Classification of Bacteriology - Complete Guide with Flow Charts

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pres.layout = "LAYOUT_WIDE"; // 13.3" x 7.5"
pres.title = "Diagnostic Bacteriology - Gram Stain Classification";
pres.author = "Microbiology Teaching";

// ─── Color palette ───────────────────────────────────────────────────────────
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  teal:    "1B6CA8",
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  white:   "FFFFFF",
  offWhite:"F5F7FA",
  gpcBlue: "1565C0",   // GPC node
  gncOrange:"E65100",  // GNC node
  gnbGreen:"2E7D32",   // GNB node
  gpbPurp: "6A1B9A",   // GPB node
  posGreen:"2E7D32",
  negRed:  "C62828",
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// ═══════════════════════════════════════════════════════════════════════════════
// SLIDE 1 — TITLE
// ═══════════════════════════════════════════════════════════════════════════════
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  s.addText("Gram Stain Classification & Identification Flowcharts", {
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    { label: "GPC", sub: "Gram-Positive Cocci", color: C.gpcBlue, x: 1.3 },
    { label: "GNC", sub: "Gram-Negative Cocci", color: C.gncOrange, x: 4.3 },
    { label: "GNB", sub: "Gram-Negative Bacilli", color: C.gnbGreen, x: 7.3 },
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  s.addText("Biochemical Tests  •  Key Organisms  •  Clinical Examples", {
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// ═══════════════════════════════════════════════════════════════════════════════
// SLIDE 2 — MASTER ALGORITHM (Gram Stain → 4 groups)
// ═══════════════════════════════════════════════════════════════════════════════
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  // Arrow down to GRAM STAIN
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  // GRAM STAIN diamond
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  addHLine(s, 2.0, 3.0, 4.15, C.gpcBlue);
  labelText(s, "Cocci", 1.3, 3.95, 1.2, C.gpcBlue, 9, true);
  addNode(s, "GPC\nGram-Positive Cocci", 1.2, 4.65, 2.5, 0.85, C.gpcBlue, C.white, 11);

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  addHLine(s, 3.5, 4.5, 4.15, C.gpbPurp);
  labelText(s, "Bacilli", 4.0, 3.95, 1.2, C.gpbPurp, 9, true);
  addNode(s, "GPB\nGram-Positive Bacilli", 3.6, 4.65, 2.5, 0.85, C.gpbPurp, C.white, 11);

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  addHLine(s, 9.0, 9.9, 4.15, C.gncOrange);
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  addNode(s, "GNC\nGram-Negative Cocci", 8.7, 4.65, 2.5, 0.85, C.gncOrange, C.white, 11);

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    { x: 3.6, color: C.gpbPurp, next: "→ Slide 6" },
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// ═══════════════════════════════════════════════════════════════════════════════
// SLIDE 3 — GPC FLOWCHART
// ═══════════════════════════════════════════════════════════════════════════════
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  addVLine(s, 8.5, 5.2, 5.5, C.midBlue);
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  addDiamond(s, "BACITRACIN\nLANCEFIELD", 10.0, 5.6, 1.7, 0.75, C.teal);

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// ═══════════════════════════════════════════════════════════════════════════════
// SLIDE 4 — GNB FLOWCHART
// ═══════════════════════════════════════════════════════════════════════════════
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  addDiamond(s, "LACTOSE\nMacConkey", 1.5, 3.7, 2.3, 0.85, C.teal);

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  labelText(s, "PINK (+)", 0.3, 3.95, 0.85, C.posGreen, 8.5, true);
  addNode(s, "E. coli\nKlebsiella\nEnterobacter", 0.05, 4.65, 1.8, 0.9, C.gnbGreen, C.white, 9);
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  addVLine(s, 0.95, 5.55, 5.75, C.gnbGreen);
  addNode(s, "IMViC Tests\n(see Slide 7)", 0.2, 5.75, 1.5, 0.65, C.midBlue, C.white, 9);

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  labelText(s, "COLORLESS (−)", 3.5, 3.95, 1.4, C.negRed, 8.5, true);
  addVLine(s, 3.8, 4.12, 4.4);
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  addVLine(s, 4.1, 5.25, 5.5);

