CHAPTER: PATHOGENIC ORGANISMS

mkdir -p /tmp/workspace/pathogenic-organisms/diagrams /tmp/workspace/pathogenic-organisms/output && echo "Dirs created"

python3 << 'EOF' import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt import matplotlib.patches as mpatches from matplotlib.patches import FancyBboxPatch, FancyArrowPatch import numpy as np # ── DIAGRAM 1: Classification of Pathogenic Organisms ────────────────────── fig, ax = plt.subplots(figsize=(14, 9)) ax.set_xlim(0, 14) ax.set_ylim(0, 9) ax.axis('off') ax.set_facecolor('#F0F4FF') fig.patch.set_facecolor('#F0F4FF') def box(ax, x, y, w, h, text, color, fontsize=10, bold=False): rect = FancyBboxPatch((x, y), w, h, boxstyle="round,pad=0.1", linewidth=1.5, edgecolor='#333', facecolor=color) ax.add_patch(rect) weight = 'bold' if bold else 'normal' ax.text(x + w/2, y + h/2, text, ha='center', va='center', fontsize=fontsize, fontweight=weight, wrap=True, multialignment='center', color='white' if color in ['#1A3C6E','#C0392B','#1A6E3C','#6E1A5A','#6E5A1A'] else '#111') # Root box(ax, 5.5, 7.8, 3, 0.9, 'PATHOGENIC\nORGANISMS', '#1A3C6E', fontsize=12, bold=True) ax.annotate('', xy=(2, 7.0), xytext=(7, 7.8), arrowprops=dict(arrowstyle='->', color='#333', lw=1.5)) ax.annotate('', xy=(5, 7.0), xytext=(7, 7.8), arrowprops=dict(arrowstyle='->', color='#333', lw=1.5)) ax.annotate('', xy=(8, 7.0), xytext=(7, 7.8), arrowprops=dict(arrowstyle='->', color='#333', lw=1.5)) ax.annotate('', xy=(11, 7.0), xytext=(7, 7.8), arrowprops=dict(arrowstyle='->', color='#333', lw=1.5)) ax.annotate('', xy=(13, 7.0), xytext=(7, 7.8), arrowprops=dict(arrowstyle='->', color='#333', lw=1.5)) # Level 1 box(ax, 0.5, 6.0, 3, 0.9, 'BACTERIA', '#1A5276', fontsize=11, bold=True) box(ax, 3.8, 6.0, 2.4, 0.9, 'VIRUSES', '#7B241C', fontsize=11, bold=True) box(ax, 6.7, 6.0, 2.4, 0.9, 'FUNGI', '#1A6E3C', fontsize=11, bold=True) box(ax, 9.6, 6.0, 2.4, 0.9, 'PARASITES', '#6E4C1E', fontsize=11, bold=True) box(ax, 12.2, 6.0, 1.6, 0.9, 'VECTORS &\nRODENTS', '#4A235A', fontsize=9, bold=True) # Bacteria sub-branches ax.annotate('', xy=(1, 5.1), xytext=(2, 6.0), arrowprops=dict(arrowstyle='->', color='#555', lw=1.2)) ax.annotate('', xy=(2.8, 5.1), xytext=(2, 6.0), arrowprops=dict(arrowstyle='->', color='#555', lw=1.2)) box(ax, 0.1, 4.1, 1.8, 0.9, 'COCCI\n(Spherical)', '#2E86C1', fontsize=8) box(ax, 2.1, 4.1, 1.8, 0.9, 'BACILLI\n(Rod-shaped)', '#2E86C1', fontsize=8) # Cocci sub ax.annotate('', xy=(0.5, 3.2), xytext=(1.0, 4.1), arrowprops=dict(arrowstyle='->', color='#777', lw=1)) ax.annotate('', xy=(1.5, 3.2), xytext=(1.0, 4.1), arrowprops=dict(arrowstyle='->', color='#777', lw=1)) box(ax, 0.1, 2.2, 0.8, 0.9, 'Gram\n+ve', '#85C1E9', fontsize=7) box(ax, 1.1, 2.2, 0.8, 0.9, 'Gram\n-ve', '#F1948A', fontsize=7) # Bacilli sub ax.annotate('', xy=(2.5, 3.2), xytext=(3.0, 4.1), arrowprops=dict(arrowstyle='->', color='#777', lw=1)) ax.annotate('', xy=(3.5, 3.2), xytext=(3.0, 4.1), arrowprops=dict(arrowstyle='->', color='#777', lw=1)) box(ax, 2.1, 2.2, 0.8, 0.9, 'Gram\n+ve', '#85C1E9', fontsize=7) box(ax, 3.1, 2.2, 0.8, 0.9, 'Gram\n-ve', '#F1948A', fontsize=7) # Virus sub ax.annotate('', xy=(4.5, 5.1), xytext=(5.0, 6.0), arrowprops=dict(arrowstyle='->', color='#555', lw=1.2)) ax.annotate('', xy=(5.5, 5.1), xytext=(5.0, 6.0), arrowprops=dict(arrowstyle='->', color='#555', lw=1.2)) box(ax, 3.9, 4.1, 0.9, 0.9, 'DNA\nVirus', '#E59866', fontsize=7) box(ax, 5.0, 4.1, 0.9, 0.9, 'RNA\nVirus', '#E59866', fontsize=7) # Fungi sub ax.annotate('', xy=(7.3, 5.1), xytext=(7.9, 6.0), arrowprops=dict(arrowstyle='->', color='#555', lw=1.2)) ax.annotate('', xy=(8.5, 5.1), xytext=(7.9, 6.0), arrowprops=dict(arrowstyle='->', color='#555', lw=1.2)) box(ax, 6.8, 4.1, 1.0, 0.9, 'Super-\nficial', '#52BE80', fontsize=7) box(ax, 8.0, 4.1, 0.9, 0.9, 'Deep\n(Systemic)', '#52BE80', fontsize=7) # Parasites sub ax.annotate('', xy=(10.1, 5.1), xytext=(10.8, 6.0), arrowprops=dict(arrowstyle='->', color='#555', lw=1.2)) ax.annotate('', xy=(11.2, 5.1), xytext=(10.8, 6.0), arrowprops=dict(arrowstyle='->', color='#555', lw=1.2)) box(ax, 9.7, 4.1, 0.8, 0.9, 'Proto-\nzoa', '#D4AC0D', fontsize=7) box(ax, 10.8, 4.1, 1.2, 0.9, 'Helminths\n& Ecto', '#D4AC0D', fontsize=7) ax.set_title('Classification of Pathogenic Organisms', fontsize=14, fontweight='bold', pad=10, color='#1A3C6E') plt.tight_layout() plt.savefig('/tmp/workspace/pathogenic-organisms/diagrams/fig1_classification.png', dpi=150, bbox_inches='tight') plt.close() print("Fig1 done") EOF

python3 << 'EOF' import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt import matplotlib.patches as mpatches import numpy as np # ── DIAGRAM 2: Gram Positive vs Gram Negative Cell Wall ────────────────────── fig, axes = plt.subplots(1, 2, figsize=(13, 7)) fig.patch.set_facecolor('#F8F9FA') fig.suptitle('Gram-Positive vs Gram-Negative Cell Wall Structure', fontsize=14, fontweight='bold', color='#1A3C6E', y=1.01) for ax in axes: ax.set_xlim(0, 10) ax.set_ylim(0, 10) ax.axis('off') # --- Gram Positive --- ax = axes[0] ax.set_facecolor('#FFF8F0') ax.set_title('GRAM-POSITIVE\n(Appears PURPLE)', fontsize=12, fontweight='bold', color='#4A235A', pad=8) # Cytoplasm rect = plt.Rectangle((0.5, 0.5), 9, 3.5, color='#AED6F1', zorder=1) ax.add_patch(rect) ax.text(5, 2.3, 'CYTOPLASM', ha='center', va='center', fontsize=10, fontweight='bold', color='#1A5276') # Cell membrane rect = plt.Rectangle((0.5, 4.0), 9, 0.5, color='#F0B27A', zorder=2) ax.add_patch(rect) ax.text(5, 4.25, 'Cell Membrane', ha='center', va='center', fontsize=9, fontweight='bold') # Thick peptidoglycan rect = plt.Rectangle((0.5, 4.5), 9, 2.8, color='#82E0AA', zorder=2) ax.add_patch(rect) ax.text(5, 5.9, 'THICK PEPTIDOGLYCAN\nLAYER (20-80 nm)', ha='center', va='center', fontsize=10, fontweight='bold', color='#1A6E3C') # Teichoic acid lines for x in [2, 3.5, 5, 6.5, 8]: ax.plot([x, x], [4.5, 7.3], color='#922B21', linewidth=2, linestyle='--', zorder=3) ax.text(5, 7.7, 'Teichoic Acids', ha='center', fontsize=8, color='#922B21', style='italic') # Label ax.text(5, 9.0, 'Crystal Violet RETAINED → Purple', ha='center', fontsize=9, fontweight='bold', color='#4A235A', bbox=dict(boxstyle='round', facecolor='#D7BDE2', alpha=0.8)) ax.text(0.5, 0.1, 'Examples: Staphylococcus, Streptococcus,\nBacillus, Clostridium, Mycobacterium', fontsize=8, color='#1A3C6E') # Arrows + labels ax.annotate('', xy=(0.3, 5.9), xytext=(-0.2, 5.9), arrowprops=dict(arrowstyle='<->', color='#1A6E3C', lw=2)) # --- Gram Negative --- ax = axes[1] ax.set_facecolor('#F0F8FF') ax.set_title('GRAM-NEGATIVE\n(Appears PINK/RED)', fontsize=12, fontweight='bold', color='#922B21', pad=8) # Cytoplasm rect = plt.Rectangle((0.5, 0.5), 9, 3.0, color='#AED6F1', zorder=1) ax.add_patch(rect) ax.text(5, 2.0, 'CYTOPLASM', ha='center', va='center', fontsize=10, fontweight='bold', color='#1A5276') # Inner membrane rect = plt.Rectangle((0.5, 3.5), 9, 0.45, color='#F0B27A', zorder=2) ax.add_patch(rect) ax.text(5, 3.73, 'Inner (Cytoplasmic) Membrane', ha='center', va='center', fontsize=8, fontweight='bold') # Periplasmic space rect = plt.Rectangle((0.5, 3.95), 9, 0.35, color='#FDFEFE', zorder=2) ax.add_patch(rect) ax.text(5, 4.13, 'Periplasmic Space', ha='center', va='center', fontsize=7, color='#555') # Thin peptidoglycan rect = plt.Rectangle((0.5, 4.3), 9, 0.55, color='#82E0AA', zorder=2) ax.add_patch(rect) ax.text(5, 4.58, 'Thin Peptidoglycan (2-7 nm)', ha='center', va='center', fontsize=8, fontweight='bold', color='#1A6E3C') # Outer membrane rect = plt.Rectangle((0.5, 4.85), 9, 0.5, color='#F1948A', zorder=2) ax.add_patch(rect) ax.text(5, 5.1, 'Outer Membrane', ha='center', va='center', fontsize=9, fontweight='bold', color='#922B21') # LPS spikes for x in np.arange(1, 10, 0.7): ax.annotate('', xy=(x, 6.4), xytext=(x, 5.35), arrowprops=dict(arrowstyle='->', color='#C0392B', lw=1.5)) ax.text(5, 6.8, 'LPS (Lipopolysaccharide / Endotoxin)', ha='center', fontsize=8, color='#922B21', fontweight='bold') ax.text(5, 9.0, 'Crystal Violet LOST → Pink (Safranin)', ha='center', fontsize=9, fontweight='bold', color='#922B21', bbox=dict(boxstyle='round', facecolor='#FADBD8', alpha=0.8)) ax.text(0.5, 0.1, 'Examples: E.coli, Salmonella, Vibrio,\nNeisseria, Pseudomonas, Klebsiella', fontsize=8, color='#1A3C6E') plt.tight_layout() plt.savefig('/tmp/workspace/pathogenic-organisms/diagrams/fig2_gramstain.png', dpi=150, bbox_inches='tight') plt.close() print("Fig2 done") EOF

python3 << 'EOF' import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt import matplotlib.patches as mpatches import numpy as np # ── DIAGRAM 3: Bacteria Shapes & Arrangements ─────────────────────────────── fig, ax = plt.subplots(figsize=(13, 5)) ax.set_xlim(0, 13) ax.set_ylim(0, 5) ax.axis('off') ax.set_facecolor('#F8F9FA') fig.patch.set_facecolor('#F8F9FA') ax.set_title('Bacterial Shapes and Arrangements', fontsize=14, fontweight='bold', color='#1A3C6E', pad=10) shapes = [ # (x_center, y_center, label, sublabel) ] def draw_coccus(ax, cx, cy, r=0.25, color='#5DADE2'): c = plt.Circle((cx, cy), r, color=color, zorder=3) ax.add_patch(c) def draw_rod(ax, cx, cy, w=0.7, h=0.3, color='#58D68D', angle=0): from matplotlib.patches import FancyBboxPatch rect = FancyBboxPatch((cx - w/2, cy - h/2), w, h, boxstyle="round,pad=0.05", color=color, zorder=3) ax.add_patch(rect) # ---- Cocci arrangements ---- # Monococcus draw_coccus(ax, 1.0, 3.5) ax.text(1.0, 2.9, 'Monococcus', ha='center', fontsize=8, color='#1A3C6E') # Diplococcus draw_coccus(ax, 2.3, 3.5); draw_coccus(ax, 2.9, 3.5) ax.text(2.6, 2.9, 'Diplococcus\n(e.g. Neisseria)', ha='center', fontsize=8, color='#1A3C6E') # Streptococcus (chain) for i in range(5): draw_coccus(ax, 4.0 + i*0.55, 3.5) ax.text(5.1, 2.9, 'Streptococcus\n(Chain)', ha='center', fontsize=8, color='#1A3C6E') # Staphylococcus (cluster) positions = [(7.0,3.8),(7.55,3.8),(7.27,3.3),(7.0,3.3),(7.55,3.3),(7.27,3.8)] for x,y in positions: draw_coccus(ax, x, y, color='#AF7AC5') ax.text(7.27, 2.9, 'Staphylococcus\n(Cluster)', ha='center', fontsize=8, color='#1A3C6E') # Tetrad for dx,dy in [(-0.3,0.3),(0.3,0.3),(-0.3,-0.3),(0.3,-0.3)]: draw_coccus(ax, 9.0+dx, 3.5+dy, color='#F39C12') ax.text(9.0, 2.9, 'Tetrad', ha='center', fontsize=8, color='#1A3C6E') # Sarcina (8-pack) for dx in [-0.3, 0.3]: for dy in [0.3, -0.3]: draw_coccus(ax, 10.7+dx, 3.5+dy, color='#EC7063') ax.text(10.7, 2.9, 'Sarcina\n(Packet)', ha='center', fontsize=8, color='#1A3C6E') # ---- Bacilli arrangements ---- ax.text(0.5, 2.3, 'BACILLI:', fontsize=10, fontweight='bold', color='#1A6E3C') # Single bacillus draw_rod(ax, 1.5, 1.6, color='#58D68D') ax.text(1.5, 1.1, 'Single\nBacillus', ha='center', fontsize=8, color='#1A6E3C') # Diplobacillus draw_rod(ax, 3.0, 1.6); draw_rod(ax, 3.85, 1.6) ax.text(3.4, 1.1, 'Diplobacillus', ha='center', fontsize=8, color='#1A6E3C') # Streptobacillus for i in range(4): draw_rod(ax, 5.2+i*0.85, 1.6) ax.text(6.35, 1.1, 'Streptobacillus\n(Chain)', ha='center', fontsize=8, color='#1A6E3C') # Coccobacillus for i in range(3): draw_rod(ax, 8.3+i*0.7, 1.6, w=0.4, h=0.35, color='#76D7C4') ax.text(8.85, 1.1, 'Cocco-\nbacillus', ha='center', fontsize=8, color='#1A6E3C') # Vibrio (curved) theta = np.linspace(0.3, 1.4, 50) x_v = 10.8 + 0.5*np.cos(theta) y_v = 1.4 + 0.6*np.sin(theta) ax.plot(x_v, y_v, color='#E74C3C', linewidth=6, solid_capstyle='round', zorder=3) ax.text(10.8, 1.1, 'Vibrio\n(Curved)', ha='center', fontsize=8, color='#1A6E3C') # Spirillum theta2 = np.linspace(0, 3*np.pi, 200) x_s = 12.0 + 0.3*np.sin(theta2*1.5)*0.5 + theta2*0.08 y_s = 1.6 + 0.25*np.sin(theta2) ax.plot(x_s, y_s, color='#8E44AD', linewidth=3, solid_capstyle='round', zorder=3) ax.text(12.3, 1.1, 'Spirillum', ha='center', fontsize=8, color='#1A6E3C') # Dividers ax.axhline(2.5, color='#AAA', lw=1, linestyle='--', xmin=0.03, xmax=0.97) ax.text(0.5, 4.5, 'COCCI:', fontsize=10, fontweight='bold', color='#1A5276') plt.tight_layout() plt.savefig('/tmp/workspace/pathogenic-organisms/diagrams/fig3_shapes.png', dpi=150, bbox_inches='tight') plt.close() print("Fig3 done") EOF

python3 << 'EOF' import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt import matplotlib.patches as mpatches import numpy as np # ── DIAGRAM 4: Virus Structure ─────────────────────────────────────────────── fig, axes = plt.subplots(1, 2, figsize=(12, 6)) fig.patch.set_facecolor('#F8F9FA') fig.suptitle('Virus Structure', fontsize=14, fontweight='bold', color='#1A3C6E') # --- Non-enveloped virus --- ax = axes[0] ax.set_xlim(-4, 4); ax.set_ylim(-4, 4); ax.set_aspect('equal'); ax.axis('off') ax.set_facecolor('#FFF8F0') ax.set_title('Non-Enveloped Virus\n(e.g. Adenovirus, Poliovirus)', fontsize=10, fontweight='bold', color='#7B241C') # Nucleic acid core core = plt.Circle((0,0), 1.0, color='#F1948A', zorder=4) ax.add_patch(core) ax.text(0, 0, 'Nucleic Acid\n(DNA/RNA)', ha='center', va='center', fontsize=8, fontweight='bold', color='white', zorder=5) # Capsid for angle in np.linspace(0, 2*np.pi, 20, endpoint=False): x = 1.7*np.cos(angle); y = 1.7*np.sin(angle) c = plt.Circle((x, y), 0.28, color='#5DADE2', zorder=3) ax.add_patch(c) ax.text(0, -2.4, 'Capsid (Capsomeres)', ha='center', fontsize=9, color='#1A5276', fontweight='bold') ax.annotate('', xy=(1.65, 0.5), xytext=(2.8, 1.2), arrowprops=dict(arrowstyle='->', color='#1A5276', lw=1.5)) ax.text(3.0, 1.4, 'Capsomere', fontsize=8, color='#1A5276') # --- Enveloped virus --- ax = axes[1] ax.set_xlim(-4, 4); ax.set_ylim(-4, 4); ax.set_aspect('equal'); ax.axis('off') ax.set_facecolor('#F0FFF4') ax.set_title('Enveloped Virus\n(e.g. HIV, Influenza, Herpes)', fontsize=10, fontweight='bold', color='#1A6E3C') # Nucleic acid core = plt.Circle((0,0), 0.9, color='#F1948A', zorder=5) ax.add_patch(core) ax.text(0, 0, 'Nucleic\nAcid', ha='center', va='center', fontsize=8, fontweight='bold', color='white', zorder=6) # Capsid ring capsid = plt.Circle((0,0), 1.4, fill=False, edgecolor='#5DADE2', linewidth=4, zorder=4) ax.add_patch(capsid) ax.text(-2.5, -1.4, 'Capsid', fontsize=8, color='#1A5276', fontweight='bold') # Envelope envelope = plt.Circle((0,0), 2.2, fill=False, edgecolor='#82E0AA', linewidth=6, zorder=3) ax.add_patch(envelope) # Glycoprotein spikes for angle in np.linspace(0, 2*np.pi, 16, endpoint=False): x1 = 2.2*np.cos(angle); y1 = 2.2*np.sin(angle) x2 = 2.9*np.cos(angle); y2 = 2.9*np.sin(angle) ax.plot([x1, x2], [y1, y2], color='#C0392B', linewidth=2.5, zorder=4) tip = plt.Circle((x2, y2), 0.15, color='#C0392B', zorder=5) ax.add_patch(tip) ax.text(0, -3.4, 'Envelope (Lipid Bilayer)', ha='center', fontsize=9, color='#1A6E3C', fontweight='bold') ax.annotate('', xy=(2.3, 1.5), xytext=(3.2, 2.2), arrowprops=dict(arrowstyle='->', color='#C0392B', lw=1.5)) ax.text(3.3, 2.4, 'Glycoprotein\nSpikes', fontsize=8, color='#C0392B') plt.tight_layout() plt.savefig('/tmp/workspace/pathogenic-organisms/diagrams/fig4_virus.png', dpi=150, bbox_inches='tight') plt.close() # ── DIAGRAM 5: Fungal Classification Diagram ────────────────────────────── fig, ax = plt.subplots(figsize=(13, 7)) ax.set_xlim(0, 13); ax.set_ylim(0, 7); ax.axis('off') ax.set_facecolor('#F5FFF5') fig.patch.set_facecolor('#F5FFF5') ax.set_title('Classification of Medically Important Fungi', fontsize=14, fontweight='bold', color='#1A6E3C', pad=10) def fbox(ax, x, y, w, h, text, fc, tc='white', fs=9): from matplotlib.patches import FancyBboxPatch r = FancyBboxPatch((x,y), w, h, boxstyle='round,pad=0.1', facecolor=fc, edgecolor='#333', lw=1.2) ax.add_patch(r) ax.text(x+w/2, y+h/2, text, ha='center', va='center', fontsize=fs, color=tc, fontweight='bold', multialignment='center') # Root fbox(ax, 5.0, 5.8, 3.0, 0.9, 'FUNGI\n(Eukaryotes, Chitin cell wall)', '#1A6E3C', fs=10) # Branches for xto in [1.5, 5.0, 9.5]: ax.annotate('', xy=(xto+1.0, 4.9), xytext=(6.5, 5.8), arrowprops=dict(arrowstyle='->', color='#555', lw=1.5)) fbox(ax, 0.3, 3.8, 2.5, 0.9, 'SUPERFICIAL\nMYCOSES', '#7D3C98', fs=9) fbox(ax, 4.2, 3.8, 2.5, 0.9, 'CUTANEOUS\nDERMATOPHYTES', '#1A5276', fs=9) fbox(ax, 8.3, 3.8, 2.5, 0.9, 'DEEP/SYSTEMIC\nMYCOSES', '#922B21', fs=9) # Superficial sub organisms_sup = ['Malassezia furfur\n(Tinea versicolor)', 'Piedraia hortae\n(Black piedra)'] for i, org in enumerate(organisms_sup): fx = 0.1 + i*2.0 fbox(ax, fx, 2.3, 1.8, 1.2, org, '#C39BD3', tc='#1A1A1A', fs=7) ax.annotate('', xy=(fx+0.9, 3.5), xytext=(1.55, 3.8), arrowprops=dict(arrowstyle='->', color='#7D3C98', lw=1)) # Cutaneous sub organisms_cut = ['Trichophyton\n(Tinea capitis,\npedis, unguium)', 'Microsporum\n(Tinea capitis)', 'Epidermophyton\n(Tinea cruris)'] for i, org in enumerate(organisms_cut): fx = 3.0 + i*2.2 fbox(ax, fx, 2.3, 2.0, 1.2, org, '#85C1E9', tc='#1A1A1A', fs=7) ax.annotate('', xy=(fx+1.0, 3.5), xytext=(5.45, 3.8), arrowprops=dict(arrowstyle='->', color='#1A5276', lw=1)) # Systemic sub organisms_sys = ['Histoplasma\ncapsulatum', 'Cryptococcus\nneoformans', 'Candida\nalbicans', 'Aspergillus\nfumigatus'] for i, org in enumerate(organisms_sys): fx = 7.5 + i*1.4 fbox(ax, fx, 2.3, 1.3, 1.2, org, '#F1948A', tc='#1A1A1A', fs=7) ax.annotate('', xy=(fx+0.65, 3.5), xytext=(9.55, 3.8), arrowprops=dict(arrowstyle='->', color='#922B21', lw=1)) # Legend boxes at bottom legend_items = [ (0.5, 0.7, '#7D3C98', 'Superficial: only skin surface, hair shaft'), (0.5, 0.3, '#1A5276', 'Cutaneous: keratinized skin, hair, nails'), (6.5, 0.7, '#922B21', 'Systemic: internal organs, lungs'), (6.5, 0.3, '#1A6E3C', 'Dimorphic fungi: yeast (37°C) vs mold (25°C)'), ] for lx, ly, lc, lt in legend_items: rect = plt.Rectangle((lx, ly), 0.4, 0.25, color=lc) ax.add_patch(rect) ax.text(lx+0.55, ly+0.12, lt, va='center', fontsize=8, color='#333') plt.tight_layout() plt.savefig('/tmp/workspace/pathogenic-organisms/diagrams/fig5_fungi.png', dpi=150, bbox_inches='tight') plt.close() print("Fig4 and Fig5 done") EOF

python3 << 'EOF' import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt import matplotlib.patches as mpatches import numpy as np # ── DIAGRAM 6: Vector-Borne Diseases ───────────────────────────────────────── fig, ax = plt.subplots(figsize=(13, 7)) ax.set_xlim(0, 13); ax.set_ylim(0, 7); ax.axis('off') ax.set_facecolor('#FFFDF0') fig.patch.set_facecolor('#FFFDF0') ax.set_title('Important Vectors and Diseases They Transmit', fontsize=14, fontweight='bold', color='#1A3C6E', pad=10) vectors = [ ('Anopheles\nMosquito', '#3498DB', ['Malaria', 'Lymphatic Filariasis'], 1.2), ('Aedes\nMosquito', '#E74C3C', ['Dengue', 'Yellow Fever', 'Zika', 'Chikungunya'], 3.4), ('Culex\nMosquito', '#9B59B6', ['Japanese Encephalitis', 'West Nile Fever'], 5.6), ('Sandfly\n(Phlebotomus)', '#E67E22', ['Kala-azar', 'Sandfly Fever'], 7.8), ('Tsetse Fly', '#27AE60', ['Sleeping Sickness\n(Trypanosomiasis)'], 9.8), ('Tick\n(Ixodes)', '#C0392B', ['Lyme Disease', 'RMSF', 'Tick Typhus'], 11.3), ] for (name, color, diseases, x) in vectors: # Vector box from matplotlib.patches import FancyBboxPatch r = FancyBboxPatch((x-0.85, 4.8), 1.7, 1.2, boxstyle='round,pad=0.1', facecolor=color, edgecolor='#333', lw=1.2) ax.add_patch(r) ax.text(x, 5.4, name, ha='center', va='center', fontsize=8, color='white', fontweight='bold', multialignment='center') # Arrow for i, disease in enumerate(diseases): yd = 3.6 - i*1.1 ax.annotate('', xy=(x, yd+0.3), xytext=(x, 4.8), arrowprops=dict(arrowstyle='->', color=color, lw=1.5)) dr = FancyBboxPatch((x-0.8, yd-0.2), 1.6, 0.7, boxstyle='round,pad=0.05', facecolor=color+'33', edgecolor=color, lw=1) ax.add_patch(dr) ax.text(x, yd+0.15, disease, ha='center', va='center', fontsize=7, color='#111', multialignment='center') ax.text(0.2, 6.5, 'VECTOR', fontsize=11, fontweight='bold', color='#1A3C6E', bbox=dict(boxstyle='round', facecolor='#D6EAF8')) ax.text(0.2, 5.3, 'DISEASE', fontsize=11, fontweight='bold', color='#1A6E3C', bbox=dict(boxstyle='round', facecolor='#D5F5E3')) # Bottom row - more vectors extra = [ ('Rat Flea\n(Xenopsylla)', '#795548', ['Plague', 'Murine Typhus'], 1.5), ('Body Louse\n(Pediculus)', '#607D8B', ['Epidemic Typhus', 'Relapsing Fever'], 4.2), ('Reduviid\n(Triatoma)', '#FF5722', ['Chagas Disease'], 7.0), ('Blackfly\n(Simulium)', '#455A64', ['Onchocerciasis\n(River Blindness)'], 9.5), ('Mite\n(Sarcoptes)', '#8D6E63', ['Scabies', 'Scrub Typhus'], 11.5), ] ax.text(0.2, 2.0, 'More Vectors:', fontsize=9, fontweight='bold', color='#555') for (name, color, diseases, x) in extra: from matplotlib.patches import FancyBboxPatch r = FancyBboxPatch((x-0.8, 1.2), 1.6, 0.75, boxstyle='round,pad=0.07', facecolor=color, edgecolor='#333', lw=1) ax.add_patch(r) ax.text(x, 1.575, name, ha='center', va='center', fontsize=7, color='white', fontweight='bold', multialignment='center') ax.text(x, 0.5, ' / '.join(diseases), ha='center', va='center', fontsize=6.5, color='#333', multialignment='center') plt.tight_layout() plt.savefig('/tmp/workspace/pathogenic-organisms/diagrams/fig6_vectors.png', dpi=150, bbox_inches='tight') plt.close() # ── DIAGRAM 7: Parasite Life