General bacteriology

Last updated: August 5, 2022

Summarytoggle arrow icon

Bacteria constitute a domain of unicellular prokaryotes that, unlike the eukaryotic domain (e.g., animals and plants), do not have a nucleus. They can be classified as pathogens or commensals. Microscopy (with staining) and culture are the most important methods of identifying bacteria. For a table of the bacteria with the highest clinical relevance see “Bacteria overview.”

Occurrence in humanstoggle arrow icon

Commensals of the human body [1][2]

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 (e.g., by inhibiting the growth of pathogens or helping with digestion)

Pathogens [1][2]

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

Immunocompromise (e.g., due to AIDS, organ transplant), disruption of resident flora balance (e.g., due to antibiotics), or spread of resident flora to otherwise sterile areas (e.g., gastrointestinal E.coli entering the urethra) can facilitate the excessive multiplication and/or spread of organisms, causing infection.

Bacterial structuretoggle arrow icon

See “Prokaryotes vs. eukaryotes.”

Overview of bacterial structure
Structure Gram positive Gram negative Composition Function
Cell wall
  • Present (thick)
  • Present (thin)
Outer membrane
  • Absent
  • Present
Cytoplasmic membrane
  • Present
  • Present
Bacterial capsule
  • Present
  • Present

Glycocalyx (slime layer)

  • Present
  • Present
  • Adhesion of bacteria to cell surface and foreign surface (e.g., central lines)
  • Absent
  • Present
  • Stores substances for excretion/elimination
  • Present
  • Present
  • Adhesion
  • Motility
Pilus (fimbria)
  • Present
  • Present
  • Glycoproteins
  • Adhesion of bacteria to cell surface
  • Function as sex pilus (an appendage encoded for the F factor that attaches two bacterial cells together) during conjugation
  • Absent
  • Coating layer composed of
  • Metabolically inactive (spores are usually formed when nutrients are reduced)
  • Aids in bacterial survival by protecting against:

Distinguishing characteristicstoggle arrow icon


Cell wall structure

Gram staining

Acid-fast staining

These Atypical Microbes Usually Lack Color Because these Microbes are Bare (no cell wall), Emaciated (thin), and Remain inside:” Treponema, Anaplasma, Mycobacteria, Ureaplasma, Leptospira, Chlamydia, Borrelia, Mycoplasma, Bartonella, Ehrlichia, and Rickettsia do not Gram stain well.


Intracellular bacteria

Survival in oxygenated environment

Oxygen level is used to differentiate between the following:

Foul Anaerobes Can't Breathe:” Fusobacterium, Actinomyces israelii, Clostridium, and Bacteroides are obligate anaerobic.


Hemolysis serves to differentiate streptococci based on the various types of hemoglobin degradation

Enzymatic testing

Resistance testing

  • Performed with antibiotics to yield an antibiogram: a microbiological test that assesses the susceptibility of a bacterial pathogen to various antibiotics.
  • Reports the sensitivity of a pathogen as "susceptible", "intermediate", or "resistant" (e.g., Enterococci are resistant to cephalosporins).
  • Minimum inhibitory concentration: the lowest concentration of an antimicrobial that inhibits the growth of a specific microorganism isolate
  • Are used as a guide for selecting antibiotic therapy

Growth in culture (bacterial culture)

  • Description
    • To multiply bacteria for a microbial assay, a tissue or fluid sample is taken from the patient and cultivated on a culture medium.
    • Generation time refers to the time required by bacteria to double in number in a culture medium; depends on:
    • The different properties observed in culture allow for the identification of different types of bacteria.
      • Substances in the media (e.g., blood components for the growth of Haemophilus influenzae)
      • Surrounding temperature (e.g., cold enrichment for Yersinia )
  • Types of culture media
    • Enrichment culture media: provides optimal conditions for general bacterial growth
    • Selective culture media
      • Used to grow only select bacteria and thus to isolate specific pathogens
      • Contain substances (e.g., antibiotics) that prevent the growth of other organisms
      • Example: Thayer-Martin agar
    • Indicator media (differential media)
      • Contain indicator substances that undergo a change in color when coming in contact with metabolic products of certain organisms
      • Example: MacConkey agar
Most common bacterial cultures
Type of culture Composition Pathogen isolated Colony morphology
Thayer-Martin agar
  • Neisseria gonorrhoeae: small in size with defined margins, mucoid appearance, colorless or grayish-white color, smooth consistency [3]
MacConkey agar
Bordet-Gengou agar
  • Small, round, shiny colonies with mercury-silver appearance
Regan-Lowe medium
  • Small, glistening, greyish-white colonies [4]
Chocolate agar
  • Contains X factor (hematin) and V factor (NAD+) to promote growth of fastidious organisms (organisms with complex or stringent nutritional requirements that are difficult to culture and only grow with specific nutritional supplementation and precise environmental control)
  • Small, pale-grayish, mucoid colonies with coccobacillary shape
Eaton agar
  • “Fried egg” appearance

