Multi-drug resistance in pathogenic bacteria is a serious threat to public health. It is therefore vital to understand the factors that contribute to the development of antibiotic resistance. Here, we analyze the in-host evolution of carbapenem resistance of Klebsiella pneumoniae, a Gram-negative human pathogen causing serious infections. Three strains, FK-2624, FK-2723 and FK-2820, were isolated from the same patient in a tertiary hospital in China at different treatment stages, showing increasing antibiotic resistance in response to drug treatment. Whole-genome sequencing of these strains suggested a close phylogenetic relationship and differences in the type and number of beta-lactamases carried. A combination of porin loss, the mutation of SHV-187 to SHV-12 and acquisition of a resistance plasmid carrying the extended-spectrum beta-lactamases DHA-1 and CTX-M-14 over the course of the treatment are likely causative for the development of carbapenem resistance. Additional experiments to identify the putative resistance plasmid donor are currently in progress. Together, these results provide evidence of the evolutionary adaptations necessary and available to pathogenic bacteria to survive antibiotic treatment and develop drug-resistance in hospital settings.