🦠 Normal Flora & Host defense
Definition: Communities of microorganisms that reside on body surfaces exposed to the external environment (skin, mucous membranes, gastrointestinal tract). They are semi‑permanent and change with major life events (hormonal shifts, antibiotic use, diet).
✅ Protective & Nutritional Roles
- Colonization resistance: Maintain pH and occupy niches, preventing pathogen overgrowth.
- Nutritional synthesis: Produce vitamin K and B vitamins (e.g., biotin, folate).
- Immune stimulation: Low‑level activation of mucosal immunity.
⚠️ Endogenous infections
- Misplacement: Fecal flora into urinary tract (UTI) or skin flora into catheters.
- Immunocompromise: Overgrowth (e.g., oral thrush from Candida).
- Bacteremia vs. septicemia: Bacteremia = bacteria in blood without symptoms; septicemia = multiplying bacteria with systemic signs.
Key normal flora by site
| Site | Common organisms | Notable pathogens / conditions |
|---|---|---|
| Cutaneous (skin, urethra) | Staphylococcus epidermidis, diphtheroids | S. aureus, yeasts (Candida) |
| Nose | S. aureus (carriage ~25%) | S. epidermidis, streptococci |
| Oropharynx | Viridans streptococci (e.g., S. mutans) | Non‑typeable Haemophilus, Candida |
| Gingival crevices | Anaerobes: Bacteroides, Fusobacterium | Actinomyces, streptococci |
| Vagina (adult) | Lactobacillus (dominant), Bacteroides | Group B strep (S. agalactiae) in 15‑20% |
| Colon | Bifidobacterium (breast‑fed infants), anaerobes | E. coli, Enterococcus, Bacteroides |
💡 Clinical pearl: Group B streptococcus (GBS) colonization in the vagina is a major risk for neonatal sepsis and meningitis – routine screening at 35‑37 weeks is standard.
🔬 Gram‑positive cocci
Overview of the major genera: Staphylococcus (catalase positive, clusters), Streptococcus (catalase negative, chains), and Enterococcus (catalase negative, PYR positive).
Staphylococcus species
S. aureus – the pathogen
- Features: Coagulase positive, β‑hemolytic, ferments mannitol, salt tolerant.
- Reservoir: Nasal mucosa (25% carriers), skin.
- Virulence factors: Protein A (binds IgG Fc), enterotoxins (heat‑stable, rapid onset), TSST‑1 (superantigen), coagulase, exfoliatins, cytotoxins (PVL).
- Diseases: Abscesses, osteomyelitis (#1 cause), acute endocarditis, food poisoning (2‑6 h), toxic shock, scalded skin, bullous impetigo.
Other staphylococci
- S. epidermidis: Coagulase negative, novobiocin sensitive, biofilm producer → catheter/prosthetic infections, endocarditis in IV drug users.
- S. saprophyticus: Coagulase negative, novobiocin resistant → UTI in young sexually active females.
Treatment: Nafcillin/oxacillin for MSSA; vancomycin for MRSA; linezolid/daptomycin for VISA/VRSA.
Streptococcus species
Group A strep (S. pyogenes)
- β‑hemolytic, bacitracin sensitive, PYR positive.
- M protein (antiphagocytic), streptolysin O (immunogenic), hyaluronic acid capsule.
- Suppurative: pharyngitis, scarlet fever (rash, strawberry tongue), impetigo, cellulitis/necrotizing fasciitis.
- Nonsuppurative: rheumatic fever (type II, carditis, chorea), acute glomerulonephritis (type III, smoky urine).
Group B strep (S. agalactiae)
- β‑hemolytic, bacitracin resistant, CAMP positive, hippurate hydrolysis.
- Neonatal sepsis & meningitis: leading cause, especially with prolonged labor after membrane rupture.
- Intrapartum prophylaxis with penicillin/ampicillin for colonized women.
S. pneumoniae
- α‑hemolytic, optochin sensitive, bile soluble, lancet‑shaped diplococci.
- Polysaccharide capsule (main virulence), IgA protease, pneumolysin.
- Diseases: typical lobar pneumonia (rusty sputum), adult meningitis (↓glucose, ↑protein, PMNs), otitis/sinusitis in children.
- Vaccines: PCV13 (conjugate) for children, PPSV23 for adults ≥65.
Viridans group streptococci
- S. mutans (dextran biofilm → dental caries), S. sanguinis, S. gallolyticus (bovis) associated with colon cancer.
- α‑hemolytic, optochin resistant, bile insoluble.
- Subacute endocarditis: predisposing damaged heart valves; follows dental work (prophylaxis recommended).
