Culture Media & Culture Methods - NEET PG High-Yield Revision Guide

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

OUTPUT = "/tmp/workspace/neet-pg-microbiology/Culture_Media_NEET_PG.pdf"

doc = SimpleDocTemplate(
    OUTPUT,
    pagesize=A4,
    rightMargin=1.8*cm,
    leftMargin=1.8*cm,
    topMargin=2*cm,
    bottomMargin=2*cm
)

# ── Colour palette ──────────────────────────────────────────────────────────
DARK_BLUE   = colors.HexColor("#1a3a5c")
MED_BLUE    = colors.HexColor("#2563a8")
LIGHT_BLUE  = colors.HexColor("#dbeafe")
ACCENT      = colors.HexColor("#e65c00")
YELLOW_BG   = colors.HexColor("#fffbeb")
GREEN_BG    = colors.HexColor("#f0fdf4")
GREEN_DARK  = colors.HexColor("#166534")
TABLE_HEAD  = colors.HexColor("#1e40af")
ROW_ALT     = colors.HexColor("#f0f7ff")
WHITE       = colors.white
GREY_TEXT   = colors.HexColor("#374151")
LIGHT_GREY  = colors.HexColor("#f3f4f6")
RED_BG      = colors.HexColor("#fff1f2")
RED_DARK    = colors.HexColor("#9b1c1c")

styles = getSampleStyleSheet()

# Custom styles
title_style = ParagraphStyle(
    "Title", parent=styles["Normal"],
    fontSize=22, fontName="Helvetica-Bold",
    textColor=WHITE, alignment=TA_CENTER, spaceAfter=4
)
subtitle_style = ParagraphStyle(
    "Subtitle", parent=styles["Normal"],
    fontSize=11, fontName="Helvetica",
    textColor=colors.HexColor("#bfdbfe"), alignment=TA_CENTER, spaceAfter=2
)
h1 = ParagraphStyle(
    "H1", parent=styles["Normal"],
    fontSize=14, fontName="Helvetica-Bold",
    textColor=WHITE, spaceBefore=8, spaceAfter=4,
    leftIndent=0, leading=18
)
h2 = ParagraphStyle(
    "H2", parent=styles["Normal"],
    fontSize=11, fontName="Helvetica-Bold",
    textColor=DARK_BLUE, spaceBefore=10, spaceAfter=4,
    leftIndent=0, leading=14
)
h3 = ParagraphStyle(
    "H3", parent=styles["Normal"],
    fontSize=10, fontName="Helvetica-Bold",
    textColor=MED_BLUE, spaceBefore=6, spaceAfter=3,
    leftIndent=0, leading=13
)
body = ParagraphStyle(
    "Body", parent=styles["Normal"],
    fontSize=9, fontName="Helvetica",
    textColor=GREY_TEXT, spaceBefore=2, spaceAfter=2,
    leftIndent=0, leading=13
)
body_bold = ParagraphStyle(
    "BodyBold", parent=body,
    fontName="Helvetica-Bold", textColor=DARK_BLUE
)
mnemonic_style = ParagraphStyle(
    "Mnemonic", parent=styles["Normal"],
    fontSize=9.5, fontName="Helvetica-Bold",
    textColor=GREEN_DARK, spaceBefore=3, spaceAfter=3,
    leftIndent=8, leading=14
)
tip_style = ParagraphStyle(
    "Tip", parent=styles["Normal"],
    fontSize=9, fontName="Helvetica-Oblique",
    textColor=RED_DARK, spaceBefore=2, spaceAfter=2,
    leftIndent=8, leading=13
)
tbl_header = ParagraphStyle(
    "TblHeader", parent=styles["Normal"],
    fontSize=9, fontName="Helvetica-Bold",
    textColor=WHITE, alignment=TA_CENTER, leading=12
)
tbl_cell = ParagraphStyle(
    "TblCell", parent=styles["Normal"],
    fontSize=8.5, fontName="Helvetica",
    textColor=GREY_TEXT, alignment=TA_LEFT, leading=11
)
tbl_cell_bold = ParagraphStyle(
    "TblCellBold", parent=tbl_cell,
    fontName="Helvetica-Bold", textColor=DARK_BLUE
)

story = []