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  addNode(s, "Salmonella\nProteus", 1.75, 6.55, 1.6, 0.55, C.gnbGreen, C.white, 9);
  addVLine(s, 2.55, 6.5, 6.55, C.gnbGreen);
  addHLine(s, 4.9, 5.5, 5.87);
  labelText(s, "(−)", 5.0, 5.7, 0.6, C.negRed, 8.5, true);
  addNode(s, "Shigella\nYersinia", 4.95, 6.55, 1.6, 0.55, C.gnbGreen, C.white, 9);

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  addVLine(s, 11.0, 3.35, 3.6, C.gnbGreen);
  addDiamond(s, "GLUCOSE\nFERM.", 9.9, 3.6, 2.2, 0.8, C.teal);

  addHLine(s, 8.5, 9.9, 4.0);
  labelText(s, "(−) Oxidative", 8.2, 3.82, 1.6, C.negRed, 8.5, true);
  addNode(s, "Pseudomonas\naeruginsoa\n(Pyocyanin+)", 7.6, 4.65, 2.0, 0.85, C.gnbGreen, C.white, 9);
  addVLine(s, 8.6, 4.55, 4.65, C.gnbGreen);

  addHLine(s, 12.1, 12.5, 4.0);
  labelText(s, "(+) Ferment.", 12.0, 3.82, 1.5, C.posGreen, 8.5, true);
  addNode(s, "Vibrio cholerae\nAeromonas", 11.7, 4.65, 1.8, 0.65, C.gnbGreen, C.white, 9);
  addVLine(s, 12.6, 4.55, 4.65, C.gnbGreen);

  // Curved path — fastidious
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  addNode(s, "Fastidious GNB\nHaemophilus\nBrucella\nCampylobacter", 9.8, 4.65, 2.3, 1.0, C.midBlue, C.white, 9);

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    fill: { color: C.navy }, line: { color: C.accent, width: 1 }, rectRadius: 0.1,
  });
  s.addText("KEY TESTS — GNB", { x: 5.9, y: 5.05, w: 3.1, h: 0.4, fontSize: 10, color: C.accent, bold: true, align: "center", fontFace: "Calibri" });
  s.addText([
    { text: "• Oxidase: ", options: { bold: true } }, { text: "Divides Enterobact. vs Non\n" },
    { text: "• MacConkey: ", options: { bold: true } }, { text: "Lactose fermenters (pink)\n" },
    { text: "• H₂S: ", options: { bold: true } }, { text: "Salmonella / Proteus (black ppt)\n" },
    { text: "• IMViC: ", options: { bold: true } }, { text: "Indole, MR, VP, Citrate\n" },
    { text: "• Urease: ", options: { bold: true } }, { text: "Proteus, Klebsiella, H. pylori" },
  ], { x: 5.9, y: 5.5, w: 3.1, h: 1.65, fontSize: 9, color: C.offWhite, fontFace: "Calibri" });
}

// ═══════════════════════════════════════════════════════════════════════════════
// SLIDE 5 — GNC FLOWCHART
// ═══════════════════════════════════════════════════════════════════════════════
{
  const s = pres.addSlide();
  s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: C.offWhite } });
  s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 0.65, fill: { color: C.gncOrange } });
  s.addText("GNC — GRAM-NEGATIVE COCCI  |  Diagnostic Flowchart", {
    x: 0.3, y: 0.1, w: 12.7, h: 0.45, fontSize: 16, color: C.white, bold: true, fontFace: "Calibri", charSpacing: 2,
  });

  addNode(s, "Gram-Negative Cocci\n(Diplococci / Coffee bean shape)", 4.6, 0.9, 4.1, 0.65, C.gncOrange, C.white, 13);
  addVLine(s, 6.65, 1.55, 2.0, C.gncOrange);

  addDiamond(s, "OXIDASE\nTEST", 5.4, 2.0, 2.5, 0.85, C.teal);

