Case Study: Genome Assembly of Klebsiella pneumoniae isolates over course of treatment

We used Oxford Nanopore and Illumina MiSeq whole genome sequencing (WGS) to characterize a concurrent disseminated infection of a highly virulent hypermucoviscous (HMV) Klebsiella pneumoniae and OXA-181-producing XDR K. pneumoniae from a patient with recent hospitalization in India. During exposure to meropenem therapy, the pan-susceptible HMV K. pneumoniae became resistant to carbapenems, consistent with the acquisition of blaOXA-181 by the HMV strain. WGS was applied to all clinical K. pneumoniae isolates recovered from the patient throughout his 3-month hospitalization to demonstrate changes in the organism's resistome that occurred over time