IS Element Ecology Shapes Divergent Carbapenem Resistance Gene Mobilisation Strategies Across Clinical Gram-Negative Pathogens: A Three-Species Comparative Genomic Analysis

This repository contains the analysis code, processed results, and manuscript for a comparative genomic study examining IS element architecture around carbapenem resistance genes in 926 Chinese clinical isolates across three WHO priority pathogens: Klebsiella pneumoniae (n=492), Escherichia coli (n=266), and Acinetobacter baumannii (n=168). Key findings: IS26-mediated composite transposon architecture flanks 94.0% of K. pneumoniae, 62.1% of E. coli, and 6.8% of A. baumannii acquired carbapenemase loci. IS6 copy number predicts carbapenem resistance in both Enterobacteriaceae species (KPN AUC=0.667, p=4.2e-10; ECO PFAM-corrected AUC=0.718, p=2.3e-6). Analysis code is available at https://github.com/jiayu6954-sudo/comparative-amr-genomics