Systematic Bacteriology · Master Reference Table

Bacteriology at a glance

Compiled verbatim from Basics in Medical Microbiology and Immunology — Part III, Systematic Bacteriology & Mycology (Zagazig University, Faculty of Medicine, Medical Microbiology & Immunology Department, 2013). No external content added. Em dash (—) indicates a column not addressed by the textbook for that organism.

CategoryOrganismBiochemical ReactionsAntigenic StructureVirulence FactorsDiagnosisTreatmentSpecial Characteristic
1 · GPCStaphylococci S. aureus
S. epidermidis
S. saprophyticusGP cocci in irregular grape-like clusters; non-motile, non-sporing; usually non-capsulated
  • Catalase + (differentiates from Strep)
  • S. aureus: coagulase +, DNase +, catalase +, ferments mannitol, gelatin liquefaction +
  • Blood agar: β-hemolysis, yellow/clear zones
  • Nutrient agar: golden yellow colonies (endopigment), best at RT
  • Mannitol salt agar (7.5% NaCl): yellow colonies; selective
  • CoNS: coagulase −; S. saprophyticus novobiocin-resistant; S. epidermidis novobiocin-sensitive
 S. aureus cell-wall components
  • Peptidoglycan: elicits IL-1, opsonic Abs; PMN chemoattractant; endotoxin-like; activates complement
  • Teichoic acids: antigenic; part of phage receptors
  • Protein A: binds Fc of IgG except IgG₃; Fab free → "coagglutination" reagent
  • Capsule (some strains): polysaccharide, antiphagocytic unless specific Abs present
  • Phage surface receptors: phage typing
  • Fibronectin-binding proteins (FnBPs): adhesion/invasion
 Enzymes
  • Catalase; Coagulase (clots citrated plasma, fibrin coat → resists phagocytosis); Clumping factor (binds fibrinogen non-enzymatically, distinct from coagulase); hyaluronidase, staphylokinase, proteinases, lipases, β-lactamase
Toxins
  • Enterotoxin (A–E, G–I, K–M): superantigen, heat-resistant, acid/enzyme-resistant → food poisoning (vomiting>diarrhea)
  • TSST-1: superantigen → toxic shock (tampons, wound, nasal packing); 5–25% isolates; blood cultures typically negative
  • Exfoliative toxins A & B: proteases dissolving epidermal mucopolysaccharide → SSSS
  • Leukocidins: α (necrosis, hemolysis), β, δ
  • PVL: bicomponent (S+F); severe necrotizing pneumonia in children; CA-MRSA (phage-encoded)
Pigment
  • Staphyloxanthin: carotenoid, antioxidant evading ROS; golden color
  • Specimens by site: blood, pus swab, CSF, urine, vomitus/stool/food
  • Direct smear: GPC in grape-like clusters among pus cells
  • Culture: β-hemolysis blood agar + golden colonies; mannitol salt agar for contaminated samples
  • ID tests: catalase, coagulase, DNase, mannitol fermentation, gelatin liquefaction
  • Phage typing: epidemiologic tracing (hospital outbreaks; food handlers' nose/nailbed/fomites)
  • Routine AST; molecular typing; serology of little value
  • Food poisoning: vomitus/stool/food remnants; mannitol salt agar; demonstrate enterotoxin by gel diffusion
  • ~90% produce β-lactamase → Pen-G resistant; susceptible to β-lactamase-resistant penicillins (methicillin, oxacillin), cephalosporins, vancomycin
  • MRSA (~20%): altered PBPs → DOC vancomycin
  • Newer: linezolid, daptomycin, quinupristin/dalfopristin
  • S. epidermidis: vancomycin + rifampicin or gentamicin
  • Prevention: handwashing, asepsis; intranasal mupirocin for nasal carriage; remove shedders from OR/newborn nurseries
  • ~20% humans are long-term nasal carriers of S. aureus
  • S. epidermidis: most important cause of prosthetic valve endocarditis (biofilm/glycocalyx); CSF shunt infections; neonatal sepsis; peritoneal dialysis peritonitis; hospital-acquired
  • S. saprophyticus: 2nd commonest community UTI in sexually active young women (within 24h post-coitus)
  • CA-MRSA (PVL+) molecularly distinct from HA-MRSA; CA-MRSA: homeless, IVDU, athletes
  • Right-sided (tricuspid) endocarditis in IVDU
  • HA-MRSA causes ~50% of nosocomial S. aureus infections
  • SSSS: young children; recovery 7–10d; hair/nails may slough
  • Staph food poisoning IP 1–8h (preformed toxin in carbohydrate-rich foods, milk products)
1 · GPCStreptococci S. pyogenes (Gp A)
S. agalactiae (Gp B)
Viridans group
S. pneumoniaeGP cocci in chains; oxidase & catalase NEG; facultative anaerobes; many require enriched media
  • Oxidase & catalase negative
  • Hemolysis: β (pyogenes, agalactiae), α (viridans, pneumoniae), γ (bovis)
  • S. pyogenes: bacitracin-sensitive
  • S. agalactiae: CAMP +, hydrolyzes hippurate, NOT bacitracin-sensitive, SXT-resistant, double-zone hemolysis
  • Viridans vs pneumoniae: bile insoluble vs soluble; inulin non-fermenter vs fermenter; optochin resistant vs sensitive; mouse non-pathogenic vs pathogenic; Quellung − vs +
  • Better growth in 5–10% CO₂
 S. pyogenes
  • M protein: >150 types; antiphagocytic; rheumatogenic & nephritogenic strains; Abs protective
  • Hyaluronic acid capsule: antiphagocytic, non-immunogenic
  • Lipoteichoic acid: covers pili; mucosal adherence
  • Fibronectin-binding protein: adherence + internalization
  • C-carbohydrate: Lancefield grouping (A–W, no I/J)
S. agalactiae
  • Capsular polysaccharide (classification)
S. pneumoniae
  • ≥90 capsular serotypes; types 1–8 → 75% adult pneumonia; serotyped by Quellung
  • C-polysaccharide (CPS): cell-wall PS common to all pneumococci
 S. pyogenes — Enzymes
  • Streptokinase (fibrinolysin) — lyses thrombi; used clinically for MI
  • DNase A–D; anti-DNase B for pyoderma dx
  • Hyaluronidase — "spreading factor"
S. pyogenes — Toxins
  • Pyrogenic exotoxin A (erythrogenic): phage-encoded superantigen → STSS, scarlet fever
  • Pyrogenic exotoxin B: protease → necrotizing fasciitis ("flesh-eating")
  • Pyrogenic exotoxin C → STSS
  • Streptolysin O: O₂-labile, antigenic → ASO titer for RF dx
  • Streptolysin S: O₂-stable, non-antigenic; β-hemolysis on plate
  • C5a peptidase, neuraminidase, serum opacity factor
S. pneumoniae
  • Capsule (antiphagocytic, inhibits C3b opsonization)
  • Pneumolysin (Ply): 53-kDa pore-forming, activates complement
  • Autolysin (LytA): lyses bacteria, releases pneumolysin
  • H₂O₂: damages host cells; bactericidal vs H. influenzae
  • Pili: URT colonization, induce TNF → septic shock
  • CbpA / PspA: adhesin, inhibits complement opsonization
  • Specimens: swabs, pus, blood (bacteremia)
  • Gram stain; Ag detection (ELISA, agglutination)
  • Blood agar, 37°C, 5–10% CO₂; bacitracin disc (GpA); CAMP test (GpB)
  • Latex agglutination for serogrouping
  • Post-strep dz: ASO ≥1/200; CRP (latex w/ anti-CRP); ESR (RF triad ASO+CRP+ESR); anti-DNase B ≥80 U for AGN
  • S. pneumoniae: sheep blood ± gentamicin, 5–10% CO₂; sputum/CSF Gram; PS Ag detection (latex, ELISA); CPS ELISA in sputum; PCR (autolysin, pneumolysin); immune-complex assay; Quellung serotyping (reference labs)
  • S. pyogenes: penicillin DOC; erythromycin if allergic
  • RF prevention: prompt Pen for GAS throat; recurrence prevention with monthly benzathine penicillin for several years
  • S. pneumoniae: penicillin (resistance now prevalent, usually multi-drug); new cephalosporins, fluoroquinolones effective; vancomycin best; routine AST
Pneumococcal vaccines
  • 23-valent polysaccharide: ≥65y, chronic illness 2–64y, immunocompromised; 0.5 mL ID/IM; ≥5y protection
  • 7-valent conjugate: all children at 2, 4, 6 mo + 12–15 mo; selected 24–59 mo
  • Passive Ig for immunodeficient children; chemoprophylaxis for asplenic children
  • M types: rheumatogenic 1, 2, 5, 6, 18; nephritogenic 2, 4, 12, 49, 59–61; impetigo 49, 57, 59–61
  • ARF: 1–4 wk post-throat; anti-M cross-reacts with heart; common, recurrent; long-acting Pen prophylaxis; dx ASO/CRP/ESR; damages valves & myocardium
  • AGN: 3 wk post-skin; Ag-Ab complex on GBM; less common, non-recurrent; dx anti-DNase B; majority recover
  • S. agalactiae: most important cause of neonatal infections; 10–40% females are vaginal carriers; chains appear as paired cocci
  • Viridans (S. mutans): dental caries; SBE on damaged valves via dextran synthesis from glucose adhering to fibrin-platelet aggregates
  • Necrotizing fasciitis: M types 1, 3 + exotoxins A & B (superantigen)
  • S. pneumoniae: lancet-shaped GP diplococci, encapsulated; α-hemolytic
  • Pneumococcal risk: extremes of age, cirrhosis, DM, asplenia (sickle), CSF leak, daycare <2y
  • Scarlet fever: strawberry tongue, sore throat, sunburn rash (host lacks antitoxin)
1 · GPCEnterococci E. faecalis
E. faeciumGP cocci in short chains; formerly Streptococcus (split 1984); >17 species
  • Facultative anaerobes; grow 10–45°C
  • Ordinary media; usually non-hemolytic
  • PYR + and Voges-Proskauer +
  • H₂S production; reduction of litmus milk
  • Grow in 6.5% NaCl broth; bile esculin +
 — (textbook does not specify)
  • Gelatinase: protease (gelatin, collagen, peptides)
  • Hemolysin: cytolytic — lyses human, horse, rabbit RBC
  • Biofilm / Enterococcal Surface Protein (ESP): adhesion to bladder epithelium in UTI
  • Extracellular superoxide: enhances E. faecalis survival with B. fragilis
  • Specimens by site: urine, blood, pus
  • Culture: blood agar, MacConkey, CLED (urine), bile esculin, 6.5% NaCl broth
  • Blood culture for bacteremia/endocarditis
  • ID: morphology, Gram, biochem, PYR+, VP+, H₂S, litmus milk reduction
  • Intrinsic + acquired resistance; usually resistant to penicillins & aminoglycosides
  • VRE: major nosocomial pathogen, difficult to treat
  • VRE options: quinupristin/dalfopristin (synercid), linezolid, daptomycin, tigecycline
  • Normal intestinal flora of humans & animals; feared nosocomial pathogens
  • Diseases: UTI, endocarditis, bacteremia, catheter-related, surgical wounds, intra-abdominal & pelvic
  • Infecting strains often originate from patient's own gut flora
  • Genitourinary instrumentation often precedes enterococcal endocarditis
3 · Non-spore GPBCorynebacterium C. diphtheriaeDiphtheroids: C. ulcerans, C. pseudotuberculosis (non-lipophilic); C. jeikeium, C. urealyticum (lipophilic); Propionibacterium acnes (anaerobic)
  • GP rod, clubbed ends, pleomorphic, non-sporing
  • Chinese letter (acute angles) or palisade (parallel)
  • Beaded with methylene blue (metachromatic volutin granules)
  • Aerobic/facultative anaerobic; Loeffler's serum at 37°C
  • Blood tellurite: grey-black; 4 biotypes — gravis, mitis, intermedius, belfanti
  • Oxidase + and catalase +
 — (textbook describes only toxin antigenicity)
  • Diphtheria toxin (DT):
    • Gene on lysogenic bacteriophage; non-lysogenized strains = non-pathogenic
