Pathogen–Host Interactions & Normal Flora – Key Vocabulary

Microbe–Host Interactions: Core Concepts

• Discipline focus: how bacteria and human hosts coexist, compete, or harm one another.

• Interactions usually mediated by:

  • Cell-surface molecules on bacterium.

  • Molecules secreted into medium or directly into host cytoplasm (protein secretion, toxins).

Symbiosis Spectrum: Commensalism, Mutualism, Parasitism

• Symbiosis = any long-term biological interaction where at least one partner benefits.

• Commensalism

  • One partner benefits, other is unharmed.

  • Example: gut Bacteroides spp.

• Mutualism

  • Both partners benefit.

  • Example: certain non-pathogenic E.\ coli K-12 strains provide vitamins while obtaining nutrients.

• Parasitism / Pathogenicity

  • One partner benefits, other is harmed.

  • Example: E.\ coli O157:H7.

• Caveat: in medical microbiology the word “parasite” is often reserved for protozoa & helminths, but ecologically any pathogen is a parasite.

Definitional Revision: Pathogen, Pathogenicity, Virulence

• Pathogen: biological agent able to cause disease.

• Pathogenicity: capacity to produce infectious disease.

• Pathogenesis: step-by-step process that leads to disease onset, progression & maintenance.

• Virulence

  • Relative degree of damage produced or degree of pathogenicity.

  • “Virulent” as adjective: high degree of infectiousness / severe disease.

Outcomes of Host–Microbe Contact

• Possible fates (Casadevall & Pirofski 2000):

  • Elimination by immune or therapeutic means.

  • Mutualism/commensalism (harmless colonisation).

  • Persistent infection (chronic/latent).

  • Active disease.

  • Host death.

• Final outcome = balance between

  • Virulence factors of microbe.

  • Resistance/immune competence of host.

Opportunistic vs True Pathogens

• True (primary) pathogens infect healthy individuals. Example: E.\ coli O157:H7.

• Opportunistic pathogens

  • Cause disease only in the “wrong” place (wound, catheter) or “wrong” patient (immunocompromised).

  • Example: Staphylococcus\ aureus — normal skin commensal, dangerous in bloodstream.

• Microbes may lead double lives: commensal in one niche, pathogen in another.

• Colonisation mechanisms shared by both lifestyles.

Mechanisms & Factors of Bacterial Pathogenicity

• Pathogenicity/Virulence factors = gene products that help establish infection & damage host.

• Major categories (cf. figure):

  • Siderophores (iron acquisition)

  • Pili/Fimbriae (adhesion)

  • Flagella (motility & chemotaxis)

  • Capsule & biofilm matrix (immune evasion, surface attachment)

  • Lipopolysaccharide (endotoxin; Gram-negatives)

  • Secreted toxins (exotoxins, e.g. haemolysins)

  • Hydrolytic enzymes (proteases, lipases)

  • Protein secretion systems (Types I–VII)

  • Virulence plasmids & pathogenicity islands (genetic carriers)

Secreted Toxins: Haemolysins

• Exotoxins that form pores in host cell membranes.

• Identified by haemolysis of RBCs on blood agar.

• In vivo targets: erythrocytes, immune cells.

• Mechanism: monomers insert→oligomerise→create transmembrane pore→cell lysis.

• Example: Streptolysin O of Streptococcus\ pyogenes (binds cholesterol).

• Haemolysin video reference: https://youtu.be/8ZOTtVCqJjw

Adherence & Adhesins

• First obligatory step for colonisation & most infections.

• Functions

  • Overcome physical clearance (peristalsis, urine flow).

  • Establish tissue tropism.

  • Initiate toxin delivery / invasion cascades.

• Involves combination of

  • Non-specific forces (electrostatics, hydrophobicity).

  • Specific adhesin–receptor binding.

Pili/Fimbriae: Structure, Types, Assembly

• Synonyms: pilus (pl.) / fimbria (sg.).

• Thin protein tubes, mostly in Gram-negatives, few Gram-positives.

• Enable adhesion without close contact (negatively charged surfaces).

• Components

  • Shaft: polymer of pilin (PapA) or fimbrin.

  • Tip fibrillum: often distinct subunit (PapE).

  • Adhesin located at distal tip (PapF/PapG) — determines receptor specificity.

• Functional types in E.\ coli

  • Type 1 pili → lower urinary tract infection.

  • P-pili → bind Gal\alpha1\text{–}4Gal disaccharide on kidney cells → pyelonephritis.

