IS26-Mediated Composite Transposons Underlie the Near-Universal Flanking Architecture of Carbapenem Resistance Genes in Chinese Clinical Klebsiella pneumoniae: A Population Genomic Analysis

Analysis code, processed data, figures, and manuscript for a population genomic study of IS26-mediated carbapenem resistance gene architecture in 492 Chinese clinical Klebsiella pneumoniae genomes (200 carbapenem-resistant, 292 susceptible). Key findings: IS26-mediated composite transposons flank 94.0% (47/50, 95%CI 83.5-98.8%) of acquired carbapenemase loci. IS6 copy number predicts carbapenem resistance with AUC=0.949 (PFAM HMM-verified; Cliff's delta=0.899; p=2.2e-27). Dominant carbapenemases: KPC-2 (54.5%) and NDM variants (44%). Analysis code available at https://github.com/jiayu6954-sudo/amr-genomics-analysis