# ── Helper functions ─────────────────────────────────────────────────────────

def section_banner(title, color=DARK_BLUE):
    """A coloured banner for section headings."""
    data = [[Paragraph(title, h1)]]
    tbl = Table(data, colWidths=[17.4*cm])
    tbl.setStyle(TableStyle([
        ("BACKGROUND", (0,0), (-1,-1), color),
        ("TOPPADDING",    (0,0), (-1,-1), 6),
        ("BOTTOMPADDING", (0,0), (-1,-1), 6),
        ("LEFTPADDING",   (0,0), (-1,-1), 10),
        ("RIGHTPADDING",  (0,0), (-1,-1), 10),
        ("ROUNDEDCORNERS", [4, 4, 4, 4]),
    ]))
    return tbl

def make_table(headers, rows, col_widths=None):
    """Styled table with alternating row colours."""
    header_row = [Paragraph(h, tbl_header) for h in headers]
    data = [header_row]
    for i, row in enumerate(rows):
        styled = []
        for j, cell in enumerate(row):
            if j == 0:
                styled.append(Paragraph(cell, tbl_cell_bold))
            else:
                styled.append(Paragraph(cell, tbl_cell))
        data.append(styled)

    if col_widths is None:
        w = 17.4 / len(headers)
        col_widths = [w*cm] * len(headers)

    tbl = Table(data, colWidths=col_widths, repeatRows=1)
    style_cmds = [
        ("BACKGROUND",    (0,0), (-1,0), TABLE_HEAD),
        ("ROWBACKGROUNDS", (0,1), (-1,-1), [WHITE, ROW_ALT]),
        ("GRID",          (0,0), (-1,-1), 0.4, colors.HexColor("#c7d7f0")),
        ("VALIGN",        (0,0), (-1,-1), "TOP"),
        ("TOPPADDING",    (0,0), (-1,-1), 4),
        ("BOTTOMPADDING", (0,0), (-1,-1), 4),
        ("LEFTPADDING",   (0,0), (-1,-1), 5),
        ("RIGHTPADDING",  (0,0), (-1,-1), 5),
    ]
    tbl.setStyle(TableStyle(style_cmds))
    return tbl

def mnemonic_box(lines):
    """Green highlighted mnemonic box."""
    content = [Paragraph("💡 MNEMONIC / RECALL", ParagraphStyle(
        "MH", parent=styles["Normal"], fontSize=9, fontName="Helvetica-Bold",
        textColor=GREEN_DARK, leading=12
    ))]
    for line in lines:
        content.append(Paragraph("• " + line, mnemonic_style))
    data = [[content]]
    tbl = Table([[c] for c in content], colWidths=[17.4*cm])
    # Use single table with all content
    all_content = [Paragraph("💡 MNEMONIC / RECALL", ParagraphStyle(
        "MH", parent=styles["Normal"], fontSize=9, fontName="Helvetica-Bold",
        textColor=GREEN_DARK, leading=12, spaceBefore=2
    ))]
    for line in lines:
        all_content.append(Paragraph("  • " + line, mnemonic_style))
    
    outer = Table([[all_content]], colWidths=[17.4*cm])
    outer.setStyle(TableStyle([
        ("BACKGROUND",    (0,0), (-1,-1), GREEN_BG),
        ("BOX",           (0,0), (-1,-1), 1, GREEN_DARK),
        ("TOPPADDING",    (0,0), (-1,-1), 6),
        ("BOTTOMPADDING", (0,0), (-1,-1), 6),
        ("LEFTPADDING",   (0,0), (-1,-1), 10),
        ("RIGHTPADDING",  (0,0), (-1,-1), 10),
    ]))
    return outer

def tip_box(lines, title="⚠️ EXAM TIPS"):
    all_content = [Paragraph(title, ParagraphStyle(
        "TH", parent=styles["Normal"], fontSize=9, fontName="Helvetica-Bold",
        textColor=RED_DARK, leading=12, spaceBefore=2
    ))]
    for line in lines:
        all_content.append(Paragraph("  • " + line, tip_style))
    outer = Table([[all_content]], colWidths=[17.4*cm])
    outer.setStyle(TableStyle([
        ("BACKGROUND",    (0,0), (-1,-1), RED_BG),
        ("BOX",           (0,0), (-1,-1), 1, RED_DARK),
        ("TOPPADDING",    (0,0), (-1,-1), 6),
        ("BOTTOMPADDING", (0,0), (-1,-1), 6),
        ("LEFTPADDING",   (0,0), (-1,-1), 10),
        ("RIGHTPADDING",  (0,0), (-1,-1), 10),
    ]))
    return outer

# ═══════════════════════════════════════════════════════════════════════════
#  COVER PAGE
# ═══════════════════════════════════════════════════════════════════════════
cover_data = [[
    Paragraph("Culture Media &<br/>Culture Methods", title_style),
    Paragraph("NEET PG High-Yield Revision Guide", subtitle_style),
    Paragraph("Microbiology | Complete Rapid Revision", ParagraphStyle(
        "S2", parent=styles["Normal"], fontSize=9.5,
        textColor=colors.HexColor("#93c5fd"), alignment=TA_CENTER
    )),
]]
cover = Table([[
    Paragraph("Culture Media &amp; Culture Methods", title_style),
]], colWidths=[17.4*cm])
cover.setStyle(TableStyle([
    ("BACKGROUND",    (0,0), (-1,-1), DARK_BLUE),
    ("TOPPADDING",    (0,0), (-1,-1), 30),
    ("BOTTOMPADDING", (0,0), (-1,-1), 10),
    ("LEFTPADDING",   (0,0), (-1,-1), 20),
    ("RIGHTPADDING",  (0,0), (-1,-1), 20),
]))
story.append(cover)