• P-pilus architecture: 7\,\text{nm} rod + thinner tip, hollow core allows subunit passage through usher (PapC) in outer membrane.

• Assembly pathway

  • Chaperone–usher (CU) system.

  • Subunits translated in cytoplasm → Sec translocon → periplasm → periplasmic chaperone → usher pore in outer membrane → polymerisation at cell surface.

  • >30 pili & non-pili organelles built by CU systems.

• Conjugative (sex) pili mediate plasmid transfer.

Afimbrial & Other Adhesins

• Non-fimbrial adhesins: outer-membrane proteins (OMPs), often autotransporters or trimeric autotransporters.

• Exopolysaccharides & biofilm matrix.

• Lipopolysaccharide (O-antigen side chains).

• Teichoic acids (Gram-positives).

• Flagellar filaments can double as adhesins (e.g. V.\ cholerae, C.\ jejuni).

• Host receptors usually glyco-conjugates rich in carbohydrates.

Motility & Flagella

• Motility present in many rods, all spirals/curved, rare in cocci.

• Types of taxis: photo-, chemo-, magneto-, aero-taxis; directed movement toward/away from stimulus.

• Flagellum: only rotary organelle in nature.

  • Parts: filament (flagellin), hook (universal joint), basal body (anchor + motor + Type III secretion apparatus).

  • Arrangement: polar or peritrichous.

• Mechanism

  • Proton Motive Force (PMF) across membrane drives rotation via MotA/MotB stator proteins.

  • \text{Anticlockwise} → straight run; \text{Clockwise} → tumble.

  • Chemosensory system modulates rotation direction.

• Flagella antigenic (H-antigen); EHEC E.\ coli O157:H7 has characteristic flagellar serotype.

• Swarming motility

  • Rapid, coordinated spread over semi-solid surfaces.

  • Requires differentiation into elongated, hyper-flagellated swarm cells.

  • Seen in Proteus\ mirabilis (diagnostic) & some Clostridium spp.

Invasion & Internalization Strategies

• Why invade?

  • Shelter from some immune factors & antibiotics.

  • Access intracellular nutrients.

  • Dissemination via host cells.

• Strategies:

  1. Induce uptake by normally non-phagocytic cells (trigger or zipper mechanisms) → “bacterium-directed endocytosis”.

  2. Survive professional phagocytes.

  • Example: Salmonella spp. invade colonic epithelium, then survive within macrophages → systemic disease.

• Key effectors delivered by Type III/IV secretion systems often remodel host cytoskeleton & vesicular trafficking.

Biofilms

• 40\text{–}80\% of all environmental bacteria exist within biofilms.

• Definition: surface-attached microbial community embedded in self-produced extracellular polymeric substance (EPS).

• Functions/advantages

  • Adhesion to surfaces & host tissues.

  • Protection from immune attack (phagocytes, antibodies) & antimicrobials (diffusion barrier, altered physiology).

  • Facilitates genetic exchange & communal metabolism.

• Clinical issues: chronic infections (catheters, lungs in CF, dental plaque).

Genetic Basis: Pathogenicity Islands & Mobile Elements

• Virulence genes frequently clustered on:

  • Pathogenicity islands (PAIs) within chromosome.

  • Virulence plasmids.

• Characteristics of PAIs

  • Large (10–200 kb), distinct GC content, flanked by transposase/integrase genes.

  • Present in pathogenic strain; absent in commensal relatives.

  • Often associated with tRNA genes (integration hotspots).

  • May encode secretion systems, toxins, adhesins, iron uptake systems.

• Mobility means acquisition can instantly convert commensal to pathogen.

The Human Normal Microbiota

• Normal flora = bacteria, fungi, protozoa that colonise body sites long-term without causing disease in healthy host.

• Not absolutely essential (germ-free animals survive & reproduce), but influence health & development.

• Body harbours roughly 10^{13} human cells & comparable 10^{13}\text{–}10^{14} microbial cells; gut houses bulk.

• Principal habitats: skin, eyes, ears, oral cavity, URT, GI tract, urogenital tract (except healthy bladder), distal urethra.

• >2000 bacterial species isolated from human body (2015 estimate).

• Moist areas (axilla, groin) support highest densities; transient flora appear & disappear.

Acquisition, Distribution & Variation of Microbiota

• Foetus develops in near-sterile uterus; colonisation begins during birth (vaginal vs C-section influences).

• Microbes added continuously via contact, food, environment, inhalation.

