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  <head>
    <title>036-01 Foundations</title>
    <ownerName>Integrated Medical Foundations</ownerName>
  </head>
  <body>
    <outline text="Foundations of infection and diagnostic microbiology">
      <outline text="Infection chain and transmission">
        <outline text="Exposure does not guarantee colonisation">
          <outline text="Colonisation does not guarantee disease"/>
          <outline text="Detection does not guarantee causation"/>
        </outline>
        <outline text="Reservoirs: humans, animals, soil, water, food, equipment"/>
        <outline text="Routes: contact, droplet, aerosol, faecal-oral, blood, vertical">
          <outline text="Droplets short range; aerosols stay suspended"/>
        </outline>
        <outline text="Incubation ends with symptoms; latency with infectiousness">
          <outline text="Communicability may precede symptoms or outlast recovery"/>
        </outline>
      </outline>
      <outline text="Colonisation and invasion">
        <outline text="Adhesion via pili, surface proteins, capsules"/>
        <outline text="Tropism: receptors, temperature, nutrients, oxygen"/>
        <outline text="Resist mucus, cilia, flow, coughing, peristalsis"/>
        <outline text="Invasion via cells, phagocytes, lymph, blood, nerves"/>
        <outline text="Intracellular survival">
          <outline text="Block phagolysosome fusion or escape to cytosol"/>
        </outline>
        <outline text="Dose and portal shape presentation">
          <outline text="Devices, breached skin, aspiration create new niches"/>
        </outline>
      </outline>
      <outline text="Toxins and tissue injury">
        <outline text="Exotoxins: secreted proteins with specific targets">
          <outline text="A-B toxins: binding part plus enzymatic part"/>
          <outline text="Superantigens activate many T cells"/>
        </outline>
        <outline text="Endotoxin: Gram-negative lipopolysaccharide">
          <outline text="Lipid A activates innate sensors">
            <outline text="Fever, vasodilation, capillary leak, shock"/>
          </outline>
        </outline>
        <outline text="Virulence is relative and context-dependent">
          <outline text="Opportunists exploit altered host defences"/>
          <outline text="Damage from too little or excessive response"/>
        </outline>
      </outline>
      <outline text="Innate barriers and recognition">
        <outline text="Skin, mucus, acid, urine flow, microbiota"/>
        <outline text="Pattern-recognition receptors detect conserved structures">
          <outline text="Activate inflammasomes, interferons, cell death"/>
        </outline>
        <outline text="Complement: classical, lectin, alternative routes">
          <outline text="Opsonises, recruits inflammation, forms attack complexes"/>
          <outline text="Regulatory proteins protect host surfaces"/>
        </outline>
        <outline text="Neutrophils: phagocytosis, oxidants, extracellular traps"/>
        <outline text="Macrophages: ingest, present antigen, organise repair"/>
        <outline text="Natural killer cells kill stressed cells"/>
      </outline>
      <outline text="Adaptive defence">
        <outline text="B cells become plasma or memory cells">
          <outline text="Immunoglobulin M appears early"/>
          <outline text="Immunoglobulin G: systemic memory, crosses placenta"/>
          <outline text="Immunoglobulin A protects mucosa and milk"/>
        </outline>
        <outline text="T-cell help enables class switching">
          <outline text="Conjugate vaccines build memory to capsules"/>
        </outline>
        <outline text="CD-four cells coordinate responses by subtype"/>
        <outline text="CD-eight cells kill cells presenting class one peptide"/>
        <outline text="Vaccine protection varies and can wane"/>
      </outline>
      <outline text="Immune evasion and immunodeficiency">
        <outline text="Evasion strategies">
          <outline text="Capsules, antigenic variation, latency"/>
        </outline>
        <outline text="Defect type predicts infection">
          <outline text="Neutropenia: invasive bacteria and fungi, muted pus"/>
          <outline text="T-cell deficiency: opportunists, intracellular organisms"/>
          <outline text="Antibody deficiency: sinopulmonary, encapsulated"/>
          <outline text="Terminal complement defects: Neisseria"/>
          <outline text="Absent splenic function: encapsulated organisms"/>
        </outline>
        <outline text="Secondary impairment more common than primary">
          <outline text="Fever may be absent; act on subtle decline"/>
        </outline>
      </outline>
      <outline text="Choosing and collecting specimens">
        <outline text="Sample involved site, not colonised surface"/>
        <outline text="Collect before antimicrobials if no delay"/>
        <outline text="Aseptic, adequate volume, rapid transport"/>
        <outline text="Rejecting a poor specimen can be safer"/>
      </outline>
      <outline text="Microscopy, culture, identification">
        <outline text="Gram stain: wall class and morphology">
          <outline text="Sensitivity depends on burden and specimen"/>
        </outline>
        <outline text="Culture shows viability, enables susceptibility">
          <outline text="Negative after treatment, poor sampling, slow growth"/>
        </outline>
        <outline text="Identify by biochemistry, antigen, mass spec, sequence"/>
        <outline text="Flora significant at sterile site, expected on skin"/>
      </outline>
      <outline text="Antigen, nucleic acid, serology">
        <outline text="Nucleic-acid amplification multiplexes and quantifies">
          <outline text="May detect colonisation or non-viable material"/>
          <outline text="Gene present does not guarantee expression"/>
        </outline>
        <outline text="Serology detects antibody or antigen">
          <outline text="Immunoglobulin M may persist or cross-react"/>
          <outline text="Seroconversion or rising titre is stronger"/>
          <outline text="Absent early or with immune deficiency"/>
        </outline>
      </outline>
      <outline text="Susceptibility and interpretation">
        <outline text="Exposure-informed breakpoints">
          <outline text="Minimum inhibitory concentrations cannot rank drugs"/>
        </outline>
        <outline text="Penetration, dose, source control decide success"/>
        <outline text="Pretest probability frames results">
          <outline text="Predictive value changes with prevalence"/>
        </outline>
        <outline text="One-set skin organism may be contamination">
          <outline text="Devices or immune impairment make it real"/>
        </outline>
        <outline text="Repeated low-value testing yields incidental positives"/>
      </outline>
    </outline>
  </body>
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