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. 2019 Jan 4:8:446.
doi: 10.3389/fcimb.2018.00446. eCollection 2018.

The Genetic Structures of an Extensively Drug Resistant (XDR) Klebsiella pneumoniae and Its Plasmids

Ling Li  1 , Tao Yu  2 , Yanan Ma  1 , Zhongjun Yang  3 , Wenjia Wang  1 , Xiaobo Song  4 , Yu Shen  1 , Tingting Guo  1 , Jian Kong  1 , Mingyu Wang  1 , Hai Xu  1
Affiliations

The Genetic Structures of an Extensively Drug Resistant (XDR) Klebsiella pneumoniae and Its Plasmids

Ling Li et al. Front Cell Infect Microbiol. .

Abstract

Multi-, extensively-, and pan-drug resistant bacteria are a threat to our health today, because their wide resistance spectra make their infections difficult to cure. In this work, we isolated an extensively drug resistant (XDR) Klebsiella pneumoniae 2-1 strain from the stool sample of a patient diagnosed of colorectal cancer. K. pneumoniae 2-1 was found to be resistant to all the antibiotics tested except for cefepime, tigecycline, and ceftazidime-avibactam. By sequencing the complete genome of K. pneumoniae 2-1, we found it contains a chromosome of 5.23 Mb and two circular plasmids with the size of 246 and 90 kb. The larger plasmid, pKP21HI1 was found to be a new conjugation-defective plasmid belonging to incompatibility group HI1B and a new sequence type. Further comparative genomics analysis and antimicrobial resistance gene analysis showed that although a great deal of changes took place on the chromosome of K. pneumoniae 2-1 in comparison with the reference genome, the extensively drug resistance phenotype of K. pneumoniae 2-1 is primarily due to the two multidrug resistant plasmids it contains. This work explains the genetic and mechanistic basis of the extensive drug resistance of K. pneumoniae 2-1, and found that plasmids play key roles in the strong antibiotic resistance of bacteria.

Keywords: Klebsiella pneumoniae; antimicrobial resistance; antimicrobial resistance gene; extensively drug resistance; high throughput sequencing; multidrug resistant plasmid.

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Figures

Figure 1
Figure 1
Genome map of K. pneumoniae 2-1 chromosome and plasmids. For chromosome, from outside to inside, each ring represents encoding genes, COG, KEGG, GO, ncRNA, GC content, and genomic GC skew value. For plasmids, from outside to inside, each ring represents COG, GC content, and genomic GC skew value. Different color represents different annotation.
Figure 2
Figure 2
Phylogenetic analysis of pKP21AC2 and pKP21HI1. Phylogenetic tree of replicon sequence of pKP21HI1, pKP21AC2, and plasmids belonging to different incompatible group was shown. The phylogenetic tree was calculated from 500 individual trees. Bootstrap values were shown on each node. Bar: evolutionary distance of 0.5. Circled are the two plasmids found in K. pneumoniae 2-1 and the most similar plasmid to pKP21HI1.
See this image and copyright information in PMC

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