sub_cover = Table([[
    Paragraph("NEET PG High-Yield Revision Guide", subtitle_style),
]], colWidths=[17.4*cm])
sub_cover.setStyle(TableStyle([
    ("BACKGROUND",    (0,0), (-1,-1), DARK_BLUE),
    ("TOPPADDING",    (0,0), (-1,-1), 4),
    ("BOTTOMPADDING", (0,0), (-1,-1), 4),
    ("LEFTPADDING",   (0,0), (-1,-1), 20),
    ("RIGHTPADDING",  (0,0), (-1,-1), 20),
]))
story.append(sub_cover)

badge_data = Table([[
    Paragraph("Microbiology  |  Complete Rapid Revision  |  All Culture Media Tables", ParagraphStyle(
        "badge", parent=styles["Normal"], fontSize=9,
        textColor=DARK_BLUE, alignment=TA_CENTER, fontName="Helvetica-Bold"
    ))
]], colWidths=[17.4*cm])
badge_data.setStyle(TableStyle([
    ("BACKGROUND",    (0,0), (-1,-1), LIGHT_BLUE),
    ("TOPPADDING",    (0,0), (-1,-1), 8),
    ("BOTTOMPADDING", (0,0), (-1,-1), 8),
]))
story.append(badge_data)
story.append(Spacer(1, 0.5*cm))

# ═══════════════════════════════════════════════════════════════════════════
#  SECTION 1 – HOW TO REVISE
# ═══════════════════════════════════════════════════════════════════════════
story.append(section_banner("PART 1  |  How to Revise This Topic Effectively", MED_BLUE))
story.append(Spacer(1, 0.2*cm))

story.append(Paragraph("The 3-Column Master Strategy", h2))
story.append(Paragraph(
    "Make a table with three columns: <b>Organism | Medium | Key Feature / Reason</b>. "
    "This single table covers ~90% of NEET PG questions on this topic. "
    "Group by organism type: Bacteria → Fungi → Viruses → Parasites.", body))
story.append(Spacer(1, 0.2*cm))

strategy_rows = [
    ["Day 1",       "Read the Master Table (Part 3) once fully"],
    ["Day 2",       "Close book; write Organism → Medium from memory"],
    ["Day 3",       "Solve 20-30 MCQs on culture media only"],
    ["Day 7",       "Rapid recall: colony morphology buzzwords + transport media"],
    ["Final Week",  "Only mnemonics + Past Year Question (PYQ) patterns"],
]
story.append(make_table(["Day", "Activity"], strategy_rows, [4*cm, 13.4*cm]))
story.append(Spacer(1, 0.3*cm))
story.append(mnemonic_box([
    "Always ask WHY a medium is used - e.g. alkaline pH for Vibrio because it tolerates high pH.",
    "Reasoning helps answer unfamiliar MCQ variants without memorising every detail.",
    "Pair tables with Dr. Mamta Jawa / Apurba Sastry video lectures for visual memory."
]))
story.append(Spacer(1, 0.4*cm))

# ═══════════════════════════════════════════════════════════════════════════
#  SECTION 2 – CLASSIFICATION
# ═══════════════════════════════════════════════════════════════════════════
story.append(section_banner("PART 2  |  Classification of Culture Media"))
story.append(Spacer(1, 0.2*cm))

story.append(Paragraph("A. By Physical State", h2))
phys_rows = [
    ["Liquid (Broth)",  "Nutrient broth, Robertson's Cooked Meat, Alkaline Peptone Water"],
    ["Semisolid",       "Hugh-Leifson medium (motility testing)"],
    ["Solid",           "Nutrient agar, Blood agar, MacConkey agar"],
]
story.append(make_table(["Type", "Examples"], phys_rows, [5*cm, 12.4*cm]))
story.append(Spacer(1, 0.3*cm))

story.append(Paragraph("B. By Nutritional Composition (Most Tested in NEET PG)", h2))
nutri_rows = [
    ["Simple / Basal",   "Supports most non-fastidious organisms", "Nutrient agar, Peptone water"],
    ["Enriched",         "Basal + growth factors (blood/serum) for fastidious organisms", "Blood agar, Chocolate agar, Löffler's serum slope"],
    ["Enrichment",       "Suppresses commensals; favours pathogen in mixed specimens", "Selenite F broth (Salmonella), Alkaline peptone water (Vibrio)"],
    ["Selective",        "Inhibits commensals; isolates target organism", "MacConkey, Thayer-Martin, TCBS, Mannitol salt agar"],
    ["Differential",     "Distinguishes organisms by colony appearance", "MacConkey (LF vs NLF), CLED, XLD"],
    ["Indicator",        "Contains pH indicator that changes colour", "MacConkey (neutral red), CLED (bromothymol blue)"],
    ["Transport",        "Preserves viability during transit to lab", "Stuart's, Amies, Cary-Blair, VR medium"],
]
story.append(make_table(["Type", "Definition", "Examples"], nutri_rows,
                         [3.5*cm, 7*cm, 6.9*cm]))
story.append(Spacer(1, 0.3*cm))
story.append(tip_box([
    "Enrichment vs Selective: Enrichment is LIQUID (broth); Selective is SOLID (agar). This distinction is a common MCQ trap.",
    "Indicator medium is a sub-type of differential medium - it uses a pH indicator dye.",
]))

story.append(PageBreak())

# ═══════════════════════════════════════════════════════════════════════════
#  SECTION 3 – MASTER TABLE: BACTERIA
# ═══════════════════════════════════════════════════════════════════════════
story.append(section_banner("PART 3  |  Master Table: Bacteria → Media (HIGH YIELD)"))
story.append(Spacer(1, 0.2*cm))

story.append(Paragraph("3A. Gram-Positive Bacteria", h2))
gpos_rows = [
    ["Corynebacterium diphtheriae",
     "Löffler's Serum Slope",
     "BEST for metachromatic granules; rapid growth in 6-8 h"],
    ["Corynebacterium diphtheriae",
     "McLeod's / Hoyle's Tellurite",
     "Black colonies; SELECTIVE medium"],
    ["Corynebacterium diphtheriae",
     "Tinsdale Agar",
     "Black colonies with brown halo (tellurite + cystine)"],
    ["Staphylococcus aureus",
     "Mannitol Salt Agar (7.5% NaCl)",
     "Yellow colonies (mannitol fermentation); SELECTIVE"],
    ["Staphylococcus aureus",
     "Baird-Parker Agar",
     "Black shiny colonies + opaque (egg yolk) halo"],
    ["Streptococcus pneumoniae",
     "Blood Agar",
     "Alpha-haemolysis (green); draughtsman/coin/concentric ring colonies"],
    ["Streptococcus pyogenes",
     "Blood Agar",
     "Beta-haemolysis; dew-drop colonies"],
    ["Clostridium perfringens",
     "Nagler's Medium (Egg yolk agar)",
     "Nagler reaction - opalescence due to lecithinase"],
    ["Clostridia (anaerobes)",
     "Robertson's Cooked Meat (RCM) / Thioglycolate broth",
     "Anaerobic enrichment medium"],
    ["Lactobacillus",
     "Rogosa SL Agar",
     "Acidic pH (pH 5.5); selective for lactobacilli"],
    ["Actinomyces",
     "Brain Heart Infusion (BHI)",
     "Anaerobic; sulfur granules in pus (not cultured on simple media)"],
]
story.append(make_table(["Organism", "Medium", "Key Detail / Trick"],
                         gpos_rows, [5.5*cm, 5.5*cm, 6.4*cm]))
story.append(Spacer(1, 0.3*cm))

