Genomic characterization and comparative analysis of antibiotic resistance and virulence in Bangladeshi and global Klebsiella pneumoniae ST48 strains

Klebsiella pneumoniae is an opportunistic pathogen associated with nosocomial infections, known for its multidrug resistance (MDR) and biofilm-forming abilities. ST48 is a particularly concerning sequence type and an emerging international clone linked to global spread and MDR infections. This study examines the comprehensive genomic epidemiology of the local and global populations of K. pneumoniae ST48 strains using whole genomes sequence data. We performed phenotypic and genotypic characterization of a K. pneumoniae strain S3C and conducted molecular epidemiological analyses of local ST48 isolates in Bangladesh, followed by pan-genome and phylogenetic analyses of 397 global ST48 strains. The S3C strain was resistant to 17 out of 19 tested antibiotics and was a moderate biofilm former. Whole genome sequencing identified it as ST48 clonal type, with 13 acquired antibiotic resistance genes, 76 virulence-associated genes, and multiple mobile genetic elements. Comparative analysis of Bangladeshi ST48 strains indicated a high prevalence of MDR genes, particularly bla_CTX-M-15, and a diverse array of virulence factors associated with biofilm formation, siderophore production, capsular biosynthesis and others. Pan-genome analysis of Bangladeshi ST48 strains revealed 8,030 genes, with 56.26% classified as core genes. In contrast, global ST48 strains had 16,307 genes, with 75.3% as accessory genes, highlighting extensive genomic plasticity. The phylogenetic analysis revealed that isolates from different regions clustered within the major clade, indicating the global dissemination of this sequence type. Our findings underscore the substantial genomic diversity and high resistance levels of K. pneumoniae ST48, emphasizing the need for targeted infection control measures and continuous surveillance.