General bacteriology

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.”

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)

• 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)

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:

• Facultative pathogens
  • 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
  • Opportunistic pathogens
    • Usually benign but have the ability to cause disease in an immunocompromised host (e.g., patients with AIDS, patients that undergo chemotherapy)
    • Examples of opportunistic infections include:
      • Oral candidiasis, vaginal yeast infection
      • Pneumocystis jirovecii pneumonia
      • Cytomegalovirus infection
      • Cryptococcal meningitis, toxoplasma encephalitis
• Obligate pathogens
  • 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.

See “Prokaryotes vs. eukaryotes.”

Form

• Bacilli: rod-shaped bacteria
• Cocci: sphere-shaped bacteria that tend to have different arrangements under the microscope and are classified accordingly
  • Staphylococci (cluster of cocci): grape-like clusters
  • Streptococci (chain of cocci): usually arranged in chains
  • Diplococci: usually arranged in pairs
• Coccobacilli: very short rods almost resembling cocci
• Spirochetes
  • 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

Gram staining

• Description: a standard microbiological laboratory method used to differentiate bacteria based on their cell wall structure
• Method
  1. Application of crystal violet to a previously heat-fixed smear of a bacterial culture
  2. Addition of iodine to trap the dye
  3. Washing out of dye with acetone or ethanol
  4. Counterstain with safranin (or in some cases carbol fuchsin)
• Results
  • 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)

Acid-fast staining

• Description: a method that stains mycolic acid, which is contained in the cell wall of acid-fast bacteria (e.g., Mycobacteria, Nocardia).
• Ziehl-Neelsen stain: produces red staining
• Auramine-rhodamine stain
  • 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.

Capsule

• Description: a polysaccharide structure located outside the cell membranes of certain bacteria
• Function
  • Antiphagocytic by impeding opsonization
  • Facilitates adherance to surfaces
  • Provides protection from free radicals and heavy metal irons
• Most important encapsulated bacteria
  • Group B streptococcus
  • Streptococcus pneumoniae
  • Haemophilus influenzae type b
  • Neisseria meningitidis
  • E. coli
  • Salmonella
  • Klebsiella pneumoniae
  • Pseudomonas aeruginosa
• Clinical relevance
  • Important virulence factor
  • Target of immunization: vaccines against encapsulated bacteria usually consist of a capsular polysaccharide and a protein conjugate (serves as an antigen). See “Management of asplenic patients.”

Intracellular bacteria

• Obligate intracellular bacteria
  • Cannot produce ATP outside of their host cell
  • Examples include Rickettsia, Chlamydia, Coxiella
  • See “Obligate intracellular bacteria” in “Bacteria overview.”
• Facultative intracellular bacteria
  • Can produce ATP outside of their host cell
  • Examples include Mycobacterium, Salmonella, Neisseria, Listeria, Francisella, Legionella, Yersinia, Brucella

Survival in oxygenated environment

Oxygen level is used to differentiate between the following:

• Microaerophile bacteria: grow under subatmospheric oxygen levels (e.g., Helicobacter pylori)
• Anaerobic bacteria
  • Obligate anaerobe: grows only in the absence of oxygen (e.g., Clostridium, Actinomyces israelii, Bacteroides, Fusobacterium)
    • Occur in the gut flora (pathogenic in other places)
    • Susceptible to oxidative damage due to lack of enzymes that can detoxify oxygen radicals (e.g., catalase, superoxide dismutase
    • Often produce a foul smell (due to short-chain fatty acids) and gases (CO₂ and H₂) in tissue
    • Difficult to culture
  • 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
  • Require oxygen to produce ATP
  • Grow optimally under atmospheric oxygen levels
  • Examples include P. aeruginosa, M. tuberculosis, B. pertussis, Nocardia

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

Hemolysis

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

• Alpha hemolysis
  • Hemoglobin present in the agar is partially oxidized → methemoglobin, a substance with a characteristic biliverdin-green color (green hemolysis).
  • Characteristic of gram‑positive cocci (e.g., S. pneumoniae, viridans streptococci)
• Beta 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).

Enzymatic testing

• Indole test: diagnostic test to differentiate between different members of the Enterobacteriaceae family
  • Indole-positive: can convert tryptophan to indole → test medium turns pink (e.g., E. coli)
  • Indole-negative: cannot convert tryptophan to indole → test medium remains yellow (e.g., Klebsiella spp., Enterobacter spp.)

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:
    • Species of bacterium (e.g., 20 minutes for E. coli and 12–18 hours for M. tuberculosis)
    • Type of culture medium (e.g., the generation time is shorter in specially enriched media)
  • 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

Enzymes

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 NADPH oxidase 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
  • Microbes that produce oxidase include Campylobacter, Vibrio, Pseudomonas, Brucella
  • The colorless phenylenediamine reagent turns dark blue or purple when oxidized.
• Urease: an enzyme that hydrolyzes urea to ammonia and carbon dioxide, which increases the pH
  • Urease-producing organisms: Proteus, H. pylori, Ureaplasma, Nocardia, Klebsiella, S. epidermidis, S. saprophyticus, Cryptococcus
  • Infections with urease-positive organisms (especially with Proteus) predispose to struvite stones.
  • Urease-producing bacteria can colonize and survive in the urinary system.
• 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, Aspergillus, Candida, Escherichia coli, Staphylococci, Serratia, Burkholderia cepacia, and Helicobacter pylori are catalase-positive organisms.

Pigments produced by bacteria

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.
  • Qualitative antibody detection
  • Titer development
  • Detection of specific T-cell reactions, e.g., interferon-γ release assay
• 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

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

• Bacterial transformation
  • 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:
    • Neisseria
    • Haemophilus influenzae type b
    • Streptococcus pneumonia
  • 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 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
    • 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
• Bacterial transduction
  • 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.
  • Generalized transduction
    • 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)
    • Bacteriophage 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:
      • Erythrogenic toxin (Streptococcus pyogenes)
      • Cholera toxin (Vibrio cholerae)
      • Diphtheria toxin (Corynebacterium diphtheriae)
      • Shiga toxin (Shigella spp.)
      • Botulinum toxin (Clostridium botulinum)
• 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 ^[11]
    • These sequences can change their position within the bacterium (e.g., from one plasmid to another, to the bacterial chromosome, to a bacteriophage).
    • They can copy, insert, reinsert, and excise from different locations along the genetic material of plasmid and chromosomal DNA.
  • Development of antibiotic resistance by creating plasmids with different genetic sequences for resistance: Enterococcus (VRE) transfers the vanA gene, which provides resistance against vancomycin, to S. aureus (VRSA).

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.

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.

Bacterial toxins

General

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

• Bacterial invasion
• Cell damage
• Inhibition of cellular processes
• Stimulation of the immune system

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

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]

• Spores
• Loss target structures: such as the binding site of the drug (PBPs), RNA polymerase, ribosomes, and cell wall