  // All GNC are oxidase positive
  addVLine(s, 6.65, 2.85, 3.1, C.gncOrange);
  labelText(s, "(+) ALL clinically significant GNC are Oxidase Positive", 3.0, 2.87, 7.3, C.posGreen, 9, true);

  addNode(s, "NEISSERIA spp.", 5.1, 3.1, 3.1, 0.6, C.gncOrange, C.white, 13);
  addVLine(s, 6.65, 3.7, 4.05, C.gncOrange);

  addDiamond(s, "ACID FROM\nSUGARS", 5.4, 4.05, 2.5, 0.85, C.teal);

  // N. meningitidis branch
  addHLine(s, 3.3, 5.4, 4.47);
  labelText(s, "Glucose + Maltose", 2.3, 4.27, 2.5, C.posGreen, 8.5, true);
  addNode(s, "N. meningitidis", 2.0, 4.95, 2.5, 0.65, C.gncOrange, C.white, 12);
  addVLine(s, 3.25, 4.82, 4.95, C.gncOrange);
  addVLine(s, 3.25, 5.6, 5.85, C.gncOrange);
  s.addShape(pres.ShapeType.roundRect, {
    x: 1.2, y: 5.85, w: 4.1, h: 1.3,
    fill: { color: C.navy }, line: { color: C.gncOrange, width: 1 }, rectRadius: 0.08,
  });
  s.addText([
    { text: "KEY FEATURES\n", options: { bold: true, color: C.accent } },
    { text: "• Glucose + Maltose acid\n• Polysaccharide capsule\n• Causes: MENINGITIS, Septicaemia\n• Medium: Chocolate / Thayer-Martin\n• Droplet spread" },
  ], { x: 1.25, y: 5.9, w: 4.0, h: 1.2, fontSize: 9, color: C.offWhite, fontFace: "Calibri" });

  // N. gonorrhoeae branch
  addHLine(s, 7.9, 9.0, 4.47);
  labelText(s, "Glucose only", 8.3, 4.27, 1.8, C.negRed, 8.5, true);
  addNode(s, "N. gonorrhoeae", 8.5, 4.95, 2.5, 0.65, C.gncOrange, C.white, 12);
  addVLine(s, 9.75, 4.82, 4.95, C.gncOrange);
  addVLine(s, 9.75, 5.6, 5.85, C.gncOrange);
  s.addShape(pres.ShapeType.roundRect, {
    x: 7.7, y: 5.85, w: 4.1, h: 1.3,
    fill: { color: C.navy }, line: { color: C.gncOrange, width: 1 }, rectRadius: 0.08,
  });
  s.addText([
    { text: "KEY FEATURES\n", options: { bold: true, color: C.accent } },
    { text: "• Glucose acid only (NOT maltose)\n• No capsule, pili for attachment\n• Causes: GONORRHEA, PID, Ophthalmia neonatorum\n• Intracellular diplococci in PMNs\n• Medium: Thayer-Martin (VCNT agar)" },
  ], { x: 7.75, y: 5.9, w: 4.0, h: 1.2, fontSize: 9, color: C.offWhite, fontFace: "Calibri" });

  // Moraxella catarrhalis
  addVLine(s, 6.65, 4.9, 5.1, C.arrowGray);
  s.addShape(pres.ShapeType.roundRect, {
    x: 5.4, y: 5.1, w: 2.5, h: 0.65,
    fill: { color: "#78909C" }, line: { color: C.arrowGray, width: 0.5 }, rectRadius: 0.08,
  });
  s.addText("Moraxella catarrhalis", { x: 5.4, y: 5.1, w: 2.5, h: 0.65, fontSize: 10, color: C.white, bold: true, align: "center", fontFace: "Calibri" });
  addVLine(s, 6.65, 5.75, 5.95, C.arrowGray);
  s.addText("DNase (+), Butyrate (+), No acid from sugars\nOtitis media, LRTI, Elderly patients", {
    x: 5.3, y: 5.95, w: 2.7, h: 0.7, fontSize: 8.5, color: C.navy, align: "center", fontFace: "Calibri",
  });
}