    • Production controlled by repressor DtxR (iron-responsive)
    • A-B fragments; B binds receptor; A ADP-ribosylates EF-2 → inhibits protein synthesis
    • C. diphtheriae itself uses a different protein (not EF-2)
    • Heat-labile, highly antigenic; formalin → toxoid (antigenicity retained)
  • Diagnosis is clinical initially — do NOT delay antitoxin
  • Specimen: swab from pseudomembrane / skin lesion
  • Smears: Gram (Chinese letter/palisade); methylene blue (beaded)
  • Culture: Loeffler's serum + blood tellurite
  • Toxigenicity tests (reference labs):
    • Elek's test (immunoprecipitation w/ antitoxin paper)
    • PCR for tox gene
    • ELISA
    • Immunochromatographic assay (rapid, highly sensitive)
    • Tissue culture monolayer overlay
  • Carriers: throat swab
  • Diphtheria antitoxin: 20,000–100,000 U IM/IV after hypersensitivity skin/conjunctival test; only neutralizes circulating toxin
  • Antimicrobials: penicillin or erythromycin — arrest toxin production
  • Supportive care
  • Contacts: DT booster + erythromycin or long-acting Pen; antitoxin NOT indicated
Prevention
  • Diphtheria toxoid (0.3% formalin; adsorbed onto Al(OH)₃ / Al phosphate as adjuvants)
  • DTP/DTaP at 2, 4, 6, 18 mo + school-age booster; adults Td q10y (no pertussis after 6y → encephalopathy)
  • Hexavalent (DTP-HBV-HIB-Polio) available
  • Disease via local + systemic DT effects (organism has little invasive capacity)
  • Pseudomembrane: necrotic epithelium + fibrin + RBC/WBC over tonsils/pharynx/larynx; bleeds if pulled
  • Distant toxic damage: myocarditis (CHF, arrhythmia), nerve paralysis (soft palate, eye muscles, extremities — reversible)
  • IP 2–4d; tonsillar (droplet) commonest; cutaneous (direct contact, fomites) rare
  • C. ulcerans: may carry tox gene → diphtheria-like
  • C. jeikeium: immunocompromised, bacteremia, high mortality, multi-resistant
  • C. urealyticum: urease+, alkaline urine + crystals, slow grower, multi-resistant UTI
  • Propionibacterium acnes: anaerobic, pathogenesis of acne
3 · Non-spore GPBListeria L. monocytogenesShort GP rod, non-sporing; resembles diphtheroids on smear; blends features of Coryne & Strep
  • Catalase + (distinguishes from Strep)
  • Tumbling motility at 22°C, NOT at 37°C
  • Blood agar: small colony with narrow β-hemolysis
  • "Cold enhancement": grows well at refrigeration temperatures
 —
  • Internalin: binds host E-cadherin → endocytic uptake
  • Listeriolysin O (LLO): pore-forming → escapes phagosome to cytosol
  • Bacterial phospholipases (phagosome escape)
  • Actin rockets: actin filament propels bacteria cell-to-cell
  • Immunity primarily cell-mediated
  • Specimens by site: CSF, blood, stool
  • Direct smear: GP rods resembling diphtheroids
  • Culture: small grey colonies + narrow β-hemolysis on blood agar
  • ID: Gram, tumbling motility, catalase +
  • DOC: ampicillin + gentamicin (fulminant cases, T-cell compromise)
  • Alternative: ampicillin + TMP-SMX
  • Resistant strains rare
  • Gastroenteritis: no treatment usually needed
  • Infections primarily in fetus/newborn (transplacental or during delivery) & pregnant women + immunosuppressed (renal transplant, AIDS, lymphoma)
  • Newborn meningitis 1–4 wk post-delivery via bacteremia
  • Primarily an animal pathogen; transmission via contaminated unpasteurized milk/cheese, vegetables, undercooked meats (chicken, hot dogs)
  • Gastroenteritis: watery diarrhea, fever, headache, myalgias, cramps, little vomiting
  • Refrigerator storage of contaminated food increases gastroenteritis risk
2 · Spore-forming GPBBacillus B. anthracis
B. cereusLarge rectangular GP bacilli in long chains; B. anthracis non-motile, capsulated; oval central spores in vitro
  • Aerobic, grow at 37°C
  • B. anthracis nutrient agar: rounded, opaque, grey-white, ground-glass with comma projections — "Medusa head"
  • Blood agar: non-hemolytic
  • Gelatin stab: "inverted fir tree" (longest lateral spikes near surface)
  • B. cereus: β-lactamase producer
  • B. anthracis: unique — only bacterium with a protein capsule (poly-D-glutamic acid); gene on plasmid pXO2; antiphagocytic
 B. anthracis — Tripartite exotoxin (pXO1)
  • Edema Factor (EF): A subunit, adenyl cyclase → ↑cAMP → ↓PMN function, massive edema
  • Protective Antigen (PA): receptor binding, channel for EF/LF entry into phagocytes
  • Lethal Factor (LF): protease; with PA = lethal toxin; stimulates macrophage release of TNF-α, IL-1β
  • Both plasmids critical
B. cereus toxins
  • Emetic toxin: heat-stable, reheated rice, IP 1–5h
  • Diarrheal toxin: heat-labile, meat/sauces, IP 8–24h
  • High-risk pathogen: BSC, gloves, mask; chemical fixation (heat does not kill)
  • Specimens: vesicle fluid, exudate, sputum, stools, blood
  • Smears:
    • Gram: large GP rods in chains
    • Polychrome methylene blue (in-vivo capsule): pink rim around blue bacillus → McFadden's reaction
    • Modified ZN (0.5% H₂SO₄): spores stain pink (environmental)
    • IF for rapid dx
  • Culture: Medusa head colonies, non-hemolytic, inverted fir tree; Gram + spore stain
  • Animal inoculation: IP mice/guinea pigs
  • Indirect HA + ELISA for confirmation
  • PCR for bioterrorism
  • B. cereus: stool ≥10⁵/g of incriminated food (usually not done)
  • B. anthracis: ciprofloxacin or doxycycline; early prophylaxis crucial for inhalation
  • B. cereus: resistant to penicillin (β-lactamase); doxycycline, erythromycin, ciprofloxacin
Control/prevention (anthrax)
  • AVA (BioThrax): from avirulent, non-encapsulated strain; adsorbed onto Al(OH)₃; IM deltoid at 0, 4 wks; boost 6, 12, 18 mo; annual
  • Burn/deep-bury carcasses in lime; autoclave animal products; double-bag contaminated materials; live attenuated animal vaccines
  • Anthrax: primarily disease of herbivores (goats, sheep, cows); humans incidental
  • Spores resistant to drying, heat, UV, disinfectants — survive decades in soil
  • Routes:
    • Cutaneous (commonest) → "malignant pustule": painless black eschar with edema rim
    • Pulmonary (wool-sorters' disease): NOT pneumonia — mediastinal hemorrhage + bloody pleural effusion; ~100% lethal
    • GI: rare; vomiting, abdominal pain, bloody diarrhea
  • Spore size 1–2 μm = ideal alveolar penetration → ideal bioterrorism agent
  • B. cereus also opportunistic: post-traumatic endophthalmitis, endocarditis, osteomyelitis, pneumonia
  • B. cereus emetic: nausea, vomiting, ± diarrhea, self-limited 24h; diarrheal: profuse watery, vomiting uncommon
2 · Spore-forming GPBClostridium C. botulinum
C. tetani
C. perfringens
C. difficileNatural habitat: soil & intestinal tract of animals/humans
  • Anaerobes
  • C. tetani: drumstick appearance (terminal spore)
  • C. perfringens: hemolytic anaerobic blood agar; Nagler's reaction (visible precipitate around colonies on egg-yolk media — lecithinase)
  • ID by morphology, sugar fermentation, Nagler's; C. tetani also by gas-liquid chromatography
 — C. botulinum
  • Botulinum toxin: very potent neurotoxin; blocks ACh release from presynaptic terminals (autonomic + motor end plate) → flaccid paralysis
C. tetani
  • Tetanospasmin: blocks release of inhibitory neurotransmitters (GABA, glycine) → muscle overactivity → tetanic spasm
C. perfringens
  • α-toxin (lecithinase): degrades lecithin → cell lysis
  • θ (theta) toxin: hemolytic, necrotic
  • Proteases, DNases, hyaluronidase, collagenases — liquefy tissue, spread
  • Enterotoxin: heat-labile, produced in meat dishes → hypersecretion in jejunum/ileum
C. difficile
  • Toxin A: enterotoxin → watery diarrhea
  • Toxin B: cytotoxin → pseudomembrane formation
  • C. botulinum:
    • Adult: toxin in leftover food + patient serum by passive HA or RIA
    • Infant: toxin in bowel contents, NOT serum
  • C. tetani: clinical + history; lab generally unhelpful — wound aspirate for GP drumstick bacilli; anaerobic culture + GLC
  • C. perfringens: myonecrosis/cellulitis clinical; deep exudate for large GP rods; anaerobic blood agar (hemolytic, Nagler's reaction)
  • C. difficile: colonoscopy (red mucosa + white pseudomembrane); stool ELISA/latex for toxins A & B
 C. botulinum
  • Adult: immediate antitoxin + intubation/ventilation
  • Infant: hospitalization + supportive
C. tetani — 3 patient categories
  • Past immunized, last booster >10y → another booster
  • Never immunized → booster + human TIG
  • Active disease → human TIG + booster + wound cleaning/excision + penicillin + muscle relaxants + respiratory support
C. perfringens
  • Immediate removal of foreign material + devitalized tissue + O₂ exposure
  • Hyperbaric O₂ + penicillin + metronidazole
C. difficile
  • Discontinue initial antibiotic + oral metronidazole or vancomycin
Tetanus prevention
  • Toxoid in DPT at 2, 4, 6, 18 mo; boost 4–6y; boosters q10y
  • Botulism — classic adult: smoked fish, home-canned vegetables → bilateral cranial nerve palsies, diplopia, dysphagia, descending paralysis, respiratory failure
  • Infant botulism: fresh honey → constipation → swallowing difficulty → "floppy baby"
  • Tetanus: spores in soil + horse/animal feces; puncture wound, burn, umbilical stump, surgical sutures; non-invasive; trismus (lockjaw) → risus sardonicus → tonic spasm; death from respiratory mechanical failure
  • C. perfringens: gas gangrene — moist spongy cracking skin (gas pockets); clostridial myonecrosis: edematous, foul-smelling, dark, crepitus; clostridial endometritis after incomplete abortion / unsterile instruments
  • C. difficile: 3% general / 30% hospitalized carriers; feco-oral via hospital staff hands; precipitated by fluoroquinolones, macrolides, clindamycin, β-lactam/inhibitor, all cephalosporins; profuse mucoid greenish malodorous watery stools + cramps + fever; onset 5–10 days post-Ab (range 1d to 10 wks after cessation)
9 · GNCNeisseria N. gonorrhoeae (Gonococci)
N. meningitidis (Meningococci)Commensals: N. mucosa, N. sicca, N. flavescens; GN kidney-shaped cocci in pairs, intra-/extracellular in pus; type-IV pili (twitching motility); meningococci capsulated
  • All Neisseria: oxidase + and catalase +
  • N. gonorrhoeae: glucose only (acid)
  • N. meningitidis: glucose + maltose (acid)
  • Commensal Neisseria: variable sugar fermentation
  • Strict aerobe; better in moist atmosphere + 5–10% CO₂ at 37°C × 24h
  • Enriched media: chocolate agar & Modified Thayer-Martin (MTM) — vancomycin + colistin + nystatin + SXT
  • Carbohydrate utilization = principal basis for commercial rapid ID
