Bacteriology Hub — Zagazig University

Bacteriology Hub Zagazig University · Medical Microbiology & Immunology · 2013

Category	Organism	Biochemical Reactions	Antigenic Structure	Virulence Factors	Diagnosis	Treatment	Special 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 Providencia rettgeriGN pleomorphic, motile, non-sporing bacilli; soil, sewage, feces	Simple & enriched media; concentric wavy "swarming" growth Non-lactose fermenters Urease positive	P. vulgaris OX-10, OX-2, OX-K: share antigenic similarity with Rickettsiae → Weil-Felix reaction	—	Isolation by morphology, swarming, biochem (urease)	According to AST — resistant to many antimicrobials	Diseases: UTI, wound infection, otitis media Weil-Felix reaction = key principle for rickettsial serodiagnosis
4 · EnterobacteriaceaeSalmonella	S. typhi (Gp D) S. paratyphi A/B/C S. typhimurium S. enteritidis S. choleraesuisGN bacilli, motile, non-capsulated (S. typhi carriers acquire Vi antigen)	MacConkey: pale yellow, NLF Glucose, maltose, mannitol → acid only (S. typhi), acid + gas (S. paratyphi) H₂S + in S. typhi & S. paratyphi B & C Indole − and urease −	O (somatic), H (flagellar), Vi (capsular)	Pili: host-cell adherence Two pathogenicity islands; contact secretion system Facultative intracellular in macrophages Vi antigen: retards PMN phagocytosis	Wk 1: blood + bone marrow culture; Wk 2+: stool + urine culture Serology: Widal — 4-fold rise diagnostic; ≥1/160 in Egypt Carriers: high anti-Vi titer	Chloramphenicol, ampicillin, TMP-SMX, FQs, 3rd-gen cephalosporins Carriers: ampicillin, TMP-SMX, ciprofloxacin ± cholecystectomy	Enteric fever: endemic Egypt; M cells → Peyer's patches → bacteremia → secondary bacteremia + fever; gallbladder stones favor carriage Food poisoning (S. typhimurium): IP 12–48h; no blood invasion
4 · EnterobacteriaceaeShigella	S. dysenteriae (Gp A) S. flexneri (Gp B) S. boydii (Gp C) S. sonnei (Gp D)GN bacilli, non-motile, non-capsulated; strict human pathogens	MacConkey/DCA: pale yellow NLF S. sonnei: late lactose fermenter Anaerogenic; H₂S − and urease −	Lacks H antigen; 4 serogroups by O antigen	Invasiveness: large plasmid; contact secretion system Shiga exotoxin (S. dysenteriae type I): enterotoxic, cytotoxic, neurotoxic Endotoxin (LPS)	Stool (blood + mucus); selenite broth → MacConkey/DCA Latex agglutination	Fluid & electrolyte replacement Ampicillin, ciprofloxacin, 3rd-gen cephalosporins	Infectious dose ~100 organisms; "4 Fs": flies, feces, fingers, food Dysentery triad: cramps, tenesmus, bloody mucoid stools
5 · Non-ferm GNBPseudomonas	P. aeruginosaAerobic, non-spore-forming, motile, non-fermentative GN bacilli; ubiquitous in moist hospital environments	Non-fermentative; oxidase + and catalase + Grows at 42°C Diffusible exopigments: pyoverdin + pyocyanin → bright green Grape-like odor	—	Pili, flagella; Endotoxin; Biofilm formation Exotoxin A: ADP-ribosylates EF-2 (like DT) Elastase & phospholipase; Exoenzyme S	Culture readily; ID by morphology + pigment + biochem Bacteriophage typing for epidemiology	Multi-resistant → in-vitro testing required Serious infections: β-lactam + aminoglycoside	Community: folliculitis, swimmer's ear, corneal ulcer (contact lens), osteomyelitis (IVDU) Nosocomial: ICU respiratory, UTI, wound, CF chronic lung infection
5 · Non-ferm GNBAcinetobacter	A. baumanniiWidely distributed in soil/water; hospital environment	GN coccobacilli; oxidase NEGATIVE — differentiates from Neisseria/Moraxella	—	—	Mistaken for N. meningitidis — oxidase NEGATIVE distinguishes	Often multi-resistant; susceptibility testing required	Nosocomial pneumonia (most common); bacteremia from IV catheters
5 · Non-ferm GNBMoraxella	M. catarrhalis M. lacunata	GN bacilli/coccobacilli; non-motile, non-fermentative Oxidase + and DNase +	—	M. catarrhalis: β-lactamase producer	Distinguished from Neisseria by DNase positivity	Penicillin EXCEPT M. catarrhalis (β-lactamase)	M. catarrhalis: otitis media + LRT infection M. lacunata: angular conjunctivitis + blepharitis
