from reportlab.lib.pagesizes import A4
from reportlab.lib import colors
from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
from reportlab.lib.units import cm
from reportlab.platypus import (
    SimpleDocTemplate, Paragraph, Spacer, Table, TableStyle,
    HRFlowable, PageBreak, KeepTogether
)
from reportlab.lib.enums import TA_CENTER, TA_LEFT, TA_JUSTIFY

OUTPUT = "/tmp/workspace/bacteriology-pdf/Bacteriology_Lab_Diagnosis.pdf"

# ── colour palette ──────────────────────────────────────────────────
DARK_BLUE   = colors.HexColor("#1a3a5c")
MID_BLUE    = colors.HexColor("#2563a8")
LIGHT_BLUE  = colors.HexColor("#dbeafe")
ACCENT      = colors.HexColor("#e74c3c")
GRAM_POS    = colors.HexColor("#fff3cd")   # warm yellow for gram+
GRAM_NEG    = colors.HexColor("#d1ecf1")   # cool teal for gram-
SPECIAL     = colors.HexColor("#f3e5f5")   # lavender for special
HEADER_ROW  = colors.HexColor("#1a3a5c")
ALT_ROW     = colors.HexColor("#f0f4ff")
WHITE       = colors.white
TABLE_GRID  = colors.HexColor("#b0c4de")

doc = SimpleDocTemplate(
    OUTPUT,
    pagesize=A4,
    leftMargin=1.8*cm, rightMargin=1.8*cm,
    topMargin=2*cm,    bottomMargin=2*cm,
    title="Bacteriology Lab Diagnosis",
    author="Orris Medical Education"
)

styles = getSampleStyleSheet()

# Custom styles
S = {
    "cover_title": ParagraphStyle("cover_title", fontSize=28, textColor=WHITE,
        fontName="Helvetica-Bold", alignment=TA_CENTER, spaceAfter=10),
    "cover_sub":   ParagraphStyle("cover_sub", fontSize=14, textColor=LIGHT_BLUE,
        fontName="Helvetica", alignment=TA_CENTER, spaceAfter=6),
    "cover_note":  ParagraphStyle("cover_note", fontSize=10, textColor=LIGHT_BLUE,
        fontName="Helvetica-Oblique", alignment=TA_CENTER),
    "section":     ParagraphStyle("section", fontSize=16, textColor=WHITE,
        fontName="Helvetica-Bold", alignment=TA_LEFT, spaceAfter=4, spaceBefore=4,
        leftIndent=6, leading=22),
    "subsection":  ParagraphStyle("subsection", fontSize=11, textColor=DARK_BLUE,
        fontName="Helvetica-Bold", spaceAfter=3, spaceBefore=6),
    "body":        ParagraphStyle("body", fontSize=9.5, textColor=colors.black,
        fontName="Helvetica", spaceAfter=3, leading=14, alignment=TA_JUSTIFY),
    "bullet":      ParagraphStyle("bullet", fontSize=9.5, textColor=colors.black,
        fontName="Helvetica", spaceAfter=2, leading=13, leftIndent=14,
        bulletIndent=4),
    "toc_entry":   ParagraphStyle("toc_entry", fontSize=10.5, textColor=DARK_BLUE,
        fontName="Helvetica", spaceAfter=5, leftIndent=10),
    "toc_head":    ParagraphStyle("toc_head", fontSize=14, textColor=DARK_BLUE,
        fontName="Helvetica-Bold", spaceAfter=12, alignment=TA_CENTER),
    "footer_note": ParagraphStyle("footer_note", fontSize=7.5, textColor=colors.grey,
        fontName="Helvetica-Oblique", alignment=TA_CENTER),
    "label":       ParagraphStyle("label", fontSize=8.5, textColor=DARK_BLUE,
        fontName="Helvetica-Bold"),
    "cell_body":   ParagraphStyle("cell_body", fontSize=8.5, textColor=colors.black,
        fontName="Helvetica", leading=12),
    "cell_header": ParagraphStyle("cell_header", fontSize=9, textColor=WHITE,
        fontName="Helvetica-Bold", alignment=TA_CENTER),
}

# ── helpers ─────────────────────────────────────────────────────────
def section_banner(name, gram_type="special"):
    color_map = {"pos": colors.HexColor("#8b0000"),
                 "neg": colors.HexColor("#1a5276"),
                 "special": colors.HexColor("#4a235a"),
                 "anaerobe": colors.HexColor("#145a32")}
    bg = color_map.get(gram_type, DARK_BLUE)
    data = [[Paragraph(name, S["section"])]]
    t = Table(data, colWidths=[17*cm])
    t.setStyle(TableStyle([
        ("BACKGROUND", (0,0), (-1,-1), bg),
        ("ROUNDEDCORNERS", [6]),
        ("TOPPADDING", (0,0), (-1,-1), 8),
        ("BOTTOMPADDING", (0,0), (-1,-1), 8),
        ("LEFTPADDING", (0,0), (-1,-1), 10),
    ]))
    return t

def info_table(rows, bg=LIGHT_BLUE):
    """rows = list of (label, value) tuples"""
    data = [[Paragraph(l, S["label"]), Paragraph(v, S["cell_body"])] for l,v in rows]
    t = Table(data, colWidths=[4.5*cm, 12.5*cm])
    ts = TableStyle([
        ("BACKGROUND", (0,0), (-1,-1), bg),
        ("GRID", (0,0), (-1,-1), 0.4, TABLE_GRID),
        ("VALIGN", (0,0), (-1,-1), "TOP"),
        ("TOPPADDING", (0,0), (-1,-1), 5),
        ("BOTTOMPADDING", (0,0), (-1,-1), 5),
        ("LEFTPADDING", (0,0), (-1,-1), 6),
        ("RIGHTPADDING", (0,0), (-1,-1), 6),
    ])
    # alternate row colours
    for i in range(0, len(data), 2):
        ts.add("BACKGROUND", (0,i), (-1,i), bg)
    for i in range(1, len(data), 2):
        ts.add("BACKGROUND", (0,i), (-1,i), ALT_ROW)
    t.setStyle(ts)
    return t

def sensitivity_table(headers, rows):
    data = [[Paragraph(h, S["cell_header"]) for h in headers]]
    for row in rows:
        data.append([Paragraph(str(c), S["cell_body"]) for c in row])
    col_w = 17*cm / len(headers)
    t = Table(data, colWidths=[col_w]*len(headers))
    ts = TableStyle([
        ("BACKGROUND", (0,0), (-1,0), HEADER_ROW),
        ("GRID", (0,0), (-1,-1), 0.4, TABLE_GRID),
        ("VALIGN", (0,0), (-1,-1), "MIDDLE"),
        ("TOPPADDING", (0,0), (-1,-1), 4),
        ("BOTTOMPADDING", (0,0), (-1,-1), 4),
        ("LEFTPADDING", (0,0), (-1,-1), 5),
        ("ALIGN", (0,0), (-1,-1), "CENTER"),
    ])
    for i in range(1, len(data), 2):
        ts.add("BACKGROUND", (0,i), (-1,i), ALT_ROW)
    t.setStyle(ts)
    return t

def hr():
    return HRFlowable(width="100%", thickness=0.5, color=TABLE_GRID, spaceAfter=4, spaceBefore=4)

def sp(n=6):
    return Spacer(1, n)

# ═══════════════════════════════════════════════════════════════════
# BACTERIA DATA
# ═══════════════════════════════════════════════════════════════════
bacteria = [
  # ── GRAM POSITIVE ──────────────────────────────────────────────
  {
    "name": "1. Staphylococcus aureus",
    "gram": "pos",
    "bg": GRAM_POS,
    "basics": [
        ("Kingdom / Class", "Bacteria – Firmicutes – Bacilli"),
        ("Gram Stain", "Gram-POSITIVE cocci in clusters (grape-like)"),
        ("Shape / Arrangement", "Spherical cocci, 0.5–1.5 µm; non-motile, non-spore-forming"),
        ("Capsule", "Present in virulent strains (polysaccharide)"),
        ("Oxygen Requirement", "Facultative anaerobe"),
    ],
    "culture": [
        ("Routine Media", "Blood Agar (BAP): large, round, golden/yellow colonies; β-haemolysis"),
        ("Selective Media", "Mannitol Salt Agar (MSA): ferments mannitol → yellow halo"),
        ("Chromogenic Agar", "MRSA chromogenic agar: mauve/pink colonies for MRSA"),
        ("Special Feature", "Golden pigment (staphyloxanthin); β-haemolysin causes clear zones on BAP"),
        ("Growth Temp", "Optimal 37°C; halotolerant (grows in 7.5% NaCl)"),
        ("Incubation", "18–24 hours; colonies 1–3 mm"),
    ],
    "biochem": [
        ("Catalase", "POSITIVE (differentiates from Streptococcus)"),
        ("Coagulase", "POSITIVE (bound + free) — key differentiating test from CoNS"),
        ("Mannitol fermentation", "POSITIVE (aerobic & anaerobic)"),
        ("DNase", "POSITIVE"),
        ("Phosphatase", "POSITIVE"),
        ("Haemolysin", "α, β, γ, δ haemolysins; β-haemolysis on BAP"),
        ("Protein A", "POSITIVE (IgG binding)"),
        ("CAMP test", "Negative"),
        ("Oxidase", "Negative"),
        ("Novobiocin", "Sensitive"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Penicillin", "Usually Resistant", "β-lactamase production ~95% of strains"),
        ("Flucloxacillin/Nafcillin", "Sensitive (MSSA)", "Drug of choice for MSSA"),
        ("Vancomycin", "Sensitive", "DOC for MRSA; VISA/VRSA emerging"),
        ("Linezolid", "Sensitive", "Alternative for MRSA"),
        ("Daptomycin", "Sensitive", "For bacteraemia/endocarditis"),
        ("Clindamycin", "Variable", "Check inducible resistance (D-zone test)"),
        ("Co-trimoxazole", "Often Sensitive", "Used for community MRSA"),
        ("Fusidic acid", "Sensitive", "Skin infections; resistance develops rapidly"),
    ],
    "clinical": (
        "Causes: skin/soft tissue infections (furuncles, carbuncles, impetigo), bacteraemia, "
        "endocarditis, pneumonia, osteomyelitis, septic arthritis, food poisoning (pre-formed "
        "heat-stable enterotoxin), toxic shock syndrome (TSST-1), scalded skin syndrome (exfoliatin). "
        "MRSA is a major healthcare-associated pathogen. Virulence factors: coagulase, protein A, "
        "leukocidin (PVL), exotoxins."
    ),
  },

  {
    "name": "2. Streptococcus pneumoniae",
    "gram": "pos",
    "bg": GRAM_POS,
    "basics": [
        ("Kingdom / Class", "Bacteria – Firmicutes – Bacilli"),
        ("Gram Stain", "Gram-POSITIVE lancet-shaped diplococci"),
        ("Shape / Arrangement", "Oval cocci in pairs (diplococci), occasionally short chains"),
        ("Capsule", "LARGE polysaccharide capsule — major virulence factor (84 serotypes)"),
        ("Oxygen Requirement", "Facultative anaerobe; capnophilic (5% CO₂ enhances growth)"),
    ],
    "culture": [
        ("Routine Media", "Blood Agar: small, grey, α-haemolytic colonies (green zone); umbilicated/draughtsman appearance due to autolysis"),
        ("Selective Media", "Gentamicin blood agar; chocolate agar"),
        ("Key Tests", "Optochin (P-disc) sensitivity: SENSITIVE (zone ≥14 mm) — differentiates from viridans strep"),
        ("Bile Solubility", "POSITIVE — colonies dissolve in 10% sodium deoxycholate"),
        ("CO₂", "Enhanced growth in 5% CO₂"),
        ("Incubation", "35–37°C, 18–24 h; colonies 0.5–1.5 mm"),
    ],
    "biochem": [
        ("Catalase", "Negative"),
        ("Optochin", "SENSITIVE (key test)"),
        ("Bile solubility", "POSITIVE"),
        ("Inulin fermentation", "POSITIVE"),
        ("Haemolysis", "α-haemolysis (partial, green)"),
        ("Quellung reaction", "POSITIVE — capsular swelling with specific antisera"),
        ("Coagulase", "Negative"),
        ("CAMP test", "Negative"),
        ("Serotyping", "Capsular polysaccharide typing (1–84)"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Penicillin G", "Sensitive / Intermediate / Resistant", "MIC-based breakpoints; MDR strains increasing"),
        ("Amoxicillin", "Sensitive (most)", "High-dose for non-meningitic disease"),
        ("Ceftriaxone", "Sensitive", "DOC for meningitis"),
        ("Vancomycin", "Sensitive", "Used for penicillin-resistant meningitis"),
        ("Moxifloxacin", "Sensitive", "Respiratory quinolone"),
        ("Chloramphenicol", "Variable", "Used in resource-limited settings"),
        ("Erythromycin", "Variable resistance", "Macrolide resistance rising globally"),
    ],
    "clinical": (
        "Leading cause of community-acquired pneumonia, bacterial meningitis, otitis media, and "
        "sinusitis. Commonly colonises the nasopharynx. Risk groups: elderly, asplenic, "
        "immunocompromised, sickle cell. Virulence: polysaccharide capsule (antiphagocytic), "
        "pneumolysin, IgA protease, autolysin. Diagnosis: sputum Gram stain + culture, blood "
        "culture, urinary antigen (UAg) test. Vaccines: PCV13/PCV15/PCV20, PPSV23."
    ),
  },

  {
    "name": "3. Streptococcus pyogenes  (Group A Strep)",
    "gram": "pos",
    "bg": GRAM_POS,
    "basics": [
        ("Kingdom / Class", "Bacteria – Firmicutes – Bacilli"),
        ("Gram Stain", "Gram-POSITIVE cocci in chains"),
        ("Shape / Arrangement", "Spherical cocci 0.6–1.0 µm; chains of variable length"),
        ("Capsule", "Hyaluronic acid capsule (anti-phagocytic)"),
        ("Oxygen Requirement", "Facultative anaerobe"),
    ],
    "culture": [
        ("Routine Media", "Blood Agar: translucent, grey-white colonies; LARGE zone of β-haemolysis (complete)"),
        ("Selective Media", "Sheep blood agar; SXT-resistant phenotype aids selection"),
        ("Key Disc Tests", "Bacitracin (A-disc): SENSITIVE (zone ≥10 mm) — differentiates Group A from other β-haemolytic strep"),
        ("PYR test", "POSITIVE (pyrrolidonyl arylamidase)"),
        ("Incubation", "35–37°C, 18–24 h; 5% CO₂ enhances haemolysis"),
    ],
    "biochem": [
        ("Catalase", "Negative"),
        ("Haemolysis", "β-haemolysis (complete, clear zone)"),
        ("Bacitracin", "SENSITIVE (A-disc)"),
        ("PYR test", "POSITIVE"),
        ("CAMP test", "Negative"),
        ("Lancefield grouping", "Group A (Lancefield carbohydrate antigen)"),
        ("Streptolysin O", "POSITIVE — basis of ASO titre (rises in post-strep disease)"),
        ("Hyaluronidase", "POSITIVE"),
        ("Streptokinase", "POSITIVE"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Penicillin V/G", "ALWAYS Sensitive", "Drug of choice; no documented resistance"),
        ("Amoxicillin", "Sensitive", "Oral treatment of pharyngitis"),
        ("Cephalosporins", "Sensitive", "Alternative to penicillin"),
        ("Clindamycin", "Usually Sensitive", "Used for invasive/necrotising infections"),
        ("Erythromycin", "Variable resistance", "Alternative for penicillin allergy"),
        ("Azithromycin", "Variable resistance", "~5–10% resistance in some regions"),
        ("Vancomycin", "Sensitive", "Reserve for allergy/severe cases"),
    ],
    "clinical": (
        "Causes: pharyngitis (strep throat), scarlet fever, impetigo, erysipelas, cellulitis, "
        "necrotising fasciitis, streptococcal toxic shock syndrome. Post-infectious: acute rheumatic "
        "fever (M-protein molecular mimicry) and post-streptococcal glomerulonephritis. Virulence: "
        "M protein (antiphagocytic), streptolysin O & S, DNase B, streptokinase, erythrogenic "
        "toxins (A/B/C). ASO titre useful for rheumatic fever diagnosis."
    ),
  },

  {
    "name": "4. Corynebacterium diphtheriae",
    "gram": "pos",
    "bg": GRAM_POS,
    "basics": [
        ("Kingdom / Class", "Bacteria – Actinobacteria – Actinobacteria"),
        ("Gram Stain", "Gram-POSITIVE pleomorphic rods; club-shaped (Chinese letter / palisade arrangement)"),
        ("Shape / Arrangement", "Non-motile, non-spore-forming rods; V/L/Y palisade arrangements"),
        ("Capsule", "None"),
        ("Oxygen Requirement", "Aerobe / Facultative anaerobe"),
    ],
    "culture": [
        ("Routine Media", "Blood Agar: small, grey-white colonies"),
        ("Selective Media", "Loeffler's serum slope: rapid growth; metachromatic granules visible with Albert's/Neisser's stain"),
        ("Selective/Differential", "Tellurite medium (McLeod's / Hoyle's): grey-black colonies (tellurite reduced to metallic tellurium); three biotypes: gravis (grey, daisy-head), mitis (black, smooth), intermedius"),
        ("Tinsdale Medium", "Brown/black halo around colonies due to cystinase activity"),
        ("Albert's Stain", "Metachromatic (volutin) granules stain blue-black (Babes-Ernst granules)"),
        ("Incubation", "35–37°C, 18–24 h"),
    ],
    "biochem": [
        ("Catalase", "POSITIVE"),
        ("Urease", "Negative"),
        ("Nitrate reduction", "POSITIVE"),
        ("Cystinase", "POSITIVE (Tinsdale halo)"),
        ("Pyrazinamidase", "Negative"),
        ("Glucose fermentation", "POSITIVE (acid, no gas)"),
        ("Sucrose", "Negative (mitis positive)"),
        ("Metachromatic granules", "POSITIVE (Albert's/Neisser's stain)"),
        ("Elek test", "Immunodiffusion for diphtheria toxin — gold standard for toxigenicity"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Penicillin G", "Sensitive", "Bactericidal; must combine with antitoxin"),
        ("Erythromycin", "Sensitive", "Drug of choice for elimination of carriage"),
        ("Diphtheria Antitoxin", "N/A (immunological)", "Given immediately on clinical suspicion — MOST IMPORTANT"),
        ("Amoxicillin", "Sensitive", "Alternative"),
        ("Clindamycin", "Sensitive", "Alternative"),
        ("Rifampicin", "Sensitive", "Carrier eradication"),
    ],
    "clinical": (
        "Causes diphtheria: tough grey pseudomembrane on pharynx/larynx (fibrin, bacteria, necrotic "
        "cells) causing airway obstruction. Exotoxin (A-B toxin) inhibits EF-2 (elongation factor 2) "
        "via ADP-ribosylation → protein synthesis arrest → myocarditis, neuropathy. Bull-neck "
        "appearance from cervical lymphadenopathy. Cutaneous diphtheria also occurs. Diagnosis: "
        "throat swab on Loeffler's + Elek test for toxin. Prevention: DTP vaccine."
    ),
  },