// ═══════════════════════════════════════════════════════════════════════════════
// SLIDE 6 — GPB FLOWCHART
// ═══════════════════════════════════════════════════════════════════════════════
{
  const s = pres.addSlide();
  s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: C.offWhite } });
  s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 0.65, fill: { color: C.gpbPurp } });
  s.addText("GPB — GRAM-POSITIVE BACILLI  |  Diagnostic Flowchart", {
    x: 0.3, y: 0.1, w: 12.7, h: 0.45, fontSize: 16, color: C.white, bold: true, fontFace: "Calibri", charSpacing: 2,
  });

  addNode(s, "Gram-Positive Bacilli", 5.0, 0.85, 3.3, 0.6, C.gpbPurp, C.white, 13);
  addVLine(s, 6.65, 1.45, 1.9, C.gpbPurp);

  addDiamond(s, "SPORE\nFORMING?", 5.4, 1.9, 2.5, 0.85, C.teal);

  // Spore forming - YES
  addHLine(s, 3.1, 5.4, 2.32);
  labelText(s, "YES", 3.4, 2.12, 1.0, C.posGreen, 9, true);
  addNode(s, "SPORE-FORMING\nBACILLI", 2.0, 2.75, 2.2, 0.65, C.gpbPurp, C.white, 11);
  addVLine(s, 3.1, 2.62, 2.75, C.gpbPurp);
  addVLine(s, 3.1, 3.4, 3.7, C.gpbPurp);

  addDiamond(s, "AEROBIC /\nANAEROBIC?", 2.0, 3.7, 2.2, 0.8, C.teal);

  // Aerobic spore forming
  addHLine(s, 0.3, 2.0, 4.1);
  labelText(s, "Aerobic", 0.3, 3.9, 1.0, C.posGreen, 8.5, true);
  addNode(s, "Bacillus spp.\n(Aerobic)", 0.1, 4.65, 1.8, 0.65, C.gpbPurp, C.white, 10);
  addVLine(s, 1.0, 4.55, 4.65, C.gpbPurp);
  addVLine(s, 1.0, 5.3, 5.5, C.gpbPurp);
  s.addShape(pres.ShapeType.roundRect, { x: 0.1, y: 5.5, w: 1.8, h: 1.55, fill: { color: C.navy }, line: { color: C.gpbPurp, width: 1 }, rectRadius: 0.08 });
  s.addText("B. anthracis\n(No hemolysis,\nString of pearls)\nB. cereus\n(Food poisoning)", { x: 0.15, y: 5.55, w: 1.7, h: 1.45, fontSize: 8.5, color: C.offWhite, fontFace: "Calibri" });

  // Anaerobic spore forming
  addHLine(s, 4.2, 5.2, 4.1);
  labelText(s, "Anaerobic", 4.0, 3.9, 1.4, C.negRed, 8.5, true);
  addNode(s, "Clostridium spp.\n(Anaerobic)", 4.0, 4.65, 2.0, 0.65, C.gpbPurp, C.white, 10);
  addVLine(s, 5.0, 4.55, 4.65, C.gpbPurp);

  // Clostridium branches
  addVLine(s, 5.0, 5.3, 5.5, C.gpbPurp);
  s.addShape(pres.ShapeType.roundRect, { x: 3.6, y: 5.5, w: 2.8, h: 1.55, fill: { color: C.navy }, line: { color: C.gpbPurp, width: 1 }, rectRadius: 0.08 });
  s.addText([
    { text: "C. perfringens ", options: { bold: true } }, { text: "— Double β-hemolysis, Stormy clot, Lecithinase+\n" },
    { text: "C. tetani ", options: { bold: true } }, { text: "— Drumstick spore, Spastic paralysis\n" },
    { text: "C. botulinum ", options: { bold: true } }, { text: "— Flaccid paralysis, Honey in infants\n" },
    { text: "C. difficile ", options: { bold: true } }, { text: "— Toxin A+B, Pseudomembranous colitis" },
  ], { x: 3.65, y: 5.55, w: 2.7, h: 1.45, fontSize: 8.5, color: C.offWhite, fontFace: "Calibri" });

