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MICROBIOLOGY - COMPREHENSIVE STUDY NOTES

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SECTION 1: GENERAL MICROBIOLOGY

Microscopes

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Stains

Gram Stain (most important in bacteriology)

1. Crystal violet (primary stain) - all cells stain purple
2. Iodine (mordant) - fixes dye to cell wall
3. Acetone/alcohol (decolorizer) - washes out Gram-negative organisms
4. Safranin (counterstain) - Gram-negative organisms appear pink/red

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Acid-Fast Stain (Ziehl-Neelsen Stain)

1. Carbol fuchsin (primary stain, with heat) - all bacteria stain red
2. Acid-alcohol (decolorizer) - removes stain from non-acid-fast organisms
3. Methylene blue (counterstain) - non-acid-fast bacteria stain blue

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Albert's Stain

1. Albert's stain I (toluidine blue + malachite green) - applied 3-5 min
2. Albert's stain II (iodine solution) - applied 1 min

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Bipolar Staining (Safety Pin Appearance)

• Organism: Yersinia pestis (Plague), Klebsiella
• Stain: Wayson's stain or Giemsa
• Result: Bipolar staining gives appearance of closed safety pin

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Negative Stain (India Ink / Nigrosin)

• Used for: Capsule demonstration
• Organisms: Cryptococcus neoformans (India ink in CSF - capsule appears as clear halo), Klebsiella, Bacillus anthracis
• Principle: Background stains black; capsule repels dye and appears as clear zone around organism

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Methylene Blue Stain

• Uses:
  • Loeffler's methylene blue: Demonstrates metachromatic granules in C. diphtheriae
  • Counterstain in Ziehl-Neelsen stain
  • Albert's stain component
  • Demonstrates "bipolar" appearance in Yersinia pestis

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Bacterial Growth Curve

     ┌─────────────────────────────────────────────────┐
     │         BACTERIAL GROWTH CURVE                  │
     │                                                 │
     │                    Stationary                   │
     │              ╭─────────────╮                    │
     │            ╱               ╲                    │
     │          ╱     Log/         ╲  Decline/         │
     │        ╱     Exponential     ╲  Death           │
     │      ╱         Phase          ╲                 │
     │   ╭──   Lag phase                               │
     └─────────────────────────────────────────────────┘

• E. coli: ~20 min (fastest)
• Mycobacterium tuberculosis: ~18-24 hours (slowest - clinically important)

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Bacterial Genetics

Types of Gene Transfer

Types of Mutations

DNA Repair Mechanisms

1. Direct repair - enzymatic removal of damaged bases (e.g., photolyase for pyrimidine dimers)
2. Excision repair - cut out and replace damaged segment
3. Mismatch repair - corrects polymerase errors
4. Recombination repair (post-replication repair)
5. SOS repair - error-prone repair as last resort; induces mutagenesis

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Sterilization & Disinfection

Key Definitions

• Sterilization: Destruction of ALL microbial forms, including bacterial spores
• Disinfection: Destroys most microbes; spores may survive; divided into high-, intermediate-, low-level
• Antisepsis: Chemical agents applied to living tissue
• Germicide: Chemical that kills microbes

Methods of Sterilization

Levels of Disinfection

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SECTION 2: IMMUNOLOGY

Innate vs. Acquired Immunity

Cells of Innate Immunity

• Neutrophils: First responders; phagocytose and kill via oxidative burst (MPO, NADPH oxidase) and degranulation
• Macrophages: Phagocytosis, antigen presentation, cytokine production (IL-1, IL-6, TNF-α)
• NK cells: Kill virus-infected cells and tumor cells without MHC recognition; "missing self" hypothesis
• Dendritic cells: Bridge innate and adaptive immunity; most potent APCs

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Antigen-Antibody Reactions

Types of Reactions Used in Laboratory

Antibody Classes (Immunoglobulins)

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Complement System

Three Pathways of Activation

• C3b → opsonization (phagocytosis)
• C3a, C5a → anaphylatoxins (inflammation, mast cell degranulation)
• C5b-9 → Membrane Attack Complex (MAC) → cell lysis

• C1q, C2, C4 deficiency → recurrent infections + SLE-like syndrome
• C3 deficiency → most severe; recurrent bacterial infections
• C5-C9 (MAC) deficiency → recurrent Neisseria infections (meningococcal, gonococcal)
• DAF/CD59 deficiency → Paroxysmal nocturnal hemoglobinuria (PNH)

