righteousagoha/kp-prp-one-health-ghana

Analysis code for Persistence-Resistance Plasmids in K. pneumoniae across One Health compartments in Ghana # Persistence-Resistance Plasmids in *Klebsiella pneumoniae* across One Health Compartments in Ghana ## Overview Analysis code and computational pipeline for: **"CRISPR immune failure enables cross-niche spread of persistence-resistance plasmids in *Klebsiella pneumoniae*"** 78 *K. pneumoniae* isolates from clinical (n=20), animal (n=21), and environmental (n=37) sources in Ghana. 370 plasmids, 152 clusters, 32 cross-niche. ## Repository Structure ``` kp_prp_analysis/ ├── README.md ├── .gitignore ├── scripts/ │ ├── 01_genome_characterisation.sh # Unicycler + Kleborate + BacPipe │ ├── 02_plasmid_reconstruction.sh # MOB-suite pipeline │ ├── 03_crispr_analysis.sh # CRISPRimmunity pipeline │ ├── 04_abricate_annotation.sh # ABRicate on plasmid FASTAs │ ├── 05_blast_spacer_plasmid.sh # Spacer vs plasmid BLAST │ ├── 06_data_integration.R # Data loading, merging, QC │ ├── 07_analysis_all.R # Resistome, plasmid sharing, GLM, PRP │ ├── 08_acr_genomic_location.R # Acr chromosomal vs plasmid mapping │ └── 09_snp_analysis.sh # Core SNP analysis for clonal validation ├── data/ │ ├── sample_metadata.csv │ └── README_data.md ├── figures/ │ └── README_figures.md └── docs/ └── methods.md ``` ## Pipeline Overview ### Bioinformatics (scripts 01-05) 1. Quality control, trimming, assembly (FastQC, Trimmomatic, Unicycler) 2. Species ID, MLST, AMR/virulence detection (Kleborate, BacPipe) 3. Plasmid reconstruction and typing (MOB-suite) 4. CRISPR-Cas, anti-CRISPR, spacer extraction (CRISPRimmunity) 5. Plasmid annotation (ABRicate: NCBI, VFDB, PlasmidFinder) 6. Spacer-plasmid matching (BLASTn blastn-short) 7. Core SNP analysis for clonal validation (Snippy) ### Statistical analysis (scripts 06-08) - Data integration and cross-referencing across tools - Resistome clustering (Jaccard, PCoA, PERMANOVA) - Cross-niche plasmid sharing and Venn analysis - GC deviation analysis - Logistic reg …