 N. gonorrhoeae
  • Pili (type IV — twitching motility): mucosal attachment
  • Surface proteins: attachment
  • LOS (lipooligosaccharide): highly branched, no repeating O-Ag
  • IgA proteases: cleave secretory IgA
  • Epithelial endocytosis: vacuolar evasion
N. meningitidis
  • Capsular polysaccharide: 13 serogroups; A, B, C, Y, W-135 important; A & C epidemic, B sporadic, A common in Africa; antiphagocytic
  • Outer membrane proteins: class 1, 2, 3 → serotyping; role in internalization
  • Pili (type IV): main adhesion + internalization
  • LPS: endotoxin → septic shock, hemorrhage (RBC destruction)
  • IgA protease
  • (Antigens above act as virulence factors)
  • Gonococcal antigenic heterogeneity + antigenic variation of pili/surface proteins → repeated infections common
  • Gonococcal infection is superficial → IgG poorly protective; secretory IgA destroyed by IgA proteases
 Gonorrhea — males acute
  • Urethral discharge; Gram = GN diplococci intra-/extracellular in pus cells (diagnostic)
Chronic males / females (acute & chronic)
  • Specimen: chronic male — morning drop, centrifuged urinary deposit, prostatic fluid post-massage; female — urethral & cervical discharge
  • Gram smear: difficult (flora / low number)
  • Culture: chocolate or MTM at 37°C, 5–10% CO₂; ID by microscopy + biochem; carbohydrate utilization most sensitive
  • Recent: DFA, Gonotest (cross-reactions), DNA probe, ELISA
  • Non-venereal: conjunctival, synovial fluid, blood — same lines
Meningococcal meningitis — CSF
  • Physical: turbid, under tension
  • Cells > 20,000/mm³, PMN predominant
  • Centrifuge → Gram + chocolate agar culture
  • CSF Ag detection: latex agglutination, coagglutination (Staph CoA + anti-meningococcal Ab), counter-IEP, Quellung, DFA
  • Blood culture; PCR for CSF/blood DNA
  • Carriers: West's nasopharyngeal swab → MTM
  • Gonorrhea: ceftriaxone DOC; co-treat for Chlamydia (tetracycline or azithromycin) — 50% co-infection
  • Prevention: condoms; treat partners; erythromycin ointment for ophthalmia neonatorum prevention
  • Meningococcal meningitis: medical emergency — IV penicillin G or ceftriaxone immediately (sometimes pre-LP); 7–10d; chloramphenicol if resistant
  • Chemoprophylaxis (close contacts): rifampicin 600 mg PO BID × 2d OR ciprofloxacin (oral/IM) — secreted in saliva
Meningococcal vaccines
  • MCV4: conjugate (A/C/Y/W-135 + diphtheria toxoid carrier); 2–55y
  • MPSV4: polysaccharide; only one licensed for >55y
  • Group B polysaccharide not included — poorly immunogenic
  • N. meningitidis infects humans only: cannot obtain iron other than from transferrin/lactoferrin
  • Normal nasopharyngeal flora 5–30% adults; up to 70–80% during epidemics
  • Only bacterial meningitis known to occur in epidemics; most common 2–18 y
  • Meningococcemia: high fever, hemorrhagic rash, DIC, collapse
  • Gonococci fragile: susceptible to temperature, drying, UV
  • Female gonorrhea: ~80% asymptomatic; vagina not infected in adults (acidity + flora + stratified squamous); rectal up to 40%
  • Repeated gonococcal infections common (antigenic heterogeneity + pilus/surface variation + superficial → little IgG protection + IgA protease)
  • Ophthalmia neonatorum: cornea → blindness; vulvovaginitis in young females (vagina = simple squamous; via towels/seats)
  • Disseminated gonococcal: hemorrhagic papules/pustules, tenosynovitis/arthritis, endocarditis, meningitis
  • PID → infertility, ectopic pregnancy
4 · EnterobacteriaceaeEscherichia E. coliGN bacilli, usually motile, some capsulated; major facultative bowel anaerobe; family: facultative anaerobes, MacConkey-growing, oxidase NEG, nitrate-reducers, ferment glucose
  • Lactose fermenter — rose-pink on MacConkey
  • Ferments glucose, lactose, maltose, mannitol, sucrose, salicin with acid + gas
  • IMViC: + + − − (indole+, MR+, VP−, citrate−)
  • O (somatic) — cell-wall LPS
  • H (flagellar)
  • K (capsular) in capsulated strains
 Diarrheagenic E. coli
  • Pili (colonization factor): epithelial attachment
  • Enterotoxins LT & ST (ETEC): LT A-B → A subunit activates adenylate cyclase → ↑cAMP → Cl secretion + Na inhibition (cholera-like); ST → ↑guanylate cyclase → cGMP → fluid loss
  • Shiga toxin / verotoxin (EHEC, STEC): modifies 28S rRNA → blocks protein synthesis
Uropathogenic E. coli
  • Fimbrial adhesins, hemolysins (exotoxins), K antigen
LPS
  • Endotoxin → endotoxic shock
  • Specimens: feces, urine, wound, respiratory, blood, CSF
  • Direct detection useful only in normally sterile sites (CSF — agglutination for K1 antigen in neonatal meningitis)
  • Culture: MacConkey + blood agar @ 37°C; blood culture for septicemia/meningitis; CLED quantitatively for urine
  • ID: morphology, Gram, oxidase, biochem; slide agglutination with specific antisera; tissue culture for toxin (ETEC, EHEC) / invasiveness (EIEC) / adherence (EPEC, EaggEC); ELISA for toxins; DNA probe or PCR for toxin genes
  • Guide by in-vitro susceptibility (resistant strains emerging)
  • Diarrhea: rehydration + electrolyte correction; selected antibiotics if needed
  • Normal bowel flora — provides colonization resistance; indicator of fecal pollution of water (with E. faecalis, C. perfringens)
  • UTI — most common cause: >80% community; ascending → urethritis, cystitis, pyelitis, pyelonephritis; hospital UTI usually catheter + multi-resistant
  • Neonatal meningitis: E. coli K1 common cause
  • Pneumonia, sepsis, septicemia, endotoxic shock (esp. neonates)
  • Diarrheagenic pathotypes:
    • ETEC: severe diarrhea in infants/children & traveler's diarrhea
    • EHEC / STEC: bloody diarrhea / hemorrhagic colitis; HUS; O157:H7 commonest; ground beef outbreaks; STECs: O26, O111, O103, O121, O45, O145
    • EPEC: infantile diarrhea — tight adherence, interferes with absorption
    • EIEC: Shigella-like, no Shiga toxin
    • EaggEC: persistent diarrhea in children; O104:H4 Germany 2011 (vegetables) — acquired Shiga genes → HUS
4 · EnterobacteriaceaeKlebsiella K. pneumoniae
K. ozaenae
K. rhinoscleromatis
K. oxytocaNon-motile, usually capsulated GN bacilli; environment + intestinal/respiratory mucosa
  • MacConkey: rose-pink, mucoid colonies (slime)
  • Ferments glucose, lactose, maltose, mannitol, sucrose, salicin with acid + gas
  • K. pneumoniae IMViC: − − + +
  • Non-motile
  • 77 serotypes based on capsular polysaccharide
  • Capsule — most important virulence factor
  • Morphology, mucoid colonies, biochem
  • Intrinsically resistant to ampicillin
  • ESBL (extended-spectrum β-lactamase) — resistance to most effective cephalosporins
  • Routine AST required
  • Community & nosocomial:
    • UTI (most common)
    • Lobar pneumonia
    • Wound & bloodstream infections with focal lesions (liver/lung abscess)
    • Neonatal sepsis: septicemia, meningitis
  • K. ozaenae → atrophic rhinitis
  • K. rhinoscleromatis → rhinoscleroma (destructive granuloma of nose & pharynx)
  • Multi-drug-resistant nosocomial strains prevail in hospitals
4 · EnterobacteriaceaeCitrobacter, Enterobacter, Serratia Citrobacter
Enterobacter
SerratiaMotile GN bacilli; soil/water/occasionally human respiratory & intestinal tracts
  • Motile lactose fermenters
  • Citrobacter: like E. coli but citrate positive
  • Enterobacter: like Klebsiella but motile
  • Serratia: some strains red non-diffusible pigment — used for testing efficiency of bacterial filters
 — — — —
  • Opportunistic infections similar to K. pneumoniae
4 · EnterobacteriaceaeProteus P. vulgaris
P. mirabilis
Morganella morganii (formerly P. morganii)
Providencia rettgeri (formerly P. rettgeri)GN pleomorphic, motile, non-sporing bacilli; soil, sewage, feces; 3rd & 4th species moved to new genera based on DNA
  • Simple & enriched media; concentric wavy "swarming" growth due to high motility
  • Non-lactose fermenters
  • Urease positive — rapidly decomposes urea to ammonia
  • P. vulgaris OX-10, OX-2, OX-K: share antigenic similarity with Rickettsiae → Weil-Felix reaction (serodiagnosis of rickettsial diseases)
 —
  • Isolation from urine / wound discharge by morphology, swarming, biochem (urease)
  • According to AST — resistant to many antimicrobials
  • Saprophytes in soil, sewage, feces; normal intestinal flora
  • Diseases: UTI, wound infection, otitis media
  • M. morganii & P. rettgeri: emerging important nosocomial agents
  • Weil-Felix reaction = key principle for rickettsial serodiagnosis
4 · EnterobacteriaceaeSalmonella S. typhi (Gp D)
S. paratyphi A/B/C (Gps A, B, C)
S. typhimurium
S. enteritidis
S. choleraesuis (Gp C)GN bacilli, motile, non-capsulated; in S. typhi carriers acquires capsule (Vi antigen); facultative anaerobe
  • Grow on nutrient agar; MacConkey: pale yellow, non-lactose fermenting
  • Ferments glucose, maltose, mannitol → acid only in S. typhi, acid + gas in S. paratyphi
  • H₂S + in S. typhi & S. paratyphi B & C
  • Indole − and urease −
  • O (somatic): groups (A–I)
  • H (flagellar): serotype-specific
  • Vi (capsular): virulent strains (esp. S. typhi)
  • DNA-DNA hybridization → 7 groups; Group I = S. enterica >1400 serotypes
  • Minor O-Ag sharing between S. typhi & S. paratyphi; H is specific for each
  • Pili: host-cell adherence
  • Two pathogenicity islands: contact secretion system + effector proteins
  • Facultative intracellular in macrophages
  • Vi antigen in S. typhi: retards PMN phagocytosis, favors macrophage uptake
 Enteric fever — by week
  • Week 1 (fever): blood culture (5–10 mL in 50–100 mL trypticase soy broth); bone marrow culture (always +, vs ~66% blood); clot culture; subculture on MacConkey/DCA; ID by colony, microscopy, biochem, slide agglutination
  • Week 2 onwards: stool culture (selenite/tetrathionate broth → MacConkey/DCA); urine culture (centrifuged deposit on MacConkey/DCA); repeat as excretion is intermittent
  • Serology: Widal — 4-fold rise diagnostic; endemic areas (Egypt): ≥1/160 indicative, ≤1/80 = community titer; consider vaccination/past infection (anti-H persists longer than anti-O); false +ve from cross-reaction (non-enteric Salmonella, autoimmune); false −ve early or after antibiotics
  • ELISA, immunoblot — more sensitive than Widal
  • Carriers: high anti-Vi titer in S. typhi carriers; gall-bladder → stool (cholagogue + saline purge); urinary → urine
  • Chloramphenicol, ampicillin, TMP-SMX, fluoroquinolones, 3rd-gen cephalosporins
  • MDR via plasmids — base on susceptibility
