--- module: 035-01 language: en chapter: 35 title: "Bacteria, Viruses, Fungi, Parasites, and Microbial Genetics" module_title: "Foundations" source_sha256: e6ab040573528899bde368da2ff78985b7428f6fd8d50b1af5077a402b97b201 --- # Bacteria, viruses, fungi, parasites, microbial genetics ## Orientation ### Organisation, replication, metabolism, host dependence #### Determine diagnosis, transmission, immunity, therapy ### Bacteria prokaryotic, fungi and parasites eukaryotic ### Microbiota support colonisation resistance ### Detection does not always prove causation ## Bacterial cell structure ### No nucleus, chromosome in nucleoid, plasmids ### Peptidoglycan wall prevents osmotic rupture #### Determines staining and antibiotic susceptibility ### Gram-positive: thick exposed wall, teichoic acids ### Gram-negative: thin wall between two membranes #### Outer membrane lipopolysaccharide and porins #### Lipid A provokes powerful inflammation ### Mycobacteria: lipid-rich, acid-fast envelope ### Mycoplasmas lack a wall, resist wall-active drugs ### Capsules impede phagocytosis, support adherence ### Pili attach and transfer DNA, flagella move ### Endospores resist heat, drying, chemicals ### Biofilms alter growth, immunity, drug penetration ## Bacterial growth and metabolism ### Binary fission clonal, exchange creates diversity ### Lag, exponential, stationary, death phases ### In vivo growth shaped by nutrients and oxygen #### Slow, dormant, biofilm populations respond differently ### Aerobes, anaerobes, facultative, microaerophiles ### Respiration uses electron transport and acceptor ### Fermentation regenerates cofactors without acceptor ## Taxonomy and clinical patterns ### Cocci, rods, curved, spirals, branching filaments ### Stain, enzymes, mass spectrometry, sequence refine ### Taxonomy changes, do not rely on names alone ### Extracellular pyogenic: neutrophils, pus, abscess ### Intracellular bacteria need cell-mediated immunity ### Toxin-mediated disease with limited invasion ### Obligate intracellular: no growth on routine media ## Viruses ### DNA or RNA in capsid, sometimes enveloped #### No ribosomes or energy metabolism, use host ### Genome type dictates replication and mutation ### Receptor attachment shapes tropism ### Enveloped fragile, non-enveloped persist ### Persistence: latency, integration, long-lived cells #### Reactivation after altered immunity or stress ### Oncogenic: inflammation, cell cycle, integration ### RNA polymerases often lack proofreading #### Segmented viruses reassort during coinfection ### Evolution has no predetermined virulence direction ## Fungi ### Eukaryotes: chitin walls, ergosterol membranes ### Yeasts bud, moulds form hyphae, dimorphic switch ### Superficial, subcutaneous, systemic endemic ### Opportunists exploit neutropenia, T-cell impairment #### Candida colonises mucosa, invades vulnerable hosts #### Aspergillus: allergy, cavity, angioinvasion ### Shared eukaryotic biology limits selectivity #### Targets: ergosterol, wall, nucleic acid, mitosis ## Protozoa, helminths, and prions ### Protozoa: single cells, varied life cycles #### Cysts survive outside hosts ### Malaria cycles mosquito, liver, red cells ### Helminths: nematodes, cestodes, trematodes #### Most do not multiply, burden reflects exposure #### Strongyloides autoinfects, fatal in immunosuppression ### Tissue migration causes eosinophilic inflammation ### One negative specimen may miss intermittent shedding ### Prions template abnormal protein folding #### Resist inactivation, long incubation ## Genomes, mutation, and gene regulation ### Mutation from replication error, damage, mobile elements ### Antibiotics select resistance, do not create it ### Horizontal transfer accelerates adaptation #### Transformation takes up free DNA #### Transduction via bacteriophages #### Conjugation through cell contact #### Transposons and integrons collect genes ### Quorum sensing regulates biofilm and virulence ### Lysogenic conversion adds toxin genes ## Microbiota and laboratory identification ### Resident communities compete with pathogens ### Antibiotics reduce colonisation resistance ### Dysbiosis describes alteration, not mechanism ### Specimen quality precedes technology #### Sample the site before antimicrobials when safe #### Superficial swabs misrepresent deep infection ### Culture: viable organisms, misses treated pathogens ### Amplification detects residual non-viable material ### Sequencing does not establish causality