General Bacteriology

Arrangement adds further diagnostic information: cocci in chains (streptococci), clusters (staphylococci), or pairs, diplococci (Neisseria, S. pneumoniae).

Gram positive organisms have a thick peptidoglycan wall, teichoic acids, no outer membrane, and stain purple. Gram negative organisms have a thin peptidoglycan layer within a periplasmic space, an outer membrane bearing lipopolysaccharide, and stain pink or red.

This division is the primary organising axis across bacteriology as a discipline: Gram stain result, oxygen requirement, and morphology together form the first three questions asked of any unidentified isolate, before any further biochemical or molecular testing narrows identification to genus and species.

Organisms are classified as obligate aerobes, facultative anaerobes, obligate anaerobes, microaerophiles, or aerotolerant organisms, based on their capacity to grow in the presence or absence of atmospheric oxygen and their tolerance of the reactive oxygen species oxygen exposure generates.

Oxygen requirement determines culture conditions and is a key initial clue in organism identification, particularly relevant when interpreting a culture result that grows only under anaerobic or only under microaerophilic conditions.

Spore formation is restricted, among medically important bacteria, to two Gram positive genera: Bacillus and Clostridium.

Endospores are highly resistant to heat, desiccation, and most disinfectants. They require autoclaving, or a specifically sporicidal agent, for reliable destruction. This has direct infection control consequences: standard alcohol-based hand sanitiser does not reliably kill bacterial spores. Soap-and-water hand hygiene therefore remains mandatory whenever a spore-forming pathogen, most importantly Clostridioides difficile, is suspected or confirmed.

Motility is conferred by flagella, and both the presence or absence of flagella and their specific arrangement, monotrichous, lophotrichous, amphitrichous, or peritrichous, are used diagnostically.

Motility testing, by wet preparation or motility agar, helps distinguish otherwise biochemically similar organisms, and is particularly useful within the Enterobacterales, where motility status is one of several features separating genera that share lactose fermentation and other biochemical characteristics.

A capsule is an antiphagocytic polysaccharide surface layer, and it is a major virulence factor for every encapsulated organism that possesses one.

The key encapsulated pathogens recurring across clinical bacteriology are Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae type b, Klebsiella pneumoniae, and group B Streptococcus. The first three of these are the basis of polysaccharide conjugate vaccines. Antibody directed against the specific capsular polysaccharide is protective. The conjugate format allows an effective immune response even in young infants, whose immune systems otherwise respond poorly to unconjugated polysaccharide antigens alone.

Pili and fimbriae mediate adhesion, allowing colonisation of host tissue, and, via the specialised sex pilus, conjugation, the horizontal transfer of genetic material, most importantly plasmid-borne antibiotic resistance genes, between bacterial cells.

Type-specific pili are a defined virulence factor for several organisms. Neisseria gonorrhoeae pili undergo antigenic variation, allowing repeated reinfection despite prior exposure. Uropathogenic Escherichia coli has type 1 and P pili, which mediate specific adhesion to uroepithelium and are central to that organism's capacity to ascend and colonise the urinary tract.

Bacterial growth in culture follows a characteristic curve through lag, log, stationary, and death phases. Log phase, during which cells are actively dividing, is the window of maximum susceptibility for antibiotics that target active cell wall synthesis or active protein synthesis, since these processes are occurring at their highest rate during this phase.

Binary fission is the standard reproductive mode for bacteria. Generation time varies enormously between organisms, from approximately 20 minutes for Escherichia coli under optimal conditions to many hours, approximately 24 hours, for Mycobacterium tuberculosis. This difference directly determines how quickly a culture-based diagnosis becomes available. It is the central practical reason mycobacterial infection specifically demands rapid molecular diagnostic alternatives alongside traditional culture.

A biofilm is a structured, matrix-embedded microbial community that confers both antimicrobial tolerance and immune evasion on the organisms within it, properties well beyond what any single free-living bacterial cell of the same species would show in isolation.

Biofilms recur as a clinical theme throughout bacteriology, most importantly for Staphylococcus epidermidis in prosthetic device infection, Pseudomonas aeruginosa in chronic respiratory infection in cystic fibrosis, and the mixed organism communities responsible for dental plaque and periodontal disease.

Bacterial virulence is built from a recurring set of mechanisms: adhesion, invasion, toxin production, immune evasion, capsule formation, intracellular survival, enzyme production, biofilm formation, and antigenic variation. Individual organisms typically combine several of these mechanisms rather than relying on any single one, and recognising which combination a given organism uses is central to predicting its characteristic disease pattern.

An exotoxin is a secreted protein with a specific molecular target and generally high potency, and many exotoxins can be chemically inactivated while retaining their immunogenicity, producing a toxoid usable as a vaccine, tetanus and diphtheria toxoid vaccines being the clearest examples.

Endotoxin is the lipid A component of Gram negative lipopolysaccharide, released on bacterial cell lysis rather than actively secreted. It triggers Toll-like receptor 4-mediated cytokine release, producing fever, hypotension, and, in severe cases, septic shock, a mechanism entirely distinct from exotoxin action and unique to Gram negative organisms.

Bacterial genetic material consists of a circular chromosome and, frequently, one or more plasmids, smaller, independently replicating circular DNA elements that commonly carry antibiotic resistance genes and can be transferred between bacterial cells.

Genetic change occurs through mutation and through three mechanisms of horizontal gene transfer: transformation, uptake of free DNA from the environment; transduction, transfer via a bacteriophage; and conjugation, direct cell-to-cell transfer via a sex pilus, typically of plasmid DNA. These horizontal transfer mechanisms, conjugation in particular, are the dominant route by which antibiotic resistance genes spread between bacterial species and even between genera, often far more rapidly than resistance could arise through mutation alone.

Bacterial identification proceeds through a hierarchy of methods: solid, liquid, selective, differential, and enriched media support initial isolation and growth; Gram stain narrows the differential immediately; biochemical testing, antigen detection, and molecular testing then provide definitive identification to genus and species level.

Selective media suppress the growth of unwanted organisms while allowing the target organism to grow, and differential media allow visual distinction between organisms based on a specific metabolic property, lactose fermentation on MacConkey agar being the clearest recurring example throughout Gram negative bacteriology. Choosing the right medium for a given clinical question is as important to accurate diagnosis as the identification test performed afterward.