Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing

Yohei Doi, Tracy H. Hazen, Matthew Boitano, Yu Chih Tsai, Tyson A. Clark, Jonas Korlach, David A. Rasko

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

The whole-genome sequence of a carbapenem-resistant Klebsiella pneumoniae strain, PittNDM01, which coproduces NDM-1 and OXA-232 carbapenemases, was determined in this study. The use of single-molecule, real-time (SMRT) sequencing provided a closed genome in a single sequencing run. K. pneumoniae PittNDM01 has a single chromosome of 5,348,284 bp and four plasmids: pPKPN1 (283,371 bp), pPKPN2 (103,694 bp), pPKPN3 (70,814 bp), and pPKPN4 (6,141 bp). The contents of the chromosome were similar to that of the K. pneumoniae reference genome strain MGH 78578, with the exception of a large inversion spanning 23.3% of the chromosome. In contrast, three of the four plasmids are unique. The plasmid pPKPN1, an IncHI1B-like plasmid, carries the blaNDM-1, armA, and qnrB1 genes, along with tellurium and mercury resistance operons. blaNDM-1is carried on a unique structure in which Tn125 is further bracketed by IS26 downstream of a class 1 integron. The IncFIA-like plasmid pPKPN3 also carries an array of resistance elements, including blaCTX-M-15and a mercury resistance operon. The ColE-type plasmid pPKPN4 carrying blaOXA-232is identical to a plasmid previously reported from France. SMRT sequencing was useful in resolving the complex bacterial genomic structures in the de novo assemblies.Copyright

Original languageEnglish
Pages (from-to)5947-5953
Number of pages7
JournalAntimicrobial Agents and Chemotherapy
Volume58
Issue number10
DOIs
Publication statusPublished - 01-10-2014
Externally publishedYes

Fingerprint

Klebsiella pneumoniae
Plasmids
Genome
Operon
Mercury
Chromosomes
Tellurium
Integrons
Bacterial Structures
Chromosomes, Human, Pair 5
Carbapenems
Asp(5)-oxytocin
France
Genes

All Science Journal Classification (ASJC) codes

  • Pharmacology
  • Pharmacology (medical)
  • Infectious Diseases

Cite this

Doi, Yohei ; Hazen, Tracy H. ; Boitano, Matthew ; Tsai, Yu Chih ; Clark, Tyson A. ; Korlach, Jonas ; Rasko, David A. / Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing. In: Antimicrobial Agents and Chemotherapy. 2014 ; Vol. 58, No. 10. pp. 5947-5953.
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Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing. / Doi, Yohei; Hazen, Tracy H.; Boitano, Matthew; Tsai, Yu Chih; Clark, Tyson A.; Korlach, Jonas; Rasko, David A.

In: Antimicrobial Agents and Chemotherapy, Vol. 58, No. 10, 01.10.2014, p. 5947-5953.

Research output: Contribution to journalArticle

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AU - Doi, Yohei

AU - Hazen, Tracy H.

AU - Boitano, Matthew

AU - Tsai, Yu Chih

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