• 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
  • Absent
  • Present
  • 70S
  • 80S
Cell wall
  • Only present in plants and algae

Bacterial structure

Structure Gram positive Gram negative Composition Function
Cell wall Present (thick) Present (thin)
Outer membrane Absent Present
Cytoplasmic membrane Present Present
  • Hydrophobic layer with selective permeability
  • Carrier for metabolic enzymes for
Bacterial capsule Present Present
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

Distinguishing characteristics

Cell wall structure

For more details about the individual acid-fast bacteria, see the article on bacteria overview.


Growth in culture (Bacterial 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

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

Bacterial transformation

Uptake of free DNA via the cell wall

Bacterial conjugation

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

Bacterial transduction

Distribution of genetic information by infection of a bacterium with a bacteriophage. Bacteriophages are viruses that only infect bacteria. Infection leads to either the production of a new virus with destruction of the bacterium (lytic phage) or integration of phage DNA in the bacterial genome (prophage). Integration of phage DNA can result in uptake of pathogenicity factors.

Bacterial transposition

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
  • Chelate and import iron
Antigenic variation
  • Modification of surface antigens to avoid immune recognition and destruction
Intracellular survival

Type III secretion system

Inflammatory response

Bacterial toxins

Endotoxin Exotoxin
Bacterial source
Location of genetic material
Release mechanism
  • Bacterial lysis (death)
  • Actively secreted by living bacteria
Chemical nature
  • 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
Common effects
Likelihood of causing disease (toxicity)
  • Low
  • High
Toxoid formation
  • Forms no toxoid, so no vaccine available
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
      • 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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  • 3. Le T, Bhushan V,‎ Sochat M, Chavda Y, Zureick A. First Aid for the USMLE Step 1 2018. New York, NY: McGraw-Hill Medical; 2017.
  • 4. Pray LA. Transposons: The Jumping Genes. Nature Education. ; 1(1): p. 204. url: https://www.nature.com/scitable/topicpage/transposons-the-jumping-genes-518.
  • 5. Haiko J, Westerlund-Wikström B. The role of the bacterial flagellum in adhesion and virulence. Biology (Basel). 2013; 2(4): pp. 1242–1267. doi: 10.3390/biology2041242.
  • 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 09/04/2020
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