story.append(Paragraph("3B. Gram-Negative Bacteria", h2))
gneg_rows = [
    ["Vibrio cholerae",
     "TCBS (Thiosulphate Citrate Bile Salt Sucrose)",
     "Yellow colonies (sucrose fermenter); SELECTIVE-DIFFERENTIAL"],
    ["Vibrio cholerae",
     "Alkaline Peptone Water (APW), pH 8.6",
     "ENRICHMENT broth; Vibrio survives high pH"],
    ["Vibrio cholerae",
     "Monsur's Tellurite Taurocholate Gelatin",
     "Grey colonies with turbid halo"],
    ["Salmonella typhi",
     "Bismuth Sulphite Agar (Wilson-Blair)",
     "Black colonies + metallic green/black sheen; HIGHLY selective"],
    ["Salmonella (non-typhi)",
     "XLD (Xylose Lysine Deoxycholate)",
     "Pink with black centre (H2S); Shigella: pink without black"],
    ["Salmonella / Shigella",
     "Selenite F Broth",
     "ENRICHMENT; Salmonella >> Shigella inhibited"],
    ["Salmonella / Shigella",
     "DCA (Deoxycholate Citrate Agar)",
     "SELECTIVE-DIFFERENTIAL for enteric pathogens"],
    ["Salmonella / Shigella",
     "SS Agar",
     "Salmonella-Shigella agar; used in routine labs"],
    ["E. coli / Coliforms",
     "MacConkey Agar",
     "Lactose fermenter → pink/red colonies; NLF are colourless"],
    ["E. coli",
     "EMB Agar (Eosin Methylene Blue)",
     "Metallic green sheen (rapid LF); NLF are pink"],
    ["E. coli / Urine",
     "CLED Agar",
     "Prevents Proteus swarming; electrolyte-deficient"],
    ["Neisseria gonorrhoeae",
     "Thayer-Martin Agar",
     "Contains VCN: Vancomycin, Colistin, Nystatin"],
    ["Neisseria meningitidis",
     "Chocolate Agar",
     "Heated blood = releases X and V factors; fastidious organisms"],
    ["H. influenzae",
     "Levinthal's Agar",
     "Iridescence (satellite phenomenon)"],
    ["H. influenzae",
     "Fildes Agar",
     "Enriched with peptic digest of blood (X+V factors)"],
    ["Bordetella pertussis",
     "Bordet-Gengou (BG) Agar",
     "Mercury drop / bisected pearl colonies; 50% blood"],
    ["Bordetella pertussis",
     "Regan-Lowe Agar",
     "Charcoal-based; more sensitive than BG"],
    ["Campylobacter",
     "Skirrow's Medium",
     "Selective; incubated 42°C, microaerophilic (5% O2)"],
    ["H. pylori",
     "Skirrow's / BHIB Agar",
     "Urease positive; microaerophilic"],
    ["Pseudomonas aeruginosa",
     "Cetrimide Agar",
     "Selective; produces fluorescent pigments (pyocyanin, pyoverdin)"],
    ["Brucella",
     "Castaneda's Medium",
     "Diphasic medium (liquid + solid); CO2 required (B. abortus)"],
    ["Leptospira",
     "Fletcher's / EMJH Medium",
     "Semisolid; dark-field microscopy used to confirm"],
    ["Yersinia pestis",
     "MacConkey / Nutrient Agar",
     "Stalactite growth in broth; hammered metal appearance on agar"],
    ["Legionella",
     "BCYE Agar (Buffered Charcoal Yeast Extract)",
     "Requires L-cysteine and iron; cannot grow on blood agar"],
]
story.append(make_table(["Organism", "Medium", "Key Detail / Trick"],
                         gneg_rows, [5.5*cm, 5.5*cm, 6.4*cm]))
story.append(Spacer(1, 0.3*cm))

story.append(Paragraph("3C. Mycobacteria", h2))
myco_rows = [
    ["Mycobacterium tuberculosis",
     "Löwenstein-Jensen (LJ) Medium",
     "Rough Raised Buff-colored (RRBC) colonies; 6-8 weeks"],
    ["Mycobacterium tuberculosis",
     "Middlebrook 7H10 / 7H11",
     "Transparent agar; faster than LJ; for drug susceptibility"],
    ["Mycobacterium tuberculosis",
     "BACTEC / MGIT (Mycobacteria Growth Indicator Tube)",
     "FASTEST; radiometric/fluorescent; ~2 weeks"],
    ["Mycobacterium leprae",
     "Cannot be cultured on artificial media",
     "Cultured in armadillo footpad / mouse footpad only"],
    ["Atypical Mycobacteria (NTM)",
     "LJ at 25°C, 37°C, 42°C",
     "Growth temperature helps in species identification"],
]
story.append(make_table(["Organism", "Medium", "Key Detail"],
                         myco_rows, [5.5*cm, 5.5*cm, 6.4*cm]))
story.append(Spacer(1, 0.3*cm))

story.append(tip_box([
    "BACTEC/MGIT = FASTEST for MTB culture (NEET PG favourite).",
    "M. leprae = CANNOT be cultured on any artificial medium (armadillo footpad = only in-vivo model).",
    "LJ medium contains malachite green (inhibits other bacteria) + egg (solidifying agent).",
]))

story.append(PageBreak())

# ═══════════════════════════════════════════════════════════════════════════
#  SECTION 4 – FUNGI
# ═══════════════════════════════════════════════════════════════════════════
story.append(section_banner("PART 4  |  Fungi - Culture Media", colors.HexColor("#6d28d9")))
story.append(Spacer(1, 0.2*cm))

fungi_rows = [
    ["All fungi (standard)",     "Sabouraud's Dextrose Agar (SDA)", "pH 5.6; cycloheximide + chloramphenicol added; 25°C"],
    ["Cryptococcus neoformans",  "Birdseed / Niger Seed Agar",      "Brown colonies - phenol oxidase enzyme; urease positive"],
    ["Candida albicans",         "Corn Meal Agar",                  "Chlamydospores (terminal); germ tube test at 37°C"],
    ["Candida albicans",         "Chrome Agar",                     "Green colonies for C. albicans; other Candida spp. differ"],
    ["Dermatophytes",            "Dermatophyte Test Medium (DTM)",  "Red colour change (alkaline pH) in 10-14 days"],
    ["Dimorphic fungi (all)",    "SDA at 25°C = Mould form",        "Mould at room temp; Yeast at body temp (37°C)"],
    ["Aspergillus",              "SDA / Czapek-Dox Agar",           "Conidiophores; species identified by colony colour"],
    ["Malassezia furfur",        "SDA + olive oil overlay",         "Lipophilic; requires exogenous lipids to grow"],
]
story.append(make_table(["Organism", "Medium", "Key Detail"],
                         fungi_rows, [5.5*cm, 5.5*cm, 6.4*cm]))
story.append(Spacer(1, 0.3*cm))
story.append(mnemonic_box([
    "SDA = Standard for ALL fungi (pH 5.6 = acidic, inhibits bacteria)",
    "Birdseed agar → Cryptococcus → Brown (phenol oxidase = melanin production)",
    "Dimorphic = Dual form: Cold (25°C) = Mould; Warm (37°C) = Yeast  →  'Cold = Mould; Warm = Yeast'",
    "Malassezia = Lipophilic = needs olive oil on SDA",
]))

story.append(PageBreak())

