Chapter 4

Case Study: Biofilms, Missed Diagnosis, and Unintended Consequences

Lydia's Case History

  • Lydia was an 82-year-old active and healthy woman with good cognitive function who suffered a mild stroke.
  • She was recovering in the hospital's rehabilitation center.
  • A Foley catheter was placed to drain urine from her bladder, but the chart lacked notes on why it was placed or how long it should remain.
  • After 2 weeks, the urine bag was cloudy, and the lab culture grew copious Enterococcus and E. coli.

Chain of Events 1

  • Broad-spectrum antibiotics were ordered to combat a presumed Urinary Tract Infection (UTI).
  • There was no clinical evidence of UTI, such as fever, elevated blood count, or delirium.
  • Instead, asymptomatic bacteriuria resulted from biofilm-mediated colonization of the catheter tubing and bag from bacteria in the periurethral flora.
  • Definitions:
    • Biofilm: A community of microorganisms attached to a surface.
    • Bacteriuria: Bacteria in the urine.
    • Bacteremia: Bacteria in the blood.
    • Septicemia: Bacteria in the blood, often associated with endotoxin (from the gram-negative outer layer).

Chain of Events 2

  • On the last day of antibiotics, Lydia developed a fever, severe abdominal pain, and foul-smelling diarrhea.
  • A stool culture tested positive for Clostridium difficile (C. diff) and its toxins A & B.
  • The normal flora had been wiped out, creating an opportunity for C. diff to bloom and cause infection.
  • C. diff is a spore-forming anaerobe inadvertently transferred when patients are moved.
  • 10-20% of C. diff strains do not produce toxins.
  • C. diff is a resident in the colon flora of 3-5% of healthy individuals.

Chain of Events 3

  • Lydia's hospital stay was extended due to the C. diff nosocomial infection.
  • C. diff caused pseudomembranous colitis, but she avoided the more serious complications of toxic megacolon or bowel perforation.
  • Several weeks after returning to her independent living, Lydia was re-admitted when she contracted community-acquired pneumonia.
  • Streptococcus pneumoniae had acquired resistance to antibiotics during the long exposure to broad-spectrum antibiotics.
  • Lydia’s condition deteriorated quickly, and she died 2 weeks later.

Reflection Questions

  • List the microbiological principles in this case study.
  • What was the role of a biofilm? Was it related to Lydia’s disease? Why are biofilms so difficult to remove once established?
  • What factors directly set up the conditions for the C. diff infection?
  • Explain the interconnections between C. diff as a spore forming bacteria and C. diff as an opportunistic pathogen.
  • What was the timing and role of the Streptococcus pneumoniae infection?

Accessory Genes

  • Accessory Genes exist "in pan, not core".

Chapter 4: Archaeal Cell Structure

  • Archaea's cell structure is presented with a scale bar of 100 nm.
  • The outer surface of one archaeal cell is made inside the S-layer.
  • It transports some bacteria and most archaea.

General Archaeal Features

  • Many features in common with Eukarya
    • Genes encoding protein: replication, transcription, translation
  • Features in common with Bacteria
    • Genes for metabolism
    • Genomic organization and plasmids
  • Other elements are unique to Archaea
    • unique rRNA gene structure
    • capable of methanogenesis
    • Lipids in plasma membrane
    • Cell walls of pseudomurein – not peptidoglycan

More on Archaea

  • Highly diverse with respect to morphology, physiology, reproduction, and ecology
  • Best known for growth in anaerobic, hypersaline, pH extremes, and high-temperature habitats (although found across all ecosystems)
    • They exploit extreme environments.
    • They're found everywhere, in normal environments as well.
  • Also found in marine arctic temperature and tropical waters
  • Not a significant cause of diseases in humans.

Archaeal Cell Morphology

  • Examples include Methanosarcina mazei (a coccus that forms clusters) and Thermoproteus tenax (a branched archaeal cell).
  • Filamentous archaeon and Bacterial biofilm morphologies exist.

Bacterial vs. Archaeal Cells (Table 4.1)

  • Comparison of Bacterial and Archaeal Cells
    • Property differs between bacteria and archaea which are:
      • Plasma membrane lipids
      • Cell wall constituents
      • Inclusions present
      • Ribosome size
      • Chromosome structure
      • Plasmids present
      • External structures
      • Capsules or slime layers
  • Key Differences:
    • Plasma membrane lipids: Bacteria have ester-linked phospholipids and hopanoids forming a lipid bilayer; some have sterols. Archaea have glycerol diethers forming lipid bilayers; glycerol tetraethers form lipid monolayers.
    • Cell wall constituents: Bacteria have peptidoglycan in nearly all; some lack cell walls. Archaea lack peptidoglycan; some consist of S-layer only, others combine S-layer with polysaccharides or proteins, and some lack cell walls.
    • Ribosome size: Both Bacteria and Archaea have 70S ribosomes.
    • Chromosome structure: Both typically have circular, double-stranded (ds) DNA. Bacteria usually have a single chromosome.
    • External structures: Both have flagella. Bacteria have fimbriae (pili) common, while Archaea have pili and piluslike structures common.
    • Capsules or slime layers: Common in Bacteria, rare in Archaea.

Important Differences Between Bacteria and Archaea Cell Envelopes

  • Plasma membrane lipids: Bacteria have ester-linked phospholipids and hopanoids forming a lipid bilayer. Archaea have glycerol diethers forming lipid bilayers; glycerol tetraethers form lipid monolayers, branched isoprene subunits.
  • Cell wall: Bacteria have peptidoglycan in nearly all, some lack a cell wall, and some have an S-layer. Archaea always lack peptidoglycan and have diverse cell-wall chemistry with combinations of S-layer, polysaccharide, or proteins.
  • Capsules and slime layers: Common in Bacteria and rare in Archaea.

Archaeal Cell Envelopes

  • Differ from bacterial envelopes in the molecular makeup and organization
  • S layer may be only component outside plasma membrane
  • Some lack cell wall
  • Capsules and slime layers are rare

Archaeal Membranes

  • Composed of unique lipids
    • isoprene units (five carbon, branched)
    • ether linkages rather than ester linkages to glycerol
  • Some have a monolayer structure instead of a bilayer structure

Archaeal Membrane Lipids

  • Archaea have branched-chain hydrocarbons attached to glycerol by ether linkages.
  • Different from Bacteria and Eukarya, which have fatty acids attached to glycerol by ester linkages.
  • Archaeal isoprene-derived hydrocarbons are made by a different set of biosynthetic pathways and enzymes.
  • Archaeal membranes have polar phospholipids, sulfolipids, glycolipids, and other unique lipids

Archaeal Lipids and Membranes

  • Bacteria/Eukaryotes:
    • Fatty acids attached to glycerol by ester linkages
  • Archaea:
    • Branched-chain hydrocarbons (isoprene)
    • attached to glycerol by ether linkages
    • Some have diglycerol tetraethers
    • Ether linkage is stronger than ester linkage between archaeal and bacterial lipids.

Archaeal Lipids and Membranes

  • Bacteria/Eukaryotes: Fatty acids attached to glycerol by ester linkages.
  • Archaea: Branched chain hydrocarbons attached to glycerol by ether linkages.
  • Branched carbon precursors exist.

Pseudopeptidoglycan Repeating Unit

  • Methanogens make pseudopeptidoglycan
  • Pseudopeptidoglycan is composed of two sugars:
    • N-acetylglucosamine (NAG or GlcNAc)
    • N-acetyltalosaminuronic acid (TalANAc)
  • There is no peptidoglycan in archaea.
    • one class of archal bacteria only can produce methane using L-isomers, as opposed to D-isomers, as a waste product.

Archaeal Cell Surfaces

  • Cell envelopes
    • varied S layers attached to plasma membrane
    • pseudomurein (peptidoglycan-like polymer for some archaea)
    • complex polysaccharides, proteins, or glycoproteins found in some other species
      • There is no reason to produce or develop antibiotics, considering polysaccharides and no pathogens

Archaeal Cell Wall Properties

  • All lack peptidoglycan; methanogens have pseudomurein
  • Pseudomurein may be outermost layer, similar to Gram-positive microorganisms
  • Nearly all archaea have an S-layer.
  • S layer is glycoprotein matrix outside the membrane and separated by pseudomurein.
  • The lack of peptidoglycan makes archaea resistant to all antibiotics that target peptidoglycan biosynthesis.

S-layers in both Archaea and Bacteria

  • TEM image of a freeze-etched and metal-shadowed preparation of (a) an archaeal cell (from Methanocorpusuculum sinense), and (b) a bacterial cell (from Desulfotomaculum nigrificans).

Archaeal Motility

  • Flagella are thinner than bacteria.
  • Some made of more than one type of protein.
  • Filament is not hollow.
  • Rotation:
    • Powered by ATP hydrolysis instead of proton motive force.
    • Direction moves the cell forward or backward rather than runs and tumbles.
  • Swimming motility has extremely fast speeds.
  • Archae swim a lot faster than bacteria with a different set of motor proteins.