Cycle Overview ────────────────────────────────── fig, ax = plt.subplots(figsize=(12, 6)) ax.set_xlim(0, 12); ax.set_ylim(0, 6); ax.axis('off') ax.set_facecolor('#FFF8E1') fig.patch.set_facecolor('#FFF8E1') ax.set_title('Parasite Classification and Key Examples', fontsize=14, fontweight='bold', color='#1A3C6E', pad=10) from matplotlib.patches import FancyBboxPatch def pbox(ax, x, y, w, h, txt, fc, tc='white', fs=9): r = FancyBboxPatch((x,y), w, h, boxstyle='round,pad=0.1', facecolor=fc, edgecolor='#444', lw=1.2) ax.add_patch(r) ax.text(x+w/2, y+h/2, txt, ha='center', va='center', fontsize=fs, color=tc, fontweight='bold', multialignment='center') pbox(ax, 4.5, 4.9, 3.0, 0.8, 'PARASITES', '#1A3C6E', fs=12) # 3 major groups pbox(ax, 0.4, 3.5, 2.8, 0.8, 'PROTOZOA\n(Unicellular)', '#1A6E3C', fs=10) pbox(ax, 4.6, 3.5, 2.8, 0.8, 'HELMINTHS\n(Multicellular Worms)', '#6E3C1A', fs=9) pbox(ax, 9.0, 3.5, 2.5, 0.8, 'ECTOPARASITES\n(Surface)', '#6E1A5A', fs=9) for xto in [1.8, 6.0, 10.25]: ax.annotate('', xy=(xto, 4.3), xytext=(6.0, 4.9), arrowprops=dict(arrowstyle='->', color='#555', lw=1.5)) # Protozoa examples protozoa = [('Plasmodium\n(Malaria)', '#52BE80'), ('Entamoeba\n(Amoebiasis)', '#52BE80'), ('Leishmania\n(Kala-azar)', '#52BE80'), ('Giardia\n(Giardiasis)', '#52BE80')] for i, (name, col) in enumerate(protozoa): fx = 0.1 + i*0.9 pbox(ax, fx, 2.1, 0.8, 1.2, name, col, tc='#111', fs=6) ax.annotate('', xy=(fx+0.4, 3.3), xytext=(1.8, 3.5), arrowprops=dict(arrowstyle='->', color='#1A6E3C', lw=0.8)) # Helminths sub-groups helm_groups = [('NEMATODES\n(Roundworms)\ne.g. Ascaris,\nHookworm', '#D4AC0D', 3.8), ('TREMATODES\n(Flukes)\ne.g. Schistosoma,\nFasciola', '#E67E22', 5.5), ('CESTODES\n(Tapeworms)\ne.g. Taenia,\nEchinococcus', '#C0392B', 7.2)] for (name, col, fx) in helm_groups: pbox(ax, fx, 1.8, 1.5, 1.5, name, col, tc='white', fs=7) ax.annotate('', xy=(fx+0.75, 3.3), xytext=(6.0, 3.5), arrowprops=dict(arrowstyle='->', color='#6E3C1A', lw=0.8)) # Ectoparasites ecto = [('Lice\n(Pediculus)', '#9B59B6'), ('Mites\n(Sarcoptes)', '#9B59B6'), ('Ticks\n(Ixodes)', '#9B59B6')] for i, (name, col) in enumerate(ecto): fx = 8.7 + i*1.1 pbox(ax, fx, 2.1, 1.0, 1.0, name, col, tc='white', fs=7) ax.annotate('', xy=(fx+0.5, 3.1), xytext=(10.25, 3.5), arrowprops=dict(arrowstyle='->', color='#6E1A5A', lw=0.8)) plt.tight_layout() plt.savefig('/tmp/workspace/pathogenic-organisms/diagrams/fig7_parasites.png', dpi=150, bbox_inches='tight') plt.close() print("Fig6 and Fig7 done") EOF

python3 << 'PYEOF' from reportlab.lib.pagesizes import A4 from reportlab.lib import colors from reportlab.lib.units import cm, mm from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle from reportlab.lib.enums import TA_CENTER, TA_LEFT, TA_JUSTIFY from reportlab.platypus import (SimpleDocTemplate, Paragraph, Spacer, Table, TableStyle, Image, PageBreak, HRFlowable, KeepTogether) from reportlab.platypus.flowables import BalancedColumns from reportlab.graphics.shapes import Drawing, Rect, String import os OUTPUT = '/tmp/workspace/pathogenic-organisms/output/Pathogenic_Organisms_Chapter.pdf' DIAG_DIR = '/tmp/workspace/pathogenic-organisms/diagrams/' doc = SimpleDocTemplate( OUTPUT, pagesize=A4, leftMargin=1.8*cm, rightMargin=1.8*cm, topMargin=2.0*cm, bottomMargin=2.0*cm, title='Pathogenic Organisms - Full Chapter', author='Medical Microbiology Notes' ) W, H = A4 CONTENT_W = W - 3.6*cm # ── Colour palette ────────────────────────────────────────────────────────── C_NAVY = colors.HexColor('#1A3C6E') C_RED = colors.HexColor('#922B21') C_GREEN = colors.HexColor('#1A6E3C') C_PURPLE = colors.HexColor('#6E1A5A') C_ORANGE = colors.HexColor('#784212') C_LIGHT_BLUE = colors.HexColor('#D6EAF8') C_LIGHT_GREEN = colors.HexColor('#D5F5E3') C_LIGHT_PURPLE = colors.HexColor('#E8DAEF') C_LIGHT_ORANGE = colors.HexColor('#FDEBD0') C_LIGHT_RED = colors.HexColor('#FADBD8') C_LIGHT_GREY = colors.HexColor('#F2F3F4') C_GOLD = colors.HexColor('#B7950B') # ── Styles ────────────────────────────────────────────────────────────────── styles = getSampleStyleSheet() def S(name, **kw): return ParagraphStyle(name, **kw) cover_title = S('CoverTitle', fontSize=28, textColor=colors.white, alignment=TA_CENTER, fontName='Helvetica-Bold', spaceAfter=6) cover_sub = S('CoverSub', fontSize=14, textColor=colors.HexColor('#AED6F1'), alignment=TA_CENTER, fontName='Helvetica', spaceAfter=4) cover_info = S('CoverInfo', fontSize=11, textColor=colors.HexColor('#D6EAF8'), alignment=TA_CENTER, fontName='Helvetica') h1 = S('H1', fontSize=17, textColor=colors.white, fontName='Helvetica-Bold', spaceBefore=14, spaceAfter=6, alignment=TA_LEFT, backColor=C_NAVY, borderPad=6, leftIndent=-2) h2 = S('H2', fontSize=13, textColor=C_NAVY, fontName='Helvetica-Bold', spaceBefore=10, spaceAfter=4, borderPad=4, borderWidth=0, leftIndent=0) h3 = S('H3', fontSize=11, textColor=C_RED, fontName='Helvetica-Bold', spaceBefore=8, spaceAfter=3) h4 = S('H4', fontSize=10, textColor=C_GREEN, fontName='Helvetica-Bold', spaceBefore=6, spaceAfter=2) h5 = S('H5', fontSize=9.5, textColor=C_PURPLE, fontName='Helvetica-Bold', spaceBefore=5, spaceAfter=2) body = S('Body', fontSize=9, leading=14, alignment=TA_JUSTIFY, spaceAfter=4, fontName='Helvetica') bullet = S('Bullet', fontSize=9, leading=13, leftIndent=14, bulletIndent=4, spaceAfter=2, fontName='Helvetica') key_box = S('KeyBox', fontSize=9, leading=13, backColor=colors.HexColor('#FEF9E7'), borderColor=C_GOLD, borderWidth=1, borderPad=6, fontName='Helvetica', spaceAfter=6) caption = S('Caption', fontSize=8, textColor=colors.HexColor('#555555'), alignment=TA_CENTER, fontName='Helvetica-Oblique', spaceAfter=4) def P(text, style=body): return Paragraph(text, style) def SP(n=4): return Spacer(1, n) def HR(col=C_NAVY, t=0.7): return HRFlowable(width='100%', thickness=t, color=col, spaceAfter=4, spaceBefore=4) def IMG(fname, w=None, h=None): path = DIAG_DIR + fname if not os.path.exists(path): return SP(2) if w is None: w = CONTENT_W return Image(path, width=w, height=h or w*0.55, kind='proportional') def section_header(text, color=C_NAVY): tbl = Table([[Paragraph(f'<font color="white"><b>{text}</b></font>', ParagraphStyle('sh', fontSize=12, textColor=colors.white, fontName='Helvetica-Bold', alignment=TA_LEFT))]], colWidths=[CONTENT_W]) tbl.setStyle(TableStyle([ ('BACKGROUND', (0,0), (-1,-1), color), ('TOPPADDING', (0,0), (-1,-1), 7), ('BOTTOMPADDING', (0,0), (-1,-1), 7), ('LEFTPADDING', (0,0), (-1,-1), 10), ('ROUNDEDCORNERS', [4,4,4,4]), ])) return tbl def sub_header(text, color=C_LIGHT_BLUE, tc=C_NAVY): tbl = Table([[Paragraph(f'<b>{text}</b>', ParagraphStyle('subh', fontSize=10.5, textColor=tc, fontName='Helvetica-Bold'))]], colWidths=[CONTENT_W]) tbl.setStyle(TableStyle([ ('BACKGROUND', (0,0), (-1,-1), color), ('TOPPADDING', (0,0), (-1,-1), 5), ('BOTTOMPADDING', (0,0), (-1,-1), 5), ('LEFTPADDING', (0,0), (-1,-1), 8), ('LINEBELOW', (0,0), (-1,-1), 1.5, tc), ])) return tbl def organism_table(rows, col_headers, col_widths, header_color=C_NAVY): data = [col_headers] + rows tbl = Table(data, colWidths=col_widths, repeatRows=1) style = [ ('BACKGROUND', (0,0), (-1,0), header_color), ('TEXTCOLOR', (0,0), (-1,0), colors.white), ('FONTNAME', (0,0), (-1,0), 'Helvetica-Bold'), ('FONTSIZE', (0,0), (-1,-1), 8), ('FONTNAME', (0,1), (-1,-1), 'Helvetica'), ('ROWBACKGROUNDS', (0,1), (-1,-1), [colors.white, C_LIGHT_GREY]), ('GRID', (0,0), (-1,-1), 0.4, colors.HexColor('#CCCCCC')), ('VALIGN', (0,0), (-1,-1), 'TOP'), ('TOPPADDING', (0,0), (-1,-1), 4), ('BOTTOMPADDING', (0,0), (-1,-1), 4), ('LEFTPADDING', (0,0), (-1,-1), 4), ('WORDWRAP', (0,0), (-1,-1), True), ] tbl.setStyle(TableStyle(style)) return tbl def info_card(label, items, bg_color=C_LIGHT_BLUE, label_color=C_NAVY): """A two-column card: label on left, items on right.""" bullets = ''.join(f'• {i}<br/>' for i in items) data = [[ Paragraph(f'<b>{label}</b>', ParagraphStyle('lbl', fontSize=8.5, textColor=label_color, fontName='Helvetica-Bold')), Paragraph(bullets, ParagraphStyle('itm', fontSize=8.5, leading=12, fontName='Helvetica')) ]] tbl = Table(data, colWidths=[2.8*cm, CONTENT_W-2.8*cm]) tbl.setStyle(TableStyle([ ('BACKGROUND', (0,0), (0,0), bg_color), ('BACKGROUND', (1,0), (1,0), colors.white), ('VALIGN', (0,0), (-1,-1), 'TOP'), ('TOPPADDING', (0,0), (-1,-1), 5), ('BOTTOMPADDING', (0,0), (-1,-1), 5), ('LEFTPADDING', (0,0), (-1,-1), 5), ('BOX', (0,0), (-1,-1), 0.8, label_color), ('LINEAFTER', (0,0), (0,-1), 0.8, label_color), ])) return tbl # ════════════════════════════════════════════════════════════════════════════ # BUILD STORY # ════════════════════════════════════════════════════════════════════════════ story = [] # ── COVER PAGE ────────────────────────────────────────────────────────────── cover_bg = Table([ [Paragraph('CHAPTER', ParagraphStyle('ct', fontSize=13, textColor=colors.HexColor('#AED6F1'), alignment=TA_CENTER, fontName='Helvetica'))], [Paragraph('Pathogenic Organisms', ParagraphStyle('ct2', fontSize=30, textColor=colors.white, alignment=TA_CENTER, fontName='Helvetica-Bold', leading=34))], [SP(6)], [Paragraph('Complete Chapter Notes', ParagraphStyle('ct3', fontSize=16, textColor=colors.HexColor('#AED6F1'), alignment=TA_CENTER, fontName='Helvetica'))], [SP(8)], [HR(colors.HexColor('#5DADE2'), 1.5)], [SP(4)], [Paragraph('Covering: Bacteria (Cocci & Bacilli) • Viruses • Fungi • Parasites • Vectors & Rodents', ParagraphStyle('ct4', fontSize=11, textColor=colors.HexColor('#D6EAF8'), alignment=TA_CENTER, fontName='Helvetica', leading=16))], [SP(4)], [Paragraph('Characteristics • Source • Portal of Entry • Transmission • Disease Identification', ParagraphStyle('ct5', fontSize=10, textColor=colors.HexColor('#AED6F1'), alignment=TA_CENTER, fontName='Helvetica-Oblique'))], [SP(16)], [Paragraph('Medical Microbiology | Nursing & Allied Health Sciences', ParagraphStyle('ct6', fontSize=10, textColor=colors.HexColor('#85C1E9'), alignment=TA_CENTER, fontName='Helvetica'))], ], colWidths=[CONTENT_W]) cover_bg.setStyle(TableStyle([ ('BACKGROUND', (0,0), (-1,-1), C_NAVY), ('TOPPADDING', (0,0), (-1,-1), 10), ('BOTTOMPADDING', (0,0), (-1,-1), 10), ('BOX', (0,0), (-1,-1), 3, colors.HexColor('#5DADE2')), ('ROUNDEDCORNERS', [8,8,8,8]), ])) story.append(SP(30)) story.append(cover_bg) story.append(PageBreak()) # ── INTRODUCTION ───────────────────────────────────────────────────────────── story.append(section_header('INTRODUCTION TO PATHOGENIC ORGANISMS')) story.append(SP(6)) story.append(P('A <b>pathogenic organism</b> is any microorganism capable of causing disease in a susceptible host. The ability to cause disease (<i>pathogenicity</i>) depends on:')) story.append(SP(3)) intro_items = [ ['Virulence of the organism', 'Presence of toxins, enzymes, capsules, pili'], ['Portal of entry', 'Respiratory, GI, skin, mucosal surfaces'], ['Infective dose', 'Minimum number of organisms required to cause infection'], ['Host immune status', 'Immunocompromised hosts are more susceptible'], ] intro_tbl = Table(intro_items, colWidths=[5.5*cm, CONTENT_W-5.5*cm]) intro_tbl.setStyle(TableStyle([ ('FONTNAME', (0,0), (0,-1), 'Helvetica-Bold'), ('FONTNAME', (1,0), (1,-1), 'Helvetica'), ('FONTSIZE', (0,0), (-1,-1), 9), ('ROWBACKGROUNDS', (0,0), (-1,-1), [C_LIGHT_BLUE, colors.white]), ('GRID', (0,0), (-1,-1), 0.3, colors.HexColor('#BBBBBB')), ('TOPPADDING', (0,0), (-1,-1), 4), ('BOTTOMPADDING', (0,0), (-1,-1), 4), ('LEFTPADDING', (0,0), (-1,-1), 6), ('VALIGN', (0,0), (-1,-1), 'MIDDLE'), ])) story.append(intro_tbl) story.append(SP(8)) # Classification diagram story.append(P('<b>Overview: Classification of Pathogenic Organisms</b>', caption)) story.append(IMG('fig1_classification.png', w=CONTENT_W)) story.append(P('Figure 1: Major groups of pathogenic organisms and their sub-classifications.', caption)) story.append(SP(6)) # ── PART 1: BACTERIA ────────────────────────────────────────────────────────── story.append(PageBreak()) story.append(section_header('PART 1: BACTERIA', C_NAVY)) story.append(SP(6)) story.append(P('Bacteria are unicellular prokaryotes that lack a membrane-bound nucleus. They are classified by <b>Gram staining</b> into Gram-positive and Gram-negative based on cell wall differences.')) story.append(SP(4)) story.append(IMG('fig2_gramstain.png', w=CONTENT_W)) story.append(P('Figure 2: Gram-positive vs Gram-negative cell wall structure.', caption)) story.append(SP(4)) story.append(IMG('fig3_shapes.png', w=CONTENT_W)) story.append(P('Figure 3: Bacterial shapes and cellular arrangements.', caption)) story.append(SP(8)) # Gram stain comparison table gs_rows = [ ['Peptidoglycan layer', 'Thick (20-80 nm)', 'Thin (2-7 nm)'], ['Outer membrane', 'Absent', 'Present (contains LPS/endotoxin)'], ['Teichoic acids', 'Present', 'Absent'], ['Colour after Gram stain', 'Purple/Violet', 'Pink/Red'], ['Antibiotic sensitivity', 'Penicillin, Vancomycin sensitive', 'Often resistant; Beta-lactam variable'], ['Examples', 'Staph, Strep, Bacillus, Clostridium', 'E.coli, Salmonella, Neisseria, Vibrio'], ] story.append(organism_table(gs_rows, [Paragraph('<b>Feature</b>', ParagraphStyle('h', fontSize=8, textColor=colors.white, fontName='Helvetica-Bold')), Paragraph('<b>Gram-Positive</b>', ParagraphStyle('h', fontSize=8, textColor=colors.white, fontName='Helvetica-Bold')), Paragraph('<b>Gram-Negative</b>', ParagraphStyle('h', fontSize=8, textColor=colors.white, fontName='Helvetica-Bold'))], [5.0*cm, 6.5*cm, 6.5*cm], C_NAVY)) story.append(SP(4)) story.append(P('Table 1: Comparison of Gram-positive and Gram-negative bacteria.', caption)) # ── GRAM POSITIVE COCCI ────────────────────────────────────────────────────── story.append(PageBreak()) story.append(sub_header('A. COCCI (Spherical Bacteria)', C_LIGHT_BLUE, C_NAVY)) story.append(SP(4)) story.append(sub_header('1. GRAM-POSITIVE COCCI', colors.HexColor('#D5F5E3'), C_GREEN)) story.append(SP(6)) # Staphylococcus aureus card story.append(P('<b>(a) Staphylococcus aureus</b>', h3)) sa_data = [ ['Morphology', 'Gram+ve cocci in grape-like clusters; non-motile, non-spore forming'], ['Key Features', 'Coagulase-POSITIVE (distinguishes from CoNS); Beta-hemolytic; golden pigment on agar'], ['Virulence Factors', 'Coagulase, hyaluronidase, staphylokinase, exotoxins, TSST-1, PVL, enterotoxins'], ['Source', 'Human nose/skin (normal flora); contaminated food; hospital environment'], ['Portal of Entry', 'Skin breaks, wounds, respiratory tract, IV lines'], ['Transmission', 'Direct contact, droplet nuclei, fomites, contaminated food'], ['Diseases', 'Boils/carbuncles, impetigo, septicemia, osteomyelitis, endocarditis, food poisoning, TSS, SSSS'], ['Identification', 'Catalase+, Coagulase+; Mannitol Salt Agar (yellow); DNase+; blood agar beta-hemolysis'], ] sa_tbl = Table(sa_data, colWidths=[3.5*cm, CONTENT_W-3.5*cm]) sa_tbl.setStyle(TableStyle([ ('FONTNAME', (0,0), (0,-1), 'Helvetica-Bold'), ('FONTNAME', (1,0), (1,-1), 'Helvetica'), ('FONTSIZE', (0,0), (-1,-1), 8.5), ('ROWBACKGROUNDS', (0,0), (-1,-1), [C_LIGHT_BLUE, colors.white]), ('GRID', (0,0), (-1,-1), 0.3, colors.HexColor('#BBBBBB')), ('TOPPADDING', (0,0), (-1,-1), 4), ('BOTTOMPADDING', (0,0), (-1,-1), 4), ('LEFTPADDING', (0,0), (-1,-1), 5), ('VALIGN', (0,0), (-1,-1), 'TOP'), ])) story.append(sa_tbl) story.append(SP(8)) # Streptococcus pyogenes story.append(P('<b>(b) Streptococcus pyogenes (Group A Streptococcus)</b>', h3)) sp_data = [ ['Morphology', 'Gram+ve cocci in chains; catalase-NEGATIVE; beta-hemolytic'], ['Key Features', 'Bacitracin SENSITIVE (Disc A test); M protein (antiphagocytic); produces streptolysin O & S'], ['Source', 'Human throat/skin; carriers common'], ['Portal of Entry', 'Respiratory tract (droplets), broken skin'], ['Transmission', 'Respiratory droplets, direct contact'], ['Diseases', 'Pharyngitis ("strep throat"), scarlet fever, impetigo, erysipelas, necrotizing fasciitis; Post-strep: Rheumatic fever, APSGN'], ['Identification', 'Beta-hemolysis; Bacitracin sensitive; ASO titer for post-streptococcal disease'], ] sp_tbl = Table(sp_data, colWidths=[3.5*cm, CONTENT_W-3.5*cm]) sp_tbl.setStyle(TableStyle([ ('FONTNAME', (0,0), (0,-1), 'Helvetica-Bold'), ('FONTNAME', (1,0), (1,-1), 'Helvetica'), ('FONTSIZE', (0,0), (-1,-1), 8.5), ('ROWBACKGROUNDS', (0,0), (-1,-1), [C_LIGHT_GREEN, colors.white]), ('GRID', (0,0), (-1,-1), 0.3, colors.HexColor('#BBBBBB')), ('TOPPADDING', (0,0), (-1,-1), 4), ('BOTTOMPADDING', (0,0), (-1,-1), 4), ('LEFTPADDING', (0,0), (-1,-1), 5), ('VALIGN', (0,0), (-1,-1), 'TOP'), ])) story.append(sp_tbl) story.append(SP(8)) # Streptococcus pneumoniae story.append(P('<b>(c) Streptococcus pneumoniae (Pneumococcus)</b>', h3)) pn_data = [ ['Morphology', 'Gram+ve lancet-shaped diplococci; encapsulated; alpha-hemolytic (green)'], ['Key Features', 'Optochin SENSITIVE; bile SOLUBLE; Quellung reaction +ve'], ['Source', 'Normal flora of nasopharynx; carrier state common'], ['Portal of Entry', 'Respiratory tract'], ['Transmission', 'Respiratory droplets'], ['Diseases', 'Lobar pneumonia, bacterial meningitis, otitis media, sinusitis, bacteremia'], ['Identification', 'Optochin disc sensitivity; bile solubility test; Quellung (capsular swelling) reaction'], ] pn_tbl = Table(pn_data, colWidths=[3.5*cm, CONTENT_W-3.5*cm]) pn_tbl.setStyle(TableStyle([ ('FONTNAME', (0,0), (0,-1), 'Helvetica-Bold'), ('FONTNAME', (1,0), (1,-1), 'Helvetica'), ('FONTSIZE', (0,0), (-1,-1), 8.5), ('ROWBACKGROUNDS', (0,0), (-1,-1), [C_LIGHT_PURPLE, colors.white]), ('GRID', (0,0), (-1,-1), 0.3, colors.HexColor('#BBBBBB')), ('TOPPADDING', (0,0), (-1,-1), 4), ('BOTTOMPADDING', (0,0), (-1,-1), 4), ('LEFTPADDING', (0,0), (-1,-1), 5), ('VALIGN', (0,0), (-1,-1), 'TOP'), ])) story.append(pn_tbl) # ── GRAM NEGATIVE COCCI ────────────────────────────────────────────────────── story.append(PageBreak()) story.append(sub_header('2. GRAM-NEGATIVE COCCI', C_LIGHT_RED, C_RED)) story.append(SP(6)) neisseria_rows = [ [Paragraph('<b>Feature</b>', ParagraphStyle('h2', fontSize=8, textColor=colors.white, fontName='Helvetica-Bold')), Paragraph('<b>N. meningitidis (Meningococcus)</b>', ParagraphStyle('h2', fontSize=8, textColor=colors.white, fontName='Helvetica-Bold')), Paragraph('<b>N. gonorrhoeae (Gonococcus)</b>', ParagraphStyle('h2', fontSize=8, textColor=colors.white, fontName='Helvetica-Bold'))], ['Morphology', 'Gram-ve diplococci; encapsulated', 'Gram-ve diplococci; non-encapsulated'], ['Sugar fermented', 'Glucose AND Maltose', 'Glucose ONLY (not maltose)'], ['Source', 'Nasopharynx (carrier state)', 'Infected humans only (no animal reservoir)'], ['Portal of Entry', 'Respiratory tract', 'Urogenital mucosa, conjunctiva'], ['Transmission', 'Respiratory droplets; close contact', 'Sexual contact; vertical (mother to neonate)'], ['Diseases', 'Bacterial meningitis; Meningococcemia; Waterhouse-Friderichsen syndrome', 'Urethritis; Cervicitis; PID; Ophthalmia neonatorum; DGI'], ['Identification', 'Thayer-Martin medium; Oxidase+; Latex agglutination', 'Thayer-Martin medium; Gram stain of discharge; NAAT (gold standard)'], ] n_tbl = Table([[r] if isinstance(r, Paragraph) else [Paragraph(str(c), ParagraphStyle('cell', fontSize=8, fontName='Helvetica')) for c in r] for r in neisseria_rows], colWidths=[3.2*cm, 6.4*cm, 6.4*cm]) # Rebuild properly n_data = [neisseria_rows[0]] for row in neisseria_rows[1:]: n_data.append([Paragraph(str(c), ParagraphStyle('cell', fontSize=8, fontName='Helvetica', leading=11)) for c in row]) n_tbl2 = Table(n_data, colWidths=[3.2*cm, 6.4*cm, 6.4*cm]) n_tbl2.setStyle(TableStyle([ ('BACKGROUND', (0,0), (-1,0), C_RED), ('TEXTCOLOR', (0,0), (-1,0), colors.white), ('FONTNAME', (0,0), (-1,0), 'Helvetica-Bold'), ('FONTNAME', (0,1), (0,-1), 'Helvetica-Bold'), ('FONTSIZE', (0,0), (-1,-1), 8), ('ROWBACKGROUNDS', (0,1), (-1,-1), [C_LIGHT_RED, colors.white]), ('GRID', (0,0), (-1,-1), 0.3, colors.HexColor('#CCCCCC')), ('VALIGN', (0,0), (-1,-1), 'TOP'), ('TOPPADDING', (0,0), (-1,-1), 4), ('BOTTOMPADDING', (0,0), (-1,-1), 4), ('LEFTPADDING', (0,0), (-1,-1), 4), ])) story.append(n_tbl2) story.append(P('Table 2: Comparison of Neisseria meningitidis and Neisseria gonorrhoeae.', caption)) story.append(SP(8)) # ── BACILLI ─────────────────────────────────────────────────────────────────── story.append(sub_header('B. BACILLI (Rod-Shaped Bacteria)', C_LIGHT_BLUE, C_NAVY)) story.append(SP(4)) story.append(sub_header('1. GRAM-POSITIVE BACILLI', colors.HexColor('#D5F5E3'), C_GREEN)) story.append(SP(6)) # Summary table for Gram-positive bacilli gpb_rows = [ ['Bacillus anthracis', 'Anthrax', 'Spores in soil/animal products', 'Skin, lungs, GI', 'Contact/inhalation/ingestion', '"Medusa head" colonies; non-motile; capsule stain'], ['Clostridium tetani', 'Tetanus', 'Soil, animal feces', 'Deep wounds', 'Wound contamination with spores', '"Drumstick" shape; clinical diagnosis; strict anaerobe'], ['Clostridium perfringens', 'Gas gangrene; Food poisoning', 'Soil, intestinal flora', 'Contaminated wounds', 'Wound contamination', 'Double zone hemolysis; alpha toxin (lecithinase); stormy fermentation'], ['Clostridium botulinum', 'Botulism', 'Soil, improperly canned food', 'GI tract (ingestion)', 'Ingestion of preformed toxin', 'Flaccid paralysis; blocks ACh release at NMJ'], ['Mycobacterium tuberculosis', 'Tuberculosis', 'Active TB patients', 'Respiratory (primary)', 'Airborne droplet nuclei', 'ZN stain (AFB); LJ medium; GeneXpert MTB/RIF'], ['Corynebacterium diphtheriae', 'Diphtheria', 'Human throat/carriers', 'Respiratory tract', 'Droplet, contact', 'Chinese letter arrangement; Albert stain (metachromatic granules); Elek test'], ] story.append(organism_table(gpb_rows, ['Organism', 'Disease', 'Source', 'Portal of Entry', 'Transmission', 'Identification'], [3.0*cm, 3.0*cm, 2.8*cm, 2.5*cm, 2.8*cm, 3.9*cm], C_GREEN)) story.append(P('Table 3: Important Gram-positive bacilli - diseases, transmission and identification.', caption)) story.append(SP(8)) # Mycobacterium TB - detailed box story.append(P('<b>Note on Mycobacterium tuberculosis (Special AFB organism):</b>', h4)) tb_key = Table([ [Paragraph('• Cell wall contains mycolic acids → responsible for acid-fastness\n' '• ZN (Ziehl-Neelsen) stain: red AFB on blue background\n' '• Slow-growing: 3-8 weeks on LJ (Lowenstein-Jensen) medium\n' '• Virulence factors: cord factor (trehalose dimycolate), sulfatides\n' '• Ghon complex = primary lesion in lung + hilar lymph node\n' '• Mantoux test (PPD): >10 mm = positive in general population\n' '• GeneXpert MTB/RIF: rapid molecular diagnosis; also detects rifampicin resistance', ParagraphStyle('tb', fontSize=8.5, leading=13, fontName='Helvetica'))] ], colWidths=[CONTENT_W]) tb_key.setStyle(TableStyle([ ('BACKGROUND', (0,0), (-1,-1), colors.HexColor('#FEF9E7')), ('BOX', (0,0), (-1,-1), 1.5, C_GOLD), ('TOPPADDING', (0,0), (-1,-1), 8), ('BOTTOMPADDING', (0,0), (-1,-1), 8), ('LEFTPADDING', (0,0), (-1,-1), 10), ])) story.append(tb_key) story.append(SP(8)) # ── GRAM NEGATIVE BACILLI ──────────────────────────────────────────────────── story.append(PageBreak()) story.append(sub_header('2. GRAM-NEGATIVE BACILLI', C_LIGHT_RED, C_RED)) story.append(SP(6)) gnb_rows = [ ['Escherichia coli', 'UTI, diarrhea (ETEC/EPEC/EHEC), neonatal meningitis, septicemia', 'Human colon flora; contaminated food/water', 'GI, urinary tract', 'Fecal-oral', 'MacConkey agar: PINK colonies (lactose fermenter); IMViC: ++--'], ['Salmonella typhi', 'Enteric fever (Typhoid): stepladder fever, rose spots, bradycardia', 'Infected humans; chronic carriers', 'GI (oral)', 'Fecal-oral; contaminated food/water', 'Non-lactose fermenter; H2S+; Widal test; blood culture (1st week)'], ['Salmonella spp.', 'Salmonellosis (gastroenteritis)', 'Poultry, eggs, contaminated food', 'GI tract', 'Fecal-oral; food-borne', 'Non-lactose fermenter; H2S+; SS agar'], ['Shigella spp.', 'Bacillary dysentery (bloody diarrhea)', 'Human feces; contaminated food/water', 'GI tract', 'Fecal-oral (low infective dose)', 'Non-motile; non-lactose fermenter; no H2S'], ['Vibrio cholerae', 'Cholera: "rice-water" diarrhea, severe dehydration', 'Contaminated water, raw seafood', 'GI (oral)', 'Fecal-oral; waterborne', 'Comma-shaped; TCBS agar (YELLOW colonies); Oxidase+; String test+'], ['Pseudomonas aeruginosa', 'HAP, burn infections, UTI, CF lung infection, ecthyma gangrenosum', 'Soil, water, hospital environment', 'Wounds, respiratory, catheters', 'Contact; nosocomial', 'Blue-green pigment (pyocyanin); grape odor; Oxidase+; non-fermenter'], ['Klebsiella pneumoniae', 'Pneumonia ("currant jelly" sputum), UTI, hospital infections', 'Human GI; hospital environment', 'Respiratory, urinary tract', 'Nosocomial', 'Mucoid colonies; capsule; non-motile; lactose fermenter'], ['Yersinia pestis', 'Plague: bubonic, septicemic, pneumonic', 'Rodents (rats); rat fleas', 'Skin (flea bite)', 'Flea bite (Xenopsylla cheopis)', '"Safety pin" bipolar staining; non-motile; culture at 28°C'], ['Haemophilus influenzae', 'Meningitis (esp. children), epiglottitis, pneumonia', 'Nasopharynx of humans', 'Respiratory tract', 'Respiratory droplets', 'Chocolate agar; X and V factor requirements; satellite phenomenon'], ['Bordetella pertussis', 'Whooping cough (pertussis)', 'Human respiratory tract', 'Respiratory tract', 'Respiratory droplets', 'Bordet-Gengou agar; cough plate method'], ] story.append(organism_table(gnb_rows, ['Organism', 'Diseases', 'Source', 'Portal of Entry', 'Transmission', 'Identification'], [3.0*cm, 4.0*cm, 2.5*cm, 2.0*cm, 2.5*cm, 4.0*cm], C_RED)) story.append(P('Table 4: Important Gram-negative bacilli - summary of key features.', caption)) # ── PART 2: VIRUSES ────────────────────────────────────────────────────────── story.append(PageBreak()) story.append(section_header('PART 2: VIRUSES', colors.HexColor('#7B241C'))) story.append(SP(6)) story.append(P('Viruses are <b>obligate intracellular parasites</b> consisting of a nucleic acid core (DNA or RNA) surrounded by a protein coat (<i>capsid</i>). They are the smallest infectious agents (20-300 nm), visible only by electron microscopy.')) story.append(SP(6)) story.append(IMG('fig4_virus.png', w=CONTENT_W)) story.append(P('Figure 4: Structure of non-enveloped and enveloped viruses.', caption)) story.append(SP(6)) # Virus properties table vp_rows = [ ['Size', '20-300 nm', 'Smaller than bacteria; require electron microscopy'], ['Nucleic acid', 'DNA OR RNA (never both)', 'Each virus has only one type of nucleic acid'], ['Cell wall', 'Absent', 'Some have a lipid envelope derived from host membrane'], ['Ribosomes', 'Absent', 'Cannot synthesize own proteins; depend entirely on host'], ['Reproduction', 'Intracellular only', 'Cannot replicate outside living host cells'], ['Antibiotic response', 'No effect', 'Antibiotics ineffective; antivirals required'], ['Capsid', 'Always present', 'Protects nucleic acid; determines shape'], ['Envelope', 'Present or absent', 'Enveloped viruses more susceptible to disinfectants'], ] story.append(organism_table(vp_rows, ['Feature', 'Characteristic', 'Clinical Significance'], [3.5*cm, 4.5*cm, 10.0*cm], colors.HexColor('#7B241C'))) story.append(P('Table 5: General properties of viruses.', caption)) story.append(SP(8)) # DNA Viruses table story.append(sub_header('A. MEDICALLY IMPORTANT DNA VIRUSES', colors.HexColor('#FADBD8'), colors.HexColor('#7B241C'))) story.append(SP(4)) dna_rows = [ ['Herpesviridae', 'HSV-1, HSV-2', 'Oral/genital herpes; cold sores; encephalitis', 'Direct contact, sexual, vertical', 'Tzanck smear; viral culture; PCR'], ['Herpesviridae', 'Varicella-zoster (VZV)', 'Chickenpox (primary); Herpes zoster/shingles (reactivation)', 'Respiratory droplets; contact', 'Clinical; DFA; PCR'], ['Herpesviridae', 'CMV', 'Congenital CMV; retinitis/pneumonia in AIDS', 'Blood, saliva, sexual, transplant', 'CMV antigenemia; PCR; shell vial culture'], ['Herpesviridae', 'EBV', 'Infectious mononucleosis ("kissing disease")', 'Saliva (oral contact)', 'Monospot test; Paul-Bunnell test; EBV serology'], ['Hepadnaviridae', 'Hepatitis B virus (HBV)', 'Hepatitis B; cirrhosis; hepatocellular carcinoma', 'Blood, sexual, vertical (perinatal)', 'HBsAg, HBeAg, HBcAb, HBV DNA (PCR)'], ['Papillomaviridae', 'HPV (16, 18)', 'Genital warts; cervical/anal cancer; laryngeal papillomatosis', 'Sexual contact; vertical', 'Pap smear; colposcopy; HPV DNA typing'], ['Adenoviridae', 'Adenovirus', 'Pharyngitis, pneumonia, conjunctivitis, gastroenteritis', 'Respiratory, fecal-oral, contact', 'Rapid antigen test; PCR; culture'], ['Poxviridae', 'Molluscum contagiosum', 'Umbilicated skin papules', 'Direct contact', 'Clinical; Henderson-Patterson bodies on biopsy'], ] story.append(organism_table(dna_rows, ['Family', 'Virus', 'Diseases', 'Transmission', 'Identification'], [3.0*cm, 3.5*cm, 5.5*cm, 3.5*cm, 3.5*cm], colors.HexColor('#7B241C'))) story.append(P('Table 6: Medically important DNA viruses.', caption)) story.append(SP(8)) story.append(sub_header('B. MEDICALLY IMPORTANT RNA VIRUSES', colors.HexColor('#FADBD8'), colors.HexColor('#7B241C'))) story.append(SP(4)) rna_rows = [ ['Orthomyxoviridae', 'Influenza A, B, C', 'Influenza ("flu"): fever, cough, myalgia; can cause pandemics', 'Respiratory droplets', 'Rapid Ag test; RT-PCR; culture'], ['Paramyxoviridae', 'Measles (Rubeola)', 'Measles: Koplik spots, maculopapular rash (3 Cs: cough, coryza, conjunctivitis)', 'Respiratory droplets (highly contagious)', 'Clinical; serology; PCR'], ['Paramyxoviridae', 'Mumps', 'Parotitis; orchitis; meningitis', 'Respiratory droplets', 'Serology; PCR'], ['Paramyxoviridae', 'RSV', 'Bronchiolitis in infants; pneumonia in elderly/immunocompromised', 'Contact; respiratory droplets', 'Rapid Ag test; PCR'], ['Togaviridae', 'Rubella', 'German measles; Congenital rubella syndrome (CRS)', 'Respiratory droplets', 'Serology (IgM); PCR'], ['Flaviviridae', 'Dengue (DENV 1-4)', '"Breakbone fever"; DHF; DSS', 'Aedes aegypti mosquito bite', 'NS1 antigen; IgM/IgG ELISA; RT-PCR'], ['Flaviviridae', 'Hepatitis C (HCV)', 'Hepatitis C; cirrhosis; HCC', 'Blood (transfusion, IV drugs), sexual', 'Anti-HCV (ELISA); HCV RNA (PCR)'], ['Retroviridae', 'HIV-1, HIV-2', 'AIDS: CD4 count <200; opportunistic infections', 'Blood, sexual, vertical', 'ELISA (screening); Western blot (confirmation); CD4; viral load'], ['Rhabdoviridae', 'Rabies virus', 'Rabies: hydrophobia, aerophobia, encephalitis; always fatal if untreated', 'Bite of infected animal (dog, bat)', 'Negri bodies (histology); DFA; PCR'], ['Picornaviridae', 'Poliovirus', 'Poliomyelitis: flaccid paralysis; eradicated in most countries', 'Fecal-oral', 'Stool viral culture; PCR'], ['Coronaviridae', 'SARS-CoV-2', 'COVID-19: fever, cough, breathlessness, anosmia', 'Respiratory droplets; aerosol', 'RT-PCR (gold standard); Rapid Ag test'], ['Filoviridae', 'Ebola virus', 'Ebola hemorrhagic fever; high CFR', 'Direct contact with body fluids', 'PCR; ELISA; BSL-4 precautions required'], ] story.append(organism_table(rna_rows, ['Family', 'Virus', 'Diseases', 'Transmission', 'Identification'], [3.0*cm, 3.5*cm, 5.5*cm, 3.5*cm, 3.5*cm], colors.HexColor('#7B241C'))) story.append(P('Table 7: Medically important RNA viruses.', caption)) # ── PART 3: FUNGI ────────────────────────────────────────────────────────── story.append(PageBreak()) story.append(section_header('PART 3: FUNGI', C_GREEN)) story.append(SP(6)) story.append(P('Fungi are <b>eukaryotic organisms</b> with a rigid cell wall containing <b>chitin</b> (not