Cystine-tellurite agar

  • Black colonies with a brown halo
Löffler medium
  • Contains dextrose, beef and horse extract, sodium chloride, and proteose peptone [5]
  • Cream-colored colonies, raised centers
  • Dark-blue metachromatic granules can be visualized with methylene blue stain
Eosin methylene blue agar
  • Colonies with green metallic sheen

Charcoal yeast extract agar
  • Smooth surface and precise edges, white-gray to blue-gray color
  • Pasteurella
  • Moderate sized, smooth, greyish color
  • Small, smooth, slightly yellowish [6]
  • Francisella
  • Tiny, pinpoint, gray-white, translucent or opaque [7]
Löwenstein-Jensen agar
  • Small, brownish, granular (“buff, rough, and tough”) [9]
Middlebrook agar
  • Contains a variety of inorganic salts to promote growth of mycobacteria, oleic acid, and albumin.
Hektoen enteric agar
Triple sugar iron agar
  • Fermentation causes a color change within the medium
Mannitol salt agar
  • High level of salt inhibits the growth of most other bacteria
Bile esculin agar
  • Blackening of the medium around the colonies
Thiosulfate citrate bile salts sucrose agar
  • Round, smooth, glistening, and slightly flattened yellow colonies


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

SUCH PuNKS!” - S. epidermidis, Ureaplasma, Cryptococcus, H. pylori, Proteus, Nocardia, Klebsiella, and S. Saprophyticus are urease-positive organisms.

“A CAT Needs PLaCESS to Belch its Hairballs:” Nocardia, Pseudomonas, Listeria, Candida, Escherichia coli, Staphylococci, Serratia, Burkholderia cepacia, and Helicobacter pylori are catalase-positive organisms.

Pigments produced by bacteria

Bacterium Produces
Pseudomonas aeruginosa
Serratia marcescens
  • Red pigment
Actinomyces israelii
Staphylococcus aureus
  • Yellow pigment

To remember that Pseudomonas aeruginosa produces green pigment, think of the color of a(e)rugula.
To remember that Serratia Marcescens produces red pigment, think: “flaming hot Serloin (sirloin) Marinade.”
To remember that Actinomyces israelli produces yellow granules, think of “yellow sands of Israel”.
To remember that Staphylococcus aureus produces a golden-yellow pigment, think of the word “aurum” meaning gold in Latin.

Molecular biology and serology

Bacterial geneticstoggle arrow icon

Bacterial DNA structures

  • Plasmids: bacterial nonchromosomal DNA fragments that replicate independently from chromosomal replication
  • Integrons: bacterial nonchromosomal DNA that cannot replicate independently (these sequences integrate into chromosomal bacterial DNA via integrase)
  • Pathogenicity islands: a group of genes associated with virulence factors such as adhesins and toxins (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 binary fission (cell division).

Intracellular mechanisms

  • High mutation rate
  • Exchange of larger gene segments between bacteria that have a similar gene sequence via homologous recombination

Intercellular mechanisms

SHIN: Streptococcus pneumonia, Haemophilus Influenzae, and Neisseria are capable of bacterial transformation.

SHe DIed BECause of a toxin:” SHiga toxin, DIphtheria toxin, Botulinum toxin, Erythrogenic toxin, and Cholera toxin are transferred via bacterial transduction.

Mechanism of bacterial infection and diseasetoggle arrow icon

General mechanisms

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 a measure of the severity of a disease caused by a pathogen. Calculated by dividing the number of individuals who become severely ill or die due to an infection by the total number of individuals who have contracted the disease.

Overview of the most common virulence factors
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

Type III secretion system

Inflammatory response

Bacterial toxins


Bacterial toxins are likewise virulence factors and play a role in:

  • Bacterial invasion
  • Cell damage
  • Inhibition of cellular processes
  • Stimulation of the immune system
Overview of the most common bacterial toxins
Endotoxin Exotoxin
Bacteria type
Location of genetic material
Release mechanism
  • Bacterial lysis (death)
  • Exocytosis
  • Actively secreted by living bacteria
Biochemical structure
  • Lipopolysaccharide (LPS), which consists of: [15]
  • Polypeptides in the cytoplasm, which consist of two components:
    • Component A (active component): usually an enzyme
    • Component B (binding component): binds to cell receptors and facilitates entrance of A component
Heat tolerance
  • Heat-stable (for one hour at 100°C)
  • Low
Mechanism of action
  • Different mechanism for each toxin such as AB toxins, a two-component toxin:
    • B component facilitates binding and uptake (endocytosis) of A component
    • A component an enzyme, most commonly ADP ribosyltransferases
Common effects
Likelihood of causing disease (toxicity)
  • Low: > 100 μg required to cause death
  • High: 1 μg can cause death

Toxoid formation

  • Forms no toxoid, therefore, 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:” Lipid A, Polysaccharide, Shock, Edema, Nitric oxide, DIC, Outer membrane, TNF-α, O-antigen, eXtremely heat-stable, IL-1/6, and Neutrophil chemotaxis are important features of endotoxins.