  // Non-spore forming - NO
  addHLine(s, 7.9, 9.5, 2.32);
  labelText(s, "NO", 8.5, 2.12, 1.0, C.negRed, 9, true);
  addNode(s, "NON-SPORE\nFORMING", 8.8, 2.75, 2.2, 0.65, C.gpbPurp, C.white, 11);
  addVLine(s, 9.9, 2.62, 2.75, C.gpbPurp);
  addVLine(s, 9.9, 3.4, 3.7, C.gpbPurp);

  addDiamond(s, "MOTILITY &\nHEMOLYSIS", 8.8, 3.7, 2.2, 0.8, C.teal);

  // Listeria branch
  addHLine(s, 7.5, 8.8, 4.1);
  labelText(s, "β-hemolytic\nMotile (tumbling)", 6.6, 3.8, 2.2, C.posGreen, 8.5, true);
  addNode(s, "Listeria\nmonocytogenes", 6.5, 4.65, 2.0, 0.65, C.gpbPurp, C.white, 10);
  addVLine(s, 7.5, 4.55, 4.65, C.gpbPurp);
  addVLine(s, 7.5, 5.3, 5.5, C.gpbPurp);
  s.addShape(pres.ShapeType.roundRect, { x: 6.2, y: 5.5, w: 2.5, h: 1.55, fill: { color: C.navy }, line: { color: C.gpbPurp, width: 1 }, rectRadius: 0.08 });
  s.addText("• Tumbling motility at 4°C\n• CAMP test (+)\n• Cold enrichment\n• Meningitis: neonates/elderly\n• Unpasteurized dairy", { x: 6.25, y: 5.55, w: 2.4, h: 1.45, fontSize: 8.5, color: C.offWhite, fontFace: "Calibri" });

  // Corynebacterium branch
  addHLine(s, 11.0, 11.5, 4.1);
  labelText(s, "Non-hemolytic\nNon-motile", 10.8, 3.8, 1.8, C.negRed, 8.5, true);
  addNode(s, "Corynebacterium\ndiphtheriae", 10.5, 4.65, 2.2, 0.65, C.gpbPurp, C.white, 10);
  addVLine(s, 11.6, 4.55, 4.65, C.gpbPurp);
  addVLine(s, 11.6, 5.3, 5.5, C.gpbPurp);
  s.addShape(pres.ShapeType.roundRect, { x: 10.2, y: 5.5, w: 2.7, h: 1.55, fill: { color: C.navy }, line: { color: C.gpbPurp, width: 1 }, rectRadius: 0.08 });
  s.addText("• Metachromatic granules\n• Chinese-letter pattern\n• Elek test (toxin)\n• Tellurite agar (black)\n• Diphtheria — pseudomembrane", { x: 10.25, y: 5.55, w: 2.6, h: 1.45, fontSize: 8.5, color: C.offWhite, fontFace: "Calibri" });
}

// ═══════════════════════════════════════════════════════════════════════════════
// SLIDE 7 — BIOCHEMICAL TESTS REFERENCE TABLE
// ═══════════════════════════════════════════════════════════════════════════════
{
  const s = pres.addSlide();
  s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: C.navy } });
  s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 0.65, fill: { color: C.accent } });
  s.addText("KEY BIOCHEMICAL TESTS — Quick Reference", {
    x: 0.3, y: 0.1, w: 12.7, h: 0.45, fontSize: 18, color: C.navy, bold: true, fontFace: "Calibri", charSpacing: 2,
  });