peptidoglycan). They are heterotrophs, reproducing by spores. Pathogenic fungi are classified by the body region they infect.')) story.append(SP(4)) story.append(IMG('fig5_fungi.png', w=CONTENT_W)) story.append(P('Figure 5: Classification of medically important fungi.', caption)) story.append(SP(6)) # Key concepts table fc_rows = [ ['Hyphae', 'Thread-like filamentous extensions of fungi; may be septate or non-septate (coenocytic)'], ['Mycelium', 'Mass of hyphae forming the vegetative body of a fungus'], ['Yeast', 'Unicellular fungi; reproduce by budding; e.g. Candida, Cryptococcus'], ['Mold', 'Multicellular fungi with hyphae; e.g. Aspergillus, Dermatophytes'], ['Dimorphic fungi', 'Exhibit YEAST form at 37°C (in body) and MOLD form at 25°C (environment); e.g. Histoplasma, Coccidioides, Blastomyces, Sporothrix'], ['Pseudohyphae', 'Chains of elongated budding cells; seen in Candida albicans'], ['Germ tube', 'Short hypha-like projection from yeast cell; POSITIVE in Candida albicans (Reynolds-Braude test)'], ] story.append(organism_table(fc_rows, ['Term', 'Definition'], [4.0*cm, CONTENT_W-4.0*cm], C_GREEN)) story.append(P('Table 8: Key terminology in mycology.', caption)) story.append(SP(8)) # Superficial mycoses story.append(sub_header('A. SUPERFICIAL MYCOSES', C_LIGHT_GREEN, C_GREEN)) story.append(SP(4)) sup_rows = [ ['Malassezia furfur', 'Pityriasis versicolor (Tinea versicolor)', 'Trunk, chest, back', 'Contact; endogenous (normal skin flora)', 'Hypo/hyperpigmented macules; KOH mount: "spaghetti and meatball" (short hyphae + round yeast)'], ['Piedraia hortae', 'Black piedra', 'Hair shafts (scalp)', 'Environment; contaminated water/soil', 'Hard black nodules on scalp hair; microscopy shows thick-walled asci with ascospores'], ['Trichosporon spp.', 'White piedra', 'Hair shafts (beard, axilla)', 'Direct contact', 'Soft, cream/white nodules on hair; microscopy shows arthrospores and blastospores'], ['Exophiala werneckii', 'Tinea nigra', 'Palms and soles', 'Contact with soil/plant matter', 'Brown-black non-scaly macules; KOH: brown septate hyphae and budding cells'], ] story.append(organism_table(sup_rows, ['Organism', 'Disease', 'Site', 'Transmission', 'Identification'], [3.0*cm, 3.5*cm, 2.5*cm, 3.0*cm, 6.0*cm], C_GREEN)) story.append(P('Table 9: Superficial mycoses.', caption)) story.append(SP(8)) # Cutaneous (Dermatophytes) story.append(sub_header('B. CUTANEOUS MYCOSES (DERMATOPHYTOSES)', C_LIGHT_GREEN, C_GREEN)) story.append(SP(4)) cut_rows = [ ['Tinea capitis', 'Scalp ringworm', 'Trichophyton tonsurans, Microsporum canis', 'Endothrix or ectothrix hair invasion; broken hair stubs'], ['Tinea corporis', 'Body ringworm', 'Trichophyton rubrum', 'Ring-shaped, scaly, pruritic lesion with central clearing'], ['Tinea pedis', "Athlete's foot", 'T. rubrum, T. interdigitale', 'Interdigital maceration, scaling; most common dermatophytosis'], ['Tinea unguium', 'Nail infection (Onychomycosis)', 'T. rubrum', 'Thickened, discolored, brittle nails; subungual debris'], ['Tinea cruris', "Jock itch", 'T. rubrum, Epidermophyton floccosum', 'Ring-shaped lesion in groin; spares scrotum'], ['Tinea barbae', 'Beard ringworm', 'Trichophyton spp.', 'Inflammatory lesion in bearded area of face/neck'], ['Tinea manuum', 'Hand ringworm', 'T. rubrum', 'Scaling of palms; often associated with tinea pedis'], ] story.append(organism_table(cut_rows, ['Disease', 'Common Name', 'Organism', 'Key Features'], [3.2*cm, 3.0*cm, 4.2*cm, 7.6*cm], colors.HexColor('#1A5276'))) story.append(P('Table 10: Cutaneous mycoses (dermatophytoses) - Tinea infections.', caption)) story.append(SP(4)) story.append(P('All dermatophytes are identified by: <b>KOH mount</b> (branching hyphae), <b>Wood\'s lamp</b> (green fluorescence in Microsporum), and <b>Sabouraud Dextrose Agar (SDA)</b> culture.', key_box)) story.append(SP(8)) # Deep/Systemic Mycoses story.append(sub_header('C. DEEP (SYSTEMIC) MYCOSES', C_LIGHT_RED, C_RED)) story.append(SP(4)) deep_rows = [ ['Histoplasma capsulatum', 'Histoplasmosis', 'Soil with bird/bat droppings (Ohio-Mississippi valley)', 'Inhalation of microconidia', 'Flu-like illness; pulmonary cavitation; disseminated disease in AIDS', 'Dimorphic; PAS/GMS stain shows small intracellular yeast inside macrophages; urine antigen'], ['Coccidioides immitis', 'Coccidioidomycosis ("Valley fever")', 'Soil of arid regions (SW USA, Mexico)', 'Inhalation of arthrospores', 'Flu-like; erythema nodosum; can disseminate to meninges/bones', 'Spherules with endospores in tissue; non-dimorphic; serology'], ['Blastomyces dermatitidis', 'Blastomycosis', 'Soil; endemic in North America', 'Inhalation', 'Pulmonary + skin verrucous lesions', 'Broad-based budding yeast (8-15 µm); double wall; silver stain'], ['Cryptococcus neoformans', 'Cryptococcosis', 'Pigeon/bird droppings', 'Inhalation', 'Meningitis in AIDS (CD4 <100); "soap bubble" lesions in brain', 'India ink: halo around capsule; Capsular antigen (latex agglutination); Urease+'], ['Aspergillus fumigatus', 'Aspergillosis', 'Ubiquitous in environment; soil/compost', 'Inhalation of conidia', 'Allergic (ABPA); Invasive in immunocompromised; Aspergilloma (fungus ball)', 'Septate hyphae with acute angle (45°) branching; galactomannan antigen; CT: halo sign'], ['Candida albicans', 'Candidiasis', 'Normal flora (oral, vaginal, GI)', 'Endogenous; overgrowth in immunocompromised', 'Oral thrush; vaginal candidiasis; invasive candidiasis (ICU patients)', 'Germ tube test+; pseudohyphae + blastospores; CHROMagar'], ['Pneumocystis jirovecii', 'PCP (Pneumocystis pneumonia)', 'Ubiquitous; acquired in childhood', 'Reactivation in HIV (CD4 <200)', 'Interstitial pneumonia; frothy exudate; "ground glass" on CT', 'GMS/Silver stain: "helmet-shaped" cysts; BAL PCR'], ['Sporothrix schenckii', 'Sporotrichosis ("Rose thorn disease")', 'Soil, decaying vegetation, thorns', 'Traumatic inoculation (thorn/wood prick)', 'Nodular lymphangitic lesion along lymphatics', 'Dimorphic; cigar-shaped yeast at 37°C; culture on SDA'], ] story.append(organism_table(deep_rows, ['Organism', 'Disease', 'Source', 'Transmission', 'Diseases/Features', 'Identification'], [3.0*cm, 2.5*cm, 2.5*cm, 2.3*cm, 3.7*cm, 4.0*cm], C_RED)) story.append(P('Table 11: Deep/systemic mycoses - comprehensive overview.', caption)) # ── PART 4: PARASITES ──────────────────────────────────────────────────────── story.append(PageBreak()) story.append(section_header('PART 4: PARASITES', colors.HexColor('#6E4C1E'))) story.append(SP(6)) story.append(P('Parasites are organisms that live on or in a host and derive benefit at the host\'s expense. Medical parasitology encompasses protozoa (unicellular), helminths (multicellular worms), and ectoparasites (surface dwellers).')) story.append(SP(4)) story.append(IMG('fig7_parasites.png', w=CONTENT_W)) story.append(P('Figure 6: Classification of parasites and key examples.', caption)) story.append(SP(6)) # Protozoa table story.append(sub_header('A. PROTOZOA (Unicellular Parasites)', C_LIGHT_ORANGE, colors.HexColor('#6E4C1E'))) story.append(SP(4)) proto_rows = [ ['Plasmodium falciparum\nP. vivax, P. malariae\nP. ovale', 'Malaria', 'Infected humans', 'Bite of female Anopheles mosquito', 'Periodic fever/chills/rigors; P. falciparum: cerebral malaria, blackwater fever; P. vivax/ovale: relapsing malaria', 'Thick/thin blood smear; RDT (HRP2 antigen); PCR'], ['Entamoeba histolytica', 'Amoebiasis', 'Human feces (cysts)', 'Fecal-oral (cyst ingestion in contaminated water/food)', 'Flask-shaped ulcers in colon; bloody diarrhea; amoebic liver abscess ("anchovy sauce" pus)', 'Stool microscopy (cysts/trophozoites); serology; stool Ag ELISA'], ['Giardia lamblia (intestinalis)', 'Giardiasis', 'Contaminated water/feces', 'Fecal-oral; ingestion of cysts', '"Falling leaf" motility; steatorrhea; malabsorption; no invasive disease', 'Stool microscopy (cysts); stool Ag test; string test (Enterotest)'], ['Leishmania donovani', 'Visceral leishmaniasis (Kala-azar)', 'Infected humans; sandfly vector', 'Bite of Phlebotomus sandfly', 'High fever; massive splenomegaly, hepatomegaly; pancytopenia; hyperpigmentation', 'LD bodies in bone marrow/spleen; rK39 RDT; PCR'], ['Leishmania tropica/major', 'Cutaneous leishmaniasis ("Oriental sore")', 'Sandfly; rodents', 'Sandfly bite', 'Painless ulcer with raised edges; heals with scar', 'Slit-skin smear; LD bodies; PCR'], ['Trypanosoma cruzi', "Chagas disease (American trypanosomiasis)", 'Triatoma (kissing bug); infected humans', 'Bite + fecal contamination of wound by Triatoma bug', "Cardiomyopathy; megacolon; megaesophagus; Romaña's sign (periorbital edema)", 'Blood smear; serology; xenodiagnosis; PCR'], ['Trypanosoma brucei', "African sleeping sickness", 'Tsetse fly; wild animals', 'Bite of Tsetse fly (Glossina)', 'Chancre at bite site; lymphadenopathy (Winterbottom\'s sign); CNS invasion → coma', 'Blood/CSF smear; card agglutination test'], ['Trichomonas vaginalis', 'Trichomoniasis', 'Infected humans', 'Sexual intercourse (STI)', 'Frothy yellow-green vaginal discharge; "strawberry cervix"; dysuria', 'Wet mount: motile trophozoites; NAAT (gold standard)'], ['Toxoplasma gondii', 'Toxoplasmosis', 'Cat feces (oocysts); undercooked meat (tissue cysts)', 'Ingestion of oocysts/tissue cysts; vertical (transplacental)', 'Usually asymptomatic in immunocompetent; congenital: chorioretinitis, hydrocephalus, intracranial calcifications; encephalitis in AIDS', 'Serology (IgM/IgG); PCR; Sabin-Feldman dye test; CT brain (ring-enhancing lesions)'], ['Cryptosporidium parvum', 'Cryptosporidiosis', 'Contaminated water; animals', 'Fecal-oral; waterborne', 'Profuse watery diarrhea; self-limiting in immunocompetent; life-threatening in AIDS', 'Modified ZN stain: red oocysts on blue background; stool Ag test'], ] story.append(organism_table(proto_rows, ['Organism', 'Disease', 'Source', 'Transmission', 'Key Features/Diseases', 'Identification'], [2.8*cm, 2.8*cm, 2.2*cm, 2.8*cm, 4.5*cm, 3.9*cm], colors.HexColor('#6E4C1E'))) story.append(P('Table 12: Important pathogenic protozoa.', caption)) story.append(SP(8)) # Helminths story.append(sub_header('B. HELMINTHS (Multicellular Worms)', C_LIGHT_ORANGE, colors.HexColor('#6E4C1E'))) story.append(SP(4)) # Nematodes story.append(P('<b>(i) Nematodes (Roundworms)</b>', h4)) nem_rows = [ ['Ascaris lumbricoides', 'Ascariasis', 'Embryonated eggs in soil', 'Ingestion of eggs', 'Loeffler syndrome (larval migration through lungs); intestinal