Pangenome analysis of Tanzanian clinical <i>Klebsiella pneumoniae</i> reveals pandemic clones with high genome plasticity and versatile mobilome, virulome, and resistome profiles

<i>Klebsiella pneumoniae</i> is a rapidly evolving pathogen with a diverse pangenome whose mobilome and resistome remain elusive. Here, we aimed to delineate the pangenome of 198 isolates from Tanzanian regions. Raw Illumina reads retrieved from public repositories were assembled and analyzed using multilocus sequence typing, core-genome single nucleotide polymorphism (SNP)-based phylogeny, and capsular polysaccharide (K-locus) and lipopolysaccharide O-antigen (O-locus) typing. A total of 184 isolates were classified as <i>Klebsiella pneumoniae sensu stricto</i>, while 14 belonged to other species within the <i>Klebsiella pneumoniae</i> complex. We identified 90 sequence types (STs), including global high-risk ST45, ST39, ST336, ST14, ST1552, and ST17. KL24 and KL25 were the most common K-loci, while OL2α.1 and OL2α.2 were dominant O-loci. Pangenome analysis revealed 30,992 gene families, distributed as persistent (13.6%), shell (11.2%), and cloud (75.2%) genes, suggesting an open pangenome structure. Core-genome SNP-based phylogeny confirmed clonal expansion and lineage clustering. Virulence profiling showed yersiniabactin in 44% of isolates. Most genomes carried key fimbrial and iron uptake genes. Resistome analysis revealed near-universal presence of <i>bla_CTX-M-15</i>, <i>oqxA/B</i>, <i>fosA6</i>, <i>sul2</i>, and <i>marA</i>. Plasmid typing identified IncF-type (76%) and Col-type (54%) plasmids, while over 120 mobile genetic elements were detected, whose frequencies were on a huge spectrum of insertion sequences (e.g., IS5075 and MITE<i>Ype1</i>) and transposons (e.g., Tn5403 and Tn6082). Conclusively, Tanzanian <i>K. pneumoniae</i> strains exhibit extensive genomic plasticity, high-risk lineages, and a versatile mobilome, calling for national genomic surveillance to inform intervention strategies.IMPORTANCEThe <i>Klebsiella pneumoniae</i> complex comprises a diverse group of bacterial pathogens adapted to thrive over a wide range of environments. Isolates from clinical and environmental samples are implicated in nosocomial infections and multidrug resistance, with similar genome structures and inherent genes. Our study presents the first pangenome report underlying genomic plasticity of <i>K. pneumoniae</i> isolates from Tanzanian clinical specimens, demonstrating versatile clones, mobilome, and resistome profiles. Combining these profiles with the versatility of K and O structures, our study emphasizes the need for comprehensive multidisciplinary surveillance studies to optimize therapeutic and vaccine development.