A detailed educational flowchart for bacterial classification with example species. The flowchart starts at the top with "BACTERIA" and branches step by step: Step 1 - Gram Stain splits into two branches: - LEFT branch: "GRAM-POSITIVE (Purple)" with label "Thick peptidoglycan, no outer membrane" - RIGHT branch: "GRAM-NEGATIVE (Red/Pink)" with label "Thin peptidoglycan, has outer membrane & LPS" Step 2 - Each branch splits by Shape: GRAM-POSITIVE left side: - "Cocci (spherical)" → further splits by Catalase: - Catalase POSITIVE → "Staphylococcus" → splits by Coagulase: - Coagulase + → "S. aureus" (causes skin infections, pneumonia, toxic shock) - Coagulase − → "S. epidermidis" (causes catheter infections) - Catalase NEGATIVE → "Streptococcus" → splits by Hemolysis: - Beta-hemolysis → "S. pyogenes" (strep throat, rheumatic fever) - Alpha-hemolysis → "S. pneumoniae" (pneumonia, meningitis) - Gamma (no hemolysis) → "Enterococcus faecalis" (UTI, endocarditis) - "Bacilli (rods)" → splits by Spores: - Spore-forming → "Bacillus anthracis" (anthrax), "Clostridium tetani" (tetanus) - Non-spore-forming → "Listeria monocytogenes" (listeriosis), "Corynebacterium diphtheriae" (diphtheria) GRAM-NEGATIVE right side: - "Cocci (spherical)" → "Neisseria meningitidis" (meningitis), "N. gonorrhoeae" (gonorrhea) - "Bacilli (rods)" → splits by Oxygen requirement: - Aerobic/Facultative → "Enterobacteriaceae": "E. coli" (UTI, diarrhea), "Salmonella typhi" (typhoid), "Klebsiella pneumoniae" (pneumonia) - Anaerobic → "Bacteroides fragilis" (intra-abdominal infections) - "Spirochetes (spiral)" → "Treponema pallidum" (syphilis), "Borrelia burgdorferi" (Lyme disease) At the bottom, a separate box: "GRAM-STAIN EXCEPTIONS: Acid-fast stain → Mycobacterium tuberculosis (TB), M. leprae (leprosy). No cell wall → Mycoplasma pneumoniae (atypical pneumonia). Obligate intracellular → Chlamydia trachomatis, Rickettsia rickettsii" Use a clean white background, blue and red color coding for gram positive/negative branches, green for organism names, small italic text for disease examples. Use clear arrows and boxes. Professional medical education style, highly readable, organized layout.

A detailed professional educational taxonomy table/diagram showing full Linnaean classification for Gram-Positive Cocci (GPC) and Gram-Negative Bacilli (GNB) bacteria. Layout: Two large side-by-side columns, left column is blue-themed for GPC, right column is red-themed for GNB. Each column shows a vertical taxonomy ladder with 8 rows for the ranks: Kingdom, Division, Class, Order, Family, Genus, Species, Subtype. LEFT COLUMN - GRAM-POSITIVE COCCI (GPC) - Blue theme: Title: "GPC - Gram-Positive Cocci" Show TWO example organisms side by side within the column: Example 1: Staphylococcus aureus Kingdom: Bacteria Division: Firmicutes Class: Bacilli Order: Bacillales Family: Staphylococcaceae Genus: Staphylococcus Species: S. aureus Subtype: MRSA (Methicillin-Resistant S. aureus) Disease note: Skin infections, pneumonia, toxic shock Example 2: Streptococcus pyogenes Kingdom: Bacteria Division: Firmicutes Class: Bacilli Order: Lactobacillales Family: Streptococcaceae Genus: Streptococcus Species: S. pyogenes Subtype: Group A Streptococcus (GAS) Disease note: Strep throat, rheumatic fever RIGHT COLUMN - GRAM-NEGATIVE BACILLI (GNB) - Red/orange theme: Title: "GNB - Gram-Negative Bacilli" Show TWO example organisms side by side within the column: Example 1: Escherichia coli Kingdom: Bacteria Division: Proteobacteria Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Escherichia Species: E. coli Subtype: E. coli O157:H7 Disease note: UTI, diarrhea, neonatal meningitis Example 2: Klebsiella pneumoniae Kingdom: Bacteria Division: Proteobacteria Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Klebsiella Species: K. pneumoniae Subtype: CRKP (Carbapenem-Resistant K. pneumoniae) Disease note: Hospital pneumonia, UTI At the very top center, a title box: "Full Linnaean Taxonomy: GPC vs GNB" At the bottom, a legend box: "GPC = Gram-Positive Cocci (purple on Gram stain, thick peptidoglycan, NO outer membrane) | GNB = Gram-Negative Bacilli (pink/red on Gram stain, thin peptidoglycan, HAS outer membrane + LPS endotoxin)" Use clean white background, clear bold rank labels on left side, connecting arrows between ranks, color-coded boxes per organism, professional medical textbook style, large readable font.