• Variation determinants:

  • Age (infant, adult, elderly), hormonal state, diet, geography, occupation, antibiotic exposure, environment.

• Microbial succession throughout life enables “forensic microbiology” to identify individuals by unique microbiome.

• Different body sites impose selective pressures: nutrient, O_2, water availability, immune factors.

Roles & Impacts of Microbiota

Positive roles

• Competitive exclusion of pathogens (occupy receptors, secrete bacteriocins & acids).

• Immune education (“hygiene hypothesis”): early LPS exposure modulates autoimmune risk.

• Provide vitamins (e.g. E.\ coli synthesises vitamin K & B group).

• Metabolic contributions

  • Fermentation of indigestible carbohydrates → Short-Chain Fatty Acids (SCFAs) that affect energy balance, inflammation, even behaviour.
    Negative aspects

• Opportunistic infections when flora translocate (e.g. enteric GNRs causing UTI).

• Production of potentially carcinogenic/toxic metabolites.

Representative Microbiota by Site (selected)

• Nose: Staph.\ aureus, Staph.\ epidermidis, Corynebacterium spp.

• Throat: Streptococcus spp., Branhamella\ catarrhalis, Neisseria, Haemophilus.

• Skin: Staph.\ epidermidis, Propionibacterium\ acnes (now Cutibacterium).

• Large intestine: Bacteroides\ fragilis, E.\ coli, Clostridium spp., Enterococcus spp.

• Vagina: Lactobacillus spp. dominate (maintain low pH), plus Candida.

Case Study: Respiratory Tract Flora & LRT Infections

• Upper RT densely colonised despite mucociliary clearance & antimicrobials (lysozyme, SIgA).

• Common URT commensals: Strep.\ pneumoniae, Neisseria, Haemophilus, Moraxella.

• Same organisms become pathogens in Lower RT (trachea → alveoli) causing bronchitis, bronchiolitis, pneumonia.

• Disruption triggers

  • Viral infection (e.g. influenza damages epithelium → secondary pneumococcal pneumonia).

  • Antibiotic therapy, hospitalisation (ventilator-associated pneumonia) → replacement by Gram-negative rods (GNR) such as Pseudomonas\ aeruginosa, Acinetobacter spp.

• Pneumonia pathophysiology

  • Alveoli fill with exudate → impaired O_2 diffusion → hypoxia.

  • Strep.\ pneumoniae capsule resists phagocytosis.

Probiotics, Prebiotics & Fecal Microbiota Transplant

• Probiotics: live microbes (often lactic acid bacteria) administered to restore healthy gut flora following disruption.

  • Evidence base variable; some benefit shown for antibiotic-associated diarrhoea.

• Prebiotics: indigestible carbohydrates designed to preferentially feed beneficial commensals.

• Clostridioides (Clostridium) difficile infection (CDI)

  • Gram-positive, spore-forming; causes severe antibiotic-associated colitis.

  • First-line therapy: vancomycin; recurrence common.

  • Recurrent CDI (≥2 relapses) treated with Fecal Microbiota Transplant (FMT).

• FMT (“poo pills”) supplied by centres like Birmingham Microbiome Treatment Centre; re-establishes diverse gut flora & out-competes C.\ diff.

• Video resource: https://youtu.be/ZZxRp-f3ElY ("I Contain Multitudes").

Diagnostic Microbiology Implications

• Knowledge of normal flora distribution helps Biomedical Scientists (BMS) distinguish pathogen vs contaminant.

• “Sterile sites” (blood, CSF, lower bronchi/alveoli, internal organs) → any growth likely pathogenic.

• Non-sterile samples (sputum, wound swabs, stool) contain heavy commensal load → require selective media & careful interpretation.

• Examples

  • Throat swab culture often contaminated by oral streptococci.

  • Faecal cultures: selective agars (e.g. MacConkey, XLD) differentiate enteric pathogens from abundant gut flora.

  • Skin flora inevitably present on swabs; differentiate contaminant Staph.\ epidermidis from invasive Staph.\ aureus.

Learning Outcomes Recap

• Differentiate commensalism, mutualism, parasitism & their implications.

• Identify major virulence factors (toxins, adhesins, motility, invasion tools) & describe their mechanistic roles.

• Explain adhesion via fimbriae/afimbrial adhesins, flagellar motility driven by PMF, & internalisation processes.

• Outline construction of pili (chaperone-usher) and flagella (basal body–hook–filament assembly).

• Recognise predominant species of human microbiota by body site; assess their roles in health, disease, therapy & lab diagnosis.