  const rows = [
    ["TEST", "PRINCIPLE", "(+) RESULT", "KEY ORGANISMS", "GROUP"],
    ["Catalase", "H₂O₂ → H₂O + O₂", "Bubbles", "Staphylococcus (+) vs Streptococcus (−)", "GPC"],
    ["Coagulase", "Clots plasma fibrinogen", "Clot forms", "S. aureus (+) vs CoNS (−)", "GPC"],
    ["Oxidase", "Cytochrome c oxidase", "Blue-purple colour", "Pseudomonas, Neisseria (+)", "GNC/GNB"],
    ["Optochin", "Inhibits S. pneumoniae", "Zone of inhibition", "S. pneumoniae (S) vs Viridans (R)", "GPC"],
    ["Bacitracin", "Inhibits Group A Strep", "Zone ≥ 10 mm", "S. pyogenes (S) vs others (R)", "GPC"],
    ["CAMP Test", "Enhanced hemolysis", "Arrowhead β-hemolysis", "S. agalactiae Group B (+)", "GPC"],
    ["PYR Test", "Pyrrolidonyl peptidase", "Red colour", "S. pyogenes, E. faecalis (+)", "GPC"],
    ["Novobiocin", "Inhibits CoNS", "Zone of inhibition", "S. epidermidis (S) vs S. saprophyticus (R)", "GPC"],
    ["Indole (I)", "Tryptophanase + Kovac's", "Red ring", "E. coli (+), Klebsiella (−)", "GNB"],
    ["Methyl Red (M)", "Mixed acid fermentation", "Red colour", "E. coli, Salmonella (+)", "GNB"],
    ["Voges-Proskauer (V)", "2,3-butanediol prod.", "Red colour (VP reagent)", "Klebsiella, Enterobacter (+)", "GNB"],
    ["Citrate (C)", "Citrate as C-source", "Blue (Simmon's agar)", "Klebsiella, Enterobacter (+)", "GNB"],
    ["Urease", "Urea → NH₃ + CO₂", "Pink (Christensen's)", "Proteus, Klebsiella, H. pylori (+)", "GNB"],
    ["H₂S Production", "Sulfur reduction → FeS", "Black precipitate", "Salmonella, Proteus (+)", "GNB"],
    ["Elek Test", "Immunodiffusion toxin", "Precipitin line", "C. diphtheriae toxin (+)", "GPB"],
    ["Nagler's Reaction", "Lecithinase activity", "Turbidity halved", "C. perfringens (+)", "GPB"],
  ];

  const groupColors = { GPC: C.gpcBlue, GNC: C.gncOrange, GNB: C.gnbGreen, GPB: C.gpbPurp };
  const colW  = [1.6, 2.4, 2.1, 4.2, 0.85];
  const colX  = [0.15, 1.8, 4.25, 6.4, 10.65];
  const rowH  = 0.36;
  const startY = 0.75;

  rows.forEach((row, ri) => {
    row.forEach((cell, ci) => {
      const y = startY + ri * rowH;
      const isHeader = ri === 0;
      const grp = row[4];
      let bg = isHeader ? C.teal : (ri % 2 === 0 ? "#1A3050" : C.midBlue);
      if (!isHeader && ci === 4) bg = groupColors[grp] || C.midBlue;
      s.addShape(pres.ShapeType.rect, {
        x: colX[ci], y, w: colW[ci], h: rowH,
        fill: { color: bg }, line: { color: C.navy, width: 0.3 },
      });
      s.addText(cell, {
        x: colX[ci] + 0.05, y, w: colW[ci] - 0.1, h: rowH,
        fontSize: isHeader ? 9 : 7.8,
        color: C.white, bold: isHeader, fontFace: "Calibri",
        align: ci === 0 ? "left" : "left", valign: "middle", margin: 1,
      });
    });
  });

  // Footer
  s.addShape(pres.ShapeType.rect, { x: 0, y: 7.15, w: 13.3, h: 0.35, fill: { color: C.accent } });
  s.addText("I = Indole  •  M = Methyl Red  •  V = Voges-Proskauer  •  C = Citrate  →  IMViC pattern distinguishes E. coli (++-−) from Klebsiella (−−++) from Enterobacter (−−++)", {
    x: 0.3, y: 7.17, w: 12.7, h: 0.3, fontSize: 9, color: C.navy, bold: true, align: "center", fontFace: "Calibri",
  });
}

// ═══════════════════════════════════════════════════════════════════════════════
// SLIDE 8 — IMViC PATTERN TABLE
// ═══════════════════════════════════════════════════════════════════════════════
{
  const s = pres.addSlide();
  s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: C.offWhite } });
  s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 0.65, fill: { color: C.gnbGreen } });
  s.addText("IMViC TESTS — Differentiating Gram-Negative Bacilli", {
    x: 0.3, y: 0.1, w: 12.7, h: 0.45, fontSize: 17, color: C.white, bold: true, fontFace: "Calibri", charSpacing: 2,
  });