mkdir -p /home/daytona/workspace/gpc-gnb-chart && ls /home/daytona/workspace/gpc…

~/gpc-gnb-chart/generate_chart.py

from reportlab.lib.pagesizes import A3, landscape
from reportlab.lib import colors
from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
from reportlab.lib.units import cm, mm
from reportlab.platypus import (
    SimpleDocTemplate, Table, TableStyle, Paragraph,
    Spacer, HRFlowable, KeepTogether
)
from reportlab.lib.enums import TA_CENTER, TA_LEFT
from reportlab.platypus import PageBreak

OUTPUT = "/home/daytona/workspace/gpc-gnb-chart/GPC_vs_GNB_Antibiotic_Susceptibility.pdf"

# ── Colours ──────────────────────────────────────────────────────────────────
DARK_BLUE   = colors.HexColor("#1a3a5c")
MID_BLUE    = colors.HexColor("#2e6da4")
LIGHT_BLUE  = colors.HexColor("#d0e4f7")
PALE_BLUE   = colors.HexColor("#eaf3fb")

DARK_RED    = colors.HexColor("#8b1a1a")
MID_RED     = colors.HexColor("#c0392b")
LIGHT_RED   = colors.HexColor("#fdd5d0")
PALE_RED    = colors.HexColor("#fff0ee")

DARK_GREEN  = colors.HexColor("#1a5c2e")
LIGHT_GREEN = colors.HexColor("#d4edda")

DARK_ORANGE = colors.HexColor("#7d4e00")
LIGHT_ORANGE= colors.HexColor("#fff3cd")

GREY_HEADER = colors.HexColor("#2c3e50")
LIGHT_GREY  = colors.HexColor("#f2f4f6")
WHITE       = colors.white
BLACK       = colors.black

# Susceptibility cell colours
S_COLOR  = colors.HexColor("#27ae60")   # Susceptible  - green
R_COLOR  = colors.HexColor("#e74c3c")   # Resistant    - red
V_COLOR  = colors.HexColor("#f39c12")   # Variable     - amber
I_COLOR  = colors.HexColor("#8e44ad")   # Intermediate - purple
NA_COLOR = colors.HexColor("#95a5a6")   # N/A          - grey

doc = SimpleDocTemplate(
    OUTPUT,
    pagesize=landscape(A3),
    leftMargin=1.2*cm, rightMargin=1.2*cm,
    topMargin=1.5*cm,  bottomMargin=1.5*cm,
    title="GPC vs GNB Antibiotic Susceptibility Chart",
    author="Orris Medical Reference"
)

styles = getSampleStyleSheet()

def style(name, **kw):
    s = ParagraphStyle(name, parent=styles["Normal"], **kw)
    return s

title_style = style("Title2", fontSize=20, fontName="Helvetica-Bold",
                    textColor=WHITE, alignment=TA_CENTER, spaceAfter=4)
subtitle_style = style("Sub", fontSize=11, fontName="Helvetica",
                       textColor=colors.HexColor("#ccddee"), alignment=TA_CENTER)
section_style = style("Sec", fontSize=13, fontName="Helvetica-Bold",
                      textColor=WHITE, alignment=TA_CENTER)
cell_hdr = style("CH", fontSize=8.5, fontName="Helvetica-Bold",
                 textColor=WHITE, alignment=TA_CENTER, leading=10)
cell_body = style("CB", fontSize=7.5, fontName="Helvetica",
                  textColor=BLACK, alignment=TA_LEFT, leading=9)
cell_center = style("CC", fontSize=7.5, fontName="Helvetica",
                    textColor=BLACK, alignment=TA_CENTER, leading=9)
legend_style = style("Leg", fontSize=8, fontName="Helvetica",
                     textColor=BLACK, alignment=TA_LEFT)
note_style = style("Note", fontSize=7.5, fontName="Helvetica-Oblique",
                   textColor=colors.HexColor("#555555"), alignment=TA_CENTER)

