Unit 5: Microbe-host interactions, microbial diseases and clinical microbiology

Microorganisms and their human hosts exist along a continuum from cooperation to conflict. This unit establishes the ecological framework of that relationship, then examines representative pathogens across four microbial groups, and closes with the laboratory methods used to name a causative agent from a clinical specimen.

I. Host–Microbe Interaction (Orientation)

The relationship between a microbe and its host is defined by the net effect each has on the other's fitness, and this effect is context-dependent rather than fixed.

• Symbiosis (Greek sym + bios, "living together"): any long-term physical association between two species, subclassified by outcome.
• Mutualism: both partners benefit — e.g. Bacteroides in the colon ferment dietary fibre to short-chain fatty acids (butyrate) while gaining a nutrient-rich niche.
• Commensalism: one benefits, the other is unaffected — e.g. Staphylococcus epidermidis on skin.
• Parasitism: microbe benefits at host expense — the basis of infectious disease.
• Normal microbiota (flora): resident communities of skin, gut, mouth, and vagina (~10^13–10^14 cells total) providing colonisation resistance by competing for space and nutrients.
• Opportunism: a normally harmless microbe causing disease when host defences fail — e.g. Candida albicans overgrowth after antibiotics.
• Koch's postulates: the classical criteria linking a microbe to a disease — organism present in all cases, isolated in pure culture, reproduces disease when inoculated, re-isolated from the new host.

II. Harmful Microbial Interaction with Humans

Harmful interaction is the conversion of contact into disease through virulence factors that let a microbe enter, persist, and damage the host.

A. Stages of Pathogenesis

The infection cycle proceeds through an ordered sequence, each step requiring specific molecular tools.

• Exposure and adherence: attachment via adhesins, pili/fimbriae, and surface proteins — e.g. E. coli type-1 fimbriae binding mannose on uroepithelium.
• Invasion: breach of epithelium using invasins and enzymes such as hyaluronidase and collagenase.
• Immune evasion: antiphagocytic capsules (Streptococcus pneumoniae), antigenic variation, and intracellular survival.
• Multiplication and damage: measured by infectious dose ID₅₀ (organisms needed to infect 50% of hosts).

B. Mechanisms of Damage — Toxins

Damage is delivered chiefly by two classes of toxin that differ in origin and action.

1. Exotoxins: secreted proteins, often A-B structured (B binds, A is enzymatic), highly potent and heat-labile — e.g. Clostridium tetani tetanospasmin blocking inhibitory neurotransmitter release.
2. Endotoxin: the lipid A of Gram-negative lipopolysaccharide (LPS), released on lysis, heat-stable, triggering fever and, in excess, septic shock via cytokine surge (TNF-α, IL-1).

• Virulence quantifier LD₅₀: dose lethal to 50% of hosts; lower value = higher virulence.

III. Microbial Diseases: Representative Examples

Each major microbial group causes disease by group-specific strategies; one representative pathogen illustrates each.

A. Bacterial — Mycobacterium tuberculosis (Tuberculosis)

An acid-fast intracellular bacterium causing chronic granulomatous lung disease.

• Agent: slow-growing (~20 h doubling) bacillus with a waxy mycolic-acid cell wall giving acid-fastness on Ziehl–Neelsen stain (red bacilli on blue).
• Transmission: airborne droplet nuclei; primary complex forms in the lung.
• Pathogenesis: survives inside macrophages by blocking phagosome–lysosome fusion; walled off in a caseating granuloma (tubercle); type-IV hypersensitivity drives tissue damage.
• Clinical: chronic cough, haemoptysis, night sweats, weight loss.
• Diagnosis and control: Mantoux/tuberculin test, sputum smear, culture on Löwenstein–Jensen medium; BCG vaccine; multidrug therapy (isoniazid, rifampicin) to counter resistance.

B. Viral — Influenza Virus

An enveloped RNA virus causing acute respiratory infection with pandemic potential.

• Agent: Orthomyxovirus with a segmented (8-piece) negative-sense RNA genome; envelope carries haemagglutinin (HA) and neuraminidase (NA) spikes defining subtype (e.g. H1N1).
• Entry and replication: HA binds sialic-acid receptors; RNA replicates in the nucleus; NA cleaves sialic acid to release progeny.
• Antigenic change:
  • Antigenic drift: minor point mutations → seasonal epidemics.
  • Antigenic shift: reassortment of genome segments between strains → novel subtype and pandemics.
• Clinical: fever, myalgia, cough; risk of secondary bacterial pneumonia.
• Control: annual reformulated vaccine; NA inhibitors (oseltamivir).

C. Fungal — Candida albicans (Candidiasis)

A dimorphic commensal yeast turned opportunistic pathogen.

