Hybrid Genome Assembly and Annotation of a Pandrug-Resistant Klebsiella pneumoniae Strain Using Nanopore and Illumina Sequencing

The prevalence of multidrug-resistant is increasingly being implicated worldwide in a variety of infections with high mortalities. Here, we report the complete genome sequence of strain KP58, a pandrug-resistant strain that exhibits high levels of resistance to colistin and tigecycline in China. The strain KP58 was recovered from a urine sample of a female patient hospitalized in a tertiary hospital in Hangzhou, China. Antimicrobial susceptibility testing was performed and the minimum inhibitory concentrations (MICs) were determined. Whole-genome sequencing was performed using Illumina and Oxford nanopore sequencing technologies. Genomic features, antimicrobial resistance genes and virulence genes were comprehensively analysed by various bioinformatics approaches. In addition, genomic epidemiological and phylogenetic analyses of KP58 and closely related isolates were performed using the core genome multilocus sequence typing (cgMLST) analysis in BacWGSTdb, an online bacterial whole-genome sequence typing and source tracking database. KP58 was resistant to all antimicrobial agents tested, including tigecycline and colistin. Combining the two sequencing technologies allowed a high-quality complete genome sequence of KP58 comprising one circular chromosome and five circular plasmids to be obtained. This strain harbours a variety of acquired antimicrobial resistance and virulence determinants. It also carried an IS -like insertion in the disrupted gene, which confers colistin resistance. The tigecycline resistance was associated with overexpression of the AcrAB efflux system. The closest relative of KP58 was another clinical isolate recovered from Hangzhou that differed by only 10 cgMLST loci. The dataset presented in this study provides essential insights into the evolution of antimicrobial-resistant in hospital settings and assists in the development of effective control strategies. Appropriate surveillance and control measures are essential to prevent its further dissemination.