# ── Helper: coloured susceptibility cell ─────────────────────────────────────
def sc(text, bg=None):
    """Return a (Paragraph, bg_color) tuple for susceptibility cells."""
    mapping = {
        "S":  (S_COLOR,  WHITE, "S"),
        "R":  (R_COLOR,  WHITE, "R"),
        "V":  (V_COLOR,  WHITE, "V"),
        "I":  (I_COLOR,  WHITE, "I"),
        "S*": (colors.HexColor("#1e8449"), WHITE, "S*"),
        "R*": (colors.HexColor("#b03a2e"), WHITE, "R*"),
        "V*": (colors.HexColor("#d68910"), WHITE, "V*"),
        "-":  (NA_COLOR, WHITE, "-"),
    }
    if text in mapping:
        bg_col, fg_col, label = mapping[text]
        p = Paragraph(f"<b>{label}</b>",
                      style("SC", fontSize=8, fontName="Helvetica-Bold",
                            textColor=fg_col, alignment=TA_CENTER, leading=10))
        return p, bg_col
    p = Paragraph(text, cell_center)
    return p, (bg if bg else WHITE)

# ── Data definition ──────────────────────────────────────────────────────────
# Columns: Antibiotic | Class | S.aureus(MSSA) | S.aureus(MRSA) | S.pyogenes |
#          S.pneumoniae | E.faecalis | E.faecium(VRE) ||
#          E.coli | Klebsiella | Pseudomonas | Acinetobacter | Salmonella | H.influenzae

# Key: S=Susceptible, R=Resistant, V=Variable, I=Intermediate, -=Not applicable / not used
# S* / V* / R* = with caveats (footnote)