Most common bacterial exotoxins

Overview of exotoxins
Toxin Pathogen Mechanism of action Manifestation
Streptolysin O
Erythrogenic exotoxin A
Toxic shock syndrome toxin (TSST-1)
Exfoliative toxin
Enterotoxin B
  • Forms pores in enterocyte membranes → leakage of Na+ and water into the intestinal lumen
Alpha toxin
Diphtheria toxin
Pseudomonas exotoxin A
Shiga toxin
Shiga-like toxin
Heat-stable toxin
Heat labile toxin
Cholera toxin
Anthrax toxin
Pertussis toxin
Botulinum toxin
  • Acts as a protease that cleaves SNARE proteins and prevents fusion of transmitter-containing vesicles with the presynaptic membrane → inhibition of acetylcholine release from the presynaptic axon terminals

Mechanisms of drug resistancetoggle arrow icon

Genetic mechanisms

  • Chromosomal: via chromosomal mutations that alter the binding site for the drug or affect the permeability of the drug
  • Extrachromosomal
    • Resistance plasmid
      • Carries genes for enzymes that create resistance to specific antibiotics
      • Consists of:
        • Resistance transfer factor (R factor): codes for transfer and replication of resistance genes (can also contain F factor)
        • Resistance determinant (r): genes for resistance
    • Beta-lactamase: an enzyme that breaks the beta-lactam ring of a beta-lactam antibiotic, altering the chemical structure of the drug
    • Acetyltransferase: an enzyme that transfers acetyl groups to antibiotics, altering the chemical structure of the drug
    • Protein pumps: a group of energy-dependent proteins that pump antibiotics out of the cell

Nongenetic mechanisms [16]

Referencestoggle arrow icon

  1. Modified Thayer Martin Agar. Updated: August 14, 2019. Accessed: November 25, 2020.
  3. Composition of Loeffler Medium. Updated: May 1, 2019. Accessed: November 25, 2020.
  4. Raad I, Rand K, Gaskins D. Buffered charcoal-yeast extract medium for the isolation of brucellae.. J Clin Microbiol. 1990; 28 (7): p.1671-2.doi: 10.1128/JCM.28.7.1671-1672.1990 . | Open in Read by QxMD
  5. Francisella tularensis. Updated: January 1, 2020. Accessed: November 25, 2020.
  6. Lowenstein-Jensen (LJ) Medium- Composition, Principle, Uses, Preparation and Colony Morphology. Updated: June 11, 2018. Accessed: November 25, 2020.
  7. Mycobacterium tuberculosis and Tuberculosis (page 1). Updated: January 1, 2020. Accessed: November 25, 2020.
  8. Corry JEL, et al.. Hektoen enteric (HE) agar. Progress in Industrial Microbiology. 2007.doi: 10.1016/S0079-6352(03)80056-5 . | Open in Read by QxMD
  9. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P . Molecular Biology of the Cell. Garland Science ; 2002
  10. Abbott A. Scientists bust myth that our bodies have more bacteria than human cells. Nature. 2016.doi: 10.1038/nature.2016.19136 . | Open in Read by QxMD
  11. Pray LA. Transposons: The Jumping Genes. Nature Education. ; 1 (1): p.204.
  12. Ginsburg I. Role of lipoteichoic acid in infection and inflammation. Lancet Infect Dis. 2002; 2 (3): p.171-179.doi: 10.1016/s1473-3099(02)00226-8 . | Open in Read by QxMD
  13. Costa OYA, Raaijmakers JM, Kuramae EE. Microbial Extracellular Polymeric Substances: Ecological Function and Impact on Soil Aggregation. Frontiers in Microbiology. 2018; 9.doi: 10.3389/fmicb.2018.01636 . | Open in Read by QxMD
  14. Haiko J, Westerlund-Wikström B. The role of the bacterial flagellum in adhesion and virulence. Biology (Basel). 2013; 2 (4): p.1242-1267.doi: 10.3390/biology2041242 . | Open in Read by QxMD
  15. Sampath V. Bacterial endotoxin-lipopolysaccharide; structure, function and its role in immunity in vertebrates and invertebrates. Agriculture and Natural Resources. 2018; 52 (2): p.115-120.doi: 10.1016/j.anres.2018.08.002 . | Open in Read by QxMD
  16. Setlow P. Spore Resistance Properties.. Microbiology spectrum. 2014; 2 (5).doi: 10.1128/microbiolspec.TBS-0003-2012 . | Open in Read by QxMD

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