efosternyarko/molecular-characterisation-klebsiella-pneumoniae-neonatal-sepsis-outbreak-gambia

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 …