In silico genomic analysis of resistome, virulome, and mobilome of β-lactamase-producing Klebsiella pneumoniae

Klebsiella pneumoniae (K. pneumoniae) is a major multidrug-resistant pathogen associated with nosocomial infections, particularly among immunocompromised patients, and contributes significantly to global morbidity and mortality. This study provides a comprehensive genomic analysis of β-lactamase-producing K. pneumoniae isolates. Whole-genome sequences of clinical isolates were retrieved from the National Center for Biotechnology Information-Sequence Read Archive (NCBI-SRA) repository and systematically analyzed to characterize antimicrobial resistance (AMR) genes, virulence factors, mobile genetic elements, and defense systems. Clonal diversity was assessed using multilocus sequence typing and capsule typing. Pan-genome analysis revealed pronounced heterogeneity, with ST15 as the predominant sequence type. The presence of a large accessory genome indicates substantial genomic plasticity. In total, 244 unique AMR genes were identified, predominantly encoding β-lactamases and efflux pumps. Genes conferring resistance to penams, aminoglycosides, tetracyclines, and fluoroquinolones were also highly represented. Over 6203 insertion sequence (IS) elements were detected, mainly from the IS3 family. Integron-associated resistance genes were frequently observed, particularly those conferring resistance to β-lactams and aminoglycosides. Collectively, these findings highlight K. pneumoniae’s rapid genetic diversification and high potential for resistance, which are intrinsically linked to the complex dynamics of its resistome, virulome, and mobilome. This reinforces the urgent need for alternative therapeutic strategies, antimicrobial stewardship, and enhanced genomic surveillance to curb the increasing threat of AMR.