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Genome Announc. 2017 March; 5(13): e00066-17.
Published online 2017 March 30. doi:  10.1128/genomeA.00066-17
PMCID: PMC5374226

Complete Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae Strain 1756, Isolated from a Pus Specimen

ABSTRACT

Carbapenem-resistant Klebsiella pneumoniae strain 1756 was isolated from a pus specimen from a Taiwanese patient. Here, the complete genome sequence of strain 1756 is presented.

GENOME ANNOUNCEMENT

Klebsiella pneumoniae is a Gram-negative opportunistic bacillus in the family Enterobacteriaceae with worldwide distribution that causes pneumonia, liver abscess, septicemia, and urinary tract infection in humans. Carbapenems are considered to be the most effective broad-spectrum β-lactam antimicrobial agents for the defense of multidrug resistant Gram-negative organisms, including K. pneumoniae. However, over the past decade the carbapenem resistances of Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii have emerged as significant public health threats (1, 2). Here, we report the complete genome sequence of K. pneumoniae strain 1756, isolated from a pus specimen from a 63-year-old Taiwanese women.

K. pneumoniae strain 1756 was sequenced using the PacBio RS II platform (Pacific Biosciences, USA), generating a library containing 76,075 single reads with an average length of 14,567 bp and a 173-fold average coverage. Reads were assembled using HGAP version 3.0, which returned three contigs. One short contig (30,002 bp) without a plasmid replicon was discarded because the assembly was problematic. For the remaining two contigs, the head segment was almost identical to the tail segment, indicating the circular nature of the contigs.

The 1756 genome has a size of 5,195,816 bp and a G+C content of 57.6%. Sequences were annotated at NCBI (http://www.ncbi.nlm.nih.gov/genome/annotation_prok) or with the RAST prokaryotic genome annotation server (http://rast.nmpdr.org/) (3). RAST annotation results showed that the genome contained 4,856 coding sequences and 111 RNA genes. The MLST, ResFinder, and PlasmidFinder (http://www.genomicepidemiology.org/) databases were used to find the sequence type, antibiotic resistance genes, and the plasmid types present in the isolates (4, 5). The MLST scheme of strain 1756, based on the sequences of seven housekeeping genes (gapA2, infB1, mdh37, pgi1, phoE3, rpoB1, tonB56), indicated that this strain belongs to a new ST type (ST2549). Antimicrobial resistance genes against β-lactams (blaSHV-11), fluoroquinolones (oxqAB), and fosfomycin (fosA) were identified on its chromosome sequence. Strain 1756 harbored a IncI1-type plasmid (pKP1756, 73,952 bp) with antimicrobial resistance genes aph(3′)-Ia, aadA22, aac(3)-IId, blaCMY-2, and blaTEM-1B conferring resistance to aminoglycosides and β-lactams. IncI1 plasmids are highly prevalent in Enterobacteriaceae and associated with the spread of several resistance genes (6). An insertion mutation in the porin OmpK36 of strain 1756 was identified, which is likely to be associated with resistance to carbapenems in the absence of carbapenemase genes (7). This genome will facilitate exploration of the pathogenesis and antibiotic resistance of K. pneumoniae.

Accession number(s).

The complete genome sequence of K. pneumoniae strain 1756 has been deposited in GenBank under the accession numbers CP019219 (chromosome) and CP019220 (plasmid).

ACKNOWLEDGMENTS

We thank Robert Jonas for helpful comