• Clinical science

General bacteriology

Occurrence in humans

Commensals of the human body

Commensals are microorganisms (e.g., bacteria, fungi) living on or within humans that do not harm the host under normal circumstances and may even be beneficial


Among the vast variety of bacteria, only very few are considered pathogenic and cause disease in humans. These can be differentiated into:

In immunocompromised states (e.g., AIDS, organ transplant), when resident flora is unbalanced (e.g., antibiotic treatment), or if organisms are carried to sites where they do not belong (e.g., gastrointestinal E.coli entering the urethra), commensals may become pathogenic and cause infection.


Prokaryotes vs. eukaryotes

Prokaryotes (Archaea and Bacteria) Eukaryotes (e.g., protozoa, animals, and plants)
Genetic information
  • Contain no nucleus
  • DNA (termed “chromosome equivalent” in prokaryotes) is circular and located in the cytoplasm.
  • Haploid
  • Plasmids are extrachromosomal DNA rings that partially code for important features and pathogenicity factors (plasmid).
  • Absent
  • Present
  • 70S
  • 80S
Cell wall
  • Present in most bacteria
  • Composed of peptidoglycan, which contains muramic acid
  • Only present in plants and algae

Bacterial structure

Structure Gram positive Gram negative Composition Function
Cell wall Present (thick) Present (thin)
  • Peptidoglycan
    • Composed of alternating amino sugars, e.g. muramic acid
    • Cross-linked by transpeptidase
  • Gram-positive organisms only: contains lipoteichoic acid (extends from the membrane to the exterior)
  • Mycolic acid in acid-fast bacteria
  • Protects against osmotic pressure damage
  • Provides structural strength
  • Lipoteichoic acid: stimulates release of TNF-α, IL-1, IL-6
  • Mycolic acid provides chemical and aridity resistance
Outer membrane Absent Present
  • Only present in gram-negative organisms
  • Endotoxin
    • Contains LPS which is composed of
      • O-antigen: recognized by antibodies
      • Core polysaccharide
      • Lipid A: stimulates release of TNF-α, IL-1, IL-6
  • Porins: allows transport across the outer membrane
Cytoplasmic membrane Present Present
  • Hydrophobic layer with selective permeability
  • Carrier for metabolic enzymes for
Capsule Present Present
  • Protects against phagocytosis
Glycocalyx Present Present
  • Adhesion of bacteria to cell surface and foreign surface (e.g., central lines)
Periplasm Absent Present
  • Contains components exiting the bacteria such as hydrolytic enzymes
Flagellum Present Present
  • Adhesion
  • Motility
Pilus (fimbria) Present Present
  • Glycoproteins
  • Adhesion of bacteria to cell surface
  • Function as sex pilus during conjugation
Endospores Present Absent
  • Coating layer composed of
    • Keratin
    • Dipicolinic acid (in the core)
    • Peptidoglycan
    • DNA
    • Metabolically inactive
  • Only gram-positive organisms can form spores
  • Aids in bacterial survival by protecting against

Distinguishing characteristics

Cell wall structure

  • Depending on cell wall structure, differences can be observed in Gram staining
    • Gram-positive bacteria have a thick peptidoglycan cell wall that traps crystal violet dye: violet to blue staining
    • Gram-negative bacteria have a thin peptidoglycan cell wall that do not trap crystal violet dye, but does retain the counterstain (e.g., safranin dye): pink staining
    • There are bacteria without a cell wall that demonstrate atypical gram staining: remain colorless (e.g., Chlamydiae, Mycoplasma, Legionella)
    • Acid-fast bacteria (e.g. mycobacteria) contain mycolic acid in cell wall: red staining in Ziehl-Nielsen or yellowish-green in Auramine rhodamine stain

For more details about acid-fast bacteria, see the learning card on bacteria overview.


  • Bacilli: rod-shaped bacteria
  • Cocci: round-shaped bacteria that tend to have different arrangements under the microscope and are classified accordingly.
  • Coccobacilli: very short rods almost resembling cocci
  • Spirochetes

Growth in culture

To multiply bacteria for a microbial assay, a tissue or fluid sample is taken from the patient and cultivated on a culture medium. Selective culture media are used to grow only select bacteria and thus to isolate specific pathogens. Enrichment culture media, on the other hand, provides optimal conditions for general bacterial growth. The different properties observed in a culture allow for the identification of different types of bacteria.


Some bacteria produce enzymes or compounds that aid in survival under certain conditions or allow for colonization of specific organ systems

Pigments produced by bacteria

Bacterium Produces
Pseudomonas aeruginosa
  • Green pigment (pyoverdin)
  • Blue pigment (pyocyanin)
Serratia marcescens
  • Red pigment
Actinomyces israelii
Staphylococcus aureus
  • Yellow pigment

Molecular biology and serology

  • Molecular biological methods are used (e.g., PCR, FISH) for pathogens that are difficult to cultivate.
  • Indirect serology methods are usually used in long-term infections.
  • Bacterial toxins can be detected in animal experiments.

Bacterial genetics

Bacterial DNA structures

  • Plasmids: bacterial non-chromosomal DNA fragments that replicate independently from chromosomal replication
  • Transposons: Bacterial DNA sequences that cannot replicate independently. These sequences can change their position within the bacterium (e.g., from one plasmid to another, to the bacterial chromosome, or to a bacteriophage)
  • Integrons: Bacterial non-chromosomal DNA that cannot replicate independently. These sequences integrate into chromosomal bacterial DNA via integrase.
  • Pathogenicity islands: Genes associated with virulence factors such as adhesins and toxins. These genes contain transposase and integrase genes.