# ═══════════════════════════════════════════════════════════════════════════
#  SECTION 5 – VIRUSES
# ═══════════════════════════════════════════════════════════════════════════
story.append(section_banner("PART 5  |  Virus Culture Methods", colors.HexColor("#b45309")))
story.append(Spacer(1, 0.2*cm))

virus_rows = [
    ["Cell Culture (most common method)",
     "Cytopathic Effect (CPE) observed",
     "Most viruses; HSV, CMV, Adenovirus, Poliovirus"],
    ["Embryonated Egg - CAM route",
     "Pocks on CAM",
     "Poxviruses (smallpox, vaccinia)"],
    ["Embryonated Egg - Amniotic route",
     "Haemagglutination",
     "Influenza (primary isolation)"],
    ["Embryonated Egg - Allantoic route",
     "HA in allantoic fluid",
     "Influenza, Mumps (propagation)"],
    ["Embryonated Egg - Yolk sac",
     "Growth in yolk sac",
     "Chlamydia, Rickettsia, Arboviruses"],
    ["Animal Inoculation",
     "Signs in animal",
     "Rabies (mouse intracerebral), Arboviruses, Coxsackie A"],
    ["Cannot be cultured",
     "No growth on any artificial medium",
     "Hep B, Hep C, Parvovirus B19, Norovirus"],
]
story.append(make_table(["Method", "Indicator of Growth", "Key Viruses"],
                         virus_rows, [5*cm, 5.5*cm, 6.9*cm]))
story.append(Spacer(1, 0.3*cm))
story.append(mnemonic_box([
    "CAM = Chorioallantoic Membrane → Pocks → POXvirus",
    "Influenza: Amniotic (primary isolation) → Allantoic (propagation)",
    "Rabies → Mouse intracerebral → Negri bodies in hippocampus (Ammon's horn)",
]))

story.append(PageBreak())

# ═══════════════════════════════════════════════════════════════════════════
#  SECTION 6 – TRANSPORT MEDIA
# ═══════════════════════════════════════════════════════════════════════════
story.append(section_banner("PART 6  |  Transport Media"))
story.append(Spacer(1, 0.2*cm))

transport_rows = [
    ["Stuart's Medium",            "General bacteria; Gonococci (without charcoal)"],
    ["Amies Medium",               "Gonococci (with charcoal); general bacteria"],
    ["Cary-Blair Medium",          "Vibrio cholerae, Campylobacter, enteric organisms (faecal specimens)"],
    ["VR Medium (Venkatraman-Ramakrishnan)", "Vibrio cholerae (alkaline, pH 9.2)"],
    ["Pike's Medium",              "Streptococci from throat swabs"],
    ["Buffered Glycerol Saline",   "Shigella (in stool specimens)"],
    ["Alkaline Glycerol Saline",   "Shigella (alternative)"],
    ["Loeffler's Medium",          "Corynebacterium diphtheriae (also an enriched medium)"],
    ["Liquid Nitrogen / Glycerol broth", "Long-term storage of cultures"],
]
story.append(make_table(["Medium", "Organism / Specimen"], transport_rows, [8*cm, 9.4*cm]))
story.append(Spacer(1, 0.3*cm))
story.append(tip_box([
    "VR medium = ONLY for Vibrio cholerae transport (alkaline pH 9.2).",
    "Stuart's vs Amies: Stuart's has no charcoal; Amies has charcoal (charcoal absorbs toxic metabolites for fastidious organisms).",
    "Buffered Glycerol Saline = Shigella in stool - a common MCQ question.",
]))

story.append(PageBreak())