obstruction; malnutrition', 'Stool microscopy: thick-shelled ova; adult worm passed in stool/vomit'], ['Ancylostoma duodenale / Necator americanus', 'Hookworm infection', 'Larvae in soil', 'Skin penetration by filariform larvae (walking barefoot); Ancylostoma also oral', 'Iron-deficiency anemia; ground itch; Loeffler syndrome during migration', 'Stool: oval thin-shelled eggs; larval culture (Harada-Mori)'], ['Strongyloides stercoralis', 'Strongyloidiasis', 'Soil; larvae', 'Skin penetration', 'Autoinfection possible; hyperinfection syndrome in immunocompromised', 'Stool: rhabditiform larvae (not eggs); string test; serology'], ['Enterobius vermicularis', 'Pinworm/Threadworm', 'Human feces/perianal area', 'Fecal-oral; autoinfection; retroinfection', 'Nocturnal perianal itching; appendicitis rare', 'Scotch tape (cellophane) test: eggs collected from perianal skin in morning'], ['Trichuris trichiura', 'Whipworm', 'Contaminated soil', 'Ingestion of embryonated eggs', 'Rectal prolapse in heavy infection; dysentery', 'Stool: "lemon-shaped/barrel-shaped" eggs with polar plugs'], ['Wuchereria bancrofti', 'Lymphatic filariasis (Elephantiasis)', 'Infected humans', 'Bite of Culex mosquito', 'Lymphedema; hydrocele; elephantiasis (chronic); nocturnal periodicity of microfilariae', 'Night blood smear: microfilariae; Mf sheathed; ICT card test'], ['Trichinella spiralis', 'Trichinellosis', 'Pigs; wildlife', 'Ingestion of undercooked pork with larvae', 'Periorbital edema; myalgia; eosinophilia; larvae encyst in muscle', 'Muscle biopsy; serology; eosinophilia'], ['Loa loa', 'Loiasis', 'Chrysops fly; African rainforest', 'Chrysops (deerfly) bite', 'Calabar swelling; worm crossing conjunctiva (visible)', 'Day blood smear: sheathed microfilariae; Mf seen crossing eye'], ] story.append(organism_table(nem_rows, ['Organism', 'Disease', 'Source', 'Transmission', 'Key Features', 'Identification'], [3.2*cm, 2.8*cm, 2.0*cm, 2.5*cm, 3.5*cm, 4.0*cm], colors.HexColor('#784212'))) story.append(P('Table 13: Important nematodes (roundworms).', caption)) story.append(SP(6)) # Trematodes story.append(P('<b>(ii) Trematodes (Flukes)</b>', h4)) trem_rows = [ ['Schistosoma mansoni / S. japonicum / S. haematobium', 'Schistosomiasis (Bilharziasis)', 'Fresh water (with Bulinus/Biomphalaria snail as IH)', 'Skin penetration by cercariae while wading/swimming', 'Katayama fever (acute); hepatosplenic disease (mansoni/japonicum); hematuria, bladder cancer (haematobium)', 'Stool/urine microscopy for eggs; S. haematobium eggs: terminal spine; serology'], ['Fasciola hepatica', 'Liver fluke / Fascioliasis', 'Liver of sheep/cattle; metacercariae on water plants', 'Ingestion of metacercariae on raw watercress/vegetables', 'Biliary colic; hepatomegaly; eosinophilia; obstructive jaundice', 'Stool microscopy: large operculated eggs; serology; imaging'], ['Clonorchis sinensis', 'Clonorchiasis', 'Freshwater fish (second IH)', 'Ingestion of raw/undercooked freshwater fish', 'Cholangitis; biliary obstruction; cholangiocarcinoma (long-term)', 'Stool microscopy: small eggs with operculum and shoulder rim; serology'], ['Paragonimus westermani', 'Pulmonary paragonimiasis', 'Freshwater crabs/crayfish', 'Ingestion of undercooked crabs/crayfish', 'Hemoptysis; pleural effusion; mimics TB', 'Sputum/stool: operculated eggs; serology; ELISA'], ] story.append(organism_table(trem_rows, ['Organism', 'Disease', 'Source', 'Transmission', 'Key Features', 'Identification'], [3.0*cm, 2.5*cm, 2.5*cm, 2.8*cm, 3.7*cm, 3.5*cm], colors.HexColor('#6E4C1E'))) story.append(P('Table 14: Important trematodes (flukes).', caption)) story.append(SP(6)) # Cestodes story.append(P('<b>(iii) Cestodes (Tapeworms)</b>', h4)) ces_rows = [ ['Taenia solium', 'Taeniasis (adult worm); Cysticercosis (larval)', 'Pork (cysticerci in muscle)', 'Ingestion of undercooked pork; ingestion of eggs (cysticercosis)', 'Taeniasis: abdominal pain; cysticercosis: neurocysticercosis (seizures, hydrocephalus)', 'Stool: proglottids (uterine branches <13); CT brain: ring-enhancing calcified lesions; serology'], ['Taenia saginata', 'Taeniasis (beef tapeworm)', 'Beef (cysticerci in muscle)', 'Ingestion of undercooked beef', 'Usually asymptomatic; abdominal discomfort; proglottids passed in stool', 'Stool: proglottids (uterine branches >15); no cysticercosis in humans'], ['Echinococcus granulosus', 'Cystic echinococcosis (Hydatid disease)', 'Dog (definitive host); sheep/cattle', 'Ingestion of eggs from dog feces', 'Hydatid cysts in liver/lung; anaphylaxis if cyst ruptures', 'Ultrasound/CT: cyst with daughter cysts; Casoni test; serology (ELISA); Pathans sign'], ['Diphyllobothrium latum', 'Diphyllobothriasis (Fish tapeworm)', 'Freshwater fish (second IH)', 'Ingestion of raw/undercooked freshwater fish', 'Vitamin B12 deficiency (competes for B12); megaloblastic anemia; longest tapeworm', 'Stool: operculated eggs; proglottids wider than long'], ['Hymenolepis nana', 'Hymenolepiasis (dwarf tapeworm)', 'Grain beetles/mites; autoinfection possible', 'Fecal-oral; direct human-to-human', 'Usually asymptomatic; most common tapeworm worldwide', 'Stool: small round eggs with polar filaments; smallest tapeworm'], ] story.append(organism_table(ces_rows, ['Organism', 'Disease', 'Source', 'Transmission', 'Key Features', 'Identification'], [3.0*cm, 2.8*cm, 2.3*cm, 2.5*cm, 3.7*cm, 3.7*cm], colors.HexColor('#922B21'))) story.append(P('Table 15: Important cestodes (tapeworms).', caption)) # ── PART 5: RODENTS & VECTORS ──────────────────────────────────────────────── story.append(PageBreak()) story.append(section_header('PART 5: RODENTS AND VECTORS', C_PURPLE)) story.append(SP(6)) story.append(IMG('fig6_vectors.png', w=CONTENT_W)) story.append(P('Figure 7: Important disease vectors and the diseases they transmit.', caption)) story.append(SP(6)) # Rodents story.append(sub_header('A. RODENTS AS SOURCES OF INFECTION', C_LIGHT_PURPLE, C_PURPLE)) story.append(SP(4)) rod_rows = [ ['Yersinia pestis', 'Plague', 'Rats are primary reservoir', 'Rat flea (Xenopsylla cheopis) bite; direct contact', 'Bubonic: bubo; Pneumonic: airborne spread; Septicemic: DIC', 'Blood/bubo culture; Giemsa/Wayson stain: bipolar "safety-pin" coccobacilli; PCR'], ['Leptospira interrogans', 'Leptospirosis ("Rat urine disease")', 'Rats excrete in urine; dogs, cattle', 'Contact with contaminated water/soil (flooded areas)', 'Weil\'s disease: jaundice, renal failure, hemorrhage; Fort Bragg fever', 'Dark-field microscopy; MAT (microscopic agglutination test); PCR; ELISA'], ['Rickettsia typhi', 'Murine (endemic) typhus', 'Rats are reservoir', 'Rat flea bite', 'Fever, headache, maculopapular rash; mild disease', 'Serology (Weil-Felix: OX-19; specific ELISA/IFA); PCR'], ['Hantavirus', 'Hantavirus Pulmonary Syndrome (HPS)', 'Deer mouse, other rodents', 'Inhalation of rodent urine/feces/saliva aerosols', 'Flu-like prodrome followed by rapid respiratory failure; high mortality', 'PCR; ELISA (IgM/IgG); RT-PCR on blood/BAL'], ['Streptobacillus moniliformis', 'Rat-bite fever', 'Rats, mice', 'Bite of rat/mouse; ingestion (Haverhill fever)', 'Fever, rash, polyarthritis; relapsing fever pattern', 'Blood/joint culture; serology'], ['LCM Virus', 'Lymphocytic choriomeningitis', 'House mice (Mus musculus)', 'Inhalation/ingestion of infected rodent material', 'Aseptic meningitis; flu-like illness; severe in immunocompromised', 'Serology (IgM/IgG); PCR on CSF'], ['Monkeypox virus', 'Mpox', 'Rodents (squirrels, rats) in Africa', 'Contact with infected animal/person; respiratory droplets', 'Rash (pustules including palms/soles); lymphadenopathy; milder than smallpox', 'PCR on skin lesion; electron microscopy'], ] story.append(organism_table(rod_rows, ['Pathogen', 'Disease', 'Rodent Role', 'Transmission', 'Key Features', 'Identification'], [2.8*cm, 2.5*cm, 2.5*cm, 2.8*cm, 3.5*cm, 3.9*cm], C_PURPLE)) story.append(P('Table 16: Rodent-associated diseases.', caption)) story.append(SP(8)) # Vectors story.append(sub_header('B. ARTHROPOD VECTORS AND THEIR DISEASES', C_LIGHT_PURPLE, C_PURPLE)) story.append(SP(4)) vec_rows = [ ['Anopheles mosquito\n(Female; night biter)', 'Malaria (Plasmodium spp.)\nLymphatic filariasis (Wuchereria)', 'Larvae in clean stagnant water', 'Insect repellents, bed nets, larvicides, indoor residual spraying'], ['Aedes aegypti\n(Female; day biter)', 'Dengue, Yellow fever, Zika, Chikungunya', 'Stagnant water in containers (urban)', 'Container management, larvicides, release of sterile males'], ['Culex mosquito\n(Female; night biter)', 'Japanese encephalitis, West Nile fever, Lymphatic filariasis', 'Stagnant water, rice fields, drains', 'Insecticides, biological control, drainage'], ['Phlebotomus sandfly', 'Kala-azar (Leishmania donovani)\nSandfly fever\nCutaneous leishmaniasis', 'Sandy soil, cracks in walls, animal burrows', 'DDT spraying, bed nets, sand fly proof screens'], ['Glossina (Tsetse fly)', 'African trypanosomiasis (Sleeping sickness)', 'Tropical African forests/savannahs', 'Tsetse traps, insecticides, clearing of bush'], ['Ixodes tick', 'Lyme disease (Borrelia)\nRocky Mountain spotted fever (Rickettsia)\nTick-borne encephalitis', 'Deer, mice; vegetation', 'Protective clothing, DEET repellent, tick checks'], ['Pediculus (Body louse)', 'Epidemic typhus (R. prowazekii)\nRelapsing fever (Borrelia recurrentis)\nTrench fever', 'Human body/clothing', 'Delousing (DDT/permethrin), improved hygiene'], ['Xenopsylla cheopis (Rat flea)', 'Bubonic plague (Y. pestis)\nMurine typhus (R. typhi)', 'Rats', 'Rodent control, insecticides'], ['Triatoma (Reduviid/Kissing bug)', 'Chagas disease (T. cruzi)', 'Rural houses, thatched roofs', 'House improvement, insecticides, bed nets'], ['Simulium (Blackfly)', 'Onchocerciasis/River blindness (Onchocerca volvulus)', 'Fast-flowing rivers', 'Ivermectin (mass drug administration), larviciding with temephos'], ['Sarcoptes scabiei (Mite)', 'Scabies\n(Orientia tsutsugamushi via Trombicula mite → Scrub typhus)', 'Human skin; vegetation (Trombicula)', 'Permethrin cream; clothing protection; rodent control'], ['Chrysops (Deerfly)', 'Loiasis (Loa loa)', 'African rainforest', 'Protective clothing; diethylcarbamazine prophylaxis'], ] story.append(organism_table(vec_rows, ['Vector', 'Diseases Transmitted', 'Breeding Habitat', 'Prevention/Control'], [3.5*cm, 5.0*cm, 3.5*cm, 6.0*cm], C_PURPLE)) story.append(P('Table 17: Arthropod vectors, diseases transmitted, and control measures.', caption)) # ── PART 