Klebsiella pneumoniae, an important opportunistic pathogen, is traditionally classified into classic and hypervirulent pathotypes. Convergent strains combining antimicrobial resistance (AMR) and hypervirulence have emerged globally, posing a significant health challenge. In this study, we investigated potential in-host evolution and morphotypic variation among consecutive K. pneumoniae ST147 isolates from a single patient. As described in a previous study, the isolates displayed distinct morphotypes—small white, normal white, gray, and gray/dry (g/d) colonies. In this study, we now present new genomic and phenotypic analyses, which suggest the acquisition of AMR and virulence genes through plasmid gain. The early isolates carried fewer plasmids, resulting in low resistance and virulence, while later isolates acquired a hybrid IncFIB-IncHI1B plasmid encoding different resistance and aerobactin genes, significantly increasing their geno- and phenotypic AMR and virulence potential. Chromosomal integration of this plasmid in one isolate stabilized the acquired traits. Disruptions in the K locus, mediated by insertion sequences, were linked to the gray and g/d morphotypes, impairing capsule biosynthesis. Uronic acid assays confirmed reduced capsule production in these isolates. In contrast, small colony variants showed significant transcriptomic changes, including upregulation of capsule biosynthesis, iron uptake pathways, and AMR genes, suggesting persistence through altered metabolism. Our findings suggest in-host microevolution of K. pneumoniae ST147 from a classic to a convergent pathotype and highlight the genomic and transcriptomic adaptations underlying morphotypic diversity, providing new insights into the pathogen’s adaptability and persistence in certain environments.
