Infection Flashcards
Describe the principles of “an infection” and how an individual develops an infection
Infection - invasion of host’s tissue by microorganisms. Disease caused by replication of microorganism, toxins and host response.
How you get infected - contact, inhalation, ingestion, vertical transmission.
How do microorganisms cause disease and some disease determinants
How do they cause symptoms:
Virulence factors Exotoxins(cytolytic, AB toxins, superantigens, enzymes) and
Endotoxins
Host cellular damage - direct or because of host immune response.
Disease determinants:
virulence factors
inoculum size
antimicrobial resistance
Site
Co-morbidities
Describe the 4 exotoxins produced by gram positive bacteria
Exotoxins are secreted
Cytolytic - membrane damaging
AB toxins - 2 part - B binds to cell and delivers A to cytosol which is often an enzyme that interferes with cell function.
Super antigens - microbial proteins that bind both class II MHC molecules and T-cell receptors (causing activation of the T cell)
Enzymes - destroy tissue that bacteria is trying to invade
What are endotoxins gram neg
lipopolysaccharide-protein complexes
components of cell wall of Gram Negative Bacteria
liberated only on cell lysis or death of bacteria.
Mildly toxic and do not bind to specific receptors.
Cause host cell damage either directly or as a result of the immune response e.g. cytokine determinants storms/SEPSIS.
Describe how to identify that a patient has an infection including history, examination and investigations.
How to identify:
History - symptoms - focal or systemic, severity, duration, potential exposures
Examination - organ dysfunctions
Investigations - specific and supportive
Supportive:
Full blood count(eg neutrophilia means bacterial infection)
CRP(inflammation)
Liver and kidney function tests(to see if drugs can be given)
Imaging
Histopatholoy(look at sample under microscope)
Specific(to determine cause):
Bacteriology- Collect specimen(eg swab, fluids, tissues). Then microscopy, culture and sensitivity.
Use gram stain
Or can look at antigen detection, nuclei acid detection(PCR) or antibiotic susceptibility.
Virology - ELISA tests with antigens or antibodies in well or detecting viral nuclei acid (PCR).
Microorganisms broad categorisation
bacteria - prokaryotic
viruses
parasites(eukaryotic) - Protozoa(single celled) and helminths (multi-cellular)
Fungi (eukaryotic) - yeasts (single-celled) and molds (multicellular)
Key features of bacteria
Look at diagram on notion
All are prokaryotes- do not have nucleus
Gram positive or negative
Cocci or bacilli
Aerobes or anaerobes
Gram stain
Treated with a solution of crystal violet, the bacterial cells will stain purple.
then treated with a solvent - alcohol
gram-positive organisms retain the stain, whereas gram-negative species lose the stain, becoming colourless.
Addition of the counterstain safranin stains gram-negative bacteria pink.
Agar plates
Used for culture of bacteria
Resists digestion by bacterial enzymes
Enriched medium as the plate with the protein and blood provides nutrients for a number of common bacteria.
bacterial structure
Look at notion
Virus features
Consists of DNA or RNA
Surrounded by a protein coat
A virus may also have an envelope derived from the membrane of the host cell.
Viruses contain the genetic information necessary for replication but require the host’s cellular structures and enzymatic machinery to complete the process.
The fate of the host cell following viral infection ranges from rapid lysis and release of many progeny virions to gradual, prolonged release of viral particles.
virus structure
Look at notion
Gram positive and neg diff
Look at notion
thick, multi-layered, peptidoglycan cell wall
or
negative:
have cell wall with 2 membranes which are separated by the periplasmic layer containing peptidoglycan. This layer is thin and so more susceptible to damage. Outer membrane has LPS which has a lipid portion that is toxic(endotoxin). Antigenic so can identify species.
Virulence factors - Factors that enhance pathogenicity
– Host entry (e.g. polysaccharide capsule to protect from enzymes and hostile environments)
– Adherence to host cells (e.g. pili to prevent from being washed away by mucus)
– Invasiveness (e.g. enzymes such as collagenase to degrade extracellular matrix and have easier access to host cell surfaces)
– Iron sequestration (siderophores - capture iron from host for growth)
Ses 2
Understand and describe a model of infection - see notion for flowchart
For any patient you are examining – think:
1) Patient – age, gender, social status, health status, time of year, home, recent
travel.
2)Pathogen – virus, bacteria, fungus, parasite.
3) Mechanism of infection - contiguous (direct) spread, inoculation, haematogenous, ingestion, inhalation, vector, vertical transmission.
4) Process of the infection – attachment, interaction with host defences, host.
5) Management of the patient – history, examination, investigations, treatment (specific and supportive).
6)Patient outcomes – cure, disability, chronic infection or death.
To understand how to apply the model of infection to a specific illness
Example:
Cellulitis - severe inflammation of dermal and subcutaneous layers of the skin.
Patient - children, elderly and immunocompromised.
Pathogen - Group A streptococcus, Staphylococcus aureus and Haemophilus influenza type B
Mechanism -break in skin so pathogens invade subcutaneous layers
Management- antibiotics
Patient outcomes- cure or septic shock
Thrush
Patient - Most HIV-positive individuals oral candidiasis, which often spreads to the oesophagus(AIDS).
Pathogen - yeast Candida albicans - normal body flora of skin, mouth, vagina and intestines
Mechanism - competing bacterial flora eliminated so yeast over grows
Management - nystatin or clotrimazole.
Patient outcomes
Identify microbes commonly found on the skin and other body sites
The skin
Staphylococcus aureus Staphylococcus epidermidis Streptococcus pyogenes Candida albicans
The mouth and nasopharynx
Streptococcus mutans Streptococcus pneumoniae Neisseria meningitidis Haemophilus influenza type B.