  # ── GRAM NEGATIVE ─────────────────────────────────────────────
  {
    "name": "5. Neisseria meningitidis",
    "gram": "neg",
    "bg": GRAM_NEG,
    "basics": [
        ("Kingdom / Class", "Bacteria – Proteobacteria – β-Proteobacteria"),
        ("Gram Stain", "Gram-NEGATIVE diplococci (kidney/coffee-bean shape, pairs facing each other)"),
        ("Shape / Arrangement", "Non-motile; adjacent flattened sides; 0.6–0.8 µm"),
        ("Capsule", "LARGE polysaccharide capsule — 13 serogroups (A,B,C,W135,Y most common)"),
        ("Oxygen Requirement", "Aerobe; capnophilic"),
    ],
    "culture": [
        ("Routine Media", "Blood agar: small, grey, translucent, non-haemolytic colonies"),
        ("Selective Media", "Thayer-Martin (VCN) agar: inhibits normal flora with vancomycin, colistin, nystatin"),
        ("Chocolate Agar", "Preferred — provides X and V growth factors; 5% CO₂ at 37°C"),
        ("Incubation", "35–37°C, 5% CO₂, 18–24 h; fastidious, dies quickly → process immediately"),
        ("CSF specimen", "Transport at 37°C (cold kills the organism)"),
    ],
    "biochem": [
        ("Oxidase", "POSITIVE (key test for Neisseria)"),
        ("Catalase", "POSITIVE"),
        ("Glucose fermentation", "POSITIVE (acid only)"),
        ("Maltose fermentation", "POSITIVE — differentiates from N. gonorrhoeae"),
        ("Lactose", "Negative"),
        ("Sucrose", "Negative"),
        ("DNase", "Negative"),
        ("Serogroup typing", "Capsular polysaccharide (A, B, C, W135, Y, X)"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Penicillin G / Ampicillin", "Usually Sensitive", "DOC for meningococcal meningitis"),
        ("Ceftriaxone", "Sensitive", "DOC for empiric bacterial meningitis"),
        ("Cefotaxime", "Sensitive", "Alternative third-gen cephalosporin"),
        ("Chloramphenicol", "Sensitive", "Used in resource-limited settings"),
        ("Rifampicin", "Sensitive", "Chemoprophylaxis for close contacts"),
        ("Ciprofloxacin", "Sensitive", "Single-dose prophylaxis for contacts"),
        ("Ceftriaxone IM", "Sensitive", "Preferred prophylaxis in pregnant contacts"),
    ],
    "clinical": (
        "Causes meningococcal meningitis and meningococcaemia. Presents with sudden fever, "
        "headache, photophobia, neck stiffness and a NON-BLANCHING petechial/purpuric rash "
        "(meningococcaemia). Waterhouse-Friderichsen syndrome: bilateral adrenal haemorrhage, "
        "DIC, shock. Primarily affects children and young adults; spread by respiratory droplets. "
        "Serogroup B vaccine (Bexsero), ACWY vaccines available."
    ),
  },

  {
    "name": "6. Neisseria gonorrhoeae",
    "gram": "neg",
    "bg": GRAM_NEG,
    "basics": [
        ("Kingdom / Class", "Bacteria – Proteobacteria – β-Proteobacteria"),
        ("Gram Stain", "Gram-NEGATIVE diplococci intracellularly within PMNs (urethral discharge)"),
        ("Shape / Arrangement", "Kidney-shaped pairs; 0.6–0.8 µm; non-motile, non-capsulate (in vitro)"),
        ("Capsule", "Minimal / transient"),
        ("Oxygen Requirement", "Aerobe; capnophilic"),
    ],
    "culture": [
        ("Routine Media", "Chocolate agar with CO₂"),
        ("Selective Media", "Thayer-Martin / Modified Thayer-Martin / New York City (NYC) agar — essential for genital specimens with normal flora"),
        ("Colony Morphology", "Small, grey-white, convex, glistening colonies; 4 colony types (T1–T4); T1 & T2 piliated and virulent"),
        ("Incubation", "35–37°C, 5–10% CO₂, 24–48 h; transport media (Amies/Stuart's) if delay"),
        ("NAAT", "Nucleic Acid Amplification Test — most sensitive; used for urine, swabs"),
    ],
    "biochem": [
        ("Oxidase", "POSITIVE"),
        ("Catalase", "POSITIVE"),
        ("Glucose fermentation", "POSITIVE"),
        ("Maltose fermentation", "NEGATIVE — distinguishes from N. meningitidis"),
        ("Lactose", "Negative"),
        ("Sucrose", "Negative"),
        ("DNase", "Negative"),
        ("Superoxol (30% H₂O₂)", "Strong POSITIVE reaction"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Ceftriaxone 500mg IM", "Sensitive", "Current WHO/CDC first-line for uncomplicated gonorrhoea"),
        ("Cefixime", "Sensitive (decreasing)", "Oral alternative; increasing resistance"),
        ("Azithromycin", "Increasing resistance", "No longer recommended as monotherapy"),
        ("Ciprofloxacin", "RESISTANT in most regions", "Fluoroquinolone resistance widespread"),
        ("Penicillin", "RESISTANT", "β-lactamase (PPNG) and chromosomal resistance"),
        ("Spectinomycin", "Sensitive", "Used for cephalosporin allergy"),
        ("Dual therapy", "Recommended", "Ceftriaxone + azithromycin (where resistance allows)"),
    ],
    "clinical": (
        "Causes gonorrhoea: urethritis (purulent discharge, dysuria), cervicitis, pelvic "
        "inflammatory disease (PID), epididymo-orchitis, rectal/pharyngeal infection, "
        "ophthalmia neonatorum (leading cause of preventable neonatal blindness), "
        "disseminated gonococcal infection (DGI: migratory polyarthritis, dermatitis, "
        "tenosynovitis). Diagnosis: Gram stain (intracellular GNDCs in urethral discharge ~95% "
        "sensitive in men; ~50% in women) + culture + NAAT. Antibiotic resistance is a growing concern."
    ),
  },

  {
    "name": "7. Haemophilus influenzae",
    "gram": "neg",
    "bg": GRAM_NEG,
    "basics": [
        ("Kingdom / Class", "Bacteria – Proteobacteria – γ-Proteobacteria"),
        ("Gram Stain", "Gram-NEGATIVE small pleomorphic coccobacilli (tiny rods)"),
        ("Shape / Arrangement", "Very small (0.2–0.3 × 0.5–2 µm); non-motile; pleomorphic"),
        ("Capsule", "Types a–f polysaccharide capsule; type b (Hib) most virulent (polyribitol phosphate)"),
        ("Oxygen Requirement", "Facultative anaerobe"),
    ],
    "culture": [
        ("Growth Factors", "Requires BOTH X factor (haemin) AND V factor (NAD) — neither is in blood agar alone"),
        ("Chocolate Agar", "PREFERRED medium — heat-lyses RBCs, releasing X and V factors; colonies small, grey, convex"),
        ("Satellite Phenomenon", "On BAP near Staph aureus (which provides V factor) — forms satellite colonies around Staph streak"),
        ("Levinthal's Agar", "Transparent medium; capsulated strains show iridescence"),
        ("Factor test strips", "X-only, V-only, XV discs on nutrient agar — growth only around XV strip"),
        ("Incubation", "35–37°C, 5% CO₂, 18–24 h"),
    ],
    "biochem": [
        ("Oxidase", "POSITIVE"),
        ("Catalase", "POSITIVE"),
        ("X factor requirement", "POSITIVE (needs haemin)"),
        ("V factor requirement", "POSITIVE (needs NAD)"),
        ("Indole", "Variable by biotype (I–VIII)"),
        ("Urease", "Variable"),
        ("Capsule typing", "Antisera slide agglutination (a–f)"),
        ("β-lactamase", "Often POSITIVE — TEM-1 enzyme confers ampicillin resistance"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Amoxicillin-Clavulanate", "Sensitive", "DOC for non-meningitic disease if β-lactamase positive"),
        ("Ceftriaxone", "Sensitive", "DOC for meningitis"),
        ("Ampicillin", "Resistant (~30%)", "β-lactamase production common"),
        ("Azithromycin", "Sensitive", "For respiratory infections"),
        ("Chloramphenicol", "Sensitive", "Alternative in meningitis (low-resource)"),
        ("Ciprofloxacin", "Sensitive", "Adult respiratory infections"),
        ("Rifampicin", "Sensitive", "Hib prophylaxis for contacts"),
    ],
    "clinical": (
        "Non-typeable H. influenzae (NTHi): most common cause of otitis media, sinusitis, "
        "bronchitis, exacerbations of COPD. H. influenzae type b (Hib): pre-vaccine was leading "
        "cause of bacterial meningitis in children <5 yrs; also causes epiglottitis (thumb sign on "
        "lateral X-ray), septic arthritis, pneumonia, cellulitis. Hib vaccine (conjugate) has "
        "dramatically reduced type b disease. Virulence: capsule (antiphagocytic), IgA protease."
    ),
  },

  {
    "name": "8. Escherichia coli",
    "gram": "neg",
    "bg": GRAM_NEG,
    "basics": [
        ("Kingdom / Class", "Bacteria – Proteobacteria – γ-Proteobacteria (Enterobacteriaceae)"),
        ("Gram Stain", "Gram-NEGATIVE straight rods (bacilli), 1–3 µm"),
        ("Shape / Arrangement", "Single rods; motile (peritrichous flagella) except some strains"),
        ("Capsule", "Variable (K antigen — acidic polysaccharide)"),
        ("Oxygen Requirement", "Facultative anaerobe"),
    ],
    "culture": [
        ("Routine Media", "Blood Agar: large, grey, often β-haemolytic colonies (EHEC/UPEC strains)"),
        ("MacConkey Agar", "PINK/RED lactose-fermenting colonies — key differential; characteristic metallic sheen on EMB agar"),
        ("EMB Agar (Eosin Methylene Blue)", "Metallic GREEN SHEEN colonies — highly characteristic for E. coli"),
        ("SMAC (Sorbitol-MacConkey)", "SORBITOL NON-FERMENTER = colourless colony = O157:H7 EHEC screening"),
        ("Chromogenic agar", "Pink colonies on chromogenic UTI agar"),
        ("Incubation", "35–37°C, 18–24 h; rapid grower"),
    ],
    "biochem": [
        ("Oxidase", "NEGATIVE"),
        ("Catalase", "POSITIVE"),
        ("Lactose fermentation", "POSITIVE (distinguishes from Salmonella/Shigella)"),
        ("Indole", "POSITIVE (most strains) — key IMViC test"),
        ("Methyl Red", "POSITIVE"),
        ("Voges-Proskauer", "NEGATIVE"),
        ("Citrate", "NEGATIVE (Simmons') — IMViC = +/+/-/-"),
        ("H₂S production", "NEGATIVE"),
        ("Urease", "NEGATIVE"),
        ("TSI slant", "A/A (acid/acid, no H₂S, no gas or gas)"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Nitrofurantoin", "Sensitive (UTI)", "Uncomplicated lower UTI"),
        ("Co-trimoxazole", "Variable (20–30% resistant)", "Check local resistance rates"),
        ("Ciprofloxacin", "Variable resistance", "Fluoroquinolone resistance increasing"),
        ("Amoxicillin-Clavulanate", "Often Sensitive", "For non-ESBL strains"),
        ("Ceftriaxone", "Sensitive (ESBL negative)", "Hospital-acquired: test for ESBL"),
        ("Carbapenems", "Sensitive (non-CRE)", "Reserve for ESBL/AmpC strains"),
        ("Fosfomycin", "Sensitive", "UTI due to ESBL E. coli"),
    ],
    "clinical": (
        "Most common cause of UTI (uropathogenic UPEC). Pathotypes: UPEC (UTI), ETEC (travellers' "
        "diarrhoea — LT/ST toxins), EPEC (infant diarrhoea), EHEC O157:H7 (haemorrhagic colitis, "
        "HUS via Shiga toxin), EIEC (dysentery-like), EAEC (persistent diarrhoea). Also causes "
        "neonatal meningitis (K1 capsule), bacteraemia, pneumonia. Antibiotic resistance (ESBL, "
        "carbapenemase) is a global public health crisis."
    ),
  },

  {
    "name": "9. Salmonella typhi",
    "gram": "neg",
    "bg": GRAM_NEG,
    "basics": [
        ("Kingdom / Class", "Bacteria – Proteobacteria – γ-Proteobacteria (Enterobacteriaceae)"),
        ("Gram Stain", "Gram-NEGATIVE straight rods, 2–3 µm × 0.6 µm; bipolar staining in blood cultures"),
        ("Shape / Arrangement", "Single rods; motile (peritrichous); flagella H antigen"),
        ("Capsule", "Vi (virulence) antigen — polysaccharide capsule; inhibits phagocytosis"),
        ("Oxygen Requirement", "Facultative anaerobe"),
    ],
    "culture": [
        ("Enrichment Broth", "Selenite F broth or Tetrathionate broth (suppresses coliforms for 12–24 h pre-culture)"),
        ("Selective Media", "MacConkey agar: NON-LACTOSE FERMENTER — colourless colonies"),
        ("Selective/Differential", "XLD (Xylose Lysine Deoxycholate) / DCA (Deoxycholate Citrate) / SS agar: black-centred colonies due to H₂S"),
        ("Brilliant Green Agar", "Selective for Salmonella (except S. typhi)"),
        ("Blood Culture", "BEST in first week of illness (bacteraemia phase)"),
        ("Bone marrow culture", "Most sensitive at any stage (>90%); remains positive after antibiotics"),
        ("Stool culture", "Week 2–3 (intestinal phase)"),
        ("Widal test", "Agglutination of O (somatic) and H (flagellar) antigens — supportive, not confirmatory"),
    ],
    "biochem": [
        ("Oxidase", "NEGATIVE"),
        ("Catalase", "POSITIVE"),
        ("Lactose", "NEGATIVE"),
        ("Glucose", "POSITIVE (acid + gas) — S. typhi NO GAS (unique)"),
        ("H₂S", "POSITIVE (but less than S. typhimurium)"),
        ("Urease", "NEGATIVE"),
        ("Indole", "NEGATIVE"),
        ("Citrate", "NEGATIVE"),
        ("TSI", "K/A (alkaline slant, acid butt, H₂S positive, no gas for typhi)"),
        ("Vi agglutination", "POSITIVE for S. typhi"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Ceftriaxone", "Sensitive", "DOC for severe typhoid; IV 7–14 days"),
        ("Azithromycin", "Sensitive", "DOC for uncomplicated typhoid; oral"),
        ("Ciprofloxacin", "Decreasing sensitivity (MDR)", "Nalidixic acid resistance = reduced fluoroquinolone sensitivity; avoid in Asia"),
        ("Chloramphenicol", "Sensitive (classical)", "Historical DOC; bone marrow suppression; MDR emerging"),
        ("Ampicillin", "Variable MDR resistance", "Classical drug; MDR strains common in Asia"),
        ("Co-trimoxazole", "Variable MDR resistance", "Used in susceptible strains"),
        ("Carbapenems", "Sensitive (XDR)", "For extensively drug-resistant (XDR) typhoid"),
    ],
    "clinical": (
        "Causes typhoid (enteric) fever: insidious onset, step-ladder fever, relative bradycardia, "
        "rose spots (trunk), hepatosplenomegaly, Faget sign. Transmitted faeco-orally via "
        "contaminated water/food. Complications: intestinal haemorrhage/perforation (week 3), "
        "encephalopathy, myocarditis. Chronic carrier state (gallbladder colonisation with Vi "
        "antigen). Diagnosis: blood culture (week 1), bone marrow (gold standard), Widal test "
        "(limited specificity). Vaccines: Ty21a (oral live), Vi polysaccharide, typhoid conjugate (TCV)."
    ),
  },

  {
    "name": "10. Vibrio cholerae",
    "gram": "neg",
    "bg": GRAM_NEG,
    "basics": [
        ("Kingdom / Class", "Bacteria – Proteobacteria – γ-Proteobacteria (Vibrionaceae)"),
        ("Gram Stain", "Gram-NEGATIVE curved rods (comma-shaped, 'vibrio')"),
        ("Shape / Arrangement", "Single curved rods 1.5–3 µm; highly motile — single polar flagellum; 'shooting star' motility"),
        ("Capsule", "Absent (O139 has a capsule)"),
        ("Oxygen Requirement", "Facultative anaerobe; aerophilic"),
    ],
    "culture": [
        ("Alkaline Peptone Water", "ENRICHMENT — pH 8.6 selects Vibrio; incubate 6–8 h before subculture"),
        ("TCBS Agar", "Thiosulfate Citrate Bile Salts Sucrose — YELLOW colonies (sucrose fermenter) for V. cholerae O1/O139"),
        ("MacConkey Agar", "Pale/non-lactose fermenting colonies"),
        ("Gelatin Agar", "Shows proteolytic liquefaction"),
        ("Incubation", "35–37°C, 18–24 h; pH 8.5 optimal"),
        ("Oxidase test", "String test: positive mucoid string with 0.5% sodium deoxycholate"),
    ],
    "biochem": [
        ("Oxidase", "POSITIVE — immediate reaction"),
        ("Catalase", "POSITIVE"),
        ("Indole", "POSITIVE"),
        ("String test (0.5% DOC)", "POSITIVE (mucoid string)"),
        ("TCBS", "YELLOW colonies — sucrose fermenter"),
        ("Cholera Red (Pfeffer's) reaction", "POSITIVE (sulphuric acid on culture = red colour)"),
        ("Agglutination", "O1 (Classical + El Tor biotypes) / O139 (Bengal); slide agglutination with polyvalent antisera"),
        ("El Tor vs Classical", "El Tor: VP positive, haemolysin+; Classical: VP neg"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Oral Rehydration Therapy (ORT)", "MAINSTAY", "IV/oral fluids — corrects fluid/electrolyte loss; primary treatment"),
        ("Doxycycline", "Sensitive", "Single dose DOC; reduces stool output & duration"),
        ("Azithromycin", "Sensitive", "Preferred for children and pregnancy"),
        ("Ciprofloxacin", "Sensitive (mostly)", "Fluoroquinolone; resistance emerging"),
        ("Co-trimoxazole", "Variable resistance", "Resistance widespread in many regions"),
        ("Tetracycline", "Sensitive", "Alternative adult treatment"),
    ],
    "clinical": (
        "Causes cholera: profuse, painless rice-water diarrhoea (loss of up to 1 L/h), vomiting, "
        "rapid dehydration, hypokalaemia, metabolic acidosis, muscle cramps. Can lead to hypovolaemic "
        "shock and death within hours. Pathogenesis: cholera toxin (AB₅) activates adenylyl cyclase → "
        "↑cAMP → Cl⁻ secretion, Na⁺ absorption inhibited. Pandemic O1 El Tor (7th pandemic), "
        "O139 Bengal. Faeco-oral transmission. Diagnosis: dark-field microscopy (shooting star), "
        "stool culture on TCBS, rapid dipstick tests. Oral cholera vaccines (OCV) available."
    ),
  },

  {
    "name": "11. Yersinia pestis",
    "gram": "neg",
    "bg": GRAM_NEG,
    "basics": [
        ("Kingdom / Class", "Bacteria – Proteobacteria – γ-Proteobacteria (Enterobacteriaceae)"),
        ("Gram Stain", "Gram-NEGATIVE coccobacilli; characteristic BIPOLAR STAINING (safety-pin appearance) with Giemsa/Wayson stain"),
        ("Shape / Arrangement", "Oval coccobacilli 0.5–0.8 × 1–2 µm; non-motile at 37°C, motile at 25°C"),
        ("Capsule", "F1 (fraction 1) antigen at 37°C — antiphagocytic"),
        ("Oxygen Requirement", "Facultative anaerobe"),
    ],
    "culture": [
        ("Routine Media", "Blood agar / Brain Heart Infusion agar — SLOW-GROWING (48–72 h); rough, irregular colonies"),
        ("MacConkey Agar", "Non-lactose fermenting; small, irregular colonies at 28°C"),
        ("Special Feature", "Grows better at 28°C (flea gut temperature) than 37°C; 'fried egg' colonies on BHI agar"),
        ("BSL-3 Required", "All work must be done in BSL-3 laboratory (category A bioterrorism agent)"),
        ("Wayson/Giemsa Stain", "Bipolar 'safety pin' staining pattern from smears/tissue"),
    ],
    "biochem": [
        ("Oxidase", "NEGATIVE"),
        ("Catalase", "POSITIVE"),
        ("Urease", "NEGATIVE"),
        ("Lactose", "NEGATIVE"),
        ("H₂S", "NEGATIVE or weakly positive"),
        ("Motility", "Non-motile at 37°C; motile at 22–25°C"),
        ("F1 antigen", "POSITIVE at 37°C (capsule) — detected by FA, ELISA"),
        ("PCR", "Rapid confirmatory test; most sensitive and specific"),
        ("DFP stain", "Direct fluorescent antibody — rapid identification"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Streptomycin", "Sensitive", "Traditional DOC for plague; IM administration"),
        ("Gentamicin", "Sensitive", "Alternative aminoglycoside; often used in US"),
        ("Doxycycline", "Sensitive", "Oral treatment and post-exposure prophylaxis"),
        ("Ciprofloxacin", "Sensitive", "Post-exposure prophylaxis; alternative treatment"),
        ("Chloramphenicol", "Sensitive", "For plague meningitis (CNS penetration)"),
        ("Co-trimoxazole", "Sensitive", "Prophylaxis in endemic areas"),
    ],
    "clinical": (
        "Causes plague: three forms — bubonic plague (bubo = tender, enlarged inguinal/axillary "
        "lymph node from flea bite), septicaemic plague (primary or secondary bacteraemia; "
        "'black death' skin haemorrhages), pneumonic plague (most deadly; person-to-person "
        "droplet transmission). Reservoir: rodents (rats, prairie dogs); vector: rat flea "
        "(Xenopsylla cheopis). Case fatality rate >50% untreated. BSL-3 pathogen. "
        "Category A bioterrorism agent. Diagnosis: smear (Giemsa/Wayson), culture, PCR, F1 antigen ELISA."
    ),
  },

  # ── ANAEROBES / SPORE-FORMERS ──────────────────────────────────
  {
    "name": "12. Clostridium perfringens",
    "gram": "pos",
    "bg": GRAM_POS,
    "basics": [
        ("Kingdom / Class", "Bacteria – Firmicutes – Clostridia"),
        ("Gram Stain", "Gram-POSITIVE large boxcar-shaped rods; spore rarely seen in tissue"),
        ("Shape / Arrangement", "Large (4–8 × 1–1.5 µm) rectangular rods; non-motile (unique among Clostridium)"),
        ("Spores", "Subterminal oval spores; rarely seen in clinical specimens"),
        ("Oxygen Requirement", "Obligate anaerobe"),
    ],
    "culture": [
        ("Blood Agar (Anaerobic)", "Double zone of haemolysis: inner complete β-haemolysis (θ-toxin) + outer partial haemolysis (α-toxin)"),
        ("Egg Yolk Agar (Nagler Plate)", "Lecithinase (α-toxin/phospholipase C) → opaque precipitate around colonies; INHIBITED by specific antitoxin on one side = Nagler reaction"),
        ("Litmus Milk", "Stormy clot fermentation — rapid acid production disrupts casein clot"),
        ("Robertson's Cooked Meat Medium", "Blackening with putrid smell — anaerobic growth"),
        ("Incubation", "37°C, strict anaerobic conditions, 24–48 h"),
    ],
    "biochem": [
        ("Lecithinase", "POSITIVE (α-toxin) — Nagler reaction"),
        ("Lipase", "Negative"),
        ("Stormy clot (litmus milk)", "POSITIVE"),
        ("Motility", "NON-MOTILE (unique feature)"),
        ("Haemolysis", "Double zone β-haemolysis"),
        ("Glucose/Lactose/Sucrose", "POSITIVE (acid + gas)"),
        ("H₂S", "POSITIVE"),
        ("Typing", "Toxin types A–E based on major toxin production; Type A most common human pathogen"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Penicillin G", "Sensitive", "DOC for gas gangrene with surgical debridement"),
        ("Clindamycin", "Sensitive", "Anti-toxin effect; added to penicillin for gas gangrene"),
        ("Metronidazole", "Sensitive", "For anaerobic coverage; used in combination"),
        ("Carbapenems", "Sensitive", "Broad-spectrum option"),
        ("Cephalosporins", "Sensitive", "Variable coverage"),
        ("Surgical debridement", "Essential", "Antibiotics alone insufficient for gas gangrene"),
    ],
    "clinical": (
        "Type A toxin causes: (1) Gas gangrene (myonecrosis) — traumatic wound infection with "
        "rapidly spreading necrosis, gas in tissue, foul smell, crepitus; (2) Food poisoning — "
        "heat-resistant spores survive cooking, germinate, produce enterotoxin → watery diarrhoea "
        "8–24 h after ingestion (no vomiting); (3) Necrotising enteritis (Pigbel disease — Type C). "
        "α-toxin (phospholipase C/lecithinase) is the main toxin — destroys cell membranes. "
        "Diagnosis: Gram stain of wound exudate (large boxcar GP rods), anaerobic culture, Nagler reaction."
    ),
  },

  {
    "name": "13. Clostridium tetani",
    "gram": "pos",
    "bg": GRAM_POS,
    "basics": [
        ("Kingdom / Class", "Bacteria – Firmicutes – Clostridia"),
        ("Gram Stain", "Gram-POSITIVE thin rods (may decolorise to Gram-negative with age)"),
        ("Shape / Arrangement", "Slender rods 0.5 × 2–5 µm; motile (peritrichous)"),
        ("Spores", "TERMINAL ROUND spores → classic DRUMSTICK / TENNIS RACKET appearance"),
        ("Oxygen Requirement", "Obligate anaerobe; strict"),
    ],
    "culture": [
        ("Blood Agar (Anaerobic)", "Thin spreading ('swarming') film over the plate; fine delicate colonies; β-haemolysis"),
        ("Broth Culture", "Robertson's Cooked Meat Medium: blackening; putrefaction"),
        ("Special Note", "Lab diagnosis is rarely needed — tetanus is a CLINICAL DIAGNOSIS"),
        ("Mouse Protection Test", "Gold standard for tetanospasmin (neurotoxin) detection in research settings"),
        ("Incubation", "37°C, strictly anaerobic, 48–72 h"),
    ],
    "biochem": [
        ("Indole", "POSITIVE"),
        ("Motility", "POSITIVE (motility agar) — swarming"),
        ("Proteolysis", "POSITIVE (liquefies gelatin)"),
        ("Haemolysis", "β-haemolysis (tetanolysin)"),
        ("Glucose fermentation", "NEGATIVE (non-saccharolytic)"),
        ("H₂S", "POSITIVE"),
        ("Neurotoxin", "Tetanospasmin (TeNT) — one of most potent toxins known (1 ng/kg lethal)"),
        ("Lipase", "NEGATIVE"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Metronidazole", "Sensitive", "DOC — preferred over penicillin (GABA antagonism concern)"),
        ("Penicillin G", "Sensitive", "Previously DOC; may potentiate tetanus symptoms (competes with GABA)"),
        ("Human Tetanus Immunoglobulin (HTIG)", "N/A (passive immunisation)", "Neutralises unbound toxin — give immediately"),
        ("TT Booster (Vaccine)", "N/A", "Tetanus toxoid — active immunisation"),
        ("Diazepam/Midazolam", "N/A (adjunct)", "Muscle relaxants for spasms"),
        ("Wound debridement", "Essential", "Removes source of toxin production"),
    ],
    "clinical": (
        "Tetanus is an exclusively toxin-mediated disease. Tetanospasmin blocks inhibitory "
        "neurotransmitter release (GABA and glycine) in the spinal cord → unopposed motor "
        "neuron firing → spastic paralysis. Manifestations: trismus ('lockjaw'), risus sardonicus "
        "(sardonic smile), opisthotonos (arched back), laryngeal spasm (fatal). Forms: "
        "generalised (most common), localised, cephalic, neonatal (tetanus neonatorum — "
        "umbilical stump contamination). Incubation: 3–21 days. Prevention: DTP vaccine; "
        "wound management with HTIG + booster."
    ),
  },

  # ── SPECIAL / ATYPICAL ─────────────────────────────────────────
  {
    "name": "14. Mycobacterium tuberculosis",
    "gram": "special",
    "bg": SPECIAL,
    "basics": [
        ("Kingdom / Class", "Bacteria – Actinobacteria – Actinobacteria (Mycobacteriaceae)"),
        ("Gram Stain", "DOES NOT STAIN with Gram stain — thick waxy mycolic acid cell wall"),
        ("Preferred Stain", "Ziehl-Neelsen (ZN): acid-fast bacilli (AFB) — RED rods on blue background; Auramine-rhodamine (fluorescent)"),
        ("Shape / Arrangement", "Slender, slightly curved rods 1–4 × 0.3–0.6 µm; non-motile; non-spore-forming"),
        ("Cell Wall", "High lipid content (mycolic acids, cord factor, wax D) — responsible for acid-fastness and resistance"),
        ("Oxygen Requirement", "Obligate aerobe; concentrated at lung apices"),
    ],
    "culture": [
        ("Solid Media", "Lowenstein-Jensen (LJ) medium: buff-coloured, rough, dry, crumbly EUGONIC colonies ('cauliflower' appearance); SLOW GROWTH — 3–8 weeks"),
        ("Liquid Media", "MGIT (Mycobacterial Growth Indicator Tube): fluorescence-based; detects in 1–2 weeks; BACTEC 460 radiometric"),
        ("Middlebrook 7H10/7H11", "Agar-based; observe microcolonies under microscope from 5–7 days"),
        ("Niacin test", "POSITIVE — accumulates niacin; differentiates from other mycobacteria"),
        ("Egg-based media", "LJ, Ogawa, Petragnani — traditional"),
        ("BSL-3", "Culture must be performed in BSL-3 laboratory"),
    ],
    "biochem": [
        ("Acid-fast", "POSITIVE (ZN stain — retains carbol fuchsin after acid decolorisation)"),
        ("Niacin accumulation", "POSITIVE (unique to M. tuberculosis complex)"),
        ("Nitrate reduction", "POSITIVE"),
        ("Catalase (68°C)", "NEGATIVE (heat-labile; loses catalase at 68°C — differentiates from NTM)"),
        ("Pyrazinamidase", "POSITIVE"),
        ("TCH sensitivity", "SENSITIVE to thiophen-2-carboxylic acid hydrazide (differentiates M. bovis — resistant)"),
        ("Urease", "POSITIVE"),
        ("Growth rate", "SLOW — 3–8 weeks on solid media"),
        ("Cord factor", "POSITIVE — serpentine cording pattern on microscopy"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Isoniazid (H)", "First-line", "Bactericidal; inhibits mycolic acid synthesis"),
        ("Rifampicin (R)", "First-line", "Bactericidal; inhibits RNA polymerase"),
        ("Pyrazinamide (Z)", "First-line", "Bactericidal in acidic environment"),
        ("Ethambutol (E)", "First-line", "Bacteriostatic; inhibits arabinosyl transferase"),
        ("HRZE (2 months) + HR (4 months)", "Standard regimen", "DOTS strategy"),
        ("Streptomycin", "Reserve", "Formerly first-line; used in some regimens"),
        ("MDR-TB drugs", "Bedaquiline, linezolid, clofazimine", "For RIF + INH resistant MDR-TB"),
        ("XDR-TB", "Extensive resistance", "Resistant to fluoroquinolones + injectables"),
    ],
    "clinical": (
        "Leading infectious disease killer globally. Pulmonary TB: productive cough >2 weeks, "
        "haemoptysis, night sweats, weight loss, low-grade fever. Primary TB: Ghon focus + "
        "hilar lymphadenopathy = Ghon complex. Miliary TB: haematogenous dissemination. "
        "Extrapulmonary: lymphadenopathy, pleural effusion, meningitis, spinal (Pott's disease), "
        "renal, peritoneal. Latent TB: TST (Mantoux) or IGRA (QuantiFERON). Diagnosis: "
        "AFB smear + culture + GeneXpert MTB/RIF (NAAT — detects TB + rifampicin resistance in 2 hours). "
        "BCG vaccine for prevention."
    ),
  },

  {
    "name": "15. Treponema pallidum",
    "gram": "special",
    "bg": SPECIAL,
    "basics": [
        ("Kingdom / Class", "Bacteria – Spirochaetes – Spirochaetia"),
        ("Gram Stain", "TOO THIN to visualise on Gram stain; not culturable in vitro"),
        ("Morphology", "Tightly coiled spirochaete; 6–20 µm long × 0.1–0.18 µm wide; 6–14 regular coils; corkscrew motility"),
        ("Capsule", "Outer membrane with lipoproteins; mimics host cell membrane"),
        ("Oxygen Requirement", "Microaerophile; cannot be cultured on artificial media"),
    ],
    "culture": [
        ("In vitro culture", "NOT POSSIBLE — obligate human pathogen; cannot grow on standard media"),
        ("Animal inoculation", "Rabbit testes (testicular inoculation) — reference standard for research"),
        ("Dark-field Microscopy", "PRIMARY diagnosis for primary syphilis — observe corkscrew motility of live treponemes from chancre exudate"),
        ("Direct Fluorescent Antibody (DFA-TP)", "Specific monoclonal antibody staining of smear from lesion"),
        ("Warthin-Starry / Levaditi stain", "Silver impregnation stain for tissue sections"),
    ],
    "biochem": [
        ("Dark-field microscopy", "POSITIVE — corkscrew motility from primary chancre"),
        ("Non-treponemal tests", "VDRL and RPR — measure anticardiolipin antibodies (reagin); REACTIVE in active syphilis; titre correlates with disease activity; used for screening and monitoring treatment"),
        ("Treponemal tests", "TPHA, FTA-ABS, TPPA, EIA/CLIA — specific anti-treponemal antibodies; REMAIN POSITIVE for life after infection (not used to monitor treatment)"),
        ("PCR", "POSITIVE — highly sensitive for primary lesions, CSF neurosyphilis"),
        ("Prozone phenomenon", "False-negative VDRL/RPR in secondary syphilis due to antibody excess"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Benzathine Penicillin G", "ALWAYS Sensitive — no resistance", "DOC for all stages; single IM dose 2.4 MU for primary/secondary"),
        ("Procaine Penicillin", "Sensitive", "Neurosyphilis: high-dose IV or IM"),
        ("Doxycycline", "Sensitive", "Alternative for penicillin allergy (non-pregnant)"),
        ("Ceftriaxone", "Sensitive", "Alternative; used for neurosyphilis"),
        ("Azithromycin", "RESISTANCE EMERGING", "Not recommended; chromosomal A2058G mutation in 23S rRNA"),
        ("Jarisch-Herxheimer reaction", "Not drug resistance", "Febrile reaction 2–8 h after treatment; treat with antipyretics"),
    ],
    "clinical": (
        "Causes syphilis — stages: (1) Primary: painless indurated CHANCRE + painless regional "
        "lymphadenopathy (3–90 days); (2) Secondary: maculopapular rash on palms + soles, "
        "condylomata lata, mucous patches, lymphadenopathy (6–12 weeks); (3) Latent: "
        "asymptomatic; (4) Tertiary: gummas (granulomas), cardiovascular syphilis (aortitis, "
        "aortic aneurysm), neurosyphilis (Argyll Robertson pupil, tabes dorsalis, general paresis). "
        "Congenital syphilis: interstitial keratitis, Hutchinson's teeth, saddlenose, sensorineural deafness. "
        "Transmitted sexually; transplacental."
    ),
  },