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Immunodeficiency Disorders

Primary (Congenital) Immunodeficiencies

Secondary Immunodeficiencies

• HIV/AIDS (covered under Virology)
• Malnutrition, malignancy, immunosuppressive drugs, asplenia (Strep pneumoniae, H. influenzae, Neisseria - encapsulated bacteria)

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SECTION 3: MYCOLOGY

Classification of Fungal Infections

Superficial mycoses → Outmost keratinized layers only
Cutaneous mycoses → Deeper epidermis, hair, nails
Subcutaneous mycoses → Dermis, subcutaneous tissue
Systemic/Deep mycoses → Internal organs

Superficial Mycoses

Dermatophytes (Tinea / "Ringworm")

• All are keratinophilic and keratinolytic
• Invade only outermost keratinized layers (skin, hair, nails)
• Classified by habitat: geophilic (soil), zoophilic (animals), anthropophilic (humans)

• Wood's lamp: Microsporum fluoresces green
• Culture: T. rubrum - red pigment on reverse

• Localized (no hair/nail): Topical azoles, terbinafine, haloprogin
• Scalp/nails: Oral griseofulvin, itraconazole, fluconazole, terbinafine

Piedra

Pityriasis (Tinea) Versicolor

• Agent: Malassezia furfur complex (lipophilic yeast)
• Presentation: Hypo- or hyperpigmented scaly patches on trunk
• KOH: "Spaghetti and meatballs" appearance (short hyphae + round spores)
• Treatment: Topical selenium sulfide, azoles; oral itraconazole for extensive disease

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Subcutaneous Mycoses

Mycetoma

• Eumycetoma (fungal): Madurella mycetomatis, Pseudallescheria boydii
• Actinomycetoma (bacterial): Nocardia, Actinomadura, Streptomyces
• Triad: Swelling + Sinuses + Discharge of grains (colored granules)
• Foot most common site ("Madura foot")
• Grain color: Black (Madurella), yellow (Nocardia), white/yellow (Actinomadura)

Sporotrichosis

• Agent: Sporothrix schenckii
• Transmission: Traumatic inoculation with thorny plants (rose thorn, sphagnum moss) - "Rose thorn disease"
• Presentation: Lymphocutaneous form (most common) - ulcerating nodule at inoculation site + chain of nodules along lymphatics ("sporotrichoid spread")
• Morphology: Dimorphic fungus - mold in environment (25°C), yeast at body temperature (37°C)
• "Asteroid bodies" in tissue (yeast cells surrounded by radiating Splendore-Hoeppli material)
• Treatment: Itraconazole (drug of choice), potassium iodide (for lymphocutaneous form)

Rhinosporidiosis

• Agent: Rhinosporidium seeberi (now classified as a mesomycete - Mesomycetozoa)
• Presentation: Polyps in nose, nasopharynx; "strawberry polyp" appearance
• Diagnosis: Large sporangia filled with endospores in tissue biopsy
• Common in: South Asia (India, Sri Lanka)
• Treatment: Surgical excision (no reliable antifungal)

Chromoblastomycosis (Chromomycosis)

• Agents: Fonsecaea pedrosoi, Cladophialophora carrionii, Phialophora verrucosa (dematiaceous/black molds)
• Presentation: Warty, cauliflower-like lesions on lower extremities
• Diagnosis: KOH/tissue biopsy shows Muriform (sclerotic/Medlar) bodies = copper-colored cells with cross-septa ("copper pennies")
• Treatment: Itraconazole, terbinafine; cryotherapy for small lesions

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Systemic/Deep Mycoses

Candida

• Species: C. albicans (most common), C. glabrata, C. tropicalis, C. parapsilosis, C. krusei
• Dimorphic: Yeast at 37°C; forms pseudohyphae and true hyphae
• Germ tube test: C. albicans forms germ tube at 37°C in serum within 2-3 hours
• Chlamydoconidia: Terminal thick-walled cells; only C. albicans
• Diseases: Oral thrush, vulvovaginitis, diaper rash, esophageal candidiasis (AIDS-defining), candidemia, invasive candidiasis (neutropenic patients)
• Risk factors: Antibiotics, steroids, immunosuppression, indwelling catheters, diabetes, HIV
• Treatment: Azoles (fluconazole for susceptible), echinocandins (caspofungin) for resistant/invasive, amphotericin B