The gastrointestinal tract
E. Coli
Urogenital tract - Lactobacillus
Describe how microbes, normally present as commensals (part of the microbiome) can cause disease / infections in certain situations and give
examples.
Normal flora is displaced from its normal location to sterile
location:
Breaching the skin integrity eg skin loss, surgery, IV lines
Fecal-oral route - Foodborne infection
Fecal-perineal-urethral route - Urinary tract infection (women)
Poor dental hygiene
Normal flora overgrows and becomes pathogenic
when host becomes immuno-compromised:
Diabetes o AIDS o Malignant diseases o Chemotherapy (mucositis)
When normal flora in mucosal surfaces is depleted by antibiotic therapy:
Intestine -> severe colitis (Clostridium difficile)
Vagina -> thrush (Candida albicans)
Describe the different innate barriers to infection, including physical,
physiological, chemical and biological
1) Physical barriers – skin, mucous membranes(mouth, RT, GI tract, UT) and bronchial cilia
2) Physiological barriers – diarrhoea, vomiting(hepatitis, meningitis), coughing(pneumonia) and sneezing(sinusitis).
3) Chemical barriers – low pH and antimicrobial molecules eg IgA - tears, saliva, mucous
membrane
lysozyme - sebum, perspiration,
urine
mucus
β-defensins - epithelium
gastric acid
4) Biological barriers – normal flora in strategic locations - benefits:
synthesise vitamins (e.g. K, B12) immune maturation
Compete with pathogens for
attachment sites and ressources Produce antimicrobial chemicals
Describe how these different barriers work together to maximise the response against microbes
Recognize the different interventions that affect integrity of the innate
barriers
Normal flora is displaced from its normal location to sterile location
• Breaching the skin integrity - Skin loss (burns), Surgery, IV lines, Skin diseases, Injection drug users
• Fecal-oral route - Foodborne infection. Fecal-perineal-urethral route - Urinary tract infection esp women.
Poor dental hygiene - o Gingivitis
Normal flora overgrows and becomes pathogenic when host becomes immuno-compromised:
o Diabetes o AIDS o Malignant diseases o Chemotherapy (mucositis)
When normal flora in mucosal surfaces is depleted by antibiotic therapy:
o Intestine -> severe colitis (Clostridium difficile)
o Vagina -> thrush (Candida albicans)
Understand the risk of infection associated with these interventions
State name and function of the second line of defence, including the role of phagocytes and chemicals.
3 phagocytes
4 cells of innate IS
2 chemicals
1) Phagocytes - intracellular killing by O2 dependant pathway(mostly):
macrophages - Present in all organs, Ingest and destroy microbes (Phagocytosis), Present microbial antigens to T cells (adaptive immunity), Produce cytokines/chemokines
monocytes - In blood, Recruited at infection site and differentiate into macrophages
neutrophils - in blood, Increased during infection, Recruited by chemokines to the site of infection, Ingest and destroy pyogenic bacteria - Staph. aureus and Strep. pyogenes
2) Other key cells of the innate immune system
Basophils (mast cells) - Early actors of inflammation (vasomodulation), Important in allergic responses
Eosinophils - Defence against multi-cellular parasites (worms)
Natural killer cells - Kill all abnormal host cells
Dendritic cells - Present microbial antigens to T cells (acquired immunity)
3) Chemicals – complement system and cytokines
Describe how pathogens are recognised by cells of the innate immune
system
PAMPs – pathogen associated molecular patterns - and include carbohydrates, lipids, proteins and nucleic acids, e.g. peptidoglycan (a component of bacterial cell walls), lipopolysaccharide (a lipid/carbohydrate moiety found in bacterial cell membranes), ß-glucan (found in fungal cell walls) or dsRNA (some viruses).
PRRs – pathogen recognition receptors – they are proteins that span the phagocyte membrane and they essentially bind
Opsonisation of microbes enhances the interaction between the phagocyte and the microbe. Opsonins are proteins that bind to and coat the surface of the microbe. These are produced by various components of the immune system.
Name and describe important opsonins
complement proteins - C3b, C4b.
antibodies - IgG, IgM
acute phase proteins - C-reactive protein (CRP), mannose-binding lectin (MBL).
Describe how a clinical evaluation of the innate immune response helps
to identify the presence of infection, and in particular that of acute
inflammation and acute infection.
As examples describe the role and evaluation
of neutrophils and C-reactive protein.
Neutrophilia = bacterial infection
Raised CRP - opsonise that inc phagocytosis - indicates inflammation
Ses 3
Sepsis definition
Sepsis is characterised by a life-threatening organ dysfunction due to a dysregulated host response to infection.
Sepsis effect on organs in ABCDE
Airways - no specific effect
Breathing/Respiratory: Raised respiratory rate (tachypnoea). Fluids and proteins leaking into interstitial tissues lead to lung oedema and decreased lung compliance.
Circulation: Hypovalemia (due to vasodilation and increased capillary leakage) so low blood pressure.
This would result in tachycardia.
End-organ damage (kidneys, liver, and brain)
Disability/CNS: As a result of reduced blood flow to the brain,
patients can present with confusion, drowsiness, slurred speech, agitation, anxiety,
and reduced level of consciousness.
Exposure / Pyrexial (hypothalamic response to infection) BUT remember hypothermia for
elderly.
Renal: As a result of reduced blood transfusion to the kidneys, there is reduction in
urine output.
Sepsis risk factors
• Very young (< 1 year old).
• Elderly (>75 years) or very frail. • Pregnant, post partum (within last 6 weeks).