  {
    "name": "16. Chlamydia trachomatis",
    "gram": "special",
    "bg": SPECIAL,
    "basics": [
        ("Kingdom / Class", "Bacteria – Chlamydiae – Chlamydiia (obligate intracellular)"),
        ("Gram Stain", "DOES NOT STAIN on Gram stain (no peptidoglycan in cell wall)"),
        ("Morphology", "Two forms: Elementary body (EB) — infectious, metabolically inactive (0.3 µm); Reticulate body (RB) — intracellular, metabolically active (1 µm)"),
        ("Cell Wall", "No peptidoglycan; outer membrane complex (MOMP); β-lactam antibiotics ineffective"),
        ("Oxygen Requirement", "Obligate intracellular parasite; aerobic (uses host cell ATP)"),
    ],
    "culture": [
        ("Cell Culture", "McCoy cells or HeLa 229 cells; centrifugation (shell vial assay) enhances sensitivity"),
        ("Inclusions", "Intracytoplasmic inclusion bodies — Giemsa stain: dark blue/purple; Iodine stain: brown (glycogen-rich inclusions)"),
        ("NAAT", "GOLD STANDARD — PCR/TMA on urine, endocervical, urethral, rectal swabs; sensitivity >95%"),
        ("Direct Fluorescent Antibody (DFA)", "FITC-labelled monoclonal antibodies visualise EBs in smear"),
        ("Serology", "MIF (Micro-immunofluorescence): serovars A–C (trachoma), D–K (STI), L1–L3 (LGV)"),
    ],
    "biochem": [
        ("Oxidase/Catalase", "Not applicable (obligate intracellular)"),
        ("Giemsa stain", "POSITIVE — intracytoplasmic inclusions (dark blue)"),
        ("Iodine stain", "POSITIVE — glycogen inclusions (brown)"),
        ("NAAT (PCR)", "GOLD STANDARD — detects ompA gene"),
        ("Serovars", "A–C: trachoma (hyperendemic); D–K: urogenital STI; L1–L3: Lymphogranuloma venereum (LGV)"),
        ("Complement fixation", "Group antigen — detects genus Chlamydia"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Azithromycin 1g", "Sensitive", "Single oral dose — DOC for uncomplicated urogenital Chlamydia"),
        ("Doxycycline 100mg BD × 7d", "Sensitive", "Alternative first-line; preferred for LGV (21 days)"),
        ("Erythromycin", "Sensitive", "Used in pregnancy as alternative"),
        ("Ofloxacin / Levofloxacin", "Sensitive", "Alternative for urogenital infection"),
        ("β-lactams (penicillins)", "INEFFECTIVE", "No peptidoglycan → no β-lactam target"),
        ("Tetracycline", "Sensitive", "Historical treatment; doxycycline preferred"),
    ],
    "clinical": (
        "Most common bacterial STI worldwide. Urogenital: urethritis, cervicitis, PID, "
        "epididymo-orchitis, infertility (silent disease in up to 70% of women). Neonatal: "
        "ophthalmia neonatorum (conjunctivitis 5–12 days after birth), neonatal pneumonia. "
        "Trachoma: serovars A–C; leading infectious cause of preventable blindness — conjunctival "
        "scarring → entropion → corneal abrasion. LGV (serovars L1–L3): painful inguinal "
        "lymphadenopathy (bubo) + proctitis in MSM. Reactive arthritis (Reiter's syndrome): "
        "urethritis + arthritis + conjunctivitis + mouth ulcers."
    ),
  },

  {
    "name": "17. Rickettsia species",
    "gram": "special",
    "bg": SPECIAL,
    "basics": [
        ("Kingdom / Class", "Bacteria – Proteobacteria – α-Proteobacteria (obligate intracellular)"),
        ("Gram Stain", "Gram-NEGATIVE but poorly stained; Giemsa / Gimenez stain preferred"),
        ("Morphology", "Small pleomorphic coccobacilli 0.3–0.5 × 1–2 µm; non-motile"),
        ("Cell Wall", "Gram-negative type; lipopolysaccharide; intracellular"),
        ("Oxygen Requirement", "Obligate intracellular aerobe; uses host cell ATP"),
    ],
    "culture": [
        ("Cell Culture", "Vero cells, L929 cells, embryonated eggs (yolk sac); BSL-2/3 depending on species"),
        ("Gimenez Stain", "Red/pink organisms on green background — preferred for tissue/cell smears"),
        ("Giemsa Stain", "Purple intracellular coccobacilli"),
        ("NOT culturable", "Routine lab media — will not grow; requires living cells"),
        ("Serology (Weil-Felix)", "HISTORICAL screening test — cross-reaction with Proteus OX strains (OX2, OX19, OXK); low specificity"),
        ("IFA (Indirect Fluorescent Antibody)", "GOLD STANDARD serology — specific anti-rickettsial antibodies"),
    ],
    "biochem": [
        ("Weil-Felix (Proteus agglutination)", "OX19+/OX2+ = Spotted Fever Group; OX19+ = Typhus Group; OXK+ = Scrub typhus (Orientia)"),
        ("IFA serology", "GOLD STANDARD — 4-fold rise in titre between acute & convalescent sera"),
        ("PCR", "Highly sensitive and specific; detects OmpA / OmpB genes in blood or biopsy"),
        ("Immunohistochemistry", "Detects rickettsiae in skin biopsy from rash/eschar"),
        ("Biopsy (eschar/rash)", "Histology + IHC or PCR on rash biopsy from spotted fevers"),
    ],
    "sensitivity": [
        ("Drug", "Pattern", "Notes"),
        ("Doxycycline", "ALWAYS Sensitive — DOC for ALL rickettsioses", "100mg BD × 7 days; start empirically before serology confirmed"),
        ("Chloramphenicol", "Sensitive", "Alternative in pregnancy or children <8 yrs (risk of grey baby syndrome)"),
        ("Azithromycin", "Sensitive", "Mild disease or pregnancy"),
        ("β-lactams / Aminoglycosides", "INEFFECTIVE", "Cannot penetrate intracellular compartment"),
        ("Rifampicin", "Sensitive", "Used in special circumstances"),
    ],
    "clinical": (
        "Key species: Rickettsia rickettsii (Rocky Mountain Spotted Fever — RMSF): fever, headache, "
        "centripetal rash starting on palms/soles; Rickettsia prowazekii (epidemic louse-borne "
        "typhus): classic Brill-Zinsser recurrence; Rickettsia typhi (endemic murine typhus, flea); "
        "Orientia tsutsugamushi (scrub typhus, chigger mite): pathognomonic ESCHAR at bite site. "
        "All cause fever, headache, myalgia, rash (except scrub typhus — may be faint). Vasculitis "
        "of small vessels (replicate in endothelial cells). Vectors: ticks, lice, fleas, mites. "
        "Diagnosis is primarily CLINICAL + serology (IFA). Empiric doxycycline should not be delayed."
    ),
  },
]

# ═══════════════════════════════════════════════════════════════════
# BUILD DOCUMENT
# ═══════════════════════════════════════════════════════════════════
story = []

# ── COVER PAGE ──────────────────────────────────────────────────
cover_data = [[Paragraph("BACTERIOLOGY", S["cover_title"])]]
cover_t = Table(cover_data, colWidths=[17*cm], rowHeights=[3.5*cm])
cover_t.setStyle(TableStyle([
    ("BACKGROUND", (0,0), (-1,-1), DARK_BLUE),
    ("ROUNDEDCORNERS", [10]),
    ("TOPPADDING", (0,0), (-1,-1), 30),
    ("BOTTOMPADDING", (0,0), (-1,-1), 0),
]))
story.append(sp(40))
story.append(cover_t)

sub_data = [[Paragraph("Laboratory Diagnosis Reference Guide", S["cover_sub"])]]
sub_t = Table(sub_data, colWidths=[17*cm], rowHeights=[1.2*cm])
sub_t.setStyle(TableStyle([
    ("BACKGROUND", (0,0), (-1,-1), MID_BLUE),
    ("ROUNDEDCORNERS", [0]),
    ("TOPPADDING", (0,0), (-1,-1), 10),
    ("BOTTOMPADDING", (0,0), (-1,-1), 10),
]))
story.append(sub_t)

story.append(sp(20))
story.append(Paragraph("Morphology  •  Culture  •  Biochemistry  •  Sensitivity  •  Clinical Significance", S["cover_note"]))
story.append(sp(10))
story.append(Paragraph("17 Clinically Important Bacteria  |  Medical Students Edition", S["cover_note"]))
story.append(sp(10))

# Colour legend on cover
legend_data = [
    [Paragraph("🟡 Gram-Positive", ParagraphStyle("l", fontSize=9, textColor=colors.HexColor("#7b4f00"), fontName="Helvetica-Bold")),
     Paragraph("🔵 Gram-Negative", ParagraphStyle("l", fontSize=9, textColor=colors.HexColor("#1a5276"), fontName="Helvetica-Bold")),
     Paragraph("🟣 Special / Atypical", ParagraphStyle("l", fontSize=9, textColor=colors.HexColor("#4a235a"), fontName="Helvetica-Bold")),
     Paragraph("🟢 Anaerobes", ParagraphStyle("l", fontSize=9, textColor=colors.HexColor("#145a32"), fontName="Helvetica-Bold"))],
]
lt = Table(legend_data, colWidths=[4.25*cm]*4)
lt.setStyle(TableStyle([
    ("BACKGROUND", (0,0), (-1,-1), LIGHT_BLUE),
    ("BOX", (0,0), (-1,-1), 0.5, TABLE_GRID),
    ("TOPPADDING", (0,0), (-1,-1), 6),
    ("BOTTOMPADDING", (0,0), (-1,-1), 6),
    ("ALIGN", (0,0), (-1,-1), "CENTER"),
]))
story.append(lt)
story.append(sp(20))
story.append(Paragraph("Sources: Medical Microbiology 9e (Murray), Jawetz Melnick & Adelbergs Medical Microbiology 28E, "
    "Quick Compendium of Clinical Pathology 5e, Tietz Textbook of Laboratory Medicine 7e, Sherris & Ryan Medical Microbiology 8e",
    S["footer_note"]))

story.append(PageBreak())