Cryptococcus

• Species: C. neoformans (serotypes A, D), C. gattii (serotypes B, C)
• Habitat: Pigeon droppings (C. neoformans), eucalyptus trees (C. gattii)
• Capsule: Polysaccharide capsule - virulence factor; inhibits phagocytosis
• India ink stain: Narrow-based budding yeast with large capsule (halo appearance) in CSF
• Disease: Cryptococcal meningitis (AIDS patients with CD4 <100), pneumonia, skin lesions
• Mucicarmine stain: Capsule stains red
• Latex agglutination: Detects cryptococcal antigen in CSF/serum
• Treatment: Amphotericin B + flucytosine (induction), then fluconazole (consolidation/maintenance)

Mucormycosis (Zygomycosis)

• Agents: Rhizopus (most common), Mucor, Absidia, Rhizomucor
• Risk factors: Diabetic ketoacidosis (DKA), hematologic malignancy, neutropenia, iron overload, deferoxamine therapy
• Presentation:
  • Rhinocerebral (most common) - starts as sinusitis, invades orbit and brain; black eschar on palate/nasal mucosa
  • Pulmonary, cutaneous, GI forms
• Pathology: Angioinvasion → thrombosis and infarction → "black necrotic tissue"
• Hyphae: Broad, aseptate (ribbon-like) hyphae branching at right angles (90°)
• Treatment: Amphotericin B + surgical debridement; liposomal amphotericin preferred; posaconazole/isavuconazole as alternatives

Aspergillosis

• Agent: Aspergillus fumigatus (most common), A. flavus, A. niger
• Habitat: Ubiquitous in environment; inhalation of conidia
• Hyphae: Narrow, septate hyphae branching at 45° angles (V-shaped)
• Diseases:

• Galactomannan assay: Detects Aspergillus antigen in serum/BAL
• Treatment: Voriconazole (drug of choice for invasive), isavuconazole, caspofungin; itraconazole for ABPA

PCP (Pneumocystis jirovecii Pneumonia)

• Previously: Pneumocystis carinii (name changed - rat species)
• Classification: Fungus (unique features - lacks ergosterol; has beta-glucan)
• Host: Humans (not from environment - reactivation of latent infection)
• Disease: Pneumonia in immunocompromised (HIV with CD4 <200, transplant, steroids)
• Presentation: Subacute progressive dyspnea, dry cough, fever; bilateral interstitial infiltrates ("ground glass" on CT)
• Diagnosis:
  • BAL or induced sputum: Gomori methenamine silver (GMS) stain - cysts appear as "crushed ping pong balls" / "helmet-shaped"
  • Giemsa - trophozoites
  • Beta-1,3-glucan in serum
• Treatment: TMP-SMX (first line); Pentamidine (alternative); Atovaquone
• Prophylaxis: TMP-SMX when CD4 <200

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SECTION 4: VIROLOGY

RNA vs. DNA Viruses

DNA Viruses (mnemonic: HHAPPP)

RNA Viruses

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Herpes Viruses

• Mechanism: Acyclovir → phosphorylated by viral TK → inhibits viral DNA polymerase (chain terminator)
• Resistance: TK-deficient mutants → use Foscarnet or Cidofovir

• Risk: Mother with primary genital herpes at delivery (highest risk)
• Types: Localized (skin, eye, mouth), disseminated, CNS
• Treatment: IV Acyclovir

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Parvovirus B19

• Only ssDNA virus that is pathogenic to humans
• Receptor: Globoside (blood group P antigen) on erythrocyte precursors
• Diseases:

• Diagnosis: Serology (IgM/IgG), PCR for DNA
• Treatment: No antiviral; IVIG for immunocompromised patients