• Patients with impaired immune system
Sepsis screening
A patient should be screened for sepsis when:
• a clinician or carer is worried
• the NEWS2 score is 5 or more
Scores to:
Resp rate
O2 sat
Systolic BP
Pulse rate
Consciousness
Temp
• the patient is at risk of neutropenia
• there’s evidence of organ dysfunction e.g. lactate 2mmol/l or above
Treatment for amber flag
Amber - (NEWS2 5 or 6 or 1-4 with one of lactate >2mmol, chemotherapy in last 6 weeks, organ failure, deteriorating):
Send bloods
Senior clinical review within 1 hr
Antimicrobials and escalation plan in 3 hrs
Red flag - sepsis 6
NEWS 2 more than 7
Sepsis 6 within the hour
- Senior help
- Give O2 to inc O2 sat
- Send bloods - culture and FBC
- IV antibiotics - consider likely organisms, penetration, patient factors. Source control - drain abscess.
- Consider IV fluids - correct hypovalemia
- Monitor - urine output, are they deteriorating
Consider critical care if patient continues to deteriorate. Continue reviewing patients
daily.
Understand the mechanism by which micro-organisms trigger the
inflammatory cascade
Micro-organisms trigger inflammatory responses via special methods in the following processes:
Gaining entry into the host (e.g. via respiratory, GI, urogenital, skin)
Adherence to host cells (e.g. via cell surface adhesion molecules,
fimbriae/pili)
Invasive into host cells / mucosal surfaces (e.g. via enzymes such as
collagenase and hyaluronidase)
This would then result in inflammation (either pyogenic or granulomatous)!
Understand the relevance of HIV in a global and UK context
many millions of people living with HIV.
Substantially fewer deaths due to HIV in the UK. Biggest burden of HIV infections in Africa.
Describe the principles of HIV structure, replication notion for structure
HIV is a single stranded RNA retrovirus.
Attachment to cells is accomplished via the gp120 portion of the envelope gene product on the HIV surface, which preferentially binds to the CD4 molecule.
The virus infects helper T cells, lymphocytes, monocytes, and dendritic cells, which produce this glycoprotein on their surface.
Replication - The ssRNA is converted to dsDNA and incorporated into the cell’s genome.
Apply the infection model to a patient with HIV and acquired
immunodeficiency syndrome (AIDS)
Describe the principles of infection transmission and prevention with
regard to HIV.
Transmission - Contact of infected bodily fluids with mucosal tissue / blood / broken skin eg sexual contact, blood transfusion, contaminated needles, vertical transmission to fetus during delivery.
Affected by - viral load
Prevention - Condom use, use of clean new needles, treatment during pregnancy, screening,
Post-exposure prophylaxis (PEP), Pre-exposure prophylaxis (PrEP), Male circumcision
Treatment notion
Anti-retroviral drugs (ARVs) ensure undetectable viral load and allowing CD4 count to recover. They work by:
Targeting binding - CCR5 so entry inhibitor
Target enzymes responsible for incorporation of viral DNA into host - integrase inhibitor.
Target reverse transcriptase competitively or non - NNRTI or NRTI
Prevent larger proteins breaking down into smaller proteins in viral life cycle - protease inhibitor
Virus mutates frequently so multiple drugs to resist resistance.
Who should be tested
Resp: bacterial pneumonia / TB • Neuro: meningitis/dementia • Derm: Severe psoriasis
Gastro: Chronic diarrhoea
Cancer
HIV testing
Testing - a) serology – detects both antigens (viral proteins) and antibodies to HIV in the blood, b) PCR – detects the viral nucleic acid and c) rapid testing – usually picks up the antibodies to HIV in either blood or saliva.
Ses 4
Antimicrobial classes
Antibacterial, antifungal, antiviral &
antiprotozoal agents
Anti bacterial classes - 4 (not mechanism of action)
Bactericidal or bacteriostatic
Spectrum – ‘broad’ v. ‘narrow’
Target site (mechanism of action)
Chemical structure (antibacterial class)
How to choose an antibiotic
Cause
Active
Site eg cross blood brain barrier
Right formulation
Half life - dosing
Interaction with other drugs
Toxicity - eg aminoglycosides are nephrotoxic
Monitoring - therapeutic window
different ways to measure antibiotic activity
Disc Sensitivity/Diffusion Testing – putting the organism on the agar plate and putting ‘paper discs’ containing antibiotics and reading the zone of clearance.
Minimum Inhibitory Concentration (MIC) – The first concentration of antibiotic that inhibits the growth of bacteria. Done via: broth microdilution OR E-test strip.
3 Types of antibiotic resistance:
Intrinsic - The antibiotic does not target the specific characteristics of the bacteria, therefore, unable to gain access to bacteria
Acquired - via chromosomal gene mutation/horizontal gene transfer (via plasmids). 3 ways:
Enzymatic destruction of antibiotics
Enzymatic alteration or mutations of bacterial target sites
Overexpression of efflux pumps (multi drug resistance)
Adapted: if there are a sub-therapeutic levels of antibiotics, this only causes a mild stress response to the bacteria – hence it will respond by becoming resistant to the antibiotic
Classes of antibacterials and their mechanism of action
Cell wall synthesis
Beta - lactams
Protein synthesis
Tetracycline, aminoglycosides, macrolides
Cell membrane function
Polymixins
Nucleic acid synthesis
Quinolones, Trimethoprim
Beta lactams + glycopeptides
Penicillins eg penicillin(streptococci), amoxicillin(some gram -ve)
Cephalosporins - broad spectrum but not anaerobes. Gives C.difficile infection. Eg Ceftriaxone (crosses blood-brain).