  • Chronic carriers: ampicillin, TMP-SMX, ciprofloxacin; cholecystectomy if gallbladder disease
  • Salmonella food poisoning: usually self-limited
  • Septicemia: as for typhoid
Vaccines (typhoid)
  • Ty21a live oral: attenuated S. typhi only; not <6y; boosters q5y; 50–80% protection
  • Vi polysaccharide IM: 0.5 mL 2 wk pre-travel; not <2y; boosters q2y
  • Older killed whole-cell: still used where new unavailable; more side effects
  • Enteric fever — strictly human; endemic in Egypt
  • Infectious dose ~10⁶; lower with Vi
  • Primary site: small intestine — M cells in Peyer's patches transcytose to mesenteric LN → primary bacteremia 1–2 wk (IP) → liver, gall bladder, spleen, kidney, BM → secondary bacteremia → fever; gallbladder → reinvade intestine + Peyer's patches
  • Clinical: fever, headache, malaise, tender abdomen, constipation, splenomegaly, rose spots; complications = intestinal hemorrhage/perforation; 10–30% mortality untreated
  • Carriers: gallbladder stones favor carriage; urinary bilharziasis favors urinary carriers (Egypt)
  • Food poisoning (S. typhimurium, S. enteritidis): reservoir = animals + poultry; IP 12–48h; no blood invasion; blood culture & serology of no value
  • S. choleraesuis: septicemia + metastatic abscesses on damaged tissues (infarcts, aortic aneurysms)
4 · EnterobacteriaceaeShigella S. dysenteriae (Gp A, 13 serotypes)
S. flexneri (Gp B, 8)
S. boydii (Gp C, 18)
S. sonnei (Gp D, 1)GN bacilli, non-motile, non-capsulated; strict human pathogens
  • MacConkey or DCA: pale yellow, non-lactose fermenting
  • S. dysenteriae: glucose only, acid only
  • Other species: glucose + mannitol, acid only
  • S. sonnei: late lactose fermenter
  • Anaerogenic (no gas)
  • H₂S − and urease −
  • Lacks H antigen
  • 4 serogroups by O antigen
  • Invasiveness: contact secretion system injecting invasion antigens into enterocytes; large plasmid encodes attachment
  • S. dysenteriae type I (Shiga bacillus) exotoxin: heat-labile; enterotoxic (watery diarrhea early), cytotoxic (necrosis, ulceration, pseudomembrane), neurotoxic (meningism, convulsions, coma); similar to EHEC verotoxin
  • Endotoxin (LPS): irritates bowel wall
  • Specimen: stool (visible blood + mucus)
  • Microscopy: pus cells + RBC
  • Culture: selenite broth × 24h → MacConkey/DCA
  • ID: morphology, wet film + Gram, biochem, latex agglutination
  • AST important (high resistance)
  • Fluid & electrolyte replacement
  • Antibiotics shorten illness: ampicillin, ciprofloxacin, 3rd-gen cephalosporins
  • Strict human pathogens; no animal reservoir
  • Very low infectious dose (~100 organisms) — acid-resistant survival through stomach
  • "4 Fs": flies, feces, fingers, food
  • Distal ileum + colon; invades M cells, multiplies in cytoplasm, spreads laterally via basolateral pole → apoptosis + sloughing → ulceration; submucosa inflammation; no blood invasion in healthy
  • IP 1–4d; Dysentery triad: 1) abdominal cramps, 2) tenesmus, 3) frequent small-volume bloody mucoid stools
  • Recovery spontaneous in most; children/elderly may have dehydration, acidosis, death
5 · Non-ferm GNBPseudomonas P. aeruginosaAerobic, non-spore-forming, motile, non-fermentative GN bacilli; normal flora GIT + moist body sites; ubiquitous in moist hospital environments
  • Aerobic, non-fermentative
  • Oxidase + and catalase +
  • Indole negative
  • No sugar fermentation; acid from glucose by oxidation only
  • Grows at 42°C (vs 37°C optimal)
  • Simple media; MacConkey colorless; blood agar complete hemolysis
  • Diffusible exopigments + grape-like odor: pyoverdin (yellow) + pyocyanin (blue) → bright green
 — (LPS / immunotypes mentioned only for epidemiologic typing)
  • Pili, flagella
  • Endotoxin (LPS)
  • Biofilm formation → chronic opportunistic infections (CF, ICU, elderly)
  • Exotoxin A (Exo A): ADP-ribosylates EF-2 (like DT) → tissue necrosis
  • Exoenzyme S (ExoS): delivered to cytoplasm via secretion system
  • Elastase & phospholipase: degrade proteins/lipids — nutrient acquisition + dissemination
  • Specimens: skin lesions, pus (may be greenish-blue), urine, blood, CSF
  • Gram: GN bacilli in pus
  • Culture: readily grown; ID by morphology + pigment + Gram + biochem
  • Bacteriophage typing for epidemiology; LPS immunotypes
  • Resistant to many antibiotics → in-vitro testing required
  • Serious infections: β-lactam + aminoglycoside (combined)
  • Infection control for nosocomial: moist environments (sinks, water baths, showers, hot tubs)
  • Community: folliculitis, swimmer's ear, eye infections (contact lens — corneal ulcer → blindness), osteomyelitis (children, IVDU), endocarditis (IVDU)
  • Nosocomial: respiratory in intubated ICU patients, UTI, wound + septicemia, meningitis post-LP, chronic CF lung infection
  • Characteristic grape-like odor
5 · Non-ferm GNBAcinetobacter A. baumannii (commonest)Old names: Mima polymorpha, Herellea vaginicola; widely distributed in soil/water, can be cultured from skin, mucous membranes, secretions, hospital environment
  • Aerobic
  • GN coccobacilli or cocci; diplococcal forms predominate in body fluids & on solid media
  • Oxidase NEGATIVE — differentiates from Neisseria/Moraxella
  • Grows well on most media
 — — (opportunistic; not detailed)
  • Specimens: blood, sputum, skin, pleural fluid, urine
  • Mistaken for N. meningitidis (meningitis/sepsis) or N. gonorrhoeae (female genital tract) — oxidase NEGATIVE distinguishes
  • Often multi-resistant
  • Susceptibility testing required
  • Mostly commensals; occasional nosocomial pathogen
  • Device-associated (catheters, ventilators)
  • Nosocomial pneumonia (most common): source often water of room humidifiers / vaporizers
  • Bacteremia source: IV catheters almost always
  • Burns + immunodeficient → opportunistic sepsis
5 · Non-ferm GNBMoraxella M. catarrhalis (= Branhamella catarrhalis)
M. lacunataSome species need enriched media (blood / chocolate)
  • GN bacilli, coccobacilli or cocci
  • Non-motile, non-fermentative
  • Oxidase + and DNase +
  • Morphology / fastidious growth / positive oxidase → confused with Neisseria
 —
  • M. catarrhalis: β-lactamase producer
  • Distinguished from Neisseria by morphology + oxidase + fastidious growth + DNase positivity
  • Generally susceptible to penicillin EXCEPT M. catarrhalis (β-lactamase)
  • Previously classified with Neisseria; M. catarrhalis was once called Branhamella catarrhalis
  • M. catarrhalis: normal oropharyngeal flora; occasional otitis media + lower respiratory tract infection
  • M. lacunata: angular conjunctivitis + blepharitis
6 · Curved GNBVibrios V. cholerae O1 (classical + El Tor) & O139
V. parahaemolyticus
V. vulnificusComma-shaped GN rods; saprophytes in surface (mainly salt) water and soil
  • Comma-shaped GN rods (straight on prolonged culture)
  • Motile (single polar flagellum, darting motility)
  • Highly aerobic
  • Alkaline pH 8.5–9.5 favored; sensitive to acids + cold
  • Alkaline peptone water: surface pellicle
  • TCBS: V. cholerae yellow (sucrose+); V. parahaemolyticus green
  • Ferments glucose, maltose, mannitol, sucrose
  • Oxidase +, indole +
  • Cholera red reaction + (nitrate → nitrite + indole from peptone → nitroso-indole → red with H₂SO₄)
  • String test + (0.5% Na deoxycholate → DNA strings; differentiates from Aeromonas)
  • O antigens → ≥139 serogroups
  • O1 & O139 → epidemic cholera; non-O1/non-O139 → sporadic
  • O1: serotypes Ogawa, Inaba, Hikojima; biotypes Classical & El Tor
  • Classical vs El Tor: hemolysis sheep RBC (− vs +); chicken RBC hemagglutination (− vs +); VP (− vs +); polymyxin B (sens vs res); phage IV (sens vs res)
  • TCP (Toxin-coregulated pilus): colonization; VPI pathogenicity island; co-regulated with CT
  • Heat-stable endotoxin
  • Cholera toxin (CT) / choleragen: heat-labile exotoxin, phage-encoded; A1+A2+5B subunits; B binds enterocyte receptor; A1 activates adenylate cyclase → ↑cAMP → excessive secretion of Cl⁻, K⁺, HCO₃⁻, Na⁺, water → severe diarrhea
  • Mucinase: degrades mucous layer
  • Specimens: rice-water stools, rectal swab
  • Stool → alkaline peptone water 6–8h → surface pellicle → TCBS (yellow colonies)
  • ID:
    • Wet mount: darting motility
    • Gram: GN comma-shaped bacilli
    • Biochem: sugars (glucose, maltose, mannitol, sucrose), oxidase +, indole +, cholera red +, string test +, TSI
    • Agglutination with anti-O1 and anti-O139 sera
  • Direct: IF, immunoassay for Ag, PCR for CT gene
  • Secondary cases in epidemic: microscopy + anti-O sera immobilization
  • IV fluids — most important (correct fluid/electrolyte imbalance)
  • Tetracycline: shortens excretion (resistance emerging)
Prevention
  • Sanitation; isolation; food washing; food handler observation
  • Quarantinable disease
  • Chemoprophylaxis: tetracyclines for exposed
  • Vaccines:
    • Koll's parenteral: killed whole-cell IM, 2 doses 1 wk apart; ~50% protection × 6 mo; only IgM/IgG not IgA
    • BS-WC oral: killed + B subunit; induces IgA + antitoxin Abs
    • CT B subunit vaccine
    • Recombinant oral live (CT gene in S. typhi Ty21a)
  • Endemic Indian subcontinent; epidemic + pandemic
  • IP 1–4d; rice-water diarrhea; up to 20 L fluid/day loss; severe vomiting + cramps
  • Complications: dehydration, hypokalemia, metabolic acidosis, shock, death
  • Infectious dose high (10¹⁰); lower with antacids / food (buffering)
  • Infection localized to intestine (no blood invasion)
  • Convalescent carriers: gall bladder × 4–5 wks; chronic only with El Tor
  • Sensitive to 0.05% NaOCl, 70% EtOH, 2% glutaraldehyde, 8% formaldehyde, 10% H₂O₂, iodine
  • El Tor survives longer than classical
  • V. parahaemolyticus: halophilic, warm oceans; gastroenteritis epidemics from seafood/raw fish; virulent strains make hemolysin; TCBS green (no sucrose ferment)
  • V. vulnificus: aquatic; rare septic infections in immunosuppressed
6 · Curved GNBCampylobacter C. jejuni (most important — 95% Campylobacter enterocolitis)
C. coli (also diarrhea)
C. fetus, C. lari (rare systemic: bacteremia, meningitis, pneumonia)Spiral, motile, GN, microaerophilic
  • Small GN comma-, S-, or gull-wing-shaped rods
  • Darting motility (single flagellum at one or both poles)
  • Microaerophilic + capnophilic (5% O₂, 10% CO₂)
  • Thermophilic — 42°C optimal
  • Skirrow's medium (blood + vancomycin + polymyxin + TMP)
  • 2–4 days to grow
  • Oxidase + and catalase +
  • Urease NEGATIVE (differentiates from Helicobacter)
 —