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Influenza

• Orthomyxovirus: (-) ssRNA, segmented (8 segments), enveloped
• Surface antigens:
  • Hemagglutinin (HA): 18 subtypes; attaches to sialic acid on host cells; target of neutralizing antibodies
  • Neuraminidase (NA): 11 subtypes; cleaves sialic acid (release of new virions); target of oseltamivir/zanamivir
• Types: A (most virulent, pandemic potential), B (epidemics, humans only), C (mild, no pandemics)
• Antigenic variation:
  • Antigenic drift: Point mutations in HA/NA genes; basis of seasonal epidemics; gradual change
  • Antigenic shift: Reassortment of RNA segments between two strains (requires co-infection of host); abrupt change; basis of pandemics (Influenza A only)
• Replication: Nucleus (unique for RNA virus - needs nuclear machinery to transcribe segmented genome)
• Treatment: Oseltamivir (Tamiflu), Zanamivir - neuraminidase inhibitors; Amantadine, Rimantadine - M2 ion channel blockers (Influenza A only, high resistance)
• Prevention: Annual vaccination (reformulated based on predicted strains)

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Rubella

• Togavirus (Rubivirus genus): (+) ssRNA, enveloped
• Transmission: Respiratory droplets
• Primary infection (postnatal rubella):
  • Mild febrile illness; maculopapular rash (starts on face, spreads caudally; fades in 3 days = "3-day measles")
  • Forchheimer spots: Petechiae on soft palate
  • Cervical/post-auricular lymphadenopathy
  • Arthritis (especially in adult women)
• Congenital Rubella Syndrome (CRS) - MOST IMPORTANT:
  • Risk highest in first trimester (80% risk)
  • Classic triad: Cataracts + Sensorineural deafness + Congenital heart disease (PDA, pulmonary artery stenosis)
  • Additional: "Blueberry muffin" baby (dermal erythropoiesis), microcephaly, meningoencephalitis, hepatosplenomegaly, thrombocytopenic purpura, "salt-and-pepper" retinopathy
  • Infants shed virus for months (infectious)
• Diagnosis: IgM/IgG serology, viral culture, PCR
• Prevention: MMR vaccine (live attenuated); contraindicated in pregnancy
• Treatment: Supportive (no antiviral)

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Retroviruses (HIV)

• Family: Retroviridae; (+) ssRNA diploid genome with reverse transcriptase (RNA → DNA)
• HIV Types: HIV-1 (global pandemic), HIV-2 (West Africa, less virulent)
• Structure: Enveloped; Gag (capsid/matrix), Pol (RT, integrase, protease), Env (gp120, gp41)

1. gp120 binds CD4 + CCR5 (R5-tropic) or CXCR4 (X4-tropic) → gp41 mediates membrane fusion
2. RT converts (+) ssRNA → ssDNA → dsDNA (also has RNase H activity to degrade RNA template)
3. Integrase inserts viral DNA into host chromosome (provirus - latent reservoir)
4. Provirus transcribed → viral RNA → mRNA → proteins
5. Protease cleaves Gag-Pol precursor polyprotein → mature virions
6. Budding

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Hepatitis B (VERY IMPORTANT)

Serologic Markers

The "Window Period"

• HBsAg has cleared but Anti-HBs not yet appeared
• Only Anti-HBc IgM is positive = diagnostic of acute HBV
• Patient is still infectious

Serologic Patterns

Natural History

• Incubation: 1-6 months
• Acute infection: 95% adults recover; 5% → chronic
• Neonates infected at birth: 90% → chronic (immature immune system)
• Chronic Hepatitis B → Cirrhosis → HCC (major cause globally)

Complications

• Chronic hepatitis → Cirrhosis
• Hepatocellular carcinoma (HCC) - integrates into host genome
• Fulminant hepatic failure (rare)
• Glomerulonephritis (immune complex deposition)
• Delta virus (HDV): Requires HBsAg envelope; superinfection/coinfection worsens prognosis

Treatment

• Acute: Supportive
• Chronic: Tenofovir, Entecavir (NRTIs for HBV); Pegylated interferon-alpha
• Vaccination: HBsAg subunit vaccine; 3-dose schedule; universal infant vaccination

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SECTION 5: PARASITOLOGY

Amoeba

Entamoeba histolytica

• Transmission: Fecal-oral; contaminated water/food; cysts are infective form
• Morphology: Cysts (4 nuclei; chromatoid bars with rounded ends); Trophozoites (RBC-containing)
• Diseases:
  • Intestinal amoebiasis: Dysentery (bloody diarrhea); "flask-shaped ulcers" in colon
  • Extraintestinal: Amoebic liver abscess ("anchovy sauce" pus; right lobe; odorless)
• Diagnosis: Stool microscopy; serology (liver abscess); ultrasound
• Treatment: Metronidazole (kills trophozoites) + Diloxanide furoate (kills cysts in lumen)

