Menzisk/amr-surveillance-dashboard

A multi-pathogen AMR surveillance pipeline: ESKAPE pathogens, DuckDB database, and interactive Streamlit dashboard with global coverage and African contextualization # AMR Surveillance Dashboard A multi-pathogen antimicrobial resistance (AMR) surveillance pipeline covering the six ESKAPE pathogens, the leading causes of hospital-acquired infections globally. Built to demonstrate production-style data engineering and public health analytics: automated data ingestion from BV-BRC, a structured DuckDB surveillance database, and an interactive Streamlit dashboard with global coverage and African contextualisation. --- ## ESKAPE pathogens covered | Pathogen | Abbreviation | Clinical significance | |---|---|---| | *Enterococcus faecium* | Efm | Vancomycin-resistant enterococci (VRE) | | *Staphylococcus aureus* | Sa | MRSA; leading cause of bloodstream infections | | *Klebsiella pneumoniae* | Kpn | Carbapenem-resistant; WHO critical priority | | *Acinetobacter baumannii* | Ab | Pan-drug resistant; nosocomial outbreaks | | *Pseudomonas aeruginosa* | Pa | Intrinsic multidrug resistance | | *Enterobacter* spp. | Ent | Extended-spectrum beta-lactamase producers | --- ## Tech stack - **Data source:** BV-BRC (Bacterial and Viral Bioinformatics Resource Center) API - **Database:** DuckDB — embedded analytical SQL database - **Dashboard:** Streamlit + Plotly - **Language:** Python 3.11 --- ## Project structure amr-surveillance-dashboard/ ├── data/ │ ├── raw/ # BV-BRC API downloads (JSON) - not tracked by git │ └── processed/ # Cleaned TSVs ready for DuckDB — not tracked by git ├── scripts/ # Data ingestion and processing pipeline ├── notebooks/ # Exploratory analysis and SQL development ├── dashboard/ # Streamlit app ├── tests/ # Validation scripts ├── environment.yml # Conda environment specification └── README.md --- ## Quickstart ```bash # 1. Clone the repo git clone github.com cd amr-surveillance-dashboard # 2. Create and activate conda environment conda env create -f environment.yml conda activate amr-surveillance # 3. …