ABX_DATA = [
    # [Antibiotic, Drug Class,
    #   MSSA, MRSA, S.pyo, S.pneu, E.fae, E.fae(VRE),
    #   E.coli, Klebsiella, Pseudomonas, Acinetobacter, Salmonella, H.influenzae]
    # ── Beta-lactams ──────────────────────────────────────────────
    ["Penicillin G", "Natural Penicillin",
     "S","R","S","V*","S","-",
     "R","R","R","R","R","R"],
    ["Amoxicillin", "Aminopenicillin",
     "S","R","S","S","S","-",
     "V","R","R","R","V","V"],
    ["Amoxicillin-Clavulanate", "Beta-lactam + Inhibitor",
     "S","R","S","S","S","-",
     "S","S","R","V","V","S"],
    ["Nafcillin / Oxacillin", "Antistaphylococcal PCN",
     "S","R","S","S","R","R",
     "R","R","R","R","R","R"],
    ["Piperacillin-Tazobactam", "Extended PCN + Inhibitor",
     "S","R","S","S","S","-",
     "S","S","V","V","S","S"],
    ["Cefazolin (1st gen)", "1st-Gen Cephalosporin",
     "S","R","S","S","R","R",
     "S","S","R","R","V","V"],
    ["Ceftriaxone (3rd gen)", "3rd-Gen Cephalosporin",
     "S","R","S","S","R","R",
     "S","S","R","R","S","S"],
    ["Ceftazidime (3rd gen)", "3rd-Gen Cephalosporin (anti-Pseudo)",
     "R","R","R","R","R","R",
     "S","S","S","V","S","S"],
    ["Cefepime (4th gen)", "4th-Gen Cephalosporin",
     "S","R","S","S","R","R",
     "S","S","S","V","S","S"],
    ["Ceftaroline (5th gen)", "5th-Gen Cephalosporin (anti-MRSA)",
     "S","S","S","S","R","R",
     "S","S","R","R","S","S"],
    ["Imipenem/Meropenem", "Carbapenem",
     "S","R","S","S","S","R",
     "S","S","V","V","S","S"],
    ["Ertapenem", "Carbapenem (no Pseudo)",
     "S","R","S","S","S","R",
     "S","S","R","V","S","S"],
    ["Aztreonam", "Monobactam",
     "R","R","R","R","R","R",
     "S","S","S","V","S","S"],
    # ── Glycopeptides ──────────────────────────────────────────────
    ["Vancomycin", "Glycopeptide",
     "S","S","S","S","S","R",
     "R","R","R","R","R","R"],
    ["Teicoplanin", "Glycopeptide",
     "S","S","S","S","S","R",
     "R","R","R","R","R","R"],
    # ── Lipopeptide ────────────────────────────────────────────────
    ["Daptomycin", "Lipopeptide",
     "S","S","S","S","S","V",
     "R","R","R","R","R","R"],
    # ── Oxazolidinones ─────────────────────────────────────────────
    ["Linezolid", "Oxazolidinone",
     "S","S","S","S","S","S",
     "R","R","R","R","R","R"],
    ["Tedizolid", "Oxazolidinone (2nd gen)",
     "S","S","S","S","S","S",
     "R","R","R","R","R","R"],
    # ── Aminoglycosides ────────────────────────────────────────────
    ["Gentamicin", "Aminoglycoside",
     "S","V","V","R","V*","V*",
     "S","S","S","V","V","V"],
    ["Amikacin", "Aminoglycoside",
     "S","V","V","R","V*","V*",
     "S","S","S","V","V","S"],
    # ── Fluoroquinolones ───────────────────────────────────────────
    ["Ciprofloxacin", "Fluoroquinolone",
     "S","R","V","R","V","V",
     "S","S","S","V","V","S"],
    ["Levofloxacin", "Respiratory FQ",
     "S","R","S","S","S","V",
     "S","S","S","V","S","S"],
    ["Moxifloxacin", "Respiratory FQ",
     "S","R","S","S","S","V",
     "S","S","R","V","S","S"],
    # ── Macrolides ─────────────────────────────────────────────────
    ["Azithromycin", "Macrolide",
     "V","R","S","V","R","R",
     "R","R","R","R","V","S"],
    ["Erythromycin", "Macrolide",
     "V","R","S","V","R","R",
     "R","R","R","R","R","R"],
    # ── Tetracyclines ──────────────────────────────────────────────
    ["Doxycycline", "Tetracycline",
     "S","V","S","S","V","V",
     "V","V","R","V","V","R"],
    ["Tigecycline", "Glycylcycline",
     "S","S","S","S","S","S",
     "S","S","R","S","S","S"],
    # ── Folate Inhibitors ──────────────────────────────────────────
    ["TMP-SMX", "Sulfonamide Combo",
     "S","V","V","V","R","R",
     "V","V","R","V","V","V"],
    # ── Other ──────────────────────────────────────────────────────
    ["Clindamycin", "Lincosamide",
     "S","V","S","S","R","R",
     "R","R","R","R","R","R"],
    ["Metronidazole", "Nitroimidazole",
     "R","R","R","R","R","R",
     "R","R","R","R","R","R"],
    ["Rifampicin", "Rifamycin",
     "S","S","S","S","V","V",
     "R","R","R","R","R","R"],
    ["Colistin / Polymyxin B", "Polymyxin",
     "R","R","R","R","R","R",
     "S","S","S","S","S","R"],
    ["Nitrofurantoin", "Nitrofuran",
     "S","S","S","V","S","R",
     "S","V","R","R","R","R"],
    ["Fosfomycin", "Phosphonic acid",
     "S","S","V","V","S","V",
     "S","V","V","R","V","V"],
]

# Column widths (landscape A3 = 420 x 297mm, usable ~397mm)
# Antibiotic(90), Class(80), then 12 organism cols each 19mm => 228mm => total 398mm
COL_W = [90, 80] + [19]*12
page_w = sum(COL_W)

# ── Build table rows ─────────────────────────────────────────────────────────
def hdr(txt, bg, fg=WHITE, size=8):
    return Paragraph(f"<b>{txt}</b>",
                     style("H", fontSize=size, fontName="Helvetica-Bold",
                           textColor=fg, alignment=TA_CENTER, leading=9))

