to opportunistic infection > only 3yr survival rate

-> There is no cure / vaccine = infected ones have to take antiviral drugs for life

• Virus can be resistance to the drug + its expensive

Transmitted via:

• Bodily fluids - Blood, breast milk, semen, vaginal secretions

• Mother to child - During pregnancy and delivery

Risk factors:

• Unprotected anal or vaginal sex

• Through other STIs e.g syphilis, Herpes, Chlamydia, gonorrhoea & bacterial vaginosis

• Sharing contamintated needles / needle stick injury

• Receiving unsafe injections, blood transfusions & tissue transplant or unsterile medical procedures involving cutting / piercing

lab test to measure the presence of indicators of HIV in the blood and oral fluids:

• HIV antibody test - blood or oral fluids for presence of HIV antibodies

• Nucleic acid test - blood for virus load of HIV RNA

• Antigen/antibody test - p24 antigen is made by infected cells which can be detected even before antibodies are made. Antibodies can still also be detected

HIV-1

• Accounts for 95% all infections, derived from Gorillas & chimpanzees

• Classified into 4 groups: M, N, O & P

  • Group M has 9 subtypes: A to K (Exp E&I) - 2 or more subtypes can combine to form hybrid = circulating recombinant form (CRF) of virus

    • Subtype C makes up 50% of HIV-1 infections

  • Different subtypes > challange in developing vaccine

  • Antiretroviral therapy (ART) drugs are often tested on subtype B with limited evidence on effectiveness on other subtypes.

HIV-2

• >55% genetically distinct from HIV-1 & less infectious

• Progresses much slower > lower death rate

• Concentrated in West Africa, derived from SIV from scooty mangabeys

• Known 8 strains but only A&B are pandemic

• NNRTI (non-nucleoside reverse transcriptase inhibitor) drug that Rx HIV-1 is ineffective in HIV-2

• Enveloped, +ve sense ssRNA virus with reverse transcriptase

• Contains 2 +ssRNA per virus particle

• Group 6 virus - with 2 subtypes = HIV-1 & HIV-2

• HIV is a Lentivirus (subgroup of retrovirus)

• Encodes 3 major genes:

  • Gag = the capsid or core protein

  • Pol = polymerase, integrase & protease

  • env = envelop (outer structural protein for cell-tyoe & receptor specificity

HIV undergoes different stages to replicate & spread to cells

1. Attachement - HIV binds to CD4 receptors on T cells via gp120 envelop protein (attached to gp41)

2. One of the co-receptors (CCR5 / CXCR4) then bind to gp120 > structural change > releases gp41 > allow HIV to fuse with membrane > release contents of virion into cell

3. Reverse transcriptase transforms viral ssRNA > viral dsDNA > enters nucleus > integrates into host cell genome catalysed by integrase enzyme which cuts host DNA & ligates viral DNA

4. HIV enters latency or productive cycle (below)

5. Pro-virus DNA transcribed into mRNA by host RNA polymerase & exported from nucleus

6. mRNA translated > integral membrane proteins at RER e.g gp41 & gp120

7. Also production of viral RNA & proteins via protease which is packed into emerging virions

8. Protease assembles viral proteins > virions by cleaving large p55 protein into smaller ones (p24, p17, p7, p2 > allows virus to mature & be infectious

*** Highlited stages are target for drugs

-> Key stages where interruptions possible

• Binding, fusion, reverse transcription, integration & maturation

-> There are many different classes of drugs against HIV:

• Nucleoside reverse transcriptase inhibitors (NRTIs)

• Non-nucleoside reverse transcriptase inhibitors (NNRTIs)

• Protease inhibitors (PIs)

• Fusion inhibitors (FIs - aka entry inhibitors)

• CCR5 antagonists (aka entry inhibitors)

• Integrase inhibitors (IIs)

Using single drug is ineffective -> multidrug combinations used. 3 or more drugs with different target genes are given. Typically:

• 2 different NRTIs + 1 NNRTI

• 2 different NRTIs + 1 protease inhibitor

E.g zidovudine, stavudine, lamivudine, abacavir, zalcitabine, emtricitabine, didanosine. 