Genetic variability of bacteria

The genetic variability of bacteria is attributable to intracellular and intercellular mechanisms. Bacterial replication occurs solely via mitosis (cell division).

Intracellular mechanisms

Intercellular mechanisms


Uptake of free DNA via the cell wall

  • Uptake of free segments of naked bacterial DNA from the surrounding through the cell membrane (only competent bacteria) → combination of new DNA material with bacterial pre-existing DNA degradation of unused DNA expression of new genes transformation process
  • This process can be performed by the following bacteria:


Transfer of plasmids (genetic material) by a bridge-like connection between two bacteria

  • F= fertility factor: bacterial plasmid that enables transfer of genetic material between bacteria
    • F+: bacteria with a plasmid that contain genes for sex pilus (to attach to recipient cell) and the F factor; act as donors
    • F-: bacteria without F factor and sex pilus; act as recipients
    • F+ bacteria connect with F- bacteria via the sex pilus → a single strand of plasmid DNA (no chromosomal DNA) is transferred from the F+ bacteria to the F- bacteria (mating bridge)
    • Result: 2 F+ bacteria
  • Conjugation mediated by Hfr cells (= high-frequency recombination cells)
    • Hfr cells: bacteria with a conjugative plasmid (e.g., F factor) integrated into their chromosomal DNA
    • HFr bacteria connect with F- bacteria via the sex pilus transfer and replication of DNA material on recipient F- bacteria (only the leading part of the plasmid and some adjacent genes are transferred) F- bacteria have new genes
    • Result: HFr bacteria and F- cell with new genetic material


Distribution of genetic information by infection of a bacterium with a bacteriophage

  • Generalized transduction: bacterial DNA is transferred from one bacterium to another bacterium via a bacteriophage
    • Bacteriophage infects bacterium → cleavage of bacterial DNA (this DNA does not incorporate into DNA of infected bacterium) → viral DNA is packaged into phage capsid (bacterial DNA may also be incorporated) → lysis of infected bacteria → new bacteriophage infects other bacteria
  • Specialized transduction via excision: a restricted set of bacterial genes is transferred to another bacterium (might include new virulence factors)


Exchange of genetic information via transposons (jumping genes) within the genome or between genomes of various bacteria


Mechanism of bacterial infection and disease

Bacteria use different mechanisms to colonize, invade, and infect the host in order to survive (virulence factors). In some species, these mechanisms can result in disease. Virulence is the tendency of a pathogen to cause damage to a host.

Mechanism Virulence factors Function
  • Adhesion to cell surfaces
  • Invasion of host target
Avoiding the immune system
Bacterial nutrition
  • Secretion of siderophores
  • Chelate and import iron
Antigenic variation
  • Modification of surface antigens to avoid immune recognition and destruction
Intracellular survival
  • Evasion of intracellular phagocytic cells

Type III secretion system

Inflammatory response

Bacterial toxins

  • Bacterial toxins are another virulence factor and involved in:
    • Bacterial invasion
    • Cell damage
    • Inhibition of cellular processes
    • Stimulation of the immune system
Endotoxin Exotoxin
Bacterial source
  • Present in gram-negative organisms only
  • Present in both gram-positive and gram-negative organisms (but not all species)
Location of genetic material
  • Present in plasmid or bacteriophage
Release mechanism
  • Bacterial lysis (death)
  • Actively secreted by living bacteria
Chemical nature
  • Lipopolysaccharide (LPS)
    • Lipid A
      • Composed of phosphorylated N-acetyl glucosamine dimer with fatty acids attached
      • Toxigenic component
    • O antigen
      • Composed of repeating oligosaccharide subunits
      • Immunogenic component
    • Core polysaccharide
  • Proteins in the cytoplasm
    • Often two components: A and B
    • A (active) component, usually an enzyme
    • B (binds) to cell receptors: facilitates entrance of the A component
Heat tolerance
  • Heat-stable (100o C)
  • Heat-labile (destruction at 60o C)
  • Poorly antigenic
  • Highly antigenic: induces production of antitoxin antibodies
Mechanism of action
  • Different mechanism for each toxin (e.g., alpha toxin, AB toxins)
Common effects
Likelihood of causing disease (toxicity)
  • Low
  • High
Toxoid formation
  • Forms no toxoid, so no vaccine available
  • Can be modified into a toxoid vaccine
Typical diseases

Lipid A of endotoxins activates macrophages (→ fever, hypotension), complement (→ hypotension, edema, neutrophil recruitment), and the coagulation cascade (DIC)!

LPS is an ENDOTOXIN: Edema, Nitric oxide, DIC, Outer membrane, TNF-α, O-antigen, eXtremely heat stable, IL-1 and IL-6, Neutrophil chemotaxis
LPS: (O-antigen,) Lipid A, core Polysaccharide cause Shock!


Mechanisms of drug resistance

  • Genetic mechanisms
    • Chromosomal: via chromosomal mutations that alter the binding site for the drug or affect the permeability of the drug
    • Extrachromosomal
      • Via a plasmid: carries genes for enzymes that create resistance
        • Beta-lactamase
        • Acetyltransferase
        • Protein pumps
      • Via R factor: contains transposons and insertion sequences
        • Resistance transfer factor (R-factor): plasmids that code for transfer and replication
        • Resistance determinant (r): genes for resistance and replication
  • Nongenetic mechanisms
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  • 6. Sampath V. Bacterial endotoxin-lipopolysaccharide; structure, function and its role in immunity in vertebrates and invertebrates. Agriculture and Natural Resources. 2018; 52(2): pp. 115–120. doi: 10.1016/j.anres.2018.08.002.
last updated 09/20/2019
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