6 · Curved GNBVibrios	V. cholerae O1 & O139 V. parahaemolyticus V. vulnificusComma-shaped GN rods; saprophytes in surface water and soil	Comma-shaped; single polar flagellum, darting motility Alkaline pH 8.5–9.5; TCBS: V. cholerae yellow; V. parahaemolyticus green Oxidase +, indole + Cholera red reaction +; String test +	O1: Ogawa, Inaba, Hikojima; biotypes Classical & El Tor O1 & O139 → epidemic cholera	TCP: colonization pilus Cholera toxin (CT): phage-encoded; activates adenylate cyclase → ↑cAMP → massive Cl⁻/Na⁺/water secretion Mucinase	Rice-water stools → alkaline peptone water → TCBS Agglutination with anti-O1 and anti-O139 sera; PCR for CT gene	IV fluids — most important Tetracycline (shortens excretion)	IP 1–4d; rice-water diarrhea; up to 20 L/day fluid loss V. parahaemolyticus: gastroenteritis from seafood; TCBS green
6 · Curved GNBCampylobacter	C. jejuni (95%) C. coli C. fetusSpiral, motile, GN, microaerophilic	Comma-, S-, gull-wing-shaped; microaerophilic + capnophilic Thermophilic — 42°C optimal Skirrow's medium; oxidase + catalase +; urease NEGATIVE	—	Invasiveness; enterotoxin; CDT	Stool; Skirrow's at 42°C × 2–4d; 1% basic fuchsin stain	Erythromycin or ciprofloxacin (severe)	Zoonotic; unpasteurized milk, poultry Complications: Guillain-Barré syndrome, reactive arthritis
6 · Curved GNBHelicobacter	H. pyloriMultiple polar SHEATHED flagella	Similar to Campylobacter but Skirrow's at 37°C, 1 week Urease POSITIVE — key difference from Campylobacter	—	Urease; Adhesins; VacA; CagA	Invasive: rapid urease test, histology, culture Non-invasive: urea breath test, stool ELISA, PCR, serology	Triple therapy: metronidazole + bismuth + amoxicillin/tetracycline × 14d Alternative: PPI + amoxicillin + clarithromycin/metronidazole × 1 wk	>50% world population colonized Peptic ulcer, chronic gastritis, MALT lymphoma, gastric adenocarcinoma
7 · Fastidious GNBHaemophilus	H. influenzae (Hib most pathogenic) H. ducreyi H. aegyptius H. parainfluenzae	Need factor X (hemin) + factor V (NAD) → chocolate agar Satellite phenomenon around S. aureus Catalase + and oxidase +	Types a–f; Hib most pathogenic; most normal-flora strains non-typable	IgA protease; PRP capsule (Hib); OMP + LPS	Chocolate agar 37°C 5% CO₂; satellite phenomenon Latex agglutination (LAT) for type-b PS in CSF PCR most sensitive	Cefotaxime or ceftriaxone Meningitis: steroids 15–20 min before antibiotic H. ducreyi: macrolide + ceftriaxone	Hib: meningitis, acute epiglottitis, septic arthritis, cellulitis (5 mo to 5 y) H. ducreyi: chancroid — painful genital ulcer; increases HIV risk H. aegyptius: purulent conjunctivitis + Brazilian purpuric fever
7 · Fastidious GNBBordetella	B. pertussis B. parapertussis	Bordet-Gengou or charcoal blood agar; "mercury drop" colonies	—	PT; AC toxin; TCT; FHA + pertactin (adhesion)	Saline nasal wash; direct IF; PCR most sensitive	Erythromycin DOC DTaP vaccine	Phases: catarrhal (infectious) → paroxysmal (whoop + vomiting + cyanosis) Complications: pneumonia, cerebral hemorrhage
7 · Fastidious GNBBrucella	Br. melitensis (most virulent) Br. abortus (needs 8–10% CO₂) Br. suis Br. canis	GN short coccobacilli; slow growers (blood cultures 1 month) BSC required; catalase + oxidase +; urease +	2 LPS antigens A and M; immunity mainly cell-mediated	Facultative intracellular parasite; LPS endotoxic; L antigen	Blood cultures (repeated); STAT ≥1/100; prozone avoided by dilutions; Coombs for blocking IgA; ELISA; PCR	Tetracycline + (streptomycin OR rifampicin) No human vaccine; pasteurization	Undulant fever; endemic Egypt; transmission: intestinal, mucous membranes, skin Localize in reproductive organs → sterility & abortion in animals
7 · Fastidious GNBFrancisella	F. tularensis	GN coccobacillus; modified Thayer-Martin agar	—	—	Strict lab precautions (highly infectious)	Streptomycin or gentamicin × 10d; live attenuated vaccine for lab workers	Reservoir: rabbits, rodents; ticks; tularemia; dangerous bioweapon