# ═══════════════════════════════════════════════════════════════════════════
#  SECTION 7 – SPECIAL CULTURE CONDITIONS
# ═══════════════════════════════════════════════════════════════════════════
story.append(section_banner("PART 7  |  Special Culture Conditions & Methods"))
story.append(Spacer(1, 0.2*cm))

conditions_rows = [
    ["Capnophilic (5-10% CO2)",
     "CO2 incubator / candle jar",
     "H. influenzae, Neisseria, Brucella abortus, Streptococcus pneumoniae"],
    ["Microaerophilic (5% O2, 10% CO2)",
     "GasPak jar / specific generators",
     "Campylobacter (42°C), H. pylori, Helicobacter spp."],
    ["Anaerobic culture (0% O2)",
     "Anaerobic jar / glove box",
     "Clostridia, Bacteroides, Fusobacterium, Actinomyces"],
    ["Candle jar",
     "Simple CO2 source (~3%)",
     "Neisseria, H. influenzae (field / resource-limited settings)"],
    ["BACTEC / MGIT",
     "Automated radiometric / fluorescent",
     "MTB - fastest culture method (~2 weeks)"],
    ["Cell culture",
     "CPE / immunofluorescence",
     "Viruses, Chlamydia, Rickettsia (obligate intracellular)"],
    ["Hanging drop preparation",
     "Dark-field / phase contrast microscopy",
     "Motility of Vibrio cholerae - darting (shooting star) motility"],
    ["Armadillo footpad",
     "In vivo model",
     "M. leprae (only viable model for cultivation)"],
]
story.append(make_table(["Condition / Method", "Technique", "Organisms"],
                         conditions_rows, [5*cm, 5*cm, 7.4*cm]))
story.append(Spacer(1, 0.3*cm))

# ═══════════════════════════════════════════════════════════════════════════
#  SECTION 8 – COLONY MORPHOLOGY BUZZWORDS
# ═══════════════════════════════════════════════════════════════════════════
story.append(section_banner("PART 8  |  Colony Morphology Buzzwords (Very High Yield)"))
story.append(Spacer(1, 0.2*cm))

colony_rows = [
    ["Mercury drop / Bisected pearl",     "Bordetella pertussis on Bordet-Gengou agar"],
    ["Medusa head / Inverted fir tree",   "Bacillus anthracis on nutrient agar"],
    ["String of pearls (gelatin stab)",   "Bacillus anthracis"],
    ["Draughtsman / Coin / Concentric rings", "Streptococcus pneumoniae on blood agar"],
    ["Dew drop",                          "Streptococcus pyogenes on blood agar"],
    ["Beaten copper / Cauliflower",       "Actinomyces israelii"],
    ["Black colonies + metallic sheen",   "Salmonella typhi on Bismuth Sulphite (Wilson-Blair) agar"],
    ["Metallic green sheen",              "E. coli on EMB agar"],
    ["Fried egg",                         "Mycoplasma pneumoniae (tiny, needs 2-3 weeks)"],
    ["Breadcrumb",                        "Nocardia asteroides"],
    ["Yellow sulfur granules in pus",     "Actinomyces israelii (not cultured but seen in specimen)"],
    ["Mushroom / Umbrella (in gelatin)",  "Proteus vulgaris"],
    ["Stalactite growth (in broth)",      "Yersinia pestis"],
    ["Oil paint appearance",              "Pseudomonas aeruginosa on agar"],
    ["Swarming growth",                   "Proteus mirabilis / vulgaris on blood agar"],
    ["Satellite phenomenon",              "H. influenzae around S. aureus (provides X+V factors)"],
    ["Wedge-shaped / Tenacious",          "Bacillus anthracis - non-haemolytic, non-motile"],
]
story.append(make_table(["Colony Appearance", "Organism / Medium"],
                         colony_rows, [8*cm, 9.4*cm]))

story.append(PageBreak())

# ═══════════════════════════════════════════════════════════════════════════
#  SECTION 9 – MNEMONICS
# ═══════════════════════════════════════════════════════════════════════════
story.append(section_banner("PART 9  |  Key Mnemonics for Rapid Recall", colors.HexColor("#065f46")))
story.append(Spacer(1, 0.2*cm))

mnemonics = [
    ("TCBS = Yellow for Vibrio",
     "Vibrio causes rice-water diarrhoea → think yellow watery stools → YELLOW colonies on TCBS"),
    ("LJ for MTB = BRR (Buff, Rough, Raised)",
     "BRR = 'Brrr it's cold and takes LONG' → 6-8 weeks, like winter"),
    ("Thayer-Martin = VCN",
     "V = Vancomycin (blocks Gram+ve), C = Colistin (blocks Gram-ve), N = Nystatin (blocks fungi)"),
    ("MacConkey = Pink = Lactose Fermenters",
     "PICK = Pink Is Coliforms using Ketones (LF) → E. coli, Klebsiella, Enterobacter"),
    ("CLED = No Creep",
     "CLED prevents Proteus swarming → 'Cled says No Creep allowed'"),
    ("Cold = Mould; Warm = Yeast (Dimorphic fungi)",
     "25°C → Mould (in nature); 37°C → Yeast (in body) → Mnemonic: 'Moulds in the Cold'"),
    ("Cannot culture on artificial media",
     "TRC = Treponema pallidum, Rickettsia, Chlamydia + M. leprae → all OBLIGATE intracellular / specialized"),
    ("Enrichment media = BROTH (Liquid)",
     "Enrichment = ENRICH the target in BROTH before plating on selective solid agar"),
    ("Bordet-Gengou = Bordetella",
     "Both start with 'Bord' → easy recall"),
    ("Wilson-Blair = Salmonella typhi ONLY",
     "W-B = Black sheen = Typhoid → 'Black flag for Typhoid'"),
    ("BCYE for Legionella",
     "B = Buffered, C = Charcoal, Y = Yeast extract, E = Requires L-cysteine → 'BCYE for Battlefield Legionnaire'"),
]

