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

Authors Ruan Z, Wu J, Chen H, Draz MS, Xu J, He F

Received 28 November 2019

Accepted for publication 11 January 2020

Published 21 January 2020 Volume 2020:13 Pages 199—206

DOI https://doi.org/10.2147/IDR.S240404

Checked for plagiarism Yes

Review by Single anonymous peer review

Peer reviewer comments 3

Editor who approved publication: Professor Suresh Antony


Zhi Ruan, 1 Jianyong Wu, 2 Hangfei Chen, 1 Mohamed S Draz, 3, 4 Juan Xu, 5 Fang He 6

1Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, People’s Republic of China; 2Department of Clinical Laboratory, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, People’s Republic of China; 3Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; 4Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; 5Institute of Hygiene, Zhejiang Academy of Medical Sciences, Hangzhou 310013, People’s Republic of China; 6Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou 310014, People’s Republic of China

Correspondence: Fang He Tel/Fax +86 571 88215596
Email hetrue@163.com

Background: The prevalence of multidrug-resistant Klebsiella pneumoniae is increasingly being implicated worldwide in a variety of infections with high mortalities. Here, we report the complete genome sequence of K. pneumoniae strain KP58, a pandrug-resistant K. pneumoniae strain that exhibits high levels of resistance to colistin and tigecycline in China.
Methods: The K. pneumoniae 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 K. pneumoniae 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.
Results: K. pneumoniae 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 K. pneumoniae 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 ISKpn26-like insertion in the disrupted mgrB gene, which confers colistin resistance. The tigecycline resistance was associated with overexpression of the AcrAB efflux system. The closest relative of K. pneumoniae KP58 was another clinical isolate recovered from Hangzhou that differed by only 10 cgMLST loci.
Conclusion: The dataset presented in this study provides essential insights into the evolution of antimicrobial-resistant K. pneumoniae in hospital settings and assists in the development of effective control strategies. Appropriate surveillance and control measures are essential to prevent its further dissemination.

Keywords: Klebsiella pneumoniae, whole-genome sequencing, nanopore, hybrid assembly, pandrug resistance

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