Carbapenems - broad spectrum eg imipenem. Penicillin allergy. G -ve + G+ve + anaerobes.
Glycopeptides
Vancomycin - G +ve, C.difficile oral otherwise IV.
Narrow therapeutic window.
Protein synthesis
Tetracycline (30s ribosome subunit) & doxycycline - oral, g+ve, broad. Treats protozoa, chlamydia, atypical pneumonia.
Not to children <12 years/pregnant women (causes staining of developing teeth).
Aminoglycosides - gentamicin, g-ve, nephrotoxic
Macrolides (50s) - erythromycin, g+ve
Nucleic acid synthesis
Quinolones - ciprofloxacin, Inhibit DNA gyrase, Very active against Gram negs.
Risk of tendinitis and rupture, aortic dissection, central nervous system effects and C.difficile infection.
Trimethoprim & sulphonamides - Inhibitors of folic acid synthesis, treat UTI.
Co-trimoxazole – Used to treat Pneumocystis jirovecii, Has activity against MRSA
Rifampicin - inhibits RNA polymerase
Antifungals
Azoles (active against yeasts, molds)
• Inhibit cell-membrane synthesis
• Fluconazole used to treat Candida
Polyenes (nystatin and amphotericin)
• Inhibit cell membrane function • Amphotericin for IV treatment of systemic + severe fungal
infections (e.g. aspergillus)
Nyastin for topical treatment of Candida
Antivirals
Aciclovir • When phosphorylated inhibits viral DNA polymerase
Herpes simplex – genital herpes, encephalitis
Varicella zoster – chicken pox & shingles
Oseltamivir (‘Tamiflu’) • Inhibits viral neuraminidase • Influenza A & B
Metronidazole + Nitrofurantoin
anti-bacterial (anaerobes) and anti-protozoal
Protozoal:
1. Amoebae (dysentery & systemic)
2. Giardia (diarrhoea)
3. Trichomonas (vaginitis)
SHOULD NOT TAKE THIS WITH ALCOHOL - like disulfiram
Nitrofurantoin - Mixed between preventing protein synthesis and DNA/RNA synthesis.
Antimicrobial stewardship
Do not start antibiotics in absence of clinical evidence of bacterial infection
antibiotic resistance.
The global and local relevance of Hepatitis B & Hepatitis C
Greater numbers living with hepatitis than HIV worldwide – go on to develop end stage liver disease if left untreated. Far greater numbers of untested individuals since it is not on screening programmes where it is endemic.
Hepatitis viruses - definitions
Hepatitis = inflammation of the liver
Replication specifically in hepatocyte
Destruction of hepatocytes
How to remember
A = acute
C = chronic
B = bit of both
D = double trouble - only with B
E = like A
Transmission
A + E= Faceo-oral
B + C (only blood) + D = blood, sex, vertical
B + C = chronic
Liver function tests (LFTs)
Bilirubin
Liver transaminase - hepatocyte damage
Alkaline phosphatases - Biliary tract cell
damage / cholestasis
Lower Albumin - less function
Coagulation - clotting factors made
Three causes of ALT > 1000
Viral hepatitis
Drugs/medication
Blood clots
B
Transmission - vertical but also sexual contact, intravenous drug use, close household contacts (low risk) where there is significant blood exposure and health care workers via needle stick injuries.
Symptoms - jaundice (icteric sclera), fatigue, abdominal pain, anorexia/nausea/vomiting and arthralgia (joint pain).
Replication - the virus integrates its genetic material into the host genome.
Treatment - anti- viral, vaccine given to babies
Testing - serology and HBV DNA PCR test.
Incubation - 6wekks - 6 months
Presentation- AST/ALT in 1000s
Up to 50% - no/vague symptoms
More likely to become chronic in infancy
B serology
1) Surface antigen first
2) Followed by e-antigen - Highly infectious
3) Core antibody (IgM) - First antibody to appear
4) Followed by e-antibody - Heralds disappearance of e-
antigen + infectivity
5) Surface antibody - Last antibody + Clearance of virus
6) Core antibody (IgG) - Persists for life
Chronic Hep B infection Definition
Persistence of HBsAg after 6 months
Leads to cirrhosis
C
intravenous drug users
Chronic
Symptoms - vague - fatigue, anorexia, nausea, abdominal pain (RUQ)) and about 80% have no symptoms at all
Testing - PCR, anti-Hep C antibody
Treatment - anti-virals - can be cured
No vaccine
Disease progression - cirrhosis, carcinoma
POST-EXPOSURE PROPHYLAXIS (PEP)
Risks of transmission via needle stick injury are as follow:
HIV 1/300 (or even 0 if viral low undetectable)
Hep C 1/30
Hep B 1/3 (or 0 if vaccinated).
Bleed and wash wound
Collect blood from patient and worker
Give Hep B vaccine
PEP for HIV and ARVs - earlier reduces replication.
Monitor
Use condoms
Ses 5
Describe features of Antigen Presenting Cells (APCs)
APC is a macrophage – then T-cells phagocytose the pathogen. If the APC is a B-cell then T-cells respond by stimulating the production of antibodies – the humoral response.
Dendritic and langerhan cells present to naive T cells - not exposed to antigen - become effector cells.
mucosal membranes, skin (i.e., Langerhans cells), blood (i.e., plasmacytoid cells), lymph nodes (i.e., follicular dendritic cells), and spleen.
Capture by phagocytosis and Macropinocytosis
Describe MHC molecules in relation to microbe presentation
APCs present pathogen antigenic peptide attached to major histocompatibility complexes.
MHC II complexes are expressed on dendritic cells, B-cells and macrophages (APCs)and they present microbial peptides from extracellular microbes.