Naegleria fowleri

• Free-living amoeba in warm freshwater (lakes, hot springs)
• Disease: Primary Amoebic Meningoencephalitis (PAM) - acute, rapidly fatal
• Entry: Via nasal mucosa → cribriform plate → olfactory bulb → brain
• Risk: Swimmers in warm freshwater
• CSF: PMN pleocytosis; motile amoeba visible
• Treatment: Amphotericin B (poor prognosis; nearly always fatal)

Acanthamoeba

• Free-living amoeba in soil, water, air
• Diseases:
  • Granulomatous amoebic encephalitis (GAE) - immunocompromised; subacute/chronic
  • Amoebic keratitis - contact lens wearers; painful corneal ulceration
• Treatment: Polyhexamethylene biguanide + propamidine (keratitis); Miltefosine + TMP-SMX (GAE)

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Flagellates

Giardia lamblia (intestinalis/duodenalis)

• Morphology: Trophozoite - pear-shaped with 2 nuclei; 4 pairs of flagella; "falling leaf" motility; ventral sucking disc
• Cysts - 4 nuclei; oval shape
• Transmission: Fecal-oral; contaminated water; most common intestinal parasite in developed countries
• Disease: Giardiasis - foul-smelling, greasy steatorrhea (malabsorption); abdominal bloating; no blood/mucus in stool
• Site: Duodenum and jejunum (does NOT invade)
• Diagnosis: Stool for cysts/trophozoites; antigen detection (ELISA); "string test" (Enterotest)
• Treatment: Metronidazole, tinidazole, nitazoxanide

Trichomonas vaginalis

• Trophozoite only (no cyst stage)
• Transmission: Sexually transmitted (STI)
• Disease:
  • Women: Vaginitis - frothy, yellow-green, malodorous discharge; "strawberry cervix" (punctate hemorrhages); pruritus
  • Men: Mostly asymptomatic; urethritis
• Diagnosis: Wet mount - pear-shaped trophozoite with 4 anterior flagella + undulating membrane; tumbling motility
• Treatment: Metronidazole 2g single dose (treat both partners)

Leishmania

• Transmission: Female sandfly (Phlebotomus, Lutzomyia)
• Forms: Promastigote (in sandfly/culture); Amastigote (in human macrophages - no flagella; intracellular)

• Post-kala-azar dermal leishmaniasis (PKDL): Follows visceral leishmaniasis; hypopigmented macules → nodules
• Diagnosis: Tissue/bone marrow smear showing amastigotes; rK39 rapid test; culture
• Treatment: Sodium stibogluconate (pentavalent antimony); Miltefosine; Amphotericin B liposomal

Trypanosoma

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Plasmodium (Malaria)

Mosquito injects sporozoites → Liver (exo-erythrocytic schizogony) → merozoites released
→ RBCs (erythrocytic schizogony) → ring stage → trophozoite → schizont → merozoites
→ rupture RBCs → fever paroxysm → some form gametocytes → taken up by mosquito

• Cerebral malaria (coma, seizures)
• Severe anemia
• ARDS
• Blackwater fever (massive hemolysis → hemoglobinuria)
• Hypoglycemia
• Renal failure

• Thick blood film: Screening (concentration); species cannot always be determined
• Thin blood film: Species identification; parasite count
• Rapid diagnostic test (RDT): Antigen detection (HRP-II for P. falciparum; LDH, aldolase for others)
• PCR: Most sensitive; speciation

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Coccidian Parasites

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Cestodes (Tapeworms)

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Trematodes (Flukes)

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Nematodes (Roundworms)

Intestinal Nematodes

Tissue Nematodes

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SECTION 6: BACTERIOLOGY

Gram-Positive Cocci

Staphylococcus

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Streptococcus viridans

• Group of alpha-hemolytic streptococci (not classified by Lancefield grouping due to lack of C polysaccharide)
• Species: S. mutans, S. sanguis, S. mitis, S. salivarius, S. milleri
• Optochin resistant (distinguishes from S. pneumoniae which is sensitive)
• Bile insoluble (distinguishes from S. pneumoniae which is bile soluble)
• Disease:
  • Dental caries: S. mutans (produces dextran/glucan from sucrose; adheres to teeth)
  • Subacute bacterial endocarditis (SBE): Following dental procedures; colonizes abnormal/prosthetic valves
  • Brain abscess: S. milleri group