# ── TABLE OF CONTENTS ────────────────────────────────────────────
story.append(Paragraph("TABLE OF CONTENTS", S["toc_head"]))
story.append(hr())
story.append(sp(6))
gram_cat = {
    "Gram-Positive Cocci": ["1. Staphylococcus aureus", "2. Streptococcus pneumoniae", "3. Streptococcus pyogenes  (Group A Strep)"],
    "Gram-Positive Rods": ["4. Corynebacterium diphtheriae", "12. Clostridium perfringens", "13. Clostridium tetani"],
    "Gram-Negative Cocci": ["5. Neisseria meningitidis", "6. Neisseria gonorrhoeae"],
    "Gram-Negative Rods (Enterobacteriaceae)": ["8. Escherichia coli", "9. Salmonella typhi", "11. Yersinia pestis"],
    "Gram-Negative Rods (Other)": ["7. Haemophilus influenzae", "10. Vibrio cholerae"],
    "Special / Atypical Bacteria": ["14. Mycobacterium tuberculosis", "15. Treponema pallidum",
                                     "16. Chlamydia trachomatis", "17. Rickettsia species"],
}
for cat, items in gram_cat.items():
    story.append(Paragraph(f"<b>{cat}</b>", ParagraphStyle("toc_cat", fontSize=11, textColor=MID_BLUE,
        fontName="Helvetica-Bold", spaceAfter=4, spaceBefore=8, leftIndent=0)))
    for item in items:
        story.append(Paragraph(f"   • {item}", S["toc_entry"]))
story.append(sp(10))
story.append(hr())
story.append(sp(6))
story.append(Paragraph(
    "Each entry covers: Gram stain & morphology • Culture media & colony characteristics • "
    "Biochemical tests • Antibiotic sensitivity patterns • Clinical significance",
    ParagraphStyle("toc_footer", fontSize=9, textColor=colors.grey, fontName="Helvetica-Oblique",
        alignment=TA_CENTER, spaceAfter=4)
))
story.append(PageBreak())

# ── EACH BACTERIUM ───────────────────────────────────────────────
for b in bacteria:
    bg = b["bg"]
    gram = b["gram"]

    # Header banner
    story.append(section_banner(b["name"], gram))
    story.append(sp(6))

    # ---- Morphology & Classification ----
    story.append(KeepTogether([
        Paragraph("MORPHOLOGY & CLASSIFICATION", S["subsection"]),
        info_table(b["basics"], bg=bg),
        sp(8),
    ]))

    # ---- Culture Characteristics ----
    story.append(KeepTogether([
        Paragraph("CULTURE CHARACTERISTICS", S["subsection"]),
        info_table(b["culture"], bg=bg),
        sp(8),
    ]))

    # ---- Biochemical Tests ----
    story.append(KeepTogether([
        Paragraph("BIOCHEMICAL IDENTIFICATION", S["subsection"]),
        info_table(b["biochem"], bg=bg),
        sp(8),
    ]))

    # ---- Sensitivity ----
    story.append(Paragraph("ANTIBIOTIC SENSITIVITY PATTERNS", S["subsection"]))
    headers = b["sensitivity"][0]
    rows = b["sensitivity"][1:]
    # Colour-code sensitivity cells
    raw_data = [[Paragraph(str(c), S["cell_header"]) for c in headers]]
    for row in rows:
        raw_data.append([Paragraph(str(c), S["cell_body"]) for c in row])
    col_w = [5.5*cm, 5.5*cm, 6*cm]
    sens_t = Table(raw_data, colWidths=col_w)
    ts2 = TableStyle([
        ("BACKGROUND", (0,0), (-1,0), HEADER_ROW),
        ("GRID", (0,0), (-1,-1), 0.4, TABLE_GRID),
        ("VALIGN", (0,0), (-1,-1), "MIDDLE"),
        ("TOPPADDING", (0,0), (-1,-1), 4),
        ("BOTTOMPADDING", (0,0), (-1,-1), 4),
        ("LEFTPADDING", (0,0), (-1,-1), 5),
        ("ALIGN", (0,0), (-1,0), "CENTER"),
    ])
    for i in range(1, len(raw_data), 2):
        ts2.add("BACKGROUND", (0,i), (-1,i), ALT_ROW)
    sens_t.setStyle(ts2)
    story.append(sens_t)
    story.append(sp(8))

    # ---- Clinical Significance ----
    story.append(KeepTogether([
        Paragraph("CLINICAL SIGNIFICANCE", S["subsection"]),
        Paragraph(b["clinical"], S["body"]),
        sp(4),
        hr(),
        sp(6),
    ]))

    story.append(PageBreak())

# ── QUICK REFERENCE COMPARISON TABLE ────────────────────────────
story.append(Paragraph("QUICK REFERENCE COMPARISON TABLE", S["toc_head"]))
story.append(hr())
story.append(sp(4))

qr_headers = ["Organism", "Gram", "Key Media", "Diagnostic Test", "DOC"]
qr_rows = [
    ["S. aureus", "+ve cocci", "MSA / BAP", "Coagulase +ve", "Flucloxacillin (MSSA)\nVancomycin (MRSA)"],
    ["S. pneumoniae", "+ve diplococci", "Blood agar", "Optochin S / Bile soluble", "Ceftriaxone"],
    ["S. pyogenes", "+ve cocci chains", "Blood agar", "Bacitracin S / PYR +ve", "Penicillin"],
    ["C. diphtheriae", "+ve rods", "Loeffler / Tellurite", "Elek test / Metachromatic granules", "Erythromycin + Antitoxin"],
    ["N. meningitidis", "−ve diplococci", "Thayer-Martin / CHOC", "Oxidase +ve / Maltose +ve", "Ceftriaxone"],
    ["N. gonorrhoeae", "−ve diplococci", "Thayer-Martin", "Oxidase +ve / Maltose −ve", "Ceftriaxone 500mg IM"],
    ["H. influenzae", "−ve coccobacilli", "Chocolate agar", "X+V factor requirement", "Amox-Clavulanate / Ceftriaxone"],
    ["E. coli", "−ve rods", "MacConkey / EMB", "Metallic green sheen / IMViC++--", "Nitrofurantoin (UTI)"],
    ["S. typhi", "−ve rods", "XLD / Blood culture", "Bone marrow culture / Widal", "Ceftriaxone / Azithromycin"],
    ["V. cholerae", "−ve curved rods", "TCBS (yellow)", "String test / Shooting star", "ORT + Doxycycline"],
    ["Y. pestis", "−ve coccobacilli", "BHI / Blood agar", "Bipolar safety-pin / F1 antigen", "Streptomycin / Doxycycline"],
    ["C. perfringens", "+ve rods (anaerobe)", "Egg yolk (Nagler)", "Nagler reaction / Stormy clot", "Penicillin + Clindamycin"],
    ["C. tetani", "+ve rods (anaerobe)", "Blood agar (anaerobic)", "Drumstick spores / Clinical Dx", "Metronidazole + HTIG"],
    ["M. tuberculosis", "AFB (special)", "LJ medium / MGIT", "ZN stain / GeneXpert", "HRZE (2m) + HR (4m)"],
    ["T. pallidum", "Spirochaete", "Not culturable", "Dark-field microscopy / VDRL / FTA-ABS", "Benzathine Pen G"],
    ["C. trachomatis", "Intracellular", "McCoy cells / NAAT", "NAAT (PCR) Gold standard", "Azithromycin 1g stat"],
    ["Rickettsia spp.", "Intracellular", "Vero cells / IFA serology", "IFA / Weil-Felix / PCR", "Doxycycline"],
]

qr_data = [[Paragraph(h, S["cell_header"]) for h in qr_headers]]
col_widths = [3.8*cm, 2.6*cm, 3.5*cm, 4.1*cm, 3*cm]
for row in qr_rows:
    qr_data.append([Paragraph(c, ParagraphStyle("qrc", fontSize=7.5, fontName="Helvetica", leading=10)) for c in row])

qr_t = Table(qr_data, colWidths=col_widths)
qr_ts = TableStyle([
    ("BACKGROUND", (0,0), (-1,0), HEADER_ROW),
    ("GRID", (0,0), (-1,-1), 0.4, TABLE_GRID),
    ("VALIGN", (0,0), (-1,-1), "TOP"),
    ("TOPPADDING", (0,0), (-1,-1), 4),
    ("BOTTOMPADDING", (0,0), (-1,-1), 4),
    ("LEFTPADDING", (0,0), (-1,-1), 4),
    ("RIGHTPADDING", (0,0), (-1,-1), 4),
    ("ALIGN", (0,0), (-1,0), "CENTER"),
    ("FONTSIZE", (0,1), (-1,-1), 7.5),
])
for i in range(1, len(qr_data), 2):
    qr_ts.add("BACKGROUND", (0,i), (-1,i), ALT_ROW)
qr_t.setStyle(qr_ts)
story.append(qr_t)
story.append(sp(16))
story.append(hr())
story.append(Paragraph(
    "This document is intended for medical education only. Always consult current institutional guidelines and sensitivity data for clinical decision-making. "
    "Compiled by Orris AI • Bacteriology Lab Diagnosis Reference 2026",
    S["footer_note"]))

# ── BUILD ────────────────────────────────────────────────────────
doc.build(story)
print(f"PDF saved to {OUTPUT}")