# Row 0: mega header
R0 = [
    hdr("ANTIBIOTIC", GREY_HEADER, size=9),
    hdr("DRUG CLASS", GREY_HEADER, size=9),
    hdr("GRAM-POSITIVE COCCI (GPC)", MID_BLUE, size=10),
    Paragraph(""), Paragraph(""), Paragraph(""), Paragraph(""), Paragraph(""),
    hdr("GRAM-NEGATIVE BACILLI (GNB)", MID_RED, size=10),
    Paragraph(""), Paragraph(""), Paragraph(""), Paragraph(""), Paragraph(""),
]

# Row 1: organism names
org_names_gpc = ["S. aureus\n(MSSA)", "S. aureus\n(MRSA)", "S. pyogenes\n(GAS)",
                 "S. pneumoniae", "E. faecalis", "E. faecium\n(VRE)"]
org_names_gnb = ["E. coli", "Klebsiella\npneumoniae", "Pseudomonas\naeruginosa",
                 "Acinetobacter\nbaumannii", "Salmonella\nspp.", "H. influenzae"]

R1 = [hdr("ANTIBIOTIC", DARK_BLUE, size=8),
      hdr("CLASS", DARK_BLUE, size=8)]
for n in org_names_gpc:
    R1.append(hdr(n, MID_BLUE, size=7.5))
for n in org_names_gnb:
    R1.append(hdr(n, MID_RED, size=7.5))

# Data rows
data_rows = []
style_commands = []
row_idx = 2  # rows 0,1 are headers

for i, row in enumerate(ABX_DATA):
    abx, cls = row[0], row[1]
    sus_vals = row[2:]  # 12 values

    tr = [
        Paragraph(f"<b>{abx}</b>",
                  style("A", fontSize=8, fontName="Helvetica-Bold",
                        textColor=DARK_BLUE, alignment=TA_LEFT, leading=10)),
        Paragraph(cls,
                  style("C", fontSize=7.5, fontName="Helvetica-Oblique",
                        textColor=colors.HexColor("#333333"), alignment=TA_LEFT, leading=9)),
    ]
    for j, val in enumerate(sus_vals):
        p, bg = sc(val)
        tr.append(p)
        col = 2 + j
        bg_key = f"bg_{row_idx}_{col}"
        style_commands.append(("BACKGROUND", (col, row_idx), (col, row_idx), bg))

    row_bg = PALE_BLUE if i % 2 == 0 else WHITE
    style_commands.append(("BACKGROUND", (0, row_idx), (1, row_idx), row_bg))
    data_rows.append(tr)
    row_idx += 1

all_rows = [R0, R1] + data_rows

# ── Table style ──────────────────────────────────────────────────────────────
base_style = [
    # Spanning
    ("SPAN", (2, 0), (7, 0)),    # GPC header spans cols 2-7
    ("SPAN", (8, 0), (13, 0)),   # GNB header spans cols 8-13
    ("SPAN", (0, 0), (0, 1)),    # Antibiotic header spans rows 0-1
    ("SPAN", (1, 0), (1, 1)),    # Class header spans rows 0-1

    # Fonts / alignment
    ("VALIGN", (0, 0), (-1, -1), "MIDDLE"),
    ("ALIGN",  (0, 0), (-1, -1), "CENTER"),
    ("ALIGN",  (0, 2), (1, -1),  "LEFT"),

    # Grid
    ("GRID",      (0, 0), (-1, -1), 0.4, colors.HexColor("#aaaaaa")),
    ("LINEBELOW", (0, 1), (-1, 1),  1.2, DARK_BLUE),

    # Row 0 backgrounds
    ("BACKGROUND", (0, 0), (1, 1),   GREY_HEADER),
    ("BACKGROUND", (2, 0), (7, 0),   MID_BLUE),
    ("BACKGROUND", (2, 1), (7, 1),   DARK_BLUE),
    ("BACKGROUND", (8, 0), (13, 0),  MID_RED),
    ("BACKGROUND", (8, 1), (13, 1),  DARK_RED),