8 · Yersinia / PasteurellaYersinia	Y. pestis (plague) Y. enterocolitica Y. pseudotuberculosis	Y. pestis: NLF; bipolar staining; non-motile; better at 27–30°C Y. enterocolitica: urease +, motile at 25°C, non-motile at 37°C; cold enrichment	F1 capsular antigen; V-W antigens (virulent strains)	LPS; F1 antigen; V-W antigens; YOPs (inhibit phagocytosis); exotoxin	Y. pestis: DFA; PCR; culture at 27–30°C; BSC always Y. enterocolitica: cold enrichment → MacConkey at 25°C	Y. pestis: ciprofloxacin, doxycycline, gentamicin; formalin-killed vaccine Yersiniosis: doxycycline + aminoglycoside	Plague: bubonic/septicemic/pneumonic; rat-flea cycle; bioterrorism agent Y. enterocolitica: children; may mimic appendicitis
8 · Yersinia / PasteurellaPasteurella	P. multocida	Non-motile GN coccobacilli with bipolar staining; oxidase + catalase +	—	—	Standard culture from wound discharges	—	Most common organism in cat/dog bites or scratches; cellulitis, osteomyelitis, arthritis
10 · AnaerobesBacteroides	B. fragilisPredominant anaerobe in human colon	Slim, pale-staining, capsulated GN rods; strict anaerobe	—	Superoxide dismutase; polysaccharide capsule → abscess formation; LPS less toxic; collagenase, fibrinolysin, heparinase	Anaerobic culture	Drainage + debridement; almost always β-lactamase producers Clindamycin, metronidazole; imipenem; clavulanate/sulbactam combinations	Endogenous from patient's own gut; peritonitis + intra-abdominal abscess Spreads to blood more than any other anaerobe
10 · Anaerobes / ActinomycetesActinomycetes	Actinomyces israelii (anaerobic) Nocardia asteroides (aerobic) Streptomyces Actinomadura madurae	Aerobic species: partially acid-fast, beaded branching filaments Anaerobic species (Actinomyces): GP branching filaments; anaerobic culture × 2 weeks	—	—	Actinomycosis: sulfur granules; GP branching filaments + radiating GN clubs Nocardia: GP, partially acid fast	Actinomycosis: surgical drainage + penicillin G 6–12 mo Nocardiosis: TMP-SMX	Actinomycosis: cervicofacial, thoracic, abdominal forms; sulfur granules in pus Nocardiosis: frequently misdiagnosed as TB; brain abscess Mycetoma: swelling + sinuses draining granules; feet of farmers without shoes
11 · Atypical GNBLegionella	L. pneumophila	Fastidious aerobic GN; poorly stained with Gram; BCYE agar	—	Inhibition of phagosome-lysosome fusion; C3b coating	BCYE aerobic; urinary antigen by ELISA (fastest); PCR; serology	Macrolides or fluoroquinolones Prevention: hyperchlorination + heating of water supplies	No person-to-person spread; aerosols from A/C + shower heads Legionnaire's disease (pneumonia) vs Pontiac fever (mild flu)
11 · Minor pathogensBartonella	B. bacilliformis B. quintana B. henselae	Small GN, polymorphic, motile bacilli	—	—	—	B. bacilliformis: penicillin, streptomycin, chloramphenicol B. henselae: supportive ± tetracycline/erythromycin	B. bacilliformis: Oroya fever (sand flies) B. quintana: Trench fever (body lice) B. henselae: Cat-scratch disease (2 wk post-scratch)
11 · Minor pathogensGardnerella	G. vaginalis	Gram variable coccobacilli	—	—	"Whiff" test (KOH → fishy odor); clue cells; vaginal pH ≥ 4.5	Metronidazole DOC	Bacterial vaginosis; premature rupture of membranes, preterm labor
12 · MycobacteriaMycobacterium	M. tuberculosis + M. bovis (MTC) M. leprae Atypicals: MAC, M. kansasii, M. scrofulaceum, M. marinum, M. fortuitum	Acid fastness due to mycolic acids M. tb: resists 25% H₂SO₄; M. leprae: 5% H₂SO₄ Slow growers; obligate aerobes Lowenstein-Jensen, Middlebrook 7H10/7H9, BACTEC Never reported negative before 8 wks	—	Glycolipids → granuloma formation; intracellular survival No exotoxin, no endotoxin	ZN + auramine stain; culture = gold standard; PCR Latent: Mantoux ≥10 mm or IGRA (not affected by BCG) M. leprae: NOT culturable; lepromin test	TB: INH + RIF + PZA + EMB/SM × 6–12 mo MDR-TB: resistant ≥ INH + RIF; XDR-TB: MDR + FQ + ≥3 second-line Leprosy: dapsone + rifampicin × 2 years BCG: first year of life; also for bladder carcinoma	1/3 world infected; 90% destroy; 10% active disease Primary (Ghon's) → secondary (reactivation: upper lobes, cavitation, miliary) Lepromatous (leonine facies, lepromin −) vs Tuberculoid (anesthesia, lepromin +)