for mnem, explanation in mnemonics:
    box_content = [
        Paragraph(mnem, ParagraphStyle("MH2", parent=styles["Normal"], fontSize=10,
                                        fontName="Helvetica-Bold", textColor=GREEN_DARK, leading=13)),
        Paragraph(explanation, ParagraphStyle("ME2", parent=styles["Normal"], fontSize=9,
                                               fontName="Helvetica", textColor=GREY_TEXT,
                                               leading=12, leftIndent=10))
    ]
    m_tbl = Table([[box_content]], colWidths=[17.4*cm])
    m_tbl.setStyle(TableStyle([
        ("BACKGROUND",    (0,0), (-1,-1), GREEN_BG),
        ("BOX",           (0,0), (-1,-1), 0.8, GREEN_DARK),
        ("TOPPADDING",    (0,0), (-1,-1), 5),
        ("BOTTOMPADDING", (0,0), (-1,-1), 5),
        ("LEFTPADDING",   (0,0), (-1,-1), 8),
        ("RIGHTPADDING",  (0,0), (-1,-1), 8),
    ]))
    story.append(m_tbl)
    story.append(Spacer(1, 0.15*cm))

story.append(PageBreak())

# ═══════════════════════════════════════════════════════════════════════════
#  SECTION 10 – PYQ PATTERNS
# ═══════════════════════════════════════════════════════════════════════════
story.append(section_banner("PART 10  |  Past Year NEET PG Question Patterns", ACCENT))
story.append(Spacer(1, 0.2*cm))

pyq_rows = [
    ["1", "Medium for Vibrio cholerae isolation",       "TCBS agar (yellow colonies)"],
    ["2", "Enrichment broth for Vibrio cholerae",       "Alkaline Peptone Water (pH 8.6)"],
    ["3", "Transport medium for V. cholerae",           "VR Medium / Cary-Blair"],
    ["4", "FASTEST method for MTB culture",             "BACTEC / MGIT"],
    ["5", "Medium for Bordetella pertussis",            "Bordet-Gengou (primary) / Regan-Lowe"],
    ["6", "Colony description of B. pertussis",         "Mercury drop / Bisected pearl on BG agar"],
    ["7", "Cannot be cultured on artificial media",     "Treponema pallidum, M. leprae"],
    ["8", "Enrichment medium for Salmonella",           "Selenite F Broth"],
    ["9", "Selective medium for Neisseria",             "Thayer-Martin (VCN)"],
    ["10", "Fried egg colony organism",                 "Mycoplasma pneumoniae"],
    ["11", "Medium for urine culture (standard)",       "CLED Agar (no Proteus swarming)"],
    ["12", "Medium for C. diphtheriae (granules)",      "Löffler's Serum Slope"],
    ["13", "Selective medium for C. diphtheriae",       "McLeod's Tellurite (black colonies)"],
    ["14", "Black metallic sheen on Bismuth sulphite",  "Salmonella typhi"],
    ["15", "Metallic green sheen on EMB",               "E. coli"],
    ["16", "Organism needing olive oil on SDA",         "Malassezia furfur"],
    ["17", "Brown colonies on birdseed agar",           "Cryptococcus neoformans"],
    ["18", "Dimorphic fungi temperature rule",          "25°C = Mould; 37°C = Yeast"],
    ["19", "Temperature for Campylobacter culture",     "42°C, microaerophilic"],
    ["20", "Medium requiring L-cysteine + iron",        "BCYE agar → Legionella"],
]
story.append(make_table(["#", "Question Theme", "Answer"],
                         pyq_rows, [1*cm, 9.4*cm, 7*cm]))

story.append(Spacer(1, 0.5*cm))
story.append(HRFlowable(width="100%", thickness=1, color=MED_BLUE))
story.append(Spacer(1, 0.2*cm))

footer_style = ParagraphStyle("footer", parent=styles["Normal"],
    fontSize=8.5, fontName="Helvetica", textColor=colors.HexColor("#6b7280"),
    alignment=TA_CENTER, leading=12)
story.append(Paragraph(
    "Culture Media &amp; Culture Methods | NEET PG High-Yield Revision Guide | "
    "Based on Apurba Sastry Microbiology &amp; Standard NEET PG Curriculum",
    footer_style))

# ── Build PDF ────────────────────────────────────────────────────────────
doc.build(story)
print(f"PDF created successfully: {OUTPUT}")