  • Characteristic darting / corkscrew motility
  • Invasiveness of jejunal mucosa → cell damage + inflammatory diarrhea
  • Enterotoxin: secretory diarrhea
  • Cytolethal distending toxin (CDT): arrests cell division, destroys mucosa
  • Specimen: stool
  • Wet mount (motility); Gram (morphology); 1% basic fuchsin rapid stain
  • ELISA / PCR
  • Culture: Skirrow's at 42°C × 2–4d
  • Biochem: oxidase +, catalase +, urease −
  • Serology for autoimmune complications
  • Fluid/electrolyte replacement (if indicated)
  • Severe: erythromycin or ciprofloxacin
  • Zoonotic (dogs, cats, cattle, poultry); contaminated unpasteurized milk, meat, poultry
  • Children worldwide most affected
  • Low infectious dose (few hundreds)
  • Starts in jejunum; watery foul-smelling diarrhea → bloody stools + fever + severe pain
  • Self-limited 7–10d; bacteremia rare (immunocompromised, neonates)
  • Complications (≥2 wks later): Guillain-Barré syndrome (cross-reacting Abs vs axons/myelin); reactive arthritis (autoimmune)
  • (Textbook also mentions Spirillum minus → rat-bite fever / sodoku, Japan)
6 · Curved GNBHelicobacter H. pyloriSimilar to Campylobacter but multiple polar sheathed flagella
  • Similar to Campylobacter but multiple polar SHEATHED flagella
  • Microaerophilic + humid environment
  • Skirrow's medium at 37°C (NOT 42°C)
  • 1 week to grow
  • Urease POSITIVE — key difference from Campylobacter
 —
  • Flagella: penetrate mucus layer
  • Urease: ammonia neutralizes gastric acid
  • Adhesins: deep mucosal attachment
  • Vacuolating cytotoxin (VacA): cell vacuolation + apoptosis
  • Cytotoxin-associated protein (CagA): encoded in pathogenicity island
  • Contact secretion system: protein injection into epithelial cells
 A. Invasive — gastric mucosa biopsy by endoscopy
  • Rapid urease test (biopsy in urea + pH indicator → color change)
  • Gram or special histologic stains
  • Culture: Skirrow's 37°C microaerophilic humid, 1 week
B. Non-invasive
  • Urea breath test: ¹⁴C or ¹³C-labeled urea → radiolabeled CO₂ in breath
  • Stool ELISA for Ag
  • PCR (gastric juice, biopsy, feces)
  • Serology (anti-H. pylori Abs)
  • Triple therapy: metronidazole + bismuth salt + (amoxicillin OR tetracycline) × 14d → 95% eradication
  • Alternative: PPI + amoxicillin + (metronidazole OR clarithromycin) × 1 wk
  • PPI also inhibits urease + enhances ulcer healing
  • Colonizes stomach in >50% world population; affects children + adults
  • Key role in peptic ulcer disease, chronic gastritis, MALT lymphoma, gastric adenocarcinoma
  • Acquired by oral-oral & feco-oral; iatrogenic role documented
  • Humans = only significant reservoir
7 · Fastidious GNBHaemophilus H. influenzae (Hib most pathogenic)
H. ducreyi
H. aegyptius (biogroup)
H. parainfluenzae"Blood-loving" — fastidious GN; mucous membranes of human URT as normal flora
  • Need factor X (hemin) + factor V (NAD) → chocolate agar provides both
  • On sheep blood agar: satellite phenomenon around S. aureus colonies
  • GN coccobacilli, no specific arrangement
  • Catalase + and oxidase +
  • H. ducreyi: chocolate agar + X (not V) + vancomycin, 33°C, 10% CO₂
  • Capsular polysaccharide: types a, b, c, d, e, f; Hib most pathogenic
  • Most normal-flora strains non-typable (no capsule)
  • Somatic: outer membrane proteins
  • Lipooligosaccharides (LOS): shared structures with Neisseria
  • IgA protease: degrades secretory IgA → facilitates respiratory mucosal attachment + colonization
  • Polysaccharide capsule (PRP in Hib): confers invasive virulence
  • Outer membrane proteins + LPS: invasion
  • Specimens: nasopharyngeal swab, pus, blood, CSF, sputum
  • Gram: GN coccobacilli, no specific arrangement
  • Chocolate agar 37°C 5% CO₂; X + V factor requirement; satellite phenomenon on sheep blood
  • Catalase + and oxidase +
  • Latex agglutination (LAT): direct detection of type-b PS in CSF — more sensitive than culture, unaffected by prior antibiotics, faster; culture in parallel for AST
  • PCR most sensitive
  • Cefotaxime or ceftriaxone
  • Rifampicin for nasal carriage
  • Meningitis: steroids 15–20 min before antibiotic to limit inflammatory response → prevent neurologic deficit (mental retardation, seizures, speech delay, deafness)
  • H. ducreyi: macrolide (azithromycin) + 3rd-gen ceph (ceftriaxone)
Prevention
  • Hib polysaccharide-protein conjugate vaccine (PS attached to protein carrier — recognized by young children's immune systems)
  • Combined with DTP, polio, HBV (US)
  • Rifampicin prophylaxis for unvaccinated close contacts <2y
  • Hib disease window: 5 mo to 5 y (maternal Abs protect <3 mo)
  • Hib diseases:
    • Meningitis (most serious; was most common bacterial meningitis in this age group; non-specific signs in infants)
    • Acute epiglottitis (stridor, drooling, airway obstruction)
    • Septic arthritis (most common cause in infants)
    • Cellulitis (post-bacteremia)
  • H. influenzae biogroup aegyptius: Koch discovered in Egypt during cholera studies; highly communicable purulent conjunctivitis; certain clones cause Brazilian purpuric fever (BPF) — fever, abdominal pain, purpura with preceding conjunctivitis
  • H. ducreyi: chancroid — painful bleeding genital ulcer with necrotic base, ragged edge; regional lymphadenitis; STD; open lesion increases HIV transmission risk
  • H. parainfluenzae: normal respiratory flora; rare infective endocarditis + arthritis
7 · Fastidious GNBBordetella B. pertussis
B. parapertussis (mild pertussis-like)Highly communicable; whooping cough
  • Minute GN capsulated coccobacilli (resemble H. influenzae)
  • Requires nicotinamide + additives (charcoal): Bordet-Gengou medium or charcoal blood agar
  • Grayish-white colonies with shiny convex surface — "mercury drop" appearance
 —
  • Pertussis toxin (PT): major virulence factor; damages ciliated respiratory cells → paroxysmal toxemic stage
  • Adenylate cyclase (AC): hemolytic, impairs phagocyte signaling/chemotaxis/superoxide/microbicidal function; induces apoptosis
  • Tracheal cytotoxin (TCT): peptidoglycan fragment released by multiplying cells; kills ciliated tracheal cells
  • Filamentous hemagglutinin (FHA) + pertactin: adhesion to ciliated epithelium
  • Specimen: saline nasal wash preferred; NP swab; cough plate during paroxysm
  • Direct IF
  • Culture × 7d → IF / slide agglutination / PCR (PCR most sensitive)
  • Serology: limited (Abs rise wk 3); ELISA helpful for long-term cough
  • Erythromycin DOC
  • Erythromycin prophylaxis for exposed unimmunized
Prevention
  • Heat-killed vaccine: from capsulated strains; DTP at 2, 4, 6 mo; not after 6y → encephalopathy
  • Acellular vaccine (DTaP): purified Ag (PT + FHA); fewer side effects; 2, 4, 6 mo + 15–18 mo + 6y + 10–18y booster
  • Whooping cough = acute tracheobronchitis in young children; droplet transmission
  • IP 2 weeks
  • Phases:
    • Catarrhal (infectious): mild URT — rhinorrhea, conjunctival congestion, dry cough
    • Paroxysmal: hacking coughs ending with inspiratory "whoop"; followed by vomiting, cyanosis, convulsions
  • Complications: pneumonia, otitis media, subconjunctival or cerebral hemorrhage
7 · Fastidious GNBBrucella Br. melitensis (goats, sheep — most virulent + commonest in man)
Br. abortus (cattle — needs 8–10% CO₂)
Br. suis (swine)
Br. canis (dogs)DNA evidence: only one species, Br. melitensis, with biovars; obligate parasites of animals + humans
  • GN short coccobacilli, non-motile, non-sporing, non-capsulated
  • Aerobes, 35–37°C
  • Enriched media: Brucella agar, brain heart infusion, liver extract, trypticase soy, chocolate
  • Slow growers — 4–5 days on plates; blood cultures kept up to 1 month before reporting negative
  • BSC required
  • Catalase + and oxidase +
  • Almost all urease + (variable intensity)
  • Differentiate species/biovars by: dye sensitivity (basic fuchsin, thionine), H₂S, urea hydrolysis rate, CO₂ requirement, agglutination with monoclonal anti-A/M LPS
  • 2 LPS antigens A and M in different proportions in the 4 species
  • LPS has endotoxic activity; elicits IgA, IgM, IgG
  • Immunity mainly cell-mediated (facultative intracellular)
  • Superficial L antigen: responsible for virulence
  • Facultative intracellular parasite (in phagocytic cells)
  • LPS endotoxic
  • L antigen
  • Specimens: blood, bone marrow, LN biopsy, serum
  • Repeated blood cultures at onset of febrile attacks; aerobic (most species) OR 10% CO₂ for Br. abortus; subcultures every few days × 3–4 wks before discarding
  • ID by morphology, biochem, agglutination with specific antisera
  • Serology:
    • Standard tube agglutination test (STAT): 1/20–1/5120 dilutions to avoid prozone; ≥1/100 may be diagnostic; rising titer; consider endemicity + occupation (high baseline in farmers/butchers/vets)
    • Prozone: Ab excess at low dilutions → false negative; blocking IgA antibodies (subacute) → another prozone source
    • Coombs antiglobulin method: detects blocking IgA
    • Rapid slide agglutination with stained Ag: screening farm animals + humans; not affected by prozone
    • ELISA: IgG/IgM/IgA — replaced Coombs
  • PCR for direct detection
  • Brucellin test: delayed hypersensitivity (intradermal protein extract; 24–72h induration/erythema in chronic) — rarely used
  • Prolonged + combined (chronicity + intracellular)
  • Tetracycline + (streptomycin OR rifampicin)
Prophylaxis
  • Live attenuated vaccine for cattle only
  • No human vaccine available
  • Limit/eradicate animal brucellosis; pasteurization; reduce occupational hazards
  • Brucellosis = Undulant fever / Malta fever
  • Important Egyptian health problem
  • Chronic life-long infection in animals: localize in reproductive organs; shed in milk, urine, placenta; cause sterility & abortion
  • Transmission: intestinal (undercooked meat, unpasteurized milk/cheese), mucous membranes (droplet, conjunctiva), skin abrasions (animal tissues/blood/fluids)
  • IP 1–6 weeks
  • Acute bacteremic phase → chronic stage (years)
  • Flu-like: malaise, fever, sweats, anorexia, headache, GI
  • Undulating fever: 3–4 wk fever + 3–4 wk afebrile alternating
  • Multi-organ: GI, skeletal, neurologic, CV, pulmonary; LN, liver, spleen enlargement
  • Br. melitensis more acute/severe; Br. suis more chronic
  • IgM peaks 3 mo, persists ≤2y; IgG peaks 6–8 wk; IgA parallels IgG
  • Granuloma + abscess in liver, spleen, kidneys, bone marrow, LN
7 · Fastidious GNBFrancisella F. tularensisFrom Minor Bacterial Pathogens section