13 · SpirochetesTreponema	T. pallidum	Not cultivable; microscopy + serology only	—	Outer membrane proteins (adherence); hyaluronidase	Dark-ground microscopy; Silver (Fontana); Direct IF; PCR Non-specific STS: VDRL, RPR; Specific: FTA-ABS, MHA-TP (remain + for life)	Penicillin; tetracycline/erythromycin if allergic	Primary: nontender chancre (50% serology negative) Secondary: maculopapular rash incl. palms/soles, condylomata lata Tertiary: gummas, aortitis, CNS Congenital: Hutchinson's teeth, saddle nose, interstitial keratitis
13 · SpirochetesBorrelia	B. burgdorferi (Lyme) B. recurrentis (epidemic RF) B. duttoni (endemic RF)	Spirochete morphology	—	—	Lyme: ELISA + Western immunoblot Relapsing fever: Leishman/Giemsa blood films; mouse inoculation in afebrile phase	Tetracyclines and penicillin	Lyme: "bull's eye" ECM; myocarditis; arthritis (immune complex) Epidemic RF (lice, B. recurrentis, human reservoir) vs Endemic RF (tick bite) ANUG (Vincent's): polymicrobial, immunocompromise (HIV)
13 · SpirochetesLeptospira	L. interrogans	Culture on Fletcher's or Stuart's medium at 30°C	—	—	Blood (during fever), urine (from week 2) Serology: agglutination + ELISA from week 2	Penicillin and tetracyclines	Reservoir: rats; contact with animal urine in water Weil's disease: jaundice + hemorrhages + renal failure ± meningitis Occupational: sewage workers, farmers, fishermen
14 · MycoplasmaMycoplasma	M. pneumoniae M. hominis U. urealyticum M. genitalium	No rigid cell wall (sterols in membrane); completely resistant to penicillin Fried-egg colonies ≥1 wk Cold agglutinins: titer >1/128 positive (50%)	—	—	Serology most useful: IgM or rising IgG (ELISA/CFT); cold agglutinin ≥1/128 IF for Ag; PCR/DNA probes	Tetracyclines or macrolides	M. pneumoniae: atypical pneumonia U. urealyticum: NGU; lung disease in low-birth-weight premature infants
15 · RickettsiaRickettsia & Coxiella	Typhus: R. prowazekii, R. typhi, O. tsutsugamushi Spotted: R. rickettsii, R. akari Coxiella burnetii	Non-motile GN; obligate intracellular Coxiella: endospore-like structure → heat/UV/drying resistant	Coxiella: Phase I (infectious, nature) vs Phase II (avirulent) Weil-Felix cross-reactivity with P. vulgaris OX strains	Vasculitis via intracellular multiplication in endothelial cells	Initial diagnosis clinical — do NOT delay treatment IFA, CF, ELISA; 4-fold rise diagnostic Brill-Zinsser: rapid early IgG (vs IgM in primary typhus)	Doxycycline DOC; chloramphenicol	Epidemic typhus (lice, human reservoir); centrifugal rash; Brill-Zinsser = latent reactivation Endemic typhus (rat flea); RMSF: centripetal rash (ankles/wrists → trunk/face) Q fever: pneumonia + granulomatous hepatitis, NO rash; chronic → endocarditis
16 · ChlamydiaChlamydiaceae	C. trachomatis (A–C, D–K, L1–L3) C. psittaci C. pneumoniae	Obligate intracellular; 250–400 nm; no peptidoglycan EB (infectious, extracellular) → RB (replicating, intracellular) → EB McCoy cells (trachomatis/psittaci); HEP-2 cells (pneumoniae)	Group-specific LPS; strain-specific OMPs; ≥15 serotypes	—	Cytoplasmic inclusion bodies: Giemsa, iodine, fluorescent Ab stain Ag by ELISA or IF; PCR; cell culture with iodine stain for inclusion bodies	Tetracycline or erythromycin STD: doxycycline or azithromycin; treat partners C. psittaci: quarantine imported birds	A–C: Trachoma (leading preventable infectious blindness) D–K: NGU, PID, inclusion conjunctivitis, neonatal pneumonia L1–L3: LGV → genital elephantiasis C. psittaci: psittacosis (pet parrots), atypical pneumonia C. pneumoniae: atypical pneumonia; possibly associated with atherosclerosis