• Agent: oval budding yeast that switches to hyphal/pseudohyphal form for tissue invasion — dimorphism is a key virulence trait.
• Predisposing factors: antibiotics, diabetes, immunosuppression, indwelling catheters.
• Pathogenesis: adhesins and germ-tube formation aid invasion; secreted aspartyl proteases degrade host tissue; biofilm on devices.
• Clinical: oral thrush (white plaques), vaginitis, and disseminated candidaemia in the immunocompromised.
• Diagnosis: KOH mount, germ-tube test (positive in serum), culture on Sabouraud dextrose agar; antifungals (fluconazole, amphotericin B).

D. Protozoal — Plasmodium (Malaria)

An intracellular protozoan parasite with a two-host life cycle causing febrile haemolytic disease.

• Agent: Plasmodium (five human species; P. falciparum most lethal); vector is the female Anopheles mosquito.
• Life cycle:
  • Exo-erythrocytic (liver) stage: sporozoites infect hepatocytes, forming merozoites.
  • Erythrocytic stage: merozoites cycle through red cells; synchronous rupture causes periodic fever.
• Pathogenesis: RBC lysis → anaemia; P. falciparum cytoadherence in cerebral vessels → cerebral malaria.
• Clinical: paroxysms of chills, fever, sweating; splenomegaly.
• Diagnosis: Giemsa-stained thick and thin blood films (thick = detection, thin = species ID); rapid antigen tests; treatment with artemisinin-based combination therapy.

IV. Clinical Microbiology

Clinical microbiology converts a patient specimen into an identified organism and a susceptibility profile to guide therapy.

A. Identification of Microorganisms from Specimens

Identification begins with proper specimen handling and proceeds through phenotypic characterisation.

• Specimen collection: aseptic sampling before antibiotics — blood, urine, sputum, CSF, pus, stool — with correct transport medium (e.g. Stuart's for swabs).
• Microscopy: Gram stain as the first divide — Gram-positive (purple, thick peptidoglycan) vs Gram-negative (pink, LPS outer membrane); acid-fast for mycobacteria.
• Culture: growth on selective (MacConkey), differential (blood agar haemolysis), and enriched media; colony morphology assessed.
• Biochemical tests: metabolic profiling — catalase, oxidase, coagulase, IMViC (indole, methyl-red, Voges–Proskauer, citrate) and sugar fermentation to speciate enterics.
• Antimicrobial susceptibility: Kirby–Bauer disc diffusion and MIC determination to report sensitive/resistant.

B. Rapid Methods of Identification

Rapid methods compress days of culture into hours by miniaturising or automating detection.

• Miniaturised biochemical kits: e.g. API strips — a panel of dehydrated substrates giving a numeric profile read against a database.
• Automated systems: VITEK and BD Phoenix perform combined ID and susceptibility from turbidimetric/colorimetric growth signals.
• Immunological assays:
  • ELISA: enzyme-linked antibody/antigen detection with a colour end-point.
  • Latex agglutination: antibody-coated beads clump on meeting antigen — used for streptococcal grouping.
• MALDI-TOF mass spectrometry: ionises whole-cell proteins and matches the ribosomal-protein spectral "fingerprint" to a database within minutes.

C. Molecular Methods

Molecular methods identify organisms by their nucleic-acid sequence, bypassing the need for culture.

• Polymerase chain reaction (PCR): amplifies target DNA through repeated denaturation–annealing–extension.

Cycle: 94°C denature → 55°C anneal primers → 72°C extend (Taq polymerase)
Repeated ~30× → ~10^9-fold amplification of target

• Real-time (qPCR): fluorescent probes quantify amplicon as it forms, giving load estimation.
• 16S rRNA gene sequencing: amplifies and sequences the conserved-plus-variable 16S gene to identify and phylogenetically place bacteria.
• Nucleic acid probes and FISH: labelled complementary sequences hybridise to target DNA/RNA in situ.
• Advantages and limits: high sensitivity and speed, detects unculturable and slow-growing organisms; but cannot distinguish live from dead cells and needs contamination control.

D. Analysis of Metabolic Products

Metabolic-product analysis identifies microbes by the chemical signatures of their metabolism rather than their genes or shape.

• Fermentation and gas products: detection of acid or gas (e.g. Durham tube for CO₂) distinguishing fermenters.
• Gas–liquid chromatography (GLC): separates volatile short-chain fatty acid end-products — the standard for identifying anaerobes such as Clostridium by their acid profile.
• Cellular fatty-acid analysis (FAME): whole-cell fatty-acid methyl esters chromatographed to give a taxonomic fingerprint.
• Chromogenic substrates: enzyme-cleaved dyes producing coloured colonies — e.g. chromogenic UTI agar identifying E. coli by β-glucuronidase activity.
• Significance: links a specific enzyme or end-product to a taxon, complementing microscopy, culture, and molecular data for a confident final identification.