-> It target the reverse transcriptase stage of HIV cycle

• NRTIs incorporate into virus DNA (catalysed by DNA polymerase) > compete with natural nucleosides

• Act as obligate chain terminators > inhibit transcription of RNA to DNA > inhibits HIV replication

• No effect on already infected cells

-> Specific NRTI (Zidovudine - AZT) - act as thymidine nucleoside analogue > replaces 3C’ OH group with azido (N3) > terminates incorporation of new nucleosides.

• Given as prodrug, requires phosphorylation within cell to be activated

E.g Efavirenz, Nevirapine, Delavirdine

-> Also target the reverse transcriptase stage of HIV cycle

• Bind directly to reverse transcriptase near, but not at the polymerase active site

• This distorts the RT enzyme, blocking the conversion of RNA into DNA

• Unlike NRTIs, this does not require activation by phosphorylation

E.g. Saquniavir, Indinavir, Nelfinavir, Amprenavir, Fosamprenavir, Ritonavir, Lopinavir, Atazanavir

-> PI targets the maturation stages of HIV life cycle

• HIV protease cleaves HIV polyproteins into structural proteins and enzymes required for assembly of new infectious virions

• Protease inhibitors bind the protease and inhibit the correct cleavage of viral proteins.

• This prevents HIV from being fully assembled and becoming infectious.

• Virus infects immune cells at site of infection (CD4+ T cells, dendritic cells, etc) > delivered to lymph nodes

• Active virus replication

• High levels of viraemia and dissemination

• Downregulation of virus replication by immune response

• Virus set point reached after about 6 months

Incubation period is 2-4 weeks - most pt unaware

-> Acute infection:

• CD4+ T cells decline temporarily

• CD8+ T cells increase temporarily

• Anti-HIV antibodies appear

-> Chronic infection

• CD4+ T cells gradually decline

• CD8+ T cells largely unaffected

• Cytotoxic T lymphocyte (CTL) responses and Abs evolve

• Acquisition of macrophage tropism (virus can replicate in macrophages)

-> AIDS established when CD4 Tcell count is <200cells/min

-> Associated with weight loss, malignancies & neuro Sx

There are key changes in cells during AIDS:

• CD4+ T cell depletion and loss of helper function

• HIV-specific CD4+/CD8+ T cell exhaustion

• B cells decrease/dysregulation

• NK cells’ function is impaired

AIDS-defining opportunistic infections = not usually pathogenic but become pathogenic when body’s defence is impaired. E.g

• Cryptococcal meningitis

• Toxoplasmosis

• Pneumocystis pneumonia (PCP); Pneumocystis jirovecii

• Oesophageal candidiasis

• Cancers, including Kaposi’s sarcoma (induced by HHV-8)

• HIV is an RNA virus + rapid replication = prone to error > mutation & drug resistance

  • Mutations to one drug > resistance to other drug of same family. Vaccine challenging

• HIV drugs do not cure, rather it suppress replication > needing life long Rx

• For drug to be effective, replication must be blocked

HIV is sequenced and for each mutation:

• Fold-decreased susceptibility is compared to wildtype virus

• Mutations in drug resistance positions mapped, new mutations compared to most common mutations.

NNRTIs

• Mutation > reduced interaction between RT & bound drug > steric hindrance > making it difficult for NNRTI to enter binding pocket on RT

NRTIs

• Steric hindrance

• Altered interaction with 3’OH of incoming dNTP > enchanced ATP binding & excision of NRTIs

• E.g Zidovudine (AZT) - excision involves pyrophosphorolysis (reverse of polymerisation)

• HIV has enormous genetic variability

• Glycan shielding of the envelope glycoprotein

  • HIV env is most highly glycosylated protein with half mass consists of host-drived N-linked glycans which resists penetration of Abs to envelope

• Immune escape

  • HIV mutates as it replicates > resistance to Abs

  • Original B cell clone is expanded in response to primary infections > Ab binds & neutralise founder virus but fails to neutralise rapidly emerging variants.