MHC I complexes exist in all nucleated cells and present microbial peptides from intracellular microbes.
Co-dominant expression of MHC class 1 and 2
MHC presentation 3 features
Peptide binding cleft - has polymorphic residues
Broad specificity - many peptides presented by same MHC
Responsive T cells - CD4+ by class 2 and CD8+ by class 1
Processing - Exogenous
Captured
Degradation
Peptide-rich vesicles fuse with vesicles containing MHC class II molecule
Formation of complex
Only APCs
Processing - Endogenous
Viral protein in cytosol
Marked for destruction by the
proteasome
Proteasome-generated viral peptide transported to ER by TAP proteins
Complex formation
Describe T cells and their role with regard to infections
Interact with APCs and/or nucleated cells to become activated. Then kill pathogens by cytotoxic pathway or activate B cells to produce antibodies.
Describe how antigen presenting cells activate the right adaptive immune
response
Present MHC2 to CD4+ Tcells to activate humoural immune response.
Present MHC 1 to CD8+ T cells to activate cell mediated response.
Clinical MHC
Major causes for organ transplant
rejection o HLA molecules mismatch between donor and
recipient (Allograft) o Graft-Versus-Host reaction (GVH)
association with autoimmune
disease
Ankylosing spondylitis
Insulin-dependent Diabetes Mellitus
Antimicrobial Stewardship
What is it?
Why is antimicrobial stewardship important
How does it work in practice
appropriate use of antimicrobials - limit the selection for antimicrobial resistant strains
a) MDR (multi-drug resistant) - Non-susceptibility to at least one agent in 3 or more categories
b) XDR (extensively drug resistant - Non-susceptibility to at least one agent in all but two categories
c) PDR (pan-drug resistant) - Non-susceptibility to all agents in all antimicrobial categories
- Does the patient need antibiotics? - Have they finished their course?
- Can we switch this to oral from IV? - Can they swallow?, Are they improving?
- Can we change broad to narrow-spectrum?
sensitivity results - Do you need special authorisation from microbiology?
Ses 6
Why you get surface infections and how , example of natural + prosthetics
commensals carried on
skin and mucosal surfaces. transfer to other sites can be
harmful.
Natural:
Cellulitis
Conjunctivitis
Urinary tract infection
Pneumonia
Septic arthritis
Osteomyelitis
Endocarditis
Prosthetic:
Intravascular lines
Cardiac valves
Prosthetic joints
catheters
• Adherence to host cells or prosthetic surface • Biofilm formation • Invasion and multiplication
Skin micro-organisms
Viruses
• Papilloma
• Herpes simplex
Bacteria Gram positive
• Staph aureus
• Coagulase negative staphylococci
Gram negative
• Enterobacteriaceae
Fungi
• Dermatophytes
Parasites
• mites
Other sites
Nasopharynx - Neisseria meningitidis, Streptococcus pneumoniae, Haemophilus influenzae
Mouth - Candida
Stomach - Helicobacter
Intestine - Clostridium
Vagina - Lactobacilli, coagulase-negative staphylococci, mycoplasmas
Explain a ‘biofilm’ and the implications for an infection on a surface
Biofilms comprise of microbial communities attached to surfaces and encased in an extracellular matrix of microbial origin.
Colonise medical devices - staph aureus + epidermis.
2 types of staphylococcus:
Coagulate +ve - acute
Coagulate -ve - cause problems when in a biofilm - chronic
Biofilms protect the bacteria by prevent bacterial phagocytosis, antibodies and complement recognition/binding of receptors.
only solution to treat the infection is to remove the artificial surface on which the biofilm is growing.
Describe the management of infected surfaces
sterilize tissue via antibacterial drugs, removing prosthetic material with surgery.
The challenges are poor antibacterial penetration into biofilm, low metabolic activity of biofilm micro‐organisms and difficulties of surgical procedure.
endocarditis mechanism
The endocardium is non sticky and normally resists bacterial seeding.
Biofilm binds to valves.
Aberrant flow = collection of fibrin + platelets
Microorganisms that enter the blood stream from skin, mucosa or other site bind to bio-film
Further fibrin deposition, platelet aggregation and bacterial invasion - cascade
Staph aureus - fibronectin proteins so can bind to unifected endocardium.
Hallmarks of endocarditis
- constitutional symptoms which are cytokine mediated
- local spread of infection causing destruction of myocardium
- distal blood borne septic embolisation
Clinical notion
Fever
Heart murmur
Other cardiac complications
Embolic features: These are small bits of the biofilm) that
become loose and travel to small capillaries where they can block or cause local infection:
Janeway Lesions: These are haemorrhagic nodular lesions on palms and soles. They are related to micro-abscess formation and localised necrosis.
Splinter Haemorrhages: capillary engorgements usually in distal third of the nail bed.
Oslers nodes: These are painful, erythematous nodules on pads of fingers and toes.
Prosthetic endocarditis microorganisms
With knee joints have to fuse bones
Prosthetic valve - greater than 1 year = strep, enterococcus, candida, staph a
Less than 1 = coagulase -ve strep
Prosthetic joint - coagulase -ve staph
Staph a
Pacing wire - coagulase -ve staph
Staph a
Quorum sensing
all bacteria within the biofilm express certain genes which confer some advantage to the colony such as production of a multi drug resistant (MDR) efflux pump or antibiotic production to kill other bacteria so less competition.
