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 “ .”
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 (e.g., by inhibiting the growth of pathogens or helping with digestion)
Resident flora: microorganisms that are permanently present
- Normal skin flora: Staphylococcus epidermidis
- Normal nasal flora: Staphylococcus epidermidis
- Normal oropharyngeal flora: Viridans group streptococci
- Normal flora of dental plaques: Streptococcus mutans
- Normal gut flora: Escherichia coli and Bacteroides
- Normal vaginal flora: Lactobacillus acidophilus (maintain pH)
- Normal lung flora: Neisseria catarrhalis, alpha-hemolytic streptococci, staphylococci, nonpathogenic corynebacteria, Candida albicans
- Transient flora: microorganisms that are temporarily present (e.g., E. coli or S. 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., E. coli, Vibrio cholerae, Pseudomonas aeruginosa
- Only cause disease in susceptible hosts
- Usually benign but have the ability to cause disease in an immunocompromised host (e.g., patients with , patients that undergo chemotherapy)
- Examples of opportunistic infections include:
- 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.
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.
|Overview of bacterial structure|
|Structure||Gram positive||Gram negative||Composition||Function|
|Cell wall|| || || |
|Outer membrane|| || |
|Cytoplasmic membrane|| || || |
|Bacterial capsule|| || |
Glycocalyx (slime layer)
| || || || |
|Periplasm|| || || |
|Flagellum|| || || |
|Pilus (fimbria)|| || || || |
|Endospores|| || || |
- Bacilli: rod-shaped bacteria
- Cocci: sphere-shaped bacteria that tend to have different arrangements under the microscope and are classified accordingly
- : very short rods almost resembling cocci
- Spiral-shaped organisms
- Contain axial filaments (endoflagella)
- Poorly visible on Gram stain
- Include: Treponema pallidum, Borrelia burgdorferi, and Leptospira interrogans
- Usually diagnosed by dark-field microscopy; (a microscopy technique that illuminates specimens against a dark background) and serologic studies
Cell wall structure
- Description: a standard microbiological laboratory method used to differentiate bacteria based on their cell wall structure
- Gram-positive bacteria have a thick peptidoglycan cell wall that traps crystal violet → violet-to-blue appearance
Gram-negative bacteria have a thin peptidoglycan cell wall that does not trap crystal violet but does retain the counterstain (e.g., safranin) → pink appearance
Atypical bacteria are bacteria that do not Gram stain well (remain colorless and are therefore often considered gram negative). Reasons include:
- Lack of cell wall (e.g., Mycoplasma, Ureaplasma)
- Atypical cell wall composition (e.g., high lipid percentage in Mycobacteria, lack of peptidoglycan in Chlamydia, lack of lipopolysaccharide in Treponema)
- Very thin cell wall (e.g., Leptospira)
- Bacteria are intracellular (e.g., Chlamydia, Legionella, Rickettsia, Bartonella, Ehrlichia, Anaplasma)
- Atypical bacteria are bacteria that do not Gram stain well (remain colorless and are therefore often considered gram negative). Reasons include:
- Description: a method that stains mycolic acid, which is contained in the cell wall of acid-fast bacteria (e.g., Mycobacteria, Nocardia).
- : produces red staining
- Yellowish-red staining
- More commonly used for screening due to higher sensitivity and lower cost compared to Ziehl-Neelsen 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.
- Description: a polysaccharide structure located outside the cell membranes of certain bacteria
- Most important encapsulated bacteria
- Clinical relevance
- Obligate intracellular bacteria
- Facultative intracellular bacteria
Survival in oxygenated environment
Oxygen level is used to differentiate between the following:
- Microaerophile bacteria: grow under subatmospheric oxygen levels (e.g., Helicobacter pylori)
- Obligate anaerobe: grows only in the absence of oxygen (e.g., Clostridium, Actinomyces israelii, Bacteroides, Fusobacterium)
- Facultative anaerobe: can use oxygen for ATP generation but may switch to anaerobic metabolism (e.g., fermentation) when necessary (e.g., Staphylococcus, Streptococcus, and gram‑negative bacteria in the gut)
- Aerobic bacteria
“Foul Anaerobes Can't Breathe:” Fusobacterium, Actinomyces israelii, Clostridium, and Bacteroides are obligate anaerobic.
- Alpha hemolysis
- Complete degradation of hemoglobin with a translucent halo around the bacterial colony.
- Characteristic of gram‑positive cocci (e.g., S. aureus, S. pyogenes, S. agalactiae)
- Lancefield groups: further classify β-hemolytic streptococci according to the specific bacterial cell wall carbohydrate composition
- Gamma hemolysis: no induction of hemolysis (agar around colonies remains unchanged)
- Other: Growth on bile-esculin agar as well as 6.5% NaCl is only exhibited by group D streptococci (enterococci).
