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  <head>
    <title>035-01 Foundations</title>
    <ownerName>Integrated Medical Foundations</ownerName>
  </head>
  <body>
    <outline text="Bacteria, viruses, fungi, parasites, microbial genetics">
      <outline text="Orientation">
        <outline text="Organisation, replication, metabolism, host dependence">
          <outline text="Determine diagnosis, transmission, immunity, therapy"/>
        </outline>
        <outline text="Bacteria prokaryotic, fungi and parasites eukaryotic"/>
        <outline text="Microbiota support colonisation resistance"/>
        <outline text="Detection does not always prove causation"/>
      </outline>
      <outline text="Bacterial cell structure">
        <outline text="No nucleus, chromosome in nucleoid, plasmids"/>
        <outline text="Peptidoglycan wall prevents osmotic rupture">
          <outline text="Determines staining and antibiotic susceptibility"/>
        </outline>
        <outline text="Gram-positive: thick exposed wall, teichoic acids"/>
        <outline text="Gram-negative: thin wall between two membranes">
          <outline text="Outer membrane lipopolysaccharide and porins"/>
          <outline text="Lipid A provokes powerful inflammation"/>
        </outline>
        <outline text="Mycobacteria: lipid-rich, acid-fast envelope"/>
        <outline text="Mycoplasmas lack a wall, resist wall-active drugs"/>
        <outline text="Capsules impede phagocytosis, support adherence"/>
        <outline text="Pili attach and transfer DNA, flagella move"/>
        <outline text="Endospores resist heat, drying, chemicals"/>
        <outline text="Biofilms alter growth, immunity, drug penetration"/>
      </outline>
      <outline text="Bacterial growth and metabolism">
        <outline text="Binary fission clonal, exchange creates diversity"/>
        <outline text="Lag, exponential, stationary, death phases"/>
        <outline text="In vivo growth shaped by nutrients and oxygen">
          <outline text="Slow, dormant, biofilm populations respond differently"/>
        </outline>
        <outline text="Aerobes, anaerobes, facultative, microaerophiles"/>
        <outline text="Respiration uses electron transport and acceptor"/>
        <outline text="Fermentation regenerates cofactors without acceptor"/>
      </outline>
      <outline text="Taxonomy and clinical patterns">
        <outline text="Cocci, rods, curved, spirals, branching filaments"/>
        <outline text="Stain, enzymes, mass spectrometry, sequence refine"/>
        <outline text="Taxonomy changes, do not rely on names alone"/>
        <outline text="Extracellular pyogenic: neutrophils, pus, abscess"/>
        <outline text="Intracellular bacteria need cell-mediated immunity"/>
        <outline text="Toxin-mediated disease with limited invasion"/>
        <outline text="Obligate intracellular: no growth on routine media"/>
      </outline>
      <outline text="Viruses">
        <outline text="DNA or RNA in capsid, sometimes enveloped">
          <outline text="No ribosomes or energy metabolism, use host"/>
        </outline>
        <outline text="Genome type dictates replication and mutation"/>
        <outline text="Receptor attachment shapes tropism"/>
        <outline text="Enveloped fragile, non-enveloped persist"/>
        <outline text="Persistence: latency, integration, long-lived cells">
          <outline text="Reactivation after altered immunity or stress"/>
        </outline>
        <outline text="Oncogenic: inflammation, cell cycle, integration"/>
        <outline text="RNA polymerases often lack proofreading">
          <outline text="Segmented viruses reassort during coinfection"/>
        </outline>
        <outline text="Evolution has no predetermined virulence direction"/>
      </outline>
      <outline text="Fungi">
        <outline text="Eukaryotes: chitin walls, ergosterol membranes"/>
        <outline text="Yeasts bud, moulds form hyphae, dimorphic switch"/>
        <outline text="Superficial, subcutaneous, systemic endemic"/>
        <outline text="Opportunists exploit neutropenia, T-cell impairment">
          <outline text="Candida colonises mucosa, invades vulnerable hosts"/>
          <outline text="Aspergillus: allergy, cavity, angioinvasion"/>
        </outline>
        <outline text="Shared eukaryotic biology limits selectivity">
          <outline text="Targets: ergosterol, wall, nucleic acid, mitosis"/>
        </outline>
      </outline>
      <outline text="Protozoa, helminths, and prions">
        <outline text="Protozoa: single cells, varied life cycles">
          <outline text="Cysts survive outside hosts"/>
        </outline>
        <outline text="Malaria cycles mosquito, liver, red cells"/>
        <outline text="Helminths: nematodes, cestodes, trematodes">
          <outline text="Most do not multiply, burden reflects exposure"/>
          <outline text="Strongyloides autoinfects, fatal in immunosuppression"/>
        </outline>
        <outline text="Tissue migration causes eosinophilic inflammation"/>
        <outline text="One negative specimen may miss intermittent shedding"/>
        <outline text="Prions template abnormal protein folding">
          <outline text="Resist inactivation, long incubation"/>
        </outline>
      </outline>
      <outline text="Genomes, mutation, and gene regulation">
        <outline text="Mutation from replication error, damage, mobile elements"/>
        <outline text="Antibiotics select resistance, do not create it"/>
        <outline text="Horizontal transfer accelerates adaptation">
          <outline text="Transformation takes up free DNA"/>
          <outline text="Transduction via bacteriophages"/>
          <outline text="Conjugation through cell contact"/>
          <outline text="Transposons and integrons collect genes"/>
        </outline>
        <outline text="Quorum sensing regulates biofilm and virulence"/>
        <outline text="Lysogenic conversion adds toxin genes"/>
      </outline>
      <outline text="Microbiota and laboratory identification">
        <outline text="Resident communities compete with pathogens"/>
        <outline text="Antibiotics reduce colonisation resistance"/>
        <outline text="Dysbiosis describes alteration, not mechanism"/>
        <outline text="Specimen quality precedes technology">
          <outline text="Sample the site before antimicrobials when safe"/>
          <outline text="Superficial swabs misrepresent deep infection"/>
        </outline>
        <outline text="Culture: viable organisms, misses treated pathogens"/>
        <outline text="Amplification detects residual non-viable material"/>
        <outline text="Sequencing does not establish causality"/>
      </outline>
    </outline>
  </body>
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