Enterococcus – E. faecalis & E. faecium
- Features: Catalase negative, PYR positive, bile‑esculin positive (growth in 40% bile), salt tolerant (6.5% NaCl).
- Diseases: UTI, biliary tract infections, subacute endocarditis (elderly, post‑GI/GU procedures).
- Resistance: Intrinsic and acquired; VanA strains modify D‑ala‑D‑ala to D‑ala‑D‑lactate (no vancomycin binding).
- Treatment: Ampicillin + gentamicin for susceptible; linezolid or daptomycin for VRE.
🧫 Gram‑positive rods (spore‑formers & others)
Bacillus species
B. anthracis – anthrax
- Large, boxcar‑shaped rods, aerobic, spore‑forming, polypeptide capsule (D‑glutamate).
- Anthrax toxin: protective antigen (PA), lethal factor (LF), edema factor (EF – adenylate cyclase).
- Forms: Cutaneous (eschar, malignant pustule), pulmonary (woolsorter’s, mediastinal widening), GI (rare).
- Treatment: Ciprofloxacin or doxycycline; vaccine (AVA) for high‑risk.
B. cereus – food poisoning
- Aerobic, spore‑forming, ubiquitous in soil.
- Two toxin types: Emetic (preformed, rapid 1‑6 h, fried rice) and diarrheal (8‑18 h, meat sauces, cAMP‑mediated).
- Self‑limiting gastroenteritis; rare eye infections.
Clostridium species
C. tetani – tetanus
- Anaerobic, spore‑forming; tetanospasmin (toxin) blocks glycine/GABA release → spastic paralysis (risus sardonicus, opisthotonos).
- Treatment: human tetanus immunoglobulin (TIG), metronidazole, wound debridement.
- Prevention: toxoid vaccine, wound management per tetanus‑prone status.
C. botulinum – botulism
- Anaerobic, spore‑forming; heat‑labile neurotoxin (blocks ACh release → flaccid paralysis).
- Adult: preformed toxin (canned vegetables). Infant: spores in honey/dust → constipation, “floppy baby”.
- Treatment: respiratory support, antitoxin; no honey before 1 year.
C. perfringens – gas gangrene & food poisoning
- Large anaerobic rods, double‑zone hemolysis, “stormy fermentation”.
- Gas gangrene: alpha toxin (phospholipase C) → myonecrosis, hemolysis, shock; treatment: debridement + penicillin + hyperbaric oxygen.
- Food poisoning: enterotoxin (8‑24 h) from reheated meat → watery diarrhea, self‑limiting.
C. difficile (now Clostridioides)
- Anaerobic, toxin A (enterotoxin) and toxin B (cytotoxin).
- Antibiotic‑associated diarrhea / pseudomembranous colitis (yellow plaques).
- Treatment: stop inciting antibiotic; vancomycin or metronidazole; fecal transplant for recurrent.
📊 Quick reference – key differentiating features
| Organism | Catalase | Hemolysis | Key test | Classic disease |
|---|---|---|---|---|
| S. aureus | + | β | Coagulase + | Osteomyelitis, abscess, TSS |
| S. epidermidis | + | γ | Novobiocin S | Catheter infections |
| S. saprophyticus | + | γ | Novobiocin R | UTI (young women) |
| S. pyogenes (GAS) | − | β | Bacitracin S, PYR + | Pharyngitis, scarlet fever |
| S. agalactiae (GBS) | − | β | CAMP +, hippurate + | Neonatal sepsis/meningitis |
| S. pneumoniae | − | α | Optochin S, bile soluble | Pneumonia, meningitis |
| Viridans streptococci | − | α/γ | Optochin R, bile insol. | Dental caries, subacute endocarditis |
| E. faecalis/faecium | − | var. | PYR +, bile‑esculin + | UTI, endocarditis (elderly) |
| B. anthracis | + | – | Polypeptide capsule | Anthrax (cutaneous/pulmonary) |
| C. perfringens | − | double‑zone | Stormy fermentation | Gas gangrene, food poisoning |
💡 High‑yield: S. pneumoniae is the most common cause of community‑acquired pneumonia, adult meningitis, and otitis media in children. S. pyogenes pharyngitis can lead to rheumatic fever (type II) or glomerulonephritis (type III).
Oxygen requirements & anaerobes (expand)
- Obligate aerobes: require O₂, no fermentative pathways (e.g., Mycobacterium, Pseudomonas).
- Microaerophilic: low O₂ tension (Campylobacter, Helicobacter).
- Facultative anaerobes: respire aerobically then ferment (most Enterobacteriaceae).
- Obligate anaerobes: lack superoxide dismutase/catalase, ferment, use no O₂ as electron acceptor (Actinomyces, Bacteroides, Clostridium).