Bugs & Drugs — Antimicrobial Stewardship Tool

What's New in This Version

Tab 1: Sensitivity Grid (New)

• 70+ organisms × 32 antibiotics, Sanford Guide-style color-coded matrix
• Hover any cell for antibiotic/organism context
• Filter by organism group, antibiotic class, or free-text search
• Sticky headers for easy scrolling

Tab 2: Treatment Details (Existing + Expanded)

• Tiered therapy profiles with US dosing for bacteria, fungi, viruses
• MDR Focus toggle for salvage regimens
• PDF export

Tab 3: Organism Search — AMR Database (New)

• Full AMR (for R) taxonomy database: 78,000+ taxa
• Clinical breakpoints (EUCAST/CLSI)
• Requires one-time setup (see below)

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Setup: AMR Database Integration

The AMR database tab reads pre-exported CSV files from the data/ folder. These are generated from the AMR Python package (which requires R).

Run this once on your local machine:

# 1. Install AMR Python package (requires R to be installed)
pip install AMR

# 2. Export AMR data to CSV files
python generate_amr_data.py

This creates:

• data/amr_microorganisms.csv
• data/amr_antimicrobials.csv
• data/amr_clinical_breakpoints.csv
• data/amr_top_organisms.csv

Then commit the data/ folder to your repo. Streamlit Cloud reads the CSVs directly — no R installation needed at runtime.

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Deploying to Streamlit Cloud

1. Push all files (including data/ CSVs) to GitHub
2. Connect your repo at share.streamlit.io
3. Set main file: app.py
4. No special packages.txt needed (R is not required at runtime)

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Running Locally

pip install -r requirements.txt
streamlit run app.py

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Sensitivity Data Sources

• Sanford Guide 2024
• IDSA Guidelines (MRSA, Candidiasis, CDiff, etc.)
• CDC treatment recommendations
• ASHP Clinical Practice Guidelines

For clinical decision support only. Always correlate with local antibiogram and patient factors.