6: COMPREHENSIVE SUMMARY TABLE ────────────────────────────────────── story.append(PageBreak()) story.append(section_header('COMPREHENSIVE SUMMARY: All Pathogenic Organisms', colors.HexColor('#212F3C'))) story.append(SP(6)) story.append(P('The following table provides a quick-reference summary of all major pathogenic organisms covering characteristics, source, portal of entry, transmission, and identification methods as required by the syllabus.', body)) story.append(SP(6)) summary_rows = [ # Bacteria ['Staphylococcus aureus', 'Gram+ve Cocci (clusters)', 'Skin/nose', 'Skin breaks, wounds', 'Contact, droplet, fomites', 'Coagulase+; Mannitol salt agar; Beta-hemolysis'], ['Streptococcus pyogenes', 'Gram+ve Cocci (chains)', 'Throat/skin', 'Respiratory, skin', 'Droplets, contact', 'Beta-hemolysis; Bacitracin sensitive; ASO titer'], ['S. pneumoniae', 'Gram+ve Diplococci', 'Nasopharynx', 'Respiratory', 'Droplets', 'Optochin sensitive; Bile soluble; Quellung test'], ['N. meningitidis', 'Gram-ve Diplococci', 'Nasopharynx', 'Respiratory', 'Droplets', 'Thayer-Martin; Glucose+Maltose fermenter'], ['N. gonorrhoeae', 'Gram-ve Diplococci', 'Urogenital', 'Mucous membranes', 'Sexual, vertical', 'Thayer-Martin; Glucose only; NAAT'], ['M. tuberculosis', 'AFB (Gram+ve wall)', 'Active TB patients', 'Respiratory', 'Airborne droplet nuclei', 'ZN stain; LJ medium; GeneXpert'], ['C. tetani', 'Gram+ve Bacillus', 'Soil, feces', 'Deep wounds', 'Wound contamination', 'Drumstick shape; clinical diagnosis'], ['B. anthracis', 'Gram+ve Bacillus (spores)', 'Soil, animals', 'Skin, lungs, GI', 'Contact, inhalation, ingestion', 'Non-motile; Medusa head colony; capsule stain'], ['Salmonella typhi', 'Gram-ve Bacillus', 'Infected humans/carriers', 'GI tract', 'Fecal-oral', 'Non-lactose fermenter; Widal test; Blood culture'], ['Vibrio cholerae', 'Gram-ve Curved Bacillus', 'Water, seafood', 'GI tract', 'Fecal-oral, waterborne', 'Comma shape; TCBS (yellow); Oxidase+'], ['E. coli (pathogenic)', 'Gram-ve Bacillus', 'Human colon/food/water', 'GI, urinary', 'Fecal-oral', 'MacConkey pink; IMViC: ++--'], ['Pseudomonas aeruginosa', 'Gram-ve Bacillus', 'Hospital environment', 'Wounds, respiratory', 'Nosocomial', 'Blue-green pigment; grape odor; Oxidase+'], # Viruses ['HIV', 'RNA Retrovirus', 'Blood, genital fluids, milk', 'Mucous membrane, blood', 'Sexual, blood, vertical', 'ELISA; Western blot; CD4 count; Viral load'], ['HBV', 'DNA Hepadnavirus', 'Blood, sexual fluids', 'Blood, mucous membrane', 'Sexual, blood, perinatal', 'HBsAg; HBeAg; HBV DNA PCR'], ['Dengue', 'RNA Flavivirus', 'Infected human (viremia)', 'Skin (mosquito bite)', 'Aedes aegypti mosquito', 'NS1 antigen; IgM ELISA; RT-PCR'], ['Influenza', 'RNA Orthomyxovirus', 'Humans, birds, pigs', 'Respiratory', 'Respiratory droplets', 'Rapid Ag test; RT-PCR; culture'], ['Rabies', 'RNA Rhabdovirus', 'Infected animal (dog, bat)', 'Skin (bite wound)', 'Animal bite', 'Negri bodies; DFA; PCR'], # Fungi ['Candida albicans', 'Yeast (Fungi)', 'Normal flora', 'Mucous membranes', 'Endogenous/contact', 'Germ tube+; CHROMagar; pseudohyphae'], ['Aspergillus fumigatus', 'Mold (Fungi)', 'Soil, environment', 'Respiratory', 'Inhalation of conidia', 'Septate hyphae (45°); Galactomannan; CT: halo sign'], ['Cryptococcus neoformans', 'Encapsulated yeast', 'Pigeon droppings', 'Respiratory', 'Inhalation', 'India ink; Latex agglutination (capsule Ag)'], ['Histoplasma capsulatum', 'Dimorphic fungus', 'Bat/bird droppings', 'Respiratory', 'Inhalation of microconidia', 'Intracellular yeast in macrophages; Urine antigen'], # Parasites ['Plasmodium falciparum', 'Protozoa (Intracellular)', 'Infected humans', 'Skin (mosquito)', 'Female Anopheles bite', 'Blood smear; RDT; PCR'], ['Entamoeba histolytica', 'Protozoa', 'Human feces (cysts)', 'GI tract', 'Fecal-oral', 'Stool microscopy; stool Ag ELISA'], ['Ascaris lumbricoides', 'Nematode (Roundworm)', 'Soil (embryonated eggs)', 'GI tract (oral)', 'Ingestion of eggs', 'Stool ova; adult worm passed'], ['Ancylostoma/Necator', 'Nematode (Roundworm)', 'Soil (filariform larvae)', 'Skin (feet)', 'Skin penetration', 'Stool ova; larval culture; eosinophilia'], ['Wuchereria bancrofti', 'Nematode (Filarial)', 'Infected humans', 'Skin (mosquito)', 'Culex mosquito bite', 'Night blood smear; ICT card test'], ['Taenia solium', 'Cestode (Tapeworm)', 'Infected pork', 'GI tract', 'Ingestion of undercooked pork/eggs', 'Stool proglottids; CT brain (neurocysticercosis)'], ['Schistosoma spp.', 'Trematode (Fluke)', 'Fresh water (snail)', 'Skin', 'Cercariae skin penetration', 'Stool/urine for eggs; serology'], # Vectors & Rodents ['Yersinia pestis', 'Gram-ve Bacillus (Rodent-associated)', 'Rats (reservoir)', 'Skin (flea bite)', 'Xenopsylla cheopis flea bite', 'Bipolar staining; Culture; PCR'], ['Leptospira interrogans', 'Spirochete (Rodent-associated)', 'Rat urine; contaminated water', 'Skin/mucous membrane', 'Contact with infected water/soil', 'MAT; Dark field microscopy; PCR'], ] summary_tbl = Table(summary_rows, colWidths=[3.0*cm, 2.5*cm, 2.5*cm, 2.5*cm, 2.5*cm, 5.0*cm], repeatRows=0) # Apply alternating row colors with group shading style_cmds = [ ('FONTNAME', (0,0), (-1,-1), 'Helvetica'), ('FONTSIZE', (0,0), (-1,-1), 7.5), ('GRID', (0,0), (-1,-1), 0.3, colors.HexColor('#CCCCCC')), ('VALIGN', (0,0), (-1,-1), 'TOP'), ('TOPPADDING', (0,0), (-1,-1), 3), ('BOTTOMPADDING', (0,0), (-1,-1), 3), ('LEFTPADDING', (0,0), (-1,-1), 4), ('FONTNAME', (0,0), (0,-1), 'Helvetica-Bold'), ] # Row group shading bacteria_end = 12 for i in range(bacteria_end): bg = C_LIGHT_BLUE if i % 2 == 0 else colors.white style_cmds.append(('BACKGROUND', (0,i), (-1,i), bg)) for i in range(bacteria_end, bacteria_end+5): bg = colors.HexColor('#FDEDEC') if i % 2 == 0 else colors.HexColor('#FEF9E7') style_cmds.append(('BACKGROUND', (0,i), (-1,i), bg)) for i in range(bacteria_end+5, bacteria_end+9): bg = C_LIGHT_GREEN if i % 2 == 0 else colors.white style_cmds.append(('BACKGROUND', (0,i), (-1,i), bg)) for i in range(bacteria_end+9, len(summary_rows)): bg = C_LIGHT_ORANGE if i % 2 == 0 else colors.white style_cmds.append(('BACKGROUND', (0,i), (-1,i), bg)) summary_tbl.setStyle(TableStyle(style_cmds)) story.append(summary_tbl) story.append(P('Table 18: Comprehensive summary of all pathogenic organisms (Syllabus-aligned).', caption)) # ── KEY POINTS FOR EXAM ──────────────────────────────────────────────────── story.append(PageBreak()) story.append(section_header('KEY POINTS FOR EXAMINATION', C_GOLD)) story.append(SP(6)) key_points = [ ('Gram staining', 'Gram+ve = purple (thick peptidoglycan); Gram-ve = pink (thin peptidoglycan + outer LPS membrane). LPS = endotoxin causing fever and septic shock.'), ('Coagulase test', 'Coagulase-POSITIVE = S. aureus (pathogenic). Coagulase-NEGATIVE = CoNS (S. epidermidis, S. saprophyticus).'), ('Special stains', 'ZN stain = AFB (TB, Leprosy); India ink = Cryptococcus (capsule halo); KOH mount = Fungi (hyphae); Gram stain = Bacteria; Giemsa = Parasites (malaria), Leishmania.'), ('Fecal-oral route', 'Salmonella, Shigella, Vibrio, E. coli, HAV, Poliovirus, Entamoeba, Giardia, Ascaris, Taenia (eggs).'), ('Airborne transmission', 'Mycobacterium tuberculosis (droplet nuclei, <5µm), Measles, Varicella, Influenza (also droplet).'), ('Opportunistic infections', 'Candida, Aspergillus, Cryptococcus, PCP (Pneumocystis), CMV, MAI - occur when CD4 < threshold in HIV/AIDS.'), ('Dimorphic fungi', 'Yeast at 37°C (body temperature), Mold at 25°C (room temperature). Rule: "Mold in Cold, Yeast in Heat". Examples: Histoplasma, Coccidioides, Blastomyces, Sporothrix.'), ('Vector-borne mnemonic', 'Malaria=Anopheles; Dengue/Yellow fever/Zika=Aedes; JE=Culex; Kala-azar=Sandfly; Sleeping sickness=Tsetse; Plague=Rat flea; Chagas=Reduviid; Onchocerciasis=Blackfly.'), ('Malaria diagnosis', 'Thick blood smear (screening), thin blood smear (speciation), RDT (HRP2 antigen for P. falciparum), PCR (gold standard). P. falciparum: no true relapse (no hypnozoites).'), ('Portal of entry', 'Determines type of disease. Respiratory → pneumonia/meningitis; GI → diarrhea/enteric fever; Skin → cellulitis/wound infection; Urogenital → STIs/UTI.'), ('Tetanus toxin', 'Tetanospasmin: blocks INHIBITORY neurons (glycine/GABA) at spinal cord → spastic paralysis. Botulinum toxin: blocks EXCITATORY ACh release at NMJ → flaccid paralysis.'), ('Plague forms', 'Bubonic (flea bite → bubo in groin); Pneumonic (airborne → most contagious, can cause pandemic); Septicemic (DIC, black skin → "Black Death").'), ] for label, text in key_points: row_data = [[ Paragraph(f'<b>{label}</b>', ParagraphStyle('kpl', fontSize=8.5, fontName='Helvetica-Bold', textColor=C_NAVY)), Paragraph(text, ParagraphStyle('kpt', fontSize=8.5, fontName='Helvetica', leading=12)) ]] kp_tbl = Table(row_data, colWidths=[3.5*cm, CONTENT_W-3.5*cm]) kp_tbl.setStyle(TableStyle([ ('BACKGROUND', (0,0), (0,0), C_LIGHT_BLUE), ('BACKGROUND', (1,0), (1,0), colors.white), ('VALIGN', (0,0), (-1,-1), 'TOP'), ('TOPPADDING', (0,0), (-1,-1), 5), ('BOTTOMPADDING', (0,0), (-1,-1), 5), ('LEFTPADDING', (0,0), (-1,-1), 6), ('BOX', (0,0), (-1,-1), 0.5, C_NAVY), ('LINEAFTER', (0,0), (0,-1), 1, C_NAVY), ])) story.append(kp_tbl) story.append(SP(3)) story.append(SP(10)) story.append(HR(C_NAVY)) story.append(P('<i>Sources: Jawetz, Melnick & Adelberg\'s Medical Microbiology 28th Ed; Sherris & Ryan\'s Medical Microbiology 8th Ed; Medical Microbiology 9th Ed (Murray et al.)</i>', ParagraphStyle('ref', fontSize=7.5, textColor=colors.grey, alignment=TA_CENTER, fontName='Helvetica-Oblique'))) # ════════════════════════════════════════════════════════════════════════════ # PAGE NUMBERS # ════════════════════════════════════════════════════════════════════════════ def on_page(canvas, doc): canvas.saveState() canvas.setFont('Helvetica', 8) canvas.setFillColor(colors.HexColor('#888888')) canvas.drawString(1.8*cm, 1.2*cm, 'Pathogenic Organisms - Medical Microbiology Chapter') canvas.drawRightString(W - 1.8*cm, 1.2*cm, f'Page {doc.page}') canvas.restoreState() doc.build(story, onFirstPage=on_page, onLaterPages=on_page) print(f"PDF created: {OUTPUT}") PYEOF

python3 -c " from pypdf import PdfReader r = PdfReader('/tmp/workspace/pathogenic-organisms/output/Pathogenic_Organisms_Chapter.pdf') import os size = os.path.getsize('/tmp/workspace/pathogenic-organisms/output/Pathogenic_Organisms_Chapter.pdf') print(f'Pages: {len(r.pages)}') print(f'File size: {size/1024:.1f} KB') "