Describe the antigen receptor present on T cells
T:
o T cell receptor (TCR): a and b chains
o CD3 complex
o Accessory molecules (CD4 or CD8)
Antigen recognised determined by what peptides on MHC
Understand the mechanisms leading to T cells activation notion
Signals on APCS - costimulation
Signal 1:
MHC class 1 or 2
B7
Cytokines - Il1, Il6, TNF alpha
Extracellular = CD4+ - effector is T helper cells
Intracellular = CD4+ and CD8+ - effector is cytotoxic T cells
Describe the antigen receptor present on B cells
B Cell Receptor or BCR: Membrane bound antibodies - Unique specificity for each cell
Recognises Macromolecules + small chemicals
Understand the mechanisms leading to B cells activation notion for exam diagram
1st signal: BCR engagement Signal transduction
Antigen processing and presentation
Increased B7 costimulators
2nd signal: TCR engagement
Antigen specific
Role of B7 costimulators
3rd signal
Cytokines
CD40 activation
Effect = Proliferation and differentiation
Antibody production (IgM production is T helper
independent. IgG, IgA, IgE production is T helper
dependent (isotype switch))
Heavy chain class switching
Affinity maturation in antibody
response - Prolonged or repeated exposure
Memory B cells - Upon re-challenge can give a faster,
stronger and longer antibody response
Describe the effector mechanisms of cell-mediated immunity and
humoral immunity
Notion
Effector functions of Antibodies
IgG
Fc-dependent phagocytosis
Complement activation
Neonatal Immunity
Toxin/virus neutralization
IgA
Mucosal Immunity
IgE
Immunity against helminths
Mast cell degranulation (allergies)
IgM
Complement activation
Ses 7
Hospital-acquired Infections
infections acquired in hospitals 48 hours after admission.
pathogens, patients, practice, place
Viruses: blood borne viruses (hepatitis B, C, HIV), norovirus, influenza, chickenpox, COVID-19
Bacteria - staph aureus including MRSA, Clostridioides difficile, Escherichia coli, Mycobacterium
Fungi: Candida albicans, Aspergillus species
Parasites: Malaria
Patient - extremes of age, immunosuppression, surgical patient, emergency admission.
Self infection Intervention- stop smoking, controlled diabetes, antimicrobial prophylaxis, hand hygiene.
Patient to patient - isolation of infected
Worker to patient- vaccinated, hand hygiene, PPE, Good clinical techniques (e.g. sterile non-touch)
Practice factors - Policies, engagement, leadership.
Place factors - eg no of beds in a bay.
Environment to patient transmission intervention - Cleaning (Disinfectants), Single use equipment, Sterilisation.
I fived
Identify:
Abroad
Blood borne
Colonised
Diarrhoea
Expectorating
Funny rash
Initiate
Inform
Ses 8
Describe common global and imported tropical infections and their
pathogenesis, including malaria,
Plasmodium falciparum
- most severe form - resistance emerging
Plasmodium vivax
- usually less severe & relapsing
Plasmodium ovale
- usually less severe & relapsing
Plasmodium malariae - relatively mild
Plasmodium knowlesi
- macaque monkeys – zoonotic transfer
Vector - female Anopheles mosquito.
Incubation Period: Minimum 6 days. However, P. falciparum - 4 weeks, P. vivax/ovale - 1 year! A
Symptoms and Signs: Fever, chills, headache, confusion, seizures, jaundice haemoglobinuria.
Investigation:
Blood film (thick and thin smears)
Blood test: FBC, U&E, LFT
CXR
CT-Head
Management
Removal of the vector (mosquito): bed nets, sanitation facilities.
Drugs: artesunate, quinine (IV/PO), doxycycline. Don’t use chloroquine
(unless for P.vivax). Primaquine is given for liver-related malaria. (However,
you don’t give this for G6PD patients – inc oxidative damage - MEH).
enteric fever (typhoid when secondary to )
Mechanism of infection – faecal-oral from contaminated food/water
Salmonella typhi or Salmonella parathyphi - gram neg bacilli
factors:
Only needs small dose to be infectious
Survives gastric acid
Fimbriae adhere to epithelium over ileal lymphoid tissue (Peyer’s patches) - get into blood/reticuloendothelial system
Reside within macrophages so affect spleen + liver
Susceptible patients: Usually children. Travellers from Asian countries (also African and South America).
Incubation Period: 7-14 days
Symptoms and Signs: fever, headache, abdominal discomfort, dry cough, bradycardia.
Complications - intestinal haemorrhage & perforation, seeding. chronic carrier.
Prevention - vaccination, good food and water hygiene.
Diagnostic investigations: blood culture
Treatment options: IV ceftriaxone, Azithromycin, Ciprofloxacin (but there is increasing resistance to this antibiotic)
and dengue fever
Understand and describe the life cycle of malaria.
Sporozoytes
liver cells
Merozoites
Infect RBCs
Reproduce and rupture
Infect other cells
Gametocytes remain in blood and taken up by mosquito when they are bitten again.
Describe common travel related respiratory infections, including emerging
infections
Understand the importance of a travel history
many travel related infections can have deadly consequences on patients
➢ Specific to certain areas (place) or activities so ask where have you come from? Sexual, tick bites, insect bites, animal bites?
When did the symptoms develop? - calc incubation period
➢ Different strains of pathogen (antigen/resistance) - have you taken vaccinations?
➢ Infection prevention (ward/lab)
Apply the infection model to a patient presenting with an infection linked
to travel
Expand the description of pathogen/person/practice/place as it applies to
travel related infections
Form a differential diagnosis based on region of travel, incubation period
and clinical presentation
Short - less than 10 days - bacteria = shigella
Medium - 10-21 days - protozoa- malaria
Long - more than 21 days- virus - HIV
Animal bite - rabies
Rodents - leptospirosis
Insect bite - malaria or dengue
Tick bite - Rickettsia
Undercooked meat - salmonella
Ses 9
Apply the infection model to a patient who is immunocompromised
Describe the main reasons for a patient to be immunocompromised - primary
Primary = congenital causes - intrinsic gene defect.