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Streptococcus pneumoniae (Pneumococcus)

• Lancefield: Not groupable (no C polysaccharide recognized)
• Alpha-hemolytic on blood agar; Gram-positive diplococci ("lancet-shaped")
• Virulence: Polysaccharide capsule (anti-phagocytic); pneumolysin
• Optochin sensitive; Bile soluble
• Diseases: Pneumonia (lobar), Meningitis, Otitis media, Sinusitis, Septicemia
• Most common cause of: CAP (adults), Bacterial meningitis (adults), Otitis media (children)
• Risk groups: Asplenic patients, elderly, HIV, sickle cell
• Vaccine: PCV13 (conjugate, children), PPSV23 (polysaccharide, adults/high risk)
• Treatment: Penicillin (susceptible strains); Ceftriaxone + Vancomycin (resistant strains in meningitis)

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Group A Streptococcus (GAS) - Streptococcus pyogenes

• Lancefield group A; Beta-hemolytic
• Virulence factors:

• Diseases:
  • Suppurative: Pharyngitis, Tonsillitis, Scarlet fever, Cellulitis, Impetigo, Necrotizing fasciitis, Toxic shock syndrome
  • Non-suppurative (post-streptococcal): Rheumatic fever, Acute glomerulonephritis
• Treatment: Penicillin G/V (drug of choice); Amoxicillin; Erythromycin (if allergic)
• Rheumatic fever: Penicillin prophylaxis to prevent recurrences

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Group B Streptococcus (GBS) - Streptococcus agalactiae

• Lancefield group B; Beta-hemolytic
• Hippurate hydrolysis positive (key ID test)
• CAMP test positive (enhances hemolysis of S. aureus)
• Colonizes vagina/rectum of 10-30% pregnant women
• Diseases:
  • Neonatal: Early-onset (< 7 days) - pneumonia, sepsis, meningitis from vertical transmission; Late-onset (7 days-3 months) - meningitis
  • Adults: UTI, bacteremia, postpartum endometritis
• Screening: Vaginal/rectal swab at 35-37 weeks gestation
• Prophylaxis: Intrapartum IV Penicillin G (if GBS positive or risk factors)
• Treatment: Penicillin G or Ampicillin

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Gram-Negative Cocci

Neisseria meningitidis (Meningococcus)

• Oxidase positive; Gram-negative diplococci (kidney/coffee bean shape)
• Ferments: Glucose AND maltose (distinguishes from gonorrhoeae which ferments glucose only)
• Capsule: Polysaccharide; serogroups A, B, C, W, X, Y (vaccine-preventable: A, C, W, Y by MenACWY; B by MenB/Bexsero)
• Virulence: Capsule (anti-phagocytic); LOS (lipooligosaccharide); IgA protease
• Diseases:
  • Meningococcal meningitis (fever, headache, photophobia, neck stiffness)
  • Meningococcemia: Non-blanching petechial/purpuric rash (classic), DIC
  • Waterhouse-Friderichsen syndrome: Bilateral adrenal hemorrhage; adrenal failure; shock
• Carrier state: Nasopharynx; spread by respiratory droplets
• Treatment: IV Benzylpenicillin/Ceftriaxone; Rifampicin/Ciprofloxacin for prophylaxis of close contacts

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Neisseria gonorrhoeae (Gonococcus)

• No polysaccharide capsule; IgA protease
• Ferments glucose only (not maltose)
• Pili (fimbriae): Major virulence factor; antigenic variation; adherence
• Outer membrane proteins: Opa proteins; Porin proteins
• Diseases:
  • Men: Urethritis (purulent discharge; dysuria)
  • Women: Cervicitis (majority asymptomatic); PID (salpingitis, tubo-ovarian abscess, Fitz-Hugh-Curtis syndrome)
  • Ophthalmia neonatorum (conjunctivitis in newborns - from birth canal)
  • Disseminated gonococcal infection: Septic arthritis, skin pustules, tenosynovitis
  • Pharyngitis, Proctitis (receptive anal sex)
• Diagnosis: Gram stain (intracellular Gram-negative diplococci in PMNs), culture on Thayer-Martin medium (chocolate agar + antibiotics), NAAT
• Treatment: Ceftriaxone 500mg IM single dose; Azithromycin often co-prescribed; increasing resistance