  • GN coccobacillus
  • Grows on modified Thayer-Martin agar
 — —
  • Highly infectious pathogenic nature — strict lab precautions
  • Streptomycin or gentamicin × 10 days
  • Living attenuated vaccine required for lab workers
  • Reservoir: rabbits, rodents
  • Transmission: biting arthropods (ticks, lice); direct contact with infected animal tissue; inhalation of aerosols; ingestion of contaminated food/water
  • Disease (tularemia): fever + lymphadenopathy (ulceroglandular type); typhoid-like; eye infection; pulmonary disease
  • Dangerous potential biological weapon
8 · Yersinia / PasteurellaYersinia Y. pestis (plague)
Y. enterocolitica
Y. pseudotuberculosisMember of Enterobacteriaceae; animal natural hosts
  • Y. pestis: GN short ovoid, non-motile; at 37°C develops capsule-like outer envelope
  • Wayson/Giemsa/methylene blue: marked bipolar staining
  • Blood agar / MacConkey: non-lactose fermenting
  • Growth better at 27–30°C than 37°C; colonies 2–5 days
  • Catalase +; indole, oxidase, urease NEGATIVE
  • Urease − + non-motile differentiates Y. pestis from other pathogenic Yersinia
  • Y. enterocolitica / pseudotuberculosis: NLF, urease +, oxidase −; motile at 25°C, non-motile at 37°C
  • Cold enrichment (rectal swab/feces in buffered saline pH 7.6 at 4°C × 2–4 wks)
  • Y. pestis — F1 capsular antigen (produced mainly at 37°C); antiphagocytic; induces protective Abs
  • V-W antigens: plasmid-encoded, virulent strains only; antiphagocytic; cause calcium requirement at 37°C
  • LPS (endotoxin): endotoxic shock
  • F1 antigen: capsule protein at 37°C, antiphagocytic, protective Abs
  • V-W antigens: antiphagocytic, plasmid-encoded
  • YOPs (Yersinia outer proteins): inhibit phagocytosis & cytokine production; increase replication/invasion; one Yop is a protease
  • Exotoxin: lethal to mice
 Y. pestis
  • Specimens: aspirate of LN (bubonic), sputum (pneumonic), blood (septicemic), serum
  • Direct: Wayson / Giemsa / methylene blue → bipolarity
  • Direct F1 Ag: DFA; PCR (rapid, less hazardous than culture/animal)
  • Animal inoculation in white rats / guinea pigs (autopsy)
  • Culture: blood agar / MacConkey at 27–30°C; NLF; definitive ID by IF / inoculation / PCR
  • Refer suspicious to public health lab; BSC always
  • Serology: HA / ELISA — rising titer; useful in convalescence
Y. enterocolitica / pseudotuberculosis
  • Stool, blood, surgical material
  • Cold enrichment → MacConkey at 25°C
  • NLF, urease +, oxidase −; motile at 25°C, non-motile at 37°C
  • Serology: rising agglutinin titer (cross-reacts with Vibrios, Salmonella, Brucella — may confuse)
  • Y. pestis:
    • Tetracyclines (doxycycline), fluoroquinolones (ciprofloxacin), aminoglycosides (streptomycin not widely recommended; gentamicin)
    • Early therapy crucial
    • Pneumonic plague: initiate within 24h of symptoms; continue 10 d
    • Contacts of pneumonic case: 7d prophylaxis; symptoms → 10d Tx
    • Anti-rat / anti-flea measures; standard respiratory droplet precautions
    • Formalin-killed vaccine for high-risk
  • Yersiniosis: usually self-limited; severe → doxycycline + aminoglycoside; alternatives: TMP-SMX, ceftriaxone, FQ, chloramphenicol; resistant to penicillin G, ampicillin, cephalothin
  • Pseudotuberculosis: lasts 1–3 wks untreated; complex cases — ampicillin, aminoglycosides, tetracycline, chloramphenicol or cephalosporins
  • Plague (black death) — zoonotic; epidemics; endemic in India, Far East, parts of Africa
  • Primary in rats & rodents (reservoirs); rat-to-rat by rat fleas; organism multiplies in flea gut, regurgitated through bite puncture
  • Human epidemics preceded by rat epizootics
  • Clinical forms:
    • Bubonic (Greek "boubon" = groin): painful enlarged inguinal LN (lower limb bite) / axillary (upper); fever, prostration
    • Septicemic: endotoxic shock, DIC, cutaneous hemorrhage
    • Pneumonic: hemorrhagic consolidation + sepsis; droplet spread (primary); uniformly fatal if not promptly treated
  • Bioterrorism agent: aerosol → pneumonic; infected fleas → bubonic→septicemic
  • Y. enterocolitica & Y. pseudotuberculosis: domestic + farm animals + water; food/drink fecal contamination; person-to-person rare; common in children — fever, abdominal pain, often bloody diarrhea; older children/adults — may mimic appendicitis
8 · Yersinia / PasteurellaPasteurella P. multocida (= P. septica)Worldwide in respiratory + GIT of many domestic + wild animals
  • Non-motile GN coccobacilli with bipolar staining
  • Aerobes / facultative anaerobes
  • Grow readily on blood agar / chocolate agar at 37°C
  • Oxidase + and catalase +
 — —
  • Standard culture from wound discharges (not detailed beyond morphology + biochem)
 — (not detailed in textbook)
  • Most common organism in human wound from cat / dog bites or scratches
  • Manifestations: cellulitis, lymphangitis, lymphadenitis, fever; complications: osteomyelitis, arthritis
  • Some infections without animal contact — suspected nasopharyngeal colonization → respiratory disease, meningitis
10 · AnaerobesBacteroides B. fragilis (most common opportunistic pathogen of the genus)Predominant anaerobe in human colon; opportunistic pathogen if introduced into abdominal cavity after bowel penetration
  • Slim, pale-staining, capsulated GN rods
  • Strict anaerobe
  • Form colonies overnight on blood agar — "fragility" name misleading
 —
  • Superoxide dismutase: survival in oxygenated tissues until reduced microenvironment established
  • Surface pili: adhesive
  • Polysaccharide capsule: antiphagocytic; inhibits macrophage migration; triggers T-cell responses → abscess formation (purified capsule alone — even without live bacteria — stimulates abscess; unique vs. S. pneumoniae capsule)
  • LPS endotoxin less toxic than other GNB (modified/absent lipid A)
  • Extracellular enzymes: collagenase, fibrinolysin, heparinase, hyaluronidase
  • Anaerobic culture (standard methodology in textbook)
  • Drainage of abscesses + debridement = mainstays
  • Almost always β-lactamase producers → inactivates Pen + many cephalosporins
  • Tetracycline resistance common
  • Susceptible: clindamycin, metronidazole
  • β-lactams that work: imipenem; β-lactamase inhibitor combinations (clavulanate/sulbactam + ampicillin/ticarcillin)
  • Preoperative cefoxitin recommended to prevent surgical wound contamination
  • Endogenous infections from patient's own intestinal flora; human-to-human transmission unknown
  • Deep pain + tenderness below diaphragm
  • Peritonitis + intra-abdominal abscess after bowel penetration (operation/trauma)
  • Spread to blood more common with B. fragilis than any other anaerobe
  • Course strongly influenced by other bacteria in abscess (especially Enterobacteriaceae)
10 · Anaerobes / ActinomycetesActinomycetes Actinomyces israelii (anaerobic)
Nocardia asteroides (aerobic)
Streptomyces
Actinomadura maduraeFungus-like bacteria related to Coryne & Mycobacteria; thin branching filaments breaking into bacillary + coccoid elements
  • Aerobic: Nocardia, Streptomyces — weakly GP, partially acid-fast, beaded branching filaments
  • Anaerobic: Actinomyces (most free-living in soil & aerotolerant; anaerobic species are normal oral flora) — GP branching filaments
  • Anaerobic culture, 37°C, 2 weeks
 — — (not detailed)
  • Actinomycosis: sulfur granules (microcolonies); Gram = GP branching filaments surrounded by radiating GN clubs (host origin)
  • Anaerobic media × 2 wks
  • Nocardia: GP, partially acid fast, beaded branching filaments
  • Actinomycosis: surgical drainage + penicillin G (6–12 mo); clindamycin or erythromycin if Pen-allergic
  • Nocardiosis: TMP-SMX
  • Actinomycotic mycetoma: surgical drainage + debridement + antimicrobials (vs antifungals for eumycetoma)
  • 3 diseases:
    • Actinomycosis (chronic suppurative granulomatous; drains pus + sulfur granules; lesion spreads + contagious):
      • Cervicofacial (Lump jaw): face, neck, tongue, mandible
      • Thoracic: lung with empyema
      • Abdominal: caecum/appendix/pelvic (after ruptured appendix; IUD-associated uterine)
      • Also: groin, urogenital, breast, post-op (aerotolerant species; often overlooked as contaminants)
    • Nocardiosis: frequently misdiagnosed as TB (acid-fast + lung abscess/cavitation); pleural erosion → blood-borne brain abscess + other organs; steroid-treated immunocompromised at risk
    • Actinomycotic mycetoma: chronic subcutaneous; swelling (oma) + sinuses draining granules, especially feet of farmers without shoes; spread to muscles/bones with bacterial type
      • Actinomycotic vs Eumycotic: bacteria vs fungi; yellow vs black/white granules; GP bacilli/filaments vs septate hyphae; blood agar (aer + anaer) vs Sabouraud's RT; antibiotics vs surgical debridement + long antifungals
11 · Atypical GNBLegionella L. pneumophila40 species in soil + water; multiply in free-living amebas; coexist in biofilms
  • Fastidious aerobic GN bacilli
  • Facultative intracellular
  • Poorly stained with Gram — use silver or fluorescent stain
  • Best culture: buffered charcoal yeast extract (BCYE) agar
 —
  • Inhibition of phagosome-lysosome fusion → multiplication in macrophage phagosomes
  • C3b coating → promotes macrophage phagocytosis
  • Degenerative enzymes kill infected cells; patchy lung infiltration
  • Culture: bronchial aspirate / pleural fluid / lung biopsy on BCYE aerobic → IF / nucleic acid probes
  • Urinary antigen by ELISA within hours
  • PCR
  • Serology: IgM or rising IgG ELISA (retrospective outbreak diagnosis)
  • Macrolides (erythromycin, azithromycin) OR fluoroquinolones
  • Prevention: hyperchlorination + heating of water supplies
  • Found in soil, water, biofilms, free-living amoebas
  • Chlorine tolerant
  • NO person-to-person spread
  • Inhalation of aerosols from contaminated A/C systems + shower heads → hospital outbreaks (debilitated/immunocompromised)
  • 2 diseases by host CMI:
    • Legionnaire's disease: atypical pneumonia — fever, chills, dry cough; potentially fatal in immunosuppressed
    • Pontiac fever: self-limited mild flu-like in healthy individuals
11 · Minor pathogensBartonella B. bacilliformis
B. quintana
B. henselaeFrom Minor Bacterial Pathogens section
  • Small GN, polymorphic, motile bacilli
 — — — (not detailed)
  • B. bacilliformis: penicillin, streptomycin, chloramphenicol
  • B. henselae: mainly supportive — reassurance, hot moist soaks, analgesic; tetracycline or erythromycin may help