  // IMViC explanation boxes
  const tests = [
    { letter: "I", name: "INDOLE", principle: "Tryptophanase breaks down tryptophan\n→ Indole detected by Kovac's reagent", pos: "Red ring at surface", neg: "No colour change", color: "#1565C0" },
    { letter: "M", name: "METHYL RED", principle: "Mixed acid fermentation\n→ Lowers pH below 4.4", pos: "RED colour", neg: "Yellow/orange (VP+)", color: "#2E7D32" },
    { letter: "V", name: "VOGES-PROSKAUER", principle: "2,3-butanediol production\nBarritt's reagent A+B", pos: "RED colour", neg: "No colour change", color: "#6A1B9A" },
    { letter: "C", name: "CITRATE", principle: "Citrate as sole carbon source\nAlkaline shift (Simmon's agar)", pos: "BLUE (Prussian blue)", neg: "Green (no change)", color: "#E65100" },
  ];

  tests.forEach((t, i) => {
    const x = 0.3 + i * 3.2;
    s.addShape(pres.ShapeType.roundRect, { x, y: 0.8, w: 3.0, h: 2.6, fill: { color: t.color }, line: { color: C.white, width: 0.5 }, rectRadius: 0.1 });
    s.addText(t.letter, { x, y: 0.85, w: 3.0, h: 0.8, fontSize: 32, color: C.white, bold: true, align: "center", fontFace: "Calibri" });
    s.addText(t.name, { x, y: 1.6, w: 3.0, h: 0.4, fontSize: 10, color: C.accent, bold: true, align: "center", fontFace: "Calibri" });
    s.addText(t.principle, { x: x+0.1, y: 2.0, w: 2.8, h: 0.8, fontSize: 8.5, color: C.offWhite, align: "center", fontFace: "Calibri" });
    s.addShape(pres.ShapeType.roundRect, { x: x+0.15, y: 2.85, w: 1.25, h: 0.4, fill: { color: C.posGreen }, line: { color: C.posGreen }, rectRadius: 0.05 });
    s.addText("(+) " + t.pos, { x: x+0.15, y: 2.85, w: 1.25, h: 0.4, fontSize: 7.5, color: C.white, bold: true, align: "center", fontFace: "Calibri" });
    s.addShape(pres.ShapeType.roundRect, { x: x+1.5, y: 2.85, w: 1.25, h: 0.4, fill: { color: C.negRed }, line: { color: C.negRed }, rectRadius: 0.05 });
    s.addText("(−) " + t.neg, { x: x+1.5, y: 2.85, w: 1.25, h: 0.4, fontSize: 7.5, color: C.white, bold: true, align: "center", fontFace: "Calibri" });
  });

  // IMViC result table
  s.addText("IMViC PATTERN COMPARISON TABLE", {
    x: 0.3, y: 3.5, w: 12.7, h: 0.4, fontSize: 13, color: C.navy, bold: true, fontFace: "Calibri",
  });

  const imvicData = [
    ["Organism", "Indole (I)", "Methyl Red (M)", "VP (V)", "Citrate (C)", "Lactose", "H₂S", "Urease"],
    ["E. coli", "+", "+", "−", "−", "+", "−", "−"],
    ["Klebsiella pneumoniae", "−", "−", "+", "+", "+", "−", "+"],
    ["Enterobacter cloacae", "−", "−", "+", "+", "+", "−", "−"],
    ["Salmonella typhi", "−", "+", "−", "−", "−", "+", "−"],
    ["Salmonella (non-typhi)", "−", "+", "−", "+", "−", "+", "−"],
    ["Shigella spp.", "−/+", "+", "−", "−", "−", "−", "−"],
    ["Proteus mirabilis", "−", "+", "−", "+", "−", "+", "+"],
    ["Yersinia enterocolitica", "+", "+", "−", "−", "−", "−", "+"],
    ["Vibrio cholerae", "+", "−", "+", "+", "−", "−", "−"],
  ];