    • This repeated change in Ag structure = Ag drift

  • On-going somatic hypermutation of original B cell clone > broadly neutralising Abs (bnAb) > can neutralise emerging virants

-> Continuous race between immune system & virus get slowed by HAART

• Understand the basic anatomical organisation of the immune

system of the human body

• Distinguish between the Immune System (Proper) from the

Lymphatic System of the body

• Distinguish between Primary Lymphoid Organs & Secondary

lymphoid Organs

• Understand the underlying mechanisms that underpin generation of lymph in a healthy individual

• Understand the general organisation of lymph drainage systems of the body

• Its a network of proteins, cells, tissues & organs - work together to protect the body from infectious microorganisms > prevent illnesses

• Bone marrow

• Thymus

• Spleen

• Lymph, lymph nodes and lymphatic vessels

• MALT organs and tissues

  • GI organs, nasopharynx, thyroid, lungs, salivary glands contains Mucosa-associated lymphoid tissue (MALT) - e.g Peyer’s patch in small intestine, tonsil

-> These can be split into fluids, vessels & lymphoid organs

• Involved in specific (adaptive) & non-specific (innate) immunity

• Stationed throughout the body

• Involved in growth, development and differentiation of lymphocytes.

• Interconnected by blood and lymphatic vessels through which lymphocytes circulate

Split into Primary and secondary lymphoid organs

• Primary lymphoid organs (red bone marrow & thymus) - involved in formation and maturation lymphocytes

• Secondary lymphoid organs (spleen, MALT organs & LNs) - along with the lymph vessels, they make up the lymphatic system

  • Lymphatic system drains tissue fluids from EC compartments of the body - except CNS, eyeball, inner ear, cartilage, bone & avascular planes

BM is a primary lymphoid organ

• All lymphocytes arise from here, B cells mature & differentiate here

  • Lymphocytes > circulation > interact with other lymphoid organs

In the Red bone marrow, HSCs differentiate to lymphoid cells:

• HSCs > lymphoid stem cells (common lymphoid progenitor)

• LSC > lymphoblast > develops into small immature lymphocyte or NK cells.

• Lymphocyte > develop into B cell or release into blood as undifferentiated lymphocyte

  • Latter arrives at thymus via blood > processed to form T cells.

• B cells & T cells transported to other lymphatic organs e.g LNs, lymph ducts & spleen

• Thymus is a Primary lymphoid organ - composed of 2 flask-shaped lobes joined at their medial margins

• Lies posterior to manubrium, anterior to great vessels within the superior mediastinum

  • At the base of the heart - aortic arc, brachiochephalic vein & SVC

• Inferior part in adults extends into inferior mediastinum, lying anterior to upper portion of the pericardium

• More prominent in children (max size by age 2) - After puberty > replaced by fat > mainly adipose tissue in adults with remaining true thymus tissue consists of lymphocytes

• T cells differentiate & mature here

• Produces important hormones:

  • Thymosin - stimulates T cell development

  • Thymopoietin & thymulin - enhance T cell function, help distinguish T lymphocytes

  • Thymic Humoral factor (THF) - has immunomodulatory effect during infeciton (mainly viral)

Secondary lymphoid organs (spleen, MALT organs & LN) + lymph vessels makes up the lymphatic system.

-> The lymphatic system drains tissue fluid (aka interstitial fluid) from EC compartments of the body (some exception)

• Tissue fluid is extracellular - lies outside circulatory system

• Occupies the interstitial space & bathes all cell of the body - provide essential plasma & collects waste products

• Low pressure system = movement is driven by breathing & muscle contraction

• Most of tissue fluid returns to blood via capillaries - rest enters lymphatic vessels as lymph

Functional importance:

• Return lymph contents to blood - assists capillaries to return plasma proteins that leak into EC space = role in fluid balance

• Assist transport of cellular debris that doesn’t use circulatory system

• Absorbs / transport fats from GIT

  • By Lacteals - lymphatic vessels found in villi of small intestine.

  • Chyle = Small intestine’s lymph, has high fat content

• Essential for immunological functions of the body

Clinical importance

• Major constituent of the immune system

• Conduit for spread of infections, malignancies (site for 2ndary tumours)

  • Primary infection & cancers may arise

• Blockage > lymphoedema

• Its a transudative fluid - aka interstitial fluid

• Transparent & yellow, Alkaline in nature

• Formed when blood plasma leaves capillaries (hydrostatic pressure) > EC compartment, collected at lymphatic capillaries > travels through lymphatic vessel towards LNs.