- Indole test: diagnostic test to differentiate between different members of the Enterobacteriaceae family
- 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)
- 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 )
- Surrounding temperature (e.g., cold enrichment for )
Types of culture media
- Enrichment culture media: provides optimal conditions for general bacterial growth
- Selective culture media
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|| || |
|Bordet-Gengou agar|| || |
|Regan-Lowe medium|| || |
|Chocolate agar|| |
|Eaton agar|| || |
|Löffler medium|| |
|Eosin methylene blue agar|| |
Charcoal yeast extract agar
| || |
| || |
|Löwenstein-Jensen agar|| |
|Hektoen enteric agar|
|Triple sugar iron agar|| |
|Mannitol salt agar|| |
|Bile esculin agar|| |
|Thiosulfate citrate bile salts sucrose agar|| || |
Some bacteria produce enzymes or compounds that aid in survival under certain conditions or allow for colonization of specific organ systems.
Catalase: an enzyme that visibly breaks down hydrogen peroxide into water and oxygen , preventing its breakdown into microbiocidal substances (e.g., ROS) via myeloperoxidase
- Catalase-positive organisms include: Staphylococci, E. coli, Nocardia, Serratia, Listeria, Pseudomonas, Burkholderia cepacia, H. pylori, Bordetella pertussis, Candida, Aspergillus
- Recurrent infections with catalase-positive organisms are common in individuals with chronic granulomatous disease (due to deficiency).
- Coagulase: an enzyme that converts fibrinogen into fibrin
- Oxidase (cytochrome c oxidase): an enzyme that catalyzes the donation of hydrogen atoms to oxygen, forming water or hydrogen peroxide
- Urease: an enzyme that hydrolyzes urea to ammonia and carbon dioxide, which increases the pH
- Penicillin-binding proteins (PBPs): involved in cell wall synthesis
“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
|Serratia marcescens|| |
|Actinomyces israelii|| |
|Staphylococcus aureus|| |
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
- 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 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
- 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 (released by bacterial lysis) 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
- Bacteria that can undergo transformation include:
- Deoxyribonucleases break down free DNA and prevent transformation.
Bacterial conjugation: transfer of plasmids (genetic material) by a bridge-like connection between two bacteria
Fertility factor (F factor): bacterial plasmid that enables transfer of genetic material between bacteria
- F+ bacteria (donors) have the F factor, which contains genes for sex pilus (to attach to recipient cell).
- F- (recipients) do not have the F factor
- 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
- Hfr cells (high-frequency recombination 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: recombinant F- cell with new genetic material and HFr bacteria
- Fertility factor (F factor): bacterial plasmid that enables transfer of genetic material between bacteria
- The process of gene transfer between bacteria via bacteriophages
- 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 into the bacterial genome (prophage).
- Integration of phage DNA can result in acquisition of pathogenicity factors.
- Any portion of the bacterial genome is transferred from one bacterium to another.
- Bacteriophage attaches itself to the bacterial cell wall and injects its DNA into the bacterium → cleavage of bacterial DNA and replication of viral DNA → formation of new bacteriophages with phage capsids containing fragments of bacterial DNA (“packaging error”) → lysis of bacterium and release of bacteriophages → bacteriophages infect other bacteria and thus transfer bacterial DNA
Specialized transduction (via excision)
- A specific portion of the bacterial genome is being transferred to another bacterium (might include new virulence factors)
- infects bacteria → viral DNA is incorporated into the bacterial DNA at a specific location but remains inactive (prophage stage) → upon activation; the viral DNA is replicated and, together with flanking bacterial DNA, excised from the bacterial genome → excised DNA is incorporated in new bacteriophage capsids → lysis of bacterium and release of new bacteriophages → bacteriophages infect other bacteria and thus transfer bacterial DNA
- The genes for the following toxins are transferred from one bacterium to another by specialized transduction:
- The process of gene transfer between bacteria via bacteriophages
Bacterial transposition: exchange of genetic information via transposons within the genome or between genomes of various bacteria
- Transposons: bacterial DNA sequences (jumping genes) that cannot replicate independently 
- Development of antibiotic resistance by creating plasmids with different genetic sequences for resistance: ( ) transfers the vanA gene, which provides resistance against vancomycin, to S. aureus (VRSA).
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 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|
|Colonization|| || |
|Avoiding the immune system|| |
|Bacterial nutrition|| || |
|Antigenic variation|| |
|Intracellular survival|| |
- Bacterial invasion
- Cell damage
- Inhibition of cellular processes
- Stimulation of the immune system
|Overview of the most common bacterial toxins|
|Bacteria type|| |
|Location of genetic material|
|Release mechanism|| || |
|Heat tolerance|| |
|Mechanism of action|| |
|Likelihood of causing disease (toxicity)|| || |
| || |
“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|
|Erythrogenic exotoxin A|
|Toxic shock syndrome toxin (TSST-1)|
|Enterotoxin B|| |
|Alpha toxin|| |
|Pseudomonas exotoxin A|
|Shiga toxin|| || |
|Heat labile toxin|
Mechanisms of drug resistance
- Chromosomal: via chromosomal mutations that alter the binding site for the drug or affect the permeability of the drug
- Resistance plasmid
- 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