  const imCols = [2.8, 1.0, 1.3, 1.0, 1.0, 0.9, 0.8, 0.9];
  const imX = [0.15, 3.0, 4.05, 5.4, 6.45, 7.5, 8.45, 9.3];
  const imRowH = 0.38;
  const imStartY = 3.95;

  imvicData.forEach((row, ri) => {
    row.forEach((cell, ci) => {
      const y = imStartY + ri * imRowH;
      let bg = ri === 0 ? C.navy : (ri % 2 === 0 ? "#E8F4E8" : C.white);
      if (ri > 0 && ci > 0) {
        if (cell === "+") bg = "#C8E6C9";
        else if (cell === "−") bg = "#FFCDD2";
        else bg = "#FFF9C4";
      }
      s.addShape(pres.ShapeType.rect, {
        x: imX[ci], y, w: imCols[ci], h: imRowH,
        fill: { color: bg }, line: { color: "#CCCCCC", width: 0.3 },
      });
      s.addText(cell, {
        x: imX[ci]+0.05, y, w: imCols[ci]-0.1, h: imRowH,
        fontSize: ri === 0 ? 8.5 : 9, color: ri === 0 ? C.white : C.navy,
        bold: ri === 0 || ci === 0, fontFace: "Calibri",
        align: ci === 0 ? "left" : "center", valign: "middle", margin: 1,
      });
    });
  });

  s.addShape(pres.ShapeType.rect, { x: 0, y: 7.15, w: 13.3, h: 0.35, fill: { color: C.gnbGreen } });
  s.addText("GREEN = Positive  |  RED = Negative  |  YELLOW = Variable  •  Mnemonic: IMViC = I is Indole, M is Methyl Red, V is Voges-Proskauer, C is Citrate", {
    x: 0.3, y: 7.18, w: 12.7, h: 0.28, fontSize: 8.5, color: C.white, bold: true, align: "center", fontFace: "Calibri",
  });
}

// ═══════════════════════════════════════════════════════════════════════════════
// SLIDE 9 — CLINICAL EXAMPLES SUMMARY
// ═══════════════════════════════════════════════════════════════════════════════
{
  const s = pres.addSlide();
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        "S. aureus → MRSA, Boils, Food poisoning, TSS",
        "S. pyogenes → Strep throat, Rheumatic fever",
        "S. pneumoniae → Pneumonia, Meningitis, Otitis",
        "S. agalactiae → Neonatal meningitis/sepsis",
        "S. epidermidis → Catheter biofilm, Prosthetic valve",
        "S. saprophyticus → UTI (young women)",
        "E. faecalis → Endocarditis, UTI",
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        "N. gonorrhoeae → Gonorrhea, PID, Ophthalmia neon.",
        "M. catarrhalis → Otitis media, Sinusitis, LRTI",
        "",
        "BOTH: Oxidase (+), diplococcal morphology",
        "DIFF: Maltose (+) → Meningitidis",
        "DIFF: Maltose (−) → Gonorrhoeae",
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        "Salmonella typhi → Typhoid, Rose spots, Widal+",
        "Shigella → Bloody dysentery (non-motile, H₂S−)",
        "Pseudomonas → Burns, CF, Nosocomial (pyocyanin)",
        "Vibrio cholerae → Rice-water stool, dehydration",
        "Proteus → UTI, swarming on agar, urease+",
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        "C. perfringens → Gas gangrene, Food poisoning",
        "C. tetani → Tetanus (spastic, drumstick spore)",
        "C. botulinum → Flaccid paralysis, Honey→infants",
        "C. difficile → Pseudomembranous colitis, Toxin A+B",
        "L. monocytogenes → Neonatal/elderly meningitis",
        "C. diphtheriae → Diphtheria, Pseudomembrane, Elek+",
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// ═══════════════════════════════════════════════════════════════════════════════
// SLIDE 10 — END / SUMMARY
// ═══════════════════════════════════════════════════════════════════════════════
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    { n: "3", title: "PRIMARY TESTS", body: "Coagulase / Hemolysis / Lactose (MacConkey)\nSugar fermentation / Motility / Spore stain", color: C.gnbGreen },
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// ── Write file ────────────────────────────────────────────────────────────────
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