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Gram-Positive Bacilli

Corynebacterium diphtheriae (Diphtheria)

• Club-shaped Gram-positive rods; pleomorphic; "Chinese letter" / "cuneiform" arrangement
• Metachromatic granules (volutin/Babes-Ernst granules) at poles - stain blue-black with Albert's/Loeffler's methylene blue
• Toxin: Exotoxin encoded by bacteriophage β (lysogenic conversion); A-B toxin
  • B subunit: Binds to heparin-binding EGF receptor on heart/nerve cells
  • A subunit: ADP-ribosylates EF-2 (Elongation Factor 2) → inhibits protein synthesis → cell death
• Diseases:
  • Local disease: Pharyngeal diphtheria - "bull neck" (cervical lymphadenopathy); formation of grayish-white pseudomembrane (fibrin + bacteria + necrotic cells) in throat; bleeds on removal
  • Toxin effects: Myocarditis, Polyneuropathy (palatal palsy, cranial nerve palsies, peripheral neuropathy)
  • Nasal diphtheria, cutaneous diphtheria
• Diagnosis:
  • Albert's stain / Loeffler's methylene blue
  • Culture: Loeffler's serum slope (rapid growth of metachromatic granules); Tellurite medium (gray-black colonies)
  • Elek's test / Modified Elek's test: Immunodiffusion for toxin detection (in vitro)
  • PCR for tox gene
• Treatment: Antitoxin (equine) + Benzylpenicillin or Erythromycin
• Prevention: DTP vaccine (toxoid)

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Bacillus anthracis (Anthrax)

• Large Gram-positive rods in chains; spore-forming; non-motile
• Capsule: Poly-D-glutamic acid (anti-phagocytic; unique among bacteria)
• Toxins:
  • Protective antigen (PA): Binds to host cells; "anthrax toxin receptor"
  • Edema factor (EF): Adenylate cyclase (calmodulin-dependent) → ↑cAMP → edema
  • Lethal factor (LF): Metalloprotease → cleaves MAP kinase kinase → cell death; macrophage lysis
  • PA + EF = Edema toxin; PA + LF = Lethal toxin
• Diseases:
  • Cutaneous anthrax (95%): Painless papule → vesicle → black eschar ("malignant pustule"); painless
  • Pulmonary anthrax ("Woolsorter's disease"): Inhalation of spores; mediastinal widening on CXR; biphasic illness → hemorrhagic mediastinitis; high mortality
  • GI anthrax: Ingestion; rare; abdominal pain, bloody diarrhea
• Diagnosis: Blood culture; Gram stain; capsule stain; PCR
• Treatment: Ciprofloxacin or Doxycycline; IV penicillin for susceptible strains; antitoxin
• Bioterrorism agent: Category A

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Clostridium

• Mild-moderate: Oral vancomycin or Metronidazole
• Severe/recurrent: Fidaxomicin; Bezlotoxumab (toxin B antibody); Fecal microbiota transplant (FMT)
• Do not give anti-motility agents

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Gram-Negative Organisms

Escherichia coli

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Salmonella

• Gram-negative, facultative anaerobic rods; oxidase negative; fermenter

• 2500 O serotypes; lipopolysaccharide (O antigen + core + lipid A = endotoxin)

• Strict human pathogens: S. Typhi, S. Paratyphi (typhoid/paratyphoid fever - enteric fever)
• Animal reservoirs: Salmonella Typhimurium, Enteritidis (non-typhoidal - poultry, eggs, dairy)