    # Vertical separator between GPC and GNB
    ("LINEAFTER", (7, 0), (7, -1), 2, GREY_HEADER),

    # Row heights
    ("ROWBACKGROUNDS", (0, 2), (-1, -1), [PALE_BLUE, WHITE]),

    # Padding
    ("TOPPADDING",    (0, 0), (-1, -1), 4),
    ("BOTTOMPADDING", (0, 0), (-1, -1), 4),
    ("LEFTPADDING",   (0, 0), (-1, -1), 3),
    ("RIGHTPADDING",  (0, 0), (-1, -1), 3),
]

ts = TableStyle(base_style + style_commands)

t = Table(all_rows, colWidths=COL_W, repeatRows=2)
t.setStyle(ts)

# ── Legend ────────────────────────────────────────────────────────────────────
legend_items = [
    (S_COLOR,  "S  = Susceptible (typically effective)"),
    (R_COLOR,  "R  = Resistant (not effective)"),
    (V_COLOR,  "V  = Variable (depends on strain/resistance pattern)"),
    (I_COLOR,  "I   = Intermediate / reduced susceptibility"),
    (NA_COLOR, "-   = Not applicable / not used clinically"),
]

def legend_row(col, label):
    box = Table([[""]], colWidths=[12], rowHeights=[12])
    box.setStyle(TableStyle([("BACKGROUND",(0,0),(0,0),col),
                              ("GRID",(0,0),(0,0),0.5,colors.grey)]))
    return [box, Paragraph(f"  {label}", legend_style)]

leg_data = [legend_row(c, l) for c, l in legend_items]
# Build as a single-row horizontal legend
leg_cells = []
for c, l in legend_items:
    box = Table([[""]], colWidths=[10], rowHeights=[10])
    box.setStyle(TableStyle([("BACKGROUND",(0,0),(0,0),c),
                              ("GRID",(0,0),(0,0),0.5,colors.grey)]))
    leg_cells.append(box)
    leg_cells.append(Paragraph(f" {l}   ", legend_style))

leg_table = Table([leg_cells], colWidths=([12,120]*5))
leg_table.setStyle(TableStyle([
    ("VALIGN",(0,0),(-1,-1),"MIDDLE"),
    ("ALIGN", (0,0),(-1,-1),"LEFT"),
    ("TOPPADDING",(0,0),(-1,-1),3),
    ("BOTTOMPADDING",(0,0),(-1,-1),3),
]))

notes = [
    "* V for penicillin against S. pneumoniae: susceptibility varies by site (meningitis requires higher MIC breakpoints).",
    "* Gentamicin/Amikacin used synergistically with beta-lactams for enterococcal endocarditis (not monotherapy).",
    "* MRSA = Methicillin-Resistant S. aureus; VRE = Vancomycin-Resistant Enterococcus; ESBL/CRKP strains may show further resistance.",
    "* Pseudomonas aeruginosa is intrinsically resistant to many antibiotics; always verify local antibiogram.",
    "* This chart reflects general/typical susceptibility patterns. Always consult local antibiogram and culture/sensitivity results.",
]

# ── Assemble document ─────────────────────────────────────────────────────────
elements = []

# Page title banner
title_table = Table(
    [[Paragraph("GPC vs GNB", title_style)],
     [Paragraph("Comparative Antibiotic Susceptibility Reference Chart", subtitle_style)],
     [Paragraph("Gram-Positive Cocci (GPC)  |  Gram-Negative Bacilli (GNB)  •  Orris Medical Reference 2026", subtitle_style)]],
    colWidths=[page_w]
)
title_table.setStyle(TableStyle([
    ("BACKGROUND", (0,0),(0,2), DARK_BLUE),
    ("TOPPADDING", (0,0),(0,2), 6),
    ("BOTTOMPADDING",(0,0),(0,2), 6),
    ("LEFTPADDING", (0,0),(0,2), 8),
    ("RIGHTPADDING",(0,0),(0,2), 8),
]))

elements.append(title_table)
elements.append(Spacer(1, 6))
elements.append(t)
elements.append(Spacer(1, 6))

