- Clinical science
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
- Resident flora: microorganisms that are permanently present
- Transient flora: microorganisms that are temporarily present (e.g., E.coli or Staphylococcus aureus on hands)
Among the vast variety of bacteria, only very few are considered pathogenic and cause disease in humans. These can be differentiated into:
- Are capable of survival outside of a host (e.g., in water or soil): e.g., Escherichia coli, Vibrio cholerae, Pseudomonas aeruginosa
- Only cause disease in susceptible hosts
- Opportunistic pathogens: usually benign but have the ability to cause disease in an immunocompromised host (e.g., patients with or after chemotherapy)
- Can only replicate inside the cells of a host and therefore must infect someone in order to survive: e.g., Salmonella, Treponema pallidum, Mycobacterium tuberculosis
- If a sufficient amount of bacteria is ingested (e.g., oral or contaminated foods), disease also occurs in immunocompetent individuals.
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 (Archaea and Bacteria)||Eukaryotes (e.g., protozoa, animals, and plants)|
|Mitochondria|| || |
|Ribosomes|| || |
|Cell wall|| |
|Structure||Gram positive||Gram negative||Composition||Function|
|Cell wall||Present (thick)||Present (thin)|
|Cytoplasmic membrane||Present||Present|| |
|Bacterial capsule||Present||Present|| |
|Glycocalyx||Present||Present|| || |
|Pilus (fimbria)||Present||Present|| || |
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 or yellowish-green in Auramine rhodamine stain
For more details about the individual acid-fast bacteria, see the article on .
- Bacilli: rod-shaped bacteria
- Cocci: round-shaped bacteria that tend to have different arrangements under the microscope and are classified accordingly.
- cocci: very short rods almost resembling
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.
- Substances in the media (e.g., blood components for the growth of )
- Surrounding temperature (e.g., cold enrichment for )
- Cell culture oxygen level is used to differentiate between:
- Aerobic bacteria: grow optimally under atmospheric oxygen levels
- Anaerobic bacteria: grow only in the absence of oxygen ; distinguish between
- Microaerophile bacteria: grow under subatmospheric oxygen levels (e.g., Helicobacter pylori)
Hemolysis (e.g., serves to differentiate streptococci based on the various types of hemoglobin degradation) ; ;
- Alpha hemolysis: The hemoglobin present in the agar is only partially degraded, resulting in methemoglobin, a substance with a characteristic biliverdin-green color (green hemolysis).
- Beta hemolysis: complete degradation of hemoglobin with a translucent halo around the bacterial colony
- Gamma hemolysis: no induction of hemolysis (agar around colonies remains unchanged)
- Growth on bile-esculin agar as well as 6.5% NaCl: only exhibited by group D streptococci (enterococci)
- Resistance testing for antibiotics by using antibiograms:
Some bacteria produce enzymes or compounds that aid in survival under certain conditions or allow for colonization of specific organ systems
- Catalase: Enzyme that breaks down hydrogen peroxide into water and oxygen.
- Coagulase: Enzyme that converts fibrinogen into fibrin.
- Oxidase (cytochrome C oxidase): Enzyme that transfers hydrogen to oxygen, forming water or hydrogen peroxide.
- Urease: Enzyme that converts urea to ammonia and carbon dioxide.
- ( ): involved in cell wall synthesis
Pigments produced by bacteria
|Pseudomonas aeruginosa|| |
|Serratia marcescens|| |
|Actinomyces israelii|| |
|Staphylococcus aureus|| |
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 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).
- High mutation rate
- Exchange of larger gene segments between bacteria that have a similar gene sequence via homologous recombination
- 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 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 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 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. 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.
- Generalized transduction: bacterial DNA is transferred from one bacterium to another bacterium via a bacteriophage
Specialized transduction via excision: a restricted set of bacterial genes is transferred to another bacterium (might include new virulence factors)
- infects bacteria → viral DNA from the bacteriophage incorporates into the bacterial DNA → bacterial DNA is excised with regions of both viral and bacterial genetic material → combined DNA is packed into phage capsid → lysis of infected bacteria → new infect other bacteria
- The genes for the following toxins are transferred from one bacterium to another by specialized transduction:
- Transposons (segments of ) within bacteria can copy, insert, reinsert, and excise from different locations along the genetic material of and chromosomal
Development of antibiotic resistance by creating with different genetic sequences for resistance
- ( ) and Staphylococcus aureus (VRSA) carry the vanA gene that grants resistance.
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.
|Colonization|| || |
|Avoiding the immune system|
|Bacterial nutrition|| || |
|Antigenic variation|| |
|Intracellular survival|| |
Bacterial toxins are another virulence factor and involved in:
- Bacterial invasion
- Cell damage
- Inhibition of cellular processes
- Stimulation of the immune system
|Bacterial source|| || |
|Location of genetic material|| || |
|Release mechanism|| || |
|Heat tolerance|| || |
|Antigenicity|| || |
|Mechanism of action|
|Likelihood of causing disease (toxicity)|| || |
|Toxoid formation|| || |
- Chromosomal: via chromosomal mutations that alter the binding site for the drug or affect the permeability of the drug
Via a carries genes for enzymes that create resistance
- Protein pumps
Via R factor: contains transposons and insertion sequences
- Resistance transfer factor (R-factor): that code for transfer and replication
- Resistance determinant (r): genes for resistance and replication
- Via a carries genes for enzymes that create resistance
- Nongenetic mechanisms