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Vibrio cholerae

• Gram-negative, curved rods (comma-shaped); oxidase positive; motile (single polar flagellum); non-invasive
• O groups: O1 (El Tor biotype - current pandemics), O139 (Bengal)
• Cholera toxin (CT): A-B toxin; B subunit binds GM1 ganglioside; A subunit activates Gs → adenylate cyclase → ↑↑cAMP → chloride secretion → massive watery diarrhea
• Disease: Cholera - profuse "rice water" diarrhea (no blood, no pus); vomiting; dehydration; hypokalemia; metabolic acidosis; death from dehydration
• "Rice water" stools - watery, flecks of mucus; odorless
• Dark-field microscopy of stool: "shooting stars" motility
• Treatment: Oral rehydration salts (ORS) - most important; IV fluids if severe; Doxycycline or Azithromycin (reduce duration)
• Other Vibrio: V. parahaemolyticus (raw seafood; gastroenteritis), V. vulnificus (raw oysters; bacteremia in liver disease patients; necrotizing fasciitis)

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Haemophilus influenzae

• Small Gram-negative coccobacilli; pleomorphic; non-motile
• Encapsulated (type b - Hib): Polyribosyl ribitol phosphate (PRP) capsule; major virulence factor; causes invasive disease
• Non-encapsulated (non-typeable, NTHi): Causes localized respiratory infections
• Requires: Factor X (hemin) and Factor V (NAD) for growth on chocolate agar
• Satellite phenomenon: Growth near S. aureus colonies on blood agar (S. aureus provides Factor V by hemolysis)
• Diseases:

• Epiglottitis: Acute emergency; Hib; toxic-looking child; drooling; stridor; "tripod position"; DO NOT examine throat directly (risk of complete obstruction)
• Vaccine: Hib conjugate vaccine (PRP-T); has dramatically reduced Hib meningitis/epiglottitis
• Treatment: Ceftriaxone (meningitis), Ampicillin-clavulanate; Rifampicin prophylaxis for contacts

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SECTION 7: HIGH-YIELD INFECTIONS - GENITAL ULCERS

Genital Ulcer Diseases - Comparison Table

Syphilis Stages

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What's Covered

• All 6 stains (Gram, ZN/acid-fast, Albert's, Bipolar, India ink/negative, Methylene blue) with steps, principles, and organisms
• All 4 phases of bacterial growth curve with clinical relevance
• Gene transfer mechanisms (transformation, transduction, conjugation, transposition)
• Mutation types and DNA repair mechanisms
• Full sterilization/disinfection tables with temperatures and agents

• Innate vs. adaptive immunity comparison
• All immunoglobulin classes with functions
• Complement system (3 pathways, terminal pathway, deficiency consequences)
• Primary immunodeficiency diseases (Bruton's, DiGeorge, SCID, Wiskott-Aldrich, CGD, Job's, etc.)

• All superficial/cutaneous fungi (dermatophytes by site, Piedra, Tinea versicolor)
• Subcutaneous mycoses (Mycetoma with grain colors, Sporotrichosis, Rhinosporidiosis, Chromoblastomycosis)
• Systemic mycoses (Candida, Cryptococcus, Mucormycosis, Aspergillosis, PCP) with diagnostic stains and treatments

• RNA vs. DNA virus classification tables
• All 8 herpes viruses with latency sites and diseases
• Parvovirus B19 (all presentations)
• Influenza (antigenic drift vs. shift)
• Rubella including full Congenital Rubella Syndrome
• Retrovirus/HIV life cycle + drug targets
• Hepatitis B - full serologic marker table + window period + treatment

• Amoeba (E. histolytica, Naegleria, Acanthamoeba)
• All flagellates (Giardia, Trichomonas, Leishmania, Trypanosoma) with vectors
• Plasmodium species comparison table + treatment
• Coccidian parasites (Cryptosporidium, Cyclospora, Cystoisospora) - stain and treatment differences
• Cestodes, trematodes, nematodes (intestinal + tissue) - all in tables

• S. aureus virulence factors + toxin syndromes
• Streptococcus viridans, Pneumococcus, GAS (M protein + ASO), GBS (CAMP test, neonatal disease)
• Neisseria meningitidis vs. gonorrhoeae differentiation
• C. diphtheriae (Albert's stain, toxin mechanism, Elek's test)
• B. anthracis (3 toxin components, 3 clinical forms)
• All Clostridium species with toxin mechanisms
• E. coli pathotypes, Salmonella (typhoid vs. non-typhoidal), Vibrio cholerae, H. influenzae

• Side-by-side comparison of all 5 genital ulcer causes (pain, ulcer features, lymph nodes, diagnosis, treatment)
• Syphilis stages table