# Legend box
leg_outer = Table(
    [[Paragraph("<b>LEGEND:</b>", style("LT", fontSize=8.5, fontName="Helvetica-Bold",
                                        textColor=GREY_HEADER, alignment=TA_LEFT)),
      leg_table]],
    colWidths=[55, page_w - 55]
)
leg_outer.setStyle(TableStyle([
    ("BACKGROUND",(0,0),(-1,-1), LIGHT_GREY),
    ("BOX",(0,0),(-1,-1), 0.8, colors.HexColor("#aaaaaa")),
    ("VALIGN",(0,0),(-1,-1),"MIDDLE"),
    ("TOPPADDING",(0,0),(-1,-1),5),
    ("BOTTOMPADDING",(0,0),(-1,-1),5),
    ("LEFTPADDING",(0,0),(-1,-1),6),
]))
elements.append(leg_outer)
elements.append(Spacer(1, 5))

for note in notes:
    elements.append(Paragraph(f"<i>{note}</i>", note_style))
    elements.append(Spacer(1, 2))

doc.build(elements)
print(f"PDF created: {OUTPUT}")

cd /home/daytona/workspace/gpc-gnb-chart && python generate_chart.py 2>&1

ls -lh /home/daytona/workspace/gpc-gnb-chart/

A detailed professional medical reference table for Gram-Negative Bacilli (GNB). The table should show 40+ clinically relevant species organized by category. Table with 5 columns: - Column 1: GENUS (bold, left-aligned) - Column 2: SPECIES (italicized, left-aligned) - Column 3: PHYLUM/CLASS (smaller text, center) - Column 4: SPECIAL FEATURE (concise, left-aligned) - Column 5: KEY DISEASE (left-aligned) Organize into sections with color-coded category headers: SECTION 1 - ENTEROBACTERIACEAE (FAMILY ENTEROBACTERALES, PHYLUM PROTEOBACTERIA, CLASS GAMMAPROTEOBACTERIA) - Blue header - Escherichia | E. coli | Gamma | Oxidase-, lactose ferment | UTI, neonatal meningitis, diarrhea, HUS - Escherichia | E. coli O157:H7 | Gamma | Shiga toxin producer | Hemolytic uremic syndrome - Klebsiella | K. pneumoniae | Gamma | Mucoid capsule, non-motile | Hospital pneumonia, UTI, liver abscess - Klebsiella | K. oxytoca | Gamma | ESBL producer | UTI, bacteremia - Proteus | P. mirabilis | Gamma | Urease+, swarming | Staghorn calculi, UTI - Proteus | P. vulgaris | Gamma | Urease+, indole+ | UTI, wound infections - Morganella | M. morganii | Gamma | Urease+, indole+ | UTI, wound infection - Salmonella | S. typhi | Gamma | Non-lactose ferment, H2S+ | Typhoid fever (systemic) - Salmonella | S. paratyphi | Gamma | Non-lactose ferment | Paratyphoid fever - Salmonella | S. enteritidis | Gamma | Food pathogen | Foodborne gastroenteritis - Salmonella | S. typhimurium | Gamma | Multiple serovars | Foodborne gastroenteritis - Shigella | S. dysenteriae | Gamma | Non-motile, Shiga toxin | Severe bloody dysentery - Shigella | S. flexneri | Gamma | 15 serotypes | Bacillary dysentery - Shigella | S. sonnei | Gamma | Non-motile | Mild diarrhea - Shigella | S. boydii | Gamma | Non-motile | Diarrhea - Yersinia | Y. pestis | Gamma | Biofilm | PLAGUE (bubonic/pneumonic/septicemic) - Yersinia | Y. enterocolitica | Gamma | Psychrophilic | Enterocolitis, mesenteric adenitis - Yersinia | Y. pseudotuberculosis | Gamma | Cold-loving | Mesenteric adenitis, mimics appendicitis - Enterobacter | E. cloacae | Gamma | AmpC beta-lactamase | Nosocomial infections - Enterobacter | E. aerogenes | Gamma | AmpC producer | Hospital-acquired infections - Serratia | S. marcescens | Gamma | Red pigment | Hospital infections, IV drug users - Citrobacter | C. freundii | Gamma | ESBL producer | UTI, neonatal meningitis - Citrobacter | C. koseri | Gamma | Meningitis risk | Neonatal brain abscess - Providencia | P. stuartii | Gamma | Urease+ | UTI in catheterized patients - Hafnia | H. alvei | Gamma | Lactose delayed | Rarely pathogenic SECTION 2 - NON-FERMENTATIVE GRAM-NEGATIVE BACILLI - Red header - Pseudomonas | P. aeruginosa | Gamma | Oxidase+, blue-green pigment, mucoid | Burn/wound infections, VAP, CF lung disease - Pseudomonas | P. fluorescens | Gamma | Oxidase+, fluorescence | Environmental contaminant - Pseudomonas | P. putida | Gamma | Oxidase+ | Environmental - Acinetobacter | A. baumannii | Gamma | Oxidase-, CRAB strains | Hospital VAP, wound infections - Acinetobacter | A. lwoffii | Gamma | Oxidase- | Opportunistic - Stenotrophomonas | S. maltophilia | Xanthomonas (class) | Oxidase-, carbapenem-resistant | CF pneumonia, VAP in ICU - Burkholderia | B. cepacia | Burkholderiales | Multiple genomovars | CF lung colonization - Burkholderia | B. pseudomallei | Burkholderiales | Bipolar staining | Melioidosis (endemic SE Asia) SECTION 3 - FASTIDIOUS GRAM-NEGATIVE BACILLI - Orange header - Haemophilus | H. influenzae | Pasteurellales | Requires X & V factors, type b has capsule | Meningitis, pneumonia, epiglottitis - Haemophilus | H. ducreyi | Pasteurellales | Gram-negative bacillus | Chancroid (STI) - Legionella | L. pneumophila | Legionellales | Intracellular, water systems | Legionnaire's disease, Pontiac fever - Bordetella | B. pertussis | Burkholderiales | Pertussis toxin producer | Whooping cough (pertussis) - Bordetella | B. parapertussis | Burkholderiales | Mild toxin | Parapertussis (milder) - Brucella | B. melitensis | Rhizobiales | Zoonosis (goats) | Brucellosis (undulant fever) - Brucella | B. abortus | Rhizobiales | Zoonosis (cattle) | Brucellosis - Francisella | F. tularensis | Thiotrichales | Bioterror agent, highly infectious | Tularemia (rabbit fever) - Pasteurella | P. multocida | Pasteurellales | Animal bite wound pathogen | Cat/dog bite infections - Bartonella | B. henselae | Rhizobiales | Cat flea vector | Cat scratch disease, bacillary angiomatosis SECTION 4 - CURVED/SPIRAL GRAM-NEGATIVE BACILLI - Purple header - Campylobacter | C. jejuni | Epsilonproteobacteria | Microaerophile, comma-shaped | Most common bacterial diarrhea - Campylobacter | C. fetus | Epsilonproteobacteria | Microaerophile, S-shaped | Bacteremia in elderly/immunocompromised - Helicobacter | H. pylori | Epsilonproteobacteria | Urease+, spiral, lives in stomach | Peptic ulcer, gastric cancer, MALT lymphoma - Vibrio | V. cholerae | Vibrionales | O1 & O139 epidemic strains | Cholera (rice-water diarrhea) - Vibrio | V. parahaemolyticus | Vibrionales | Halophile (salt-loving) | Seafood-associated gastroenteritis - Vibrio | V. vulnificus | Vibrionales | Highly virulent | Raw oyster infections, septicemia SECTION 5 - GRAM-NEGATIVE COCCI / COCCOBACILLI - Green header - Neisseria | N. meningitidis | Gammaproteobacteria | Gram-negative diplococcus | Bacterial meningitis, septicemia - Neisseria | N. gonorrhoeae | Gammaproteobacteria | Gram-negative diplococcus | Gonorrhea, PID, neonatal ophthalmia - Moraxella | M. catarrhalis | Gammaproteobacteria | Gram-negative diplococcus | Otitis media, sinusitis, COPD exacerbation Use white background. Section headers bold, full-width color bands. Alternate row shading (very light grey/white) for readability. Professional, high-contrast layout. Include a footer: "Data source: Henry's Clinical Diagnosis & Laboratory Methods, Red Book 2021, Medical Microbiology 9e. *Phylum = Proteobacteria unless noted; Class = Gammaproteobacteria unless noted."