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Mechanisms of Resistance

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
Yohei Doi
aDivision of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Tracy H. Hazen
bInstitute for Genome Sciences, University of Maryland, Baltimore, Maryland, USA
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Matthew Boitano
cPacific Biosciences, Menlo Park, California, USA
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Yu-Chih Tsai
cPacific Biosciences, Menlo Park, California, USA
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Tyson A. Clark
cPacific Biosciences, Menlo Park, California, USA
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Jonas Korlach
cPacific Biosciences, Menlo Park, California, USA
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David A. Rasko
bInstitute for Genome Sciences, University of Maryland, Baltimore, Maryland, USA
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DOI: 10.1128/AAC.03180-14
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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-1 is 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-15 and a mercury resistance operon. The ColE-type plasmid pPKPN4 carrying blaOXA-232 is identical to a plasmid previously reported from France. SMRT sequencing was useful in resolving the complex bacterial genomic structures in the de novo assemblies.

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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
Antimicrobial Agents and Chemotherapy Sep 2014, 58 (10) 5947-5953; DOI: 10.1128/AAC.03180-14

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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
Antimicrobial Agents and Chemotherapy Sep 2014, 58 (10) 5947-5953; DOI: 10.1128/AAC.03180-14
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