Whole-Genome Assembly of Klebsiella pneumoniae Coproducing NDM-1 and OXA-232 Carbapenemases Using Single-Molecule, Real-Time Sequencing

Abstract

ABSTRACTThe whole-genome sequence of a carbapenem-resistantKlebsiella pneumoniaestrain, 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. pneumoniaePittNDM01 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 theK. pneumoniaereference 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 theblaNDM-1,armA, andqnrB1genes, along with tellurium and mercury resistance operons.blaNDM-1is carried on a unique structure in which Tn125is further bracketed by IS26downstream of a class 1 integron. The IncFIA-like plasmid pPKPN3 also carries an array of resistance elements, includingblaCTX-M-15and a mercury resistance operon. The ColE-type plasmid pPKPN4 carryingblaOXA-232is identical to a plasmid previously reported from France. SMRT sequencing was useful in resolving the complex bacterial genomic structures in thede novoassemblies.