Antibody defects
Defect in B cell development- X-linked agammaglobulinaemia
Defect in antibody production - Common Variable Immunodeficiency, Selective IgA deficiency (asymptomatic)
T cell defects - Di George syndrome
Combined B and T cell defects - Severe combined immunodeficiency (SCID)
Phagocytic detect - defect in resp burst - Chronic granulomatous disease (CGD) - normally presents with skin abscess, pulmonary aspergillosis (Halo sign on HRCT)
secondary
Decreased production of immune components:
malnutrition
infection (eg HIV)
liver diseases
therapeutic treatment (eg corticosteroids)
splenectomy.
Increased loss of immune components:
due to protein-losing conditions or burns.
Increased susceptibility to infections:
chemotherapy
Understand the links between the innate and adaptive immune system and
situations and illnesses where a patient is immunocompromised
To consider primary immune deficiencies linked to patterns of infection.
Describe the warning signs that suggest a primary immunodeficiency
disease - SPUR + 3 more
Family history
Failure to thrive
Diagnosis of sepsis
Severe - life-threatening
Persistent
Unusual - site eg deep and nature of organisms eg opportunistic - candida
Recurrent
Is the component there?
Are they functional?
Describe the most common primary immunodeficiency diseases
CVID
Use of the clinical presentation to understand the immune defects
Onset:
Less than 6 months = Tcell or phagocyte defect
More than 6 months and less than 5 yrs = B cell, antibody or phagocyte defect.
More than 5 yrs = B-cell/antibody or 2nd
Disease:
Bacterial - complement deficiency
Bacterial + fungal = phagocytic defects
Bacterial, viral, protozoal - antibody deficiency
All 4 - T cell defects
management of primary immunodeficiency diseases
Lab investigations for antibodies, T cells, neutrophils, complements
Supportive treatment:
Infection prevention (eg prophylactic antimicrobials) Passive immunization -avoid live attenuated vaccines in patients with severe PIDs (SCID)
Nutritional support (Vitamins A-D)
Specific:
Immunoglobulin replacement therapy
Hematopoietic Stem Cell therapy
Ses 10
Describe E. coli including the identification +
serology + agar plate notion
Gram-negative rods - pink stain.
lactose-fermenting - use MacConkey agar as it contains lactose (which will grow into pink/red colonies if the pH becomes acidic – when lactose is broken down into lactic acid).
contain the O,H,K,F antigens
K - capsule
On- LPS
F - fimbriae
H- flagella
Describe the role of E. coli in health and disease
Part of bowel microbiota
Causes UTI and diarrhoea.
EPEC and EIEC are most common among young children in the developing world.
Can protect against salmonella
E. coli as a cause of diarrhoea pathogenesis, role of toxins and clinical features of ETEC and STEC.
Enterotoxigenic E. coli (ETEC) - causes ‘traveller’s diarrhoea’ through the production of 2 toxins (heat stable and heat labile) to cause watery diarrhoea - stimulate lining of intestine so secrete excess fluid. Cramping, fever, nausea.
Enteropathogenic E. coli (EPEC) - creates a translocation tube to access and anchor into the enterocyte.
Shiga toxin-producing E. coli (STEC) - Shiga toxin (A & B subunits) inhibits protein synthesis within the cell and this
causes cell death. Haemorrhagic colitis, haemolytic uraemic syndrome (HUS - triad of acute renal failure, haemolytic anemia, and thrombocytopenia).
Describe E. coli as a cause of urinary tract infections with virulence factors and clinical features
Uropathogenic E coli (UPEC)
Virulence factors:
Adhesins- Type 1 fimbriae- adhesive tips that bind to α-D-mannosylated proteins on uroepithelium, cause invasion of uroepithelium and the formation of intracellular bacterial communities (IBCs) .
Toxins - LPS, alpha haemolysins ( HlyA - pore forming toxin that is cytotoxic to epithelial cells), siderophores (acquire iron from UT).
Clinical features:
Cystitis - Uropathogenic E coli transfer from the rectum to the urethra and then migrate to the bladder.
Frequent and urgent urination, suprapubic pain, haematuria, malaise.
Can go up to kidneys and cause pyelonephritis- back pain, fever, vomiting.
Describe E. coli as a cause of blood stream infections and sepsis
commonest cause of bacterial
bloodstream infection.
Causes - UTIs, older than 75, urinary catheters, GI infections.
Describe the management of E. coli infections
Diarrhoea - related
Prevent - avoid raw / undercooked food and untreated water.
Treatment- should recover within few days, clear liquids, oral rehydration solutions, avoid antibiotics
UTI
Antibiotics - trimethoprim or nitrofurantoin.
Describe the structure of both the influenza virus
and understand their replication.
Influenza structure:
negative strand RNA genome
Encodes RNA-dependent RNA transcriptase that synthesises viral mRNAs using the template.
haemagglutinin (H) - binds to cell and neuraminidase (N) - releases the virus.
a) The flu virus is constantly replicating
b) Life cycle of approximately 6 hours
c) Viral RNA polymerases have a high error rate
the SARS-CoV-2 virus - structure and replication
large, enveloped,
spikes on surfaces
+ve single stranded RNA
used as mRNA for replication of viral particles
converted to –negative stranded RNA so template for new + strand RNA for new particles.
major antigen is spike protein used to gain entry
10hrs
RNA-dependent RNA polymerase
Define the concept of an animal reservoir for both viruses and their major
surface antigens.