  • B. bacilliformis: Oroya fever — serious infectious anemia; transmitted by sand flies
  • B. quintana: Trench fever; transmitted by body lice; human reservoir
  • B. henselae: Cat-scratch disease — usually benign self-limited; fever + lymphadenopathy 2 weeks after cat scratch / bite / flea bite
11 · Minor pathogensGardnerella G. vaginalisIsolated from normal female genitourinary tract
  • Gram variable coccobacilli
 — — Bacterial vaginosis criteria
  • Foul-smelling discharge
  • "Whiff" test: 10% KOH on discharge → fishy odor
  • "Clue cells": vaginal epithelial cells covered with Gram-variable coccobacilli
  • Vaginal pH ≥ 4.5 (normal ≤ 4.5)
  • Metronidazole DOC
  • Associated with anaerobic bacteria → causes bacterial vaginosis
  • BV associated with: premature rupture of membranes, preterm labor
12 · MycobacteriaMycobacterium M. tuberculosis + M. bovis (MTC)
M. leprae
Atypical: M. scrofulaceum, M. kansasii, MAC (M. avium-intracellulare), M. fortuitum, M. chelonae, M. marinumGenus has >125 species, mostly environmental saprophytes; slender, straight or slightly curved, non-spore-forming, aerobic
  • Acid fastness due to mycolic acids (long-chain fatty acids) in cell wall → hydrophobic, impermeable; need strong dyes + heat; resist mineral acid + acid-alcohol decolorization
  • M. tuberculosis: resists 25% H₂SO₄; M. leprae: resists only 5% H₂SO₄
  • Obligate aerobes; prefer highly oxygenated tissues
  • Slow growers
  • Survive ingestion by macrophages
  • Survive weeks in dark moist conditions, days in dried sputa/excreta
  • Rapidly killed by UV + heat
  • Solid media: Lowenstein-Jensen (egg), Middlebrook 7H10 (agar)
  • Broth: Middlebrook 7H9 — rapid & sensitive
  • Radiometric (BACTEC): ¹⁴C palmitic acid → radioactive CO₂; reduces ID to 7–10 days
  • Growth typically 2–4 wks; never reported negative before 8 wks
  • ID by: biochem, growth rate, pigment, molecular
 —
  • M. tuberculosis: glycolipids on outer surface → enhance granuloma formation, inhibit PMN migration, intracellular survival in macrophages
  • No exotoxin, no endotoxin
 Active TB
  • Specimens: sputum (commonest), BAL, endotracheal aspirate; also urine, body fluids, gastric lavage, blood, tissue
  • Decontamination/concentration for sputum/stools:
    • NALC liquefaction → 4% NaOH decontamination → centrifugation
  • Direct smear:
    • Ziehl-Neelsen: positive smear highly suggestive (negative does not rule out); grade 1+ to 4+ for follow-up
    • Auramine fluorescent: screening; confirm positives with ZN
  • Culture = gold standard
  • Molecular: PCR (DNA), RT (rRNA) — rapid but less sensitive/specific than culture
  • Serology (ELISA, ICT): not useful for active TB (frequent false +/−)
Latent TB
  • Tuberculin skin test (Mantoux): 0.1 mL PPD 5TU intradermal volar forearm; read at 48–72h; ≥10 mm induration = positive; deeper injection → false negative
  • Interpretation: positive = previous exposure / reactivation ability; suspicious in low-prevalence countries or contacts; little significance in endemic; BCG; <5y w/o exposure = suspicious; false positive from atypical Myco; false negative from severe TB (anergy), steroids, malnutrition, Hodgkin's, measles, AIDS
  • IGRA: γ-IFN release from sensitized T-cells with specific M. tb antigens; not affected by BCG; single visit
M. leprae
  • Scraping/biopsy from nasal mucosa, earlobe, skin lesions
  • Modified ZN (5% H₂SO₄): intracellular AFB (abundant in lepromatous, few in tuberculoid)
  • Histopathology of characteristic lesion
  • NOT CULTURABLE
  • Lepromin test (like tuberculin): + in tuberculoid, − in lepromatous
 TB
  • Multiple drug therapy 6–12 mo to prevent resistance; sputum non-infective 2–3 wks after starting
  • First line: isoniazid (major), rifampicin (2nd major), pyrazinamide, ethambutol, streptomycin
  • Second line (more toxic, less effective): ethionamide, kanamycin, capreomycin, cycloserine, fluoroquinolones (ciprofloxacin)
  • MDR-TB: resistant to ≥ INH + RIF
  • XDR-TB: MDR + any FQ + ≥3 second-line
Leprosy
  • Sulphones (dapsone) = main therapy
  • Combinations (e.g. dapsone + rifampicin) to prevent resistance
  • Continue up to 2 years or until lesions organism-free
Vaccination
  • BCG: live attenuated bovine ("Bacillus Calmette-Guérin"); partial immunity vs M. tb & M. bovis
  • Egypt: first year of life, single ID injection in deltoid
  • Indications: 1st year of life; TST-neg contacts; TST-neg medical/healthcare; bladder carcinoma (CMI stimulation)
  • Not for immunocompromised (AIDS)
  • TB: 1/3 of world infected; humans only reservoir for M. tb; cattle for M. bovis (rare ingestion of infected milk)
  • 90% immunocompetent destroy bacilli; 10% develop active disease; bacilli may lie dormant for years
  • 2–4 wks post-primary infection: CMI + delayed hypersensitivity (tuberculin becomes +)
  • Primary (exudative): base of lung; Ghon's lesion (calcified scar); regional LN caseate then calcify; bacilli die slowly, few remain latent
  • Secondary (reactivation): upper lobes; tubercles + caseation → fibrosis OR opens into bronchus (open TB — sputum infective); blood vessel erosion → miliary TB
  • Latent TB infection (LTBI): asymptomatic, non-infectious
  • Leprosy: skin + nasal mucosa + nerve fibers; tropical Asia + Africa; prolonged contact needed; inhalation of nasal secretions / shedding lesions of lepromatous
  • Lepromatous: severe; multiple skin nodules → leonine facies (lion-like); many bacilli, highly infectious; CMI reduced; lepromin negative
  • Tuberculoid: mild; hypopigmented macules + thickened superficial nerves + anesthesia; few bacilli; CMI intact; lepromin positive
  • Atypical Mycobacteria (opportunistic, environmental, commensal):
    • M. scrofulaceum: chronic cervical lymphadenitis in children (scrofula)
    • M. kansasii: TB-like disease
    • MAC: TB-like, especially in AIDS
    • M. fortuitum: injection site infections in drug abusers
    • M. chelonae: skin, soft tissue, bone, prosthetic joint infections
    • M. marinum: swimming pool granuloma
13 · SpirochetesTreponema T. pallidumFamily Treponemataceae; extremely thin, very long, spiral / corkscrew-shaped; outer sheath encloses endoflagella (axial fibrils) around protoplasmic cylinder
  • Spirochete morphology; not cultivable on standard media (relies on microscopy + serology)
 —
  • Outer membrane proteins: adherence to host cell surface
  • Hyaluronidase: facilitates perivascular infiltration
  • Specimens: serous exudate from chancre, maculopapular rash, condylomata lata; serum
  • Visualization:
    • Dark-ground microscopy: tiny helical organism, characteristic slow corkscrew motion
    • Silver impregnation (Fontana): dark brown against yellow
    • Direct IF using fluorescein-labeled anti-treponemal Abs
  • PCR in clinical material
  • Serologic Tests for Syphilis (STS):
    • Non-specific (treponemal): detect Abs vs non-specific cardiolipin + lecithin Ags (released by infection damage); usable on CSF
      • VDRL, RPR, ART
      • False positives: 1% adults, pregnancy, infectious mononucleosis, viral hepatitis, vaccinations, collagen-vascular dz
    • Specific (treponemal): detect Abs vs spirochete itself; confirmatory; remain positive for life even after treatment
      • FTA-ABS (Fluorescent Treponemal Antibody absorption)
      • MHA-TP: sheep RBC coated with T. pallidum extract → agglutination
  • Penicillin
  • Tetracycline or erythromycin if Pen-allergic
 Acquired syphilis — STD; also direct contact (HCW), fresh blood transfusion, transplacental
  • Primary (2–10 wks): nontender "chancre", clean indurated base at entry site; contagious; heals spontaneously 3–6 wks; dark-field/IF of lesion; 50% serology negative
  • Secondary (1–3 mo later):
    • Maculopapular copper-colored rash, diffuse, includes palms & soles; patchy alopecia
    • Condylomata lata: flat wart-like perianal + mucous membrane lesions; highly contagious
    • Syphilitic meningitis, chorioretinitis, hepatitis, nephritis (immune complex), periostitis
    • Both serologies positive
  • Latent: no clinical; serology positive
  • Tertiary (30% untreated, years): gummas (syphilitic granulomas), aortitis, CNS inflammation, cardiovascular lesions; specific serology +, non-specific may be −
  • Congenital: abortion, stillbirth, or live with congenital syphilis: interstitial keratitis, Hutchinson's teeth, saddle nose, periostitis, CNS anomalies; serology reverts negative within 3 mo if uninfected
13 · SpirochetesBorrelia B. burgdorferi (Lyme)
B. recurrentis (epidemic relapsing fever)
B. duttoni (endemic relapsing fever)Also implicated in ANUG (Vincent's angina) — polymicrobial with Prevotella, Fusobacterium, Treponema
  • Spirochete morphology (axial fibrils as in Treponema)
 — — (not specifically detailed) Lyme
  • If ECM present: biopsy from leading edge cultured for B. burgdorferi
  • Serology: anti-B. burgdorferi Abs by ELISA + Western immunoblot
Relapsing fever
  • Febrile stage: blood films stained with Leishman or Giemsa → large numbers of spirochetes
  • Afebrile stage: blood films negative → IP injection of white mice; tail blood films 2–4 d later for stained spirochetes
  • DNA probes
  • Tetracyclines and penicillin (both diseases)
 Lyme disease (B. burgdorferi)
  • Reservoir: rodents (mice) and deer
  • Transmission: bite of nymphs + adult tick
  • Invades skin → blood → heart, joints, CNS
  • Arthritis caused by immune complex
  • Erythema chronicum migrans (ECM): annular skin lesion at bite site, erythematous leading edge + central clearing — "bull's eye"; fever, chills, muscle pain, headache
  • Weeks later: myocarditis + neurologic manifestations
  • Late (months/years): arthralgias, migrating arthritis
Relapsing fever
  • Lice/ticks infected by feeding during bacteremia
  • IP 3–10d; sudden fever ~4d → afebrile 3–10d → next bout; 3–10 relapses
  • Abs appear in febrile stage → terminate attack
  • Epidemic (European): B. recurrentis; lice; crushing louse into bite wound; human reservoir; longer fever, fewer relapses
  • Endemic (African): B. duttoni + other Borrelia; tick bite; reservoir B. duttoni = human, others = rodents; shorter fever, more relapses
ANUG (Vincent's angina)
  • Necrosis + ulceration of interdental papillae/gingiva, pseudomembrane formation; painful bright red gingiva that bleeds on gentle manipulation
  • Polymicrobial: anaerobes (Prevotella intermedia, Fusobacterium) + spirochetes (Borrelia, Treponema)
