efosternyarko/gambia-kpn-pheno-geno-concordance

Analysis code and figures: phenotype-genotype AMR concordance in Klebsiella pneumoniae, rural Gambia # Phenotype-genotype correlation of the antibiotic resistance profile of *Klebsiella pneumoniae* isolates from infants in rural Gambia This repository contains the analysis code and output figures for the manuscript: > Bah A, Able-Thomas S, Dibbasey M, Kujabi M, Salaudeen R, Nyassi A, Barjo O, Adefila WO, Osei I, Bojang A, Foster-Nyarko E, Holt K, Mackenzie G, Sesay AK. *Phenotype-genotype correlation of the antibiotic resistance profile of Klebsiella pneumoniae isolates from infants in rural Gambia.* Whole-genome sequencing data (Oxford Nanopore) and phenotypic antimicrobial susceptibility testing (AST) results for 90 *K. pneumoniae* isolates were used to assess genotype-phenotype concordance across five clinically relevant antibiotics, characterise the resistome and virulence gene landscape, and screen for markers associated with the hypervirulent *K. pneumoniae* (hvKp) pathotype. ## Contents ``` code/ R scripts used for concordance analysis and figure generation figures/ Final figure PDFs as they appear in the manuscript ``` ### Code | Script | Purpose | |---|---| | `make_figure1_resistance_profile.R` | Figure 1: phenotypic resistance profile, MDR classification, top serotype/ST combinations | | `make_figure2_cooccurrence.R` | Figure 2: AMR gene co-occurrence (upset plot), pairwise co-occurrence heatmap, isolate x gene distribution matrix | | `make_concordance_plots.R` | Figure 3: genotype-phenotype concordance (sensitivity/specificity/agreement), outcome classification, resistance marker prevalence | Genotype data were derived from Kleborate v3.2.4 and Kaptive v3.0.0b6 output. Genotype-phenotype concordance was computed using the AMRgen R package (v0.1.0.9000) together with the AMR package (v3.0.1.9057) in R v4.5.3. Figures were generated with ggplot2 (v4.0.3) and patchwork (v1.3.2). ## Reproducibility note These scripts are provided as the exact code used to produce the manuscript's analysis and figures, for transparency and methodological re …