efosternyarko/molecular-characterisation-klebsiella-pneumoniae-neonatal-sepsis-outbreak-gambia
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healthcareType de record:
software
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efo
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Figure reproduction code for: Molecular characterisation of a Klebsiella pneumoniae neonatal sepsis outbreak in a rural Gambian hospital (Foster-Nyarko et al., medRxiv 2026)
# Molecular characterisation of a *Klebsiella pneumoniae* neonatal sepsis outbreak in a rural Gambian hospital
This repository contains the analysis scripts used to generate the figures in:
> Foster-Nyarko E, *et al.* **Molecular characterisation of a *Klebsiella pneumoniae* neonatal sepsis outbreak in a rural Gambian hospital: a retrospective genomic epidemiology investigation.** *medRxiv* (2026). doi.org
---
## Repository Structure
```
code/
├── README.md # This file
├── data/
│ └── README.md # Data sources and access instructions
├── fig01A_gambia_map.py # Figure 1A — Map of The Gambia
├── fig02_resistance_heatmap.py # Figure 2 — AMR heatmap (clinical + environmental)
├── fig03_flow_diagram.md # Figure 3 — Study flow diagram (Illustrator)
├── fig04_epi_curve.qmd # Figure 4 — Epidemiological curves
├── fig05_kpn_phylotree_annotated.qmd # Figure 5 — All-Kp phylogenetic tree + metadata
├── fig06_st39_global_clones.qmd # Figure 6 — Global ST39 clone distribution + AMR
├── figS1_ward_contamination.md # Figure S1 — Ward contamination sources (Illustrator)
├── figS2_transmission_clusters.md # Figure S2 — Transmission cluster analysis (note)
├── figS3_st39_plasmid.qmd # Figure S3 — ST39 multi-panel with plasmid coverage
└── figAppendix_clinker_amr_locus.md # Appendix — Chromosomal AMR locus comparison (clinker)
```
---
## Figures Summary
| Figure | Description | Script | Language |
|--------|-------------|--------|----------|
| Fig 1A | Map of The Gambia showing study sites | `fig01A_gambia_map.py` | Python |
| Fig 1B | Timeline of outbreak investigation | Assembled in Illustrator | — |
| Fig 2 | Clustered AMR heatmap (clinical + environmental isolates) | `fig02_resistance_heatmap.py` | Python |
| Fig 3 | Study flow diagram | Assembled in Illustrator | — |
| Fig 4 | Epidemiological curves — 3 pane …
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