  • Higher prevalence with immunocompromise (HIV)
13 · SpirochetesLeptospira L. interrogans (incl. L. icterohaemorrhagiae serogroup)Zoonosis
  • Spirochete morphology
  • Culture on Fletcher's or Stuart's medium at 30°C
 — —
  • Specimens: blood (during fever), CSF, urine (from week 2)
  • Serology: agglutination test + ELISA — Abs appear week 2
  • Culture: Fletcher's / Stuart's at 30°C
  • Microscopy of blood/urine deposit films: dark-ground or stained (insensitive)
  • Penicillin and tetracyclines
  • Reservoir: wild + domestic animals (rats, dogs, field mice)
  • Transmission: contact with animal urine in water → mucous membranes or breaks in epidermis
  • Occupational: sewage workers, miners, farmers, fishermen
  • Disease: Weil's disease in man — fever × few days → jaundice + hemorrhages + renal failure; severe cases complicated by meningitis
  • Organism in blood during fever; urine from week 2
14 · MycoplasmaMycoplasma M. pneumoniae (Eaton agent)
M. hominis
U. urealyticum
M. genitalium~60 species; spread by direct contact + fresh respiratory droplets
  • Smallest extracellular bacteria
  • No rigid cell wall — bounded by triple-layered "unit membrane" containing sterols
  • Stain poorly with Gram
  • Completely resistant to penicillin (no cell wall target)
  • Highly pleomorphic
  • Reproduce in cell-free media; differ from viruses (have both DNA and RNA; grow in cell-free media)
  • Pass through 450-nm pore filters (Chlamydia/virus comparable)
  • Fastidious + slow growers → diagnosis usually serological / PCR
  • Facultative anaerobes
  • Better growth in 10% CO₂
  • ≥1 wk for visible colonies → "fried-egg appearance" (center embedded beneath agar surface)
  • Induce cold agglutinins: autoantibodies agglutinating O-group RBC at 4°C after 1–2 wks of disease; titer >1/128 = positive; positive in 50% (also viral infections, malaria, acquired hemolytic anemia)
 — —
  • Specimens: sputum, nasopharyngeal aspirate
  • Smears: Giemsa
  • Culture: special media + serum/sterols, 10% CO₂; ≥1 wk for fried-egg colonies
  • Direct: IF for Ag; PCR / DNA probes for specific nucleotide
  • Serology = most useful:
    • IgM or rising IgG by ELISA or CFT
    • Cold agglutinin ≥1/128 indicates recent infection
  • Sputum isolation: difficult + time consuming
  • Tetracyclines
  • Macrolides (erythromycin or azithromycin)
  • M. pneumoniae: atypical pneumonia; associated with joint + other infections
  • M. hominis: sometimes postpartum fever; uterine tube infections (with other bacteria)
  • U. urealyticum: nongonococcal urethritis in men; lung disease in low-birth-weight premature infants
  • M. genitalium: closely related to M. pneumoniae; urethral + other infections
15 · RickettsiaRickettsia & Coxiella Typhus: R. prowazekii, R. typhi, O. tsutsugamushi
Spotted: R. rickettsii, R. akari
Coxiella burnetiiGenus of non-motile GN, non-sporing, highly pleomorphic (cocci/rods/threads); obligate intracellular parasites
  • Non-motile, GN, non-sporing, highly pleomorphic (cocci, rods, thread-like)
  • Obligate intracellular parasites — cannot live in artificial nutrient environments
  • Majority susceptible to tetracyclines
  • Coxiella burnetii: unique endospore-like structure → resistant to heat, UV, drying; extracellular survival; non-arthropod transmission; aerosolization
  • Coxiella burnetii:
    • Phase I antigen: LPS + complex carbohydrates; infectious; antigenic variation; isolated from nature
    • Phase II antigen: exposed surface protein; avirulent
  • Weil-Felix cross-reactivity with P. vulgaris OX strains (utilized for serodiagnosis)
  • Coxiella endospore-like structure (resistant; survives extracellular; aerosol-borne); ability to cause pneumonia if spores inhaled
  • Vasculitis-causing intracellular multiplication in endothelial cells of small blood vessels (typhus & spotted fevers)
  • Initial diagnosis is clinical — do NOT delay treatment
  • Serology: Abs detectable only in later stages; IFA, CF, ELISA; 4-fold rise diagnostic
  • R. rickettsii: Direct IFA of organism in tissue
  • Brill-Zinsser: rapid early IgG rise specific to R. prowazekii (vs IgM in primary)
  • Coxiella:
    • Isolation by primary guinea pig inoculation + subsequent yolk sac cultures
    • Serology: agglutination, indirect IF, CFT using Coxiella antigens
    • Phase I Abs (chronic) vs Phase I+II (acute)
  • Tetracycline (doxycycline)
  • Chloramphenicol
  • R. rickettsii: doxycycline
  • Coxiella / Q fever: doxycycline DOC
Vaccines
  • Epidemic typhus: formalin-killed R. prowazekii vaccine (useful in military during war-time)
  • Endemic typhus: live "Strain E" vaccine
  • Q fever: formalin-killed Coxiella vaccine for high-risk (vets, shepherds, abattoir workers, exposed lab personnel)
Control
  • Sanitation + eradication of human lice (epidemic typhus)
  • Control flea + rat populations; rat-proof buildings (endemic typhus)
  • Tick-bite protection + prompt eradication (RMSF)
  • Pasteurization >60°C for Coxiella spores
 Typhus group
  • Epidemic typhus (R. prowazekii): human reservoir; body louse — infection by louse feces contaminating bite; abrupt fever + headache; centrifugal rash from upper trunk → entire body; DIC + vascular occlusion; death from circulatory/renal failure
  • Brill-Zinsser: latent R. prowazekii reactivation in recovered patients without antibiotic therapy; usually mild, no rash (pre-existing Abs); untreated patient serves as reservoir between epidemics
  • Endemic typhus (R. typhi): rat reservoir; rat flea; resembles epidemic typhus but much milder, low mortality, not epidemic
  • Scrub typhus (O. tsutsugamushi): rodent reservoir; bite of mite larvae (chiggers); fever, headache, muscle pain, cough, GI symptoms; maculopapular rash, eschar, splenomegaly, lymphadenopathies; more virulent strains → hemorrhage + IVC
Spotted fever group
  • Rocky Mountain spotted fever (R. rickettsii): reservoir = rodents + dogs; Dog Tick or Rocky Mountain Wood Tick (ticks = natural hosts as reservoirs + vectors); vasculitis in brain, liver, skin, lungs, kidney, GIT; headache, fever, malaise, vomiting, confusion; rash maculopapular → petechial — starts on ankles + wrists → trunk, palms, soles, face (centripetal); CNS, DIC, circulatory collapse in severe
  • Rickettsial pox (R. akari): house mice reservoir; bite of mite living on mice; mild illness: fever + headache + vesicular rash
Coxiella burnetii / Q fever
  • Spores grow in tick → transmits to goat, sheep, cattle during bites; spores survive in dried tick feces on cattle hide + in dried cow placentas; aerosolized → human disease on inhalation
  • Transmission routes: inhalation of contaminated dust; handling infected animals/discharges; consumption of milk from infected animals
  • Q fever: febrile, influenza-like, pneumonia with granulomatous hepatitis, NO rash; Abs to phase I + II
  • Chronic Q fever: subacute infective endocarditis, fever, fatigue, dyspnea; Abs to phase I
16 · ChlamydiaChlamydiaceae C. trachomatis (15+ serotypes — A, B, Ba, C, D–K, L1, L2, L3)
Chlamydophila psittaci
Chlamydophila pneumoniaeObligate intracellular bacteria — "energy parasites" (need host ATP); 250–400 nm; classified GN but NO peptidoglycan / muramic acid
  • Obligate intracellular
  • 250–400 nm
  • Classified GN but lack peptidoglycan + muramic acid
  • Two forms in life cycle:
    • Elementary body (EB): metabolically inert, small (~300 nm), round, infectious; extensive disulfide cross-linkages stabilize extracellular existence; high affinity for host columnar epithelium (conjunctiva, cervix, respiratory tract) — enter via endocytosis
    • Initial/Reticulate body (RB): inhibits phagosome-lysosome fusion; grows to 1000 nm; divides by binary fission; differentiates back into EBs forming cytoplasmic inclusion bodies; host cell liberates by extrusion or lysis
  • Group-specific LPS
  • Strain-specific outer membrane proteins
  • C. trachomatis: ≥15 serotypes (A, B, Ba, C, D thru K, L1, L2, L3)
 — (intracellular; relies on host machinery)
  • Specimens: conjunctival, urethral discharge, cervical scraping, sputum, pus, etc.
  • Cytoplasmic inclusion bodies: Giemsa, iodine, or fluorescent antibody-stained scrapings
  • Chlamydial Ag by ELISA or IF (group LPS / strain OMPs)
  • Chlamydia nucleic acids by probes or PCR
  • Cell culture isolation:
    • McCoy cells for C. trachomatis + C. psittaci
    • HEP-2 cells for C. pneumoniae
    • Detection of inclusion bodies by iodine stain
  • Serology: cannot distinguish current vs past; IgM or 4-fold IgG rise diagnostic for psittaci/pneumoniae
  • Tetracycline and erythromycin
  • STD: doxycycline or azithromycin; treat patients + sexual partners; safe sexual practices
  • C. psittaci: quarantine imported birds; antibiotic-supplemented feed for bird infection control
 C. trachomatis (human only)
  • Serotypes A, B, Ba, C → Trachoma: chronic keratoconjunctivitis; leading cause of preventable infectious blindness; disease of poverty; acute follicular conjunctivitis → conjunctival scarring → inturned eye lashes → corneal scarring + blindness; transmission by droplets, hands, contaminated clothes, flies
  • Serotypes D–K:
    • Genital STI: males — NGU + epididymitis; females — cervicitis, salpingitis, PID → infertility + ectopic pregnancy
    • Inclusion conjunctivitis: purulent discharge, no scarring or corneal involvement; adult (fingers) or neonate (birth canal)
    • Neonatal pneumonia: birth canal acquisition
    • Respiratory tract infections: adults with inclusion conjunctivitis may develop otitis media / pharyngitis / nasal obstruction via nasolacrimal duct drainage
  • Serotypes L1, L2, L3 → Lymphogranuloma venereum (LGV): STD; painless papule/ulcer on external genitals → migrate to inguinal regional LN → enlarge, tender, suppurate; pus drains through overlying skin; healing by scar formation → stricture + lymphatic obstruction → genital elephantiasis
Chlamydophila psittaci
  • Infects >130 species of birds including pet parrots → psittacosis (bird fever)
  • Birds shed in respiratory secretions + faeces
  • Humans: inhale dust from feathers/dried feces → atypical pneumonia
  • High risk: veterinarians, poultry workers, zoo keepers, pet shop workers
Chlamydophila pneumoniae
  • Human-only; person-to-person via respiratory route; atypical pneumonia
  • Potentially associated with atherosclerosis of coronary artery + cerebrovascular disease