Comparative In Silico Profiling of Antimicrobial Resistance Genotypes in Clinical vs. Environmental Isolates of Klebsiella pneumoniae: A Global Resistome Analysis

Klebsiella pneumoniae is a critical opportunistic pathogen associated with severe healthcare-associated infections and escalating multidrug resistance (MDR). Understanding the genetic overlap between clinical resistomes and environmental reservoirs is essential for One Health surveillance. A global comparative in silico resistome analysis was conducted using genomic metadata from the NCBI Pathogen Detection browser. Isolates were categorized by origin into clinical (n > 100,000) and environmental/effluent (epi_type: "environmental/other") cohorts. Prevalences of resistance determinants annotated via AMRFinderPlus were evaluated and normalized using R. A shared core resistome dominated by efflux pump genes (emrD, oqxA, oqxB) and fosA was identified across both cohorts. Target-site mutations conferring fluoroquinolone resistance (parC_S80I, gyrA_S83I) exhibited marked enrichment in clinical isolates, reflecting high nosocomial selective pressure. Crucially, extended-spectrum beta-lactamase genes (blaCTX-M-15, blaTEM-1) and mobile determinants (sul1, sul2, aph(3'')-Ib) demonstrated high prevalence in environmental samples, mirroring circulating clinical strains. Environmental and wastewater reservoirs harbour major clinically relevant resistance genes, reinforcing the critical role of aquatic environments in AMR dissemination and the necessity for integrated One Health genomic monitoring.