C - pig and others infect animals as well
H and N proteins
Covid - zoonotic transfer from bats.
Explain how the viruses gain entry to the human host and their subsequent
uptake and spread from person to person.
Influenza:
transmitted from person to person via the respiratory route
attaches to sialic acid residues on host cell glycoproteins (NANA)
Entry by receptor-mediated endocytosis. N cleaves residue and releases.
SARS - resp route or contact with infected surfaces. Attaches to Ace2 transmembrane protein
Describe the clinical symptoms and complications of influenza infection
and SARS-CoV-2 infection.
Influenza - fever, headache, sore throat, cough
Complications- otitis media, croup, sinusitis, pneumonia
Covid - fever, sore throat, sneezing, muscle/joint pain, extreme fatigue and loss of taste/smell.
Hospitalisation and death
Describe how you would diagnose flu and COVID-19 in a clinical setting
Flu - symptoms and clinical assessment but there are rapid antigen tests and PCR.
Covid - nasopharyngeal swab which detects the viral RNA using reverse transcription polymerase chain reaction (RT-PCR). Lateral flow (antibody/antigen detection systems) tests.
Briefly outline the management of influenza & COVID-19 including
treatment options and prevention and how this is determined (for
influenza) by WHO each year.
Flu - antivirals
and neuraminidase inhibitors, vaccination against A and B.
Quadrivalent - 2A and 2B
Children - live nasal spray
WHO monitors antigenic changes each year and determines the composition of the vaccines
Covid - mRNA vaccines
Define the concepts of antigenic shift and antigenic drift in the influenza
virus.
antigenic shift - major changes in the genes of flu viruses
Diff strains combine
change in the viral subtype resulting in different H and N proteins.
reassortment of different RNA segments from each species in a new capsid
No previous immunity
Antigenic drift - random mutations in viral RNA - minor changes
Define the concepts of mutation rate and production of variants for SARS-CoV-2.
entire replication process is approximately 10 hours. This short replication period combined with the
RNA-dependent RNA polymerase (which is error prone) - means that the virus has a high mutation rate and numerous variants
Define the concepts of pandemics and epidemics (seasonality) and how
these may arise in relation to influenza.
antigenic shift - new subtype - no previous immunity - pandemics
Can respond with cytokine storm - T-cells attack and destroy the tissues in which the virus is replicating – in particular the lungs.
Ses 11
Review the microbiology and classification of streptococci
Classification by haemolysis ( ability to break down RBCs)
Alpha haemolysis - strep pneumoniae - viridans
Beta - pyogenes
Gamma - non - haemolytic
Or
Lancefield group for beta haemolytic strep based on cell wall antigens
S pyogenes = A
Highlight a range of virulence factors found in Streptococcus pyogenes
More?
Hyaluronic acid capsule - Inhibits phagocytosis by neutrophils and macrophages.
Poor immunogen because of similarity to human connective tissue hyaluronate.
M protein - Resistance to phagocytosis by inhibiting activation of alternative complement pathway on bacterial cell surface. > 150 antigenically different serotypes as a consequence of nucleotide variants of emm gene.
Adhesins, including lipoteichoic acid, M protein, fibronectin binding proteins - Adherence is first step in colonisation/infection.
Streptolysins O and S - Lysis of erythrocytes, neutrophils, platelets
Dnases A, B, C and D - Degradation of DNA
virulence factors with clinical aspects of infection - strep toxic shock syndrome what is ARF
Strep toxic shock syndrome:
Entry of group A strep into deeper tissues and bloodstream
Streptococcal pyrogenice exotoxins stimulate T-cells through binding to MHC class II APCs inducing cytokines (TNF-α, IL-1β, IL-6).
M-protein fibrinogen complex formation
Describe streptococcal pharyngitis including microbiological features,
clinical presentation and complications
• Peak incidence 5-15
years • Droplet spread • Association with over-
crowding • Untreated patients develop M protein specific antibody
Clinical features
Abrupt onset sore throat
Malaise, fever, headache
Lymphoid hyperplasia
Tonsillopharyngeal exudates
Complications:
Scarlet fever - Due to infection with
streptococcal pyrogenic exotoxin strain of S.pyogenes, Local or haematogenous
spread, High fever, sepsis, arthritis,
jaundice.
Suppurative complications - Peritonsillar
cellulitis/abscess • Retropharyngeal
abscess, Mastoiditis, sinusitis, otitis media, Meningitis, brain abscess
Disease caused by immune response not by bacteria. Happens due to antibody produced due to disease reacting with body proteins?:
Acute rheumatic fever - Inflammation of heart,
joints, CNS
Acute post-streptococcal glomerulonephritis • Acute inflammation of renal glomerulus
Describe other clinical infections caused by Streptococci
S mutans - endocarditis
S agalactiae - commensal of vagina but can invade in pregnancy
Streptococcus pyogenes skin infections
Impetigo
– Childhood infection, 2-5 years
– Initial skin colonisation, followed by intradermal innoculation
– No ARF but impetigo is most common cause of glomeruonephritis
• Erysipelas
– Dermis infection with lymphatic
involvement – Face, lower limbs – Facial lesions frequently preceded by
pharyngitis – Lower limb infection usually secondary
to invasion of skin via trauma, skin
disease or local fungal infection
• Cellulitis
– Skin and subcutaneous tissue
infection – Impaired lymphatic drainage and
illicit injecting drug use
important risk factors
• Necrotising fasciitis
– Infection of deeper
subcutaneous tissues and fascia. – Rapid, extensive necrosis – Usually secondary to skin break – Severe pain, even before gross
clinical changes – High fever, fulminant course, high
mortality (20-70%)