  • 90% returns via venous system (oncotic pressure), 10% returns via lymphatic system

• Body produce ~3-4L of lymph/day

• Flows at 120ml/hr - 100ml via thoracic duct, 20ml via lymphatic duct

  • Lymphatic vessels have valves to ensure unidirectional flow

• Contents of the lymph - water (96%) , solutes (protein, lipids, glucose, ions like Na+, K+, HCO3 & Ca2+ and cells mainly lymphocytes)

• ~400-500 LNs in adult body

  • 2/3rd in GI abdomen, rest in head, neck, arms, superficial / deep thorax, legs & pelvis

• MALT (mucosa associated lymphoid tissues) within nasopharynx (tonsils) and intestine (Peyer’s patchs) & other organs also considered LNs

• LNs are bean shaped, receives lymph via afferent channels & drains it through efferent channels.

• Lymph pass through the node, get filtered by phagocytes & macrophages

• Cancer can metastasise to nearest LN, known as sentinel LNs - its the 1st LN to drain a cancer

  • Sentinel node prcedure = identification, removal & analysis of this node

• E.g Breast cancer > mets to sentinel node (axillary LNs)

• Purple coloured soft lymphatic organ - varies in size

• Lies on left hypochondrium, posterior to mid axillary line, deep to 9th, 10th & 11th ribs.

  • 10th rib lies along the axis of spleen

• Covered entirely by peritoneum = intraperitoneal organ

• Anatomical relations:

  • Anterior – Upper part of stomach

  • Superior and partly posterior – Diaphragm

  • Deep to – 9th, 10th and 11th ribs

  • Medial - Left kidney

• Function - clear waste from blood e.g dead or dying RBC, and elaborates lymphocytes.

• Supplied by splenic artery - branch of celiac trunk

2 separate lymph drainage systems:

-> Superficial lymph vessels (superficial structures)

• Drains skin > into regional LN > deep cervical LNs

• Tend to follow the veins and drains into deep lymph vessels

-> Deep lymph vessels (deep structures)

• Drains the viscera > drains to terminal LNs

• Tend to follow the arteries (exceptions???)

Pathway of lymph drainage

• Lymphatic capillary -> lymph vessel (afferent channel) -> lymph node -> lymph vessel (efferent channel) -> lymph trunk -> collecting duct -> subclavian vein

Right lymphatic duct

• Drains right upper quadrant of the body - includes RUL, right parts of head / neck / thorax

• RLD drains into right subclavian vein at right venous angle (where subclavia & internal jugular veins unite)

Thoracic duct

• Drains rest of the body - much larger than RLD

• Drains into left subclavian vein at left venous angle

• It begins inferiorly within abdomen at cisterna chyli (dilated)

  • Here, many lymph trunks drains into thoracic duct

• Then continues superiorly > through diaphragm with aorta at T12 > along posterior & superior mediastinum

• Throughout its course, thoracic duct is along vertical midline until T5 level where it moves to left to drain into left subclavian vein

• Determined by anatomical location of head & neck tissues.

• 2 drainage system, separated by investing layer of deep fascia

• Tissues within cervical region are seperated into superficial & deep tissue depending on their relation to deep fascia.

  • Superficial cervical LNs – surround the external jugular vein. Receives drainage from some nodes in the head > drain into the deep cervical nodes.

  • Deep cervical lymph nodes – surround the internal jugular vein. Receive all drainage of the head and neck, either directly or through regional nodes present in the head.

• Superficial cervical LN & superficial LNs of head are arranged in a ring which extends from chin to occiput - ring is known as outer circle

• Within this circle, there is an inner circle of tonsillar tissue which surrounds upper airway & alimentary passages - this is Walderyer’s ring

• All these nodes drain into deep cervical nodes > jugular lymphatic trunks > right & left (thoracic) lymphatic ducts

• Infection of peritonsillar tissue following infection of palatine tonsils > accumulation of pus within retropharyngeal space

  • Space between prevertebral fascia & buccopharyngeal membrane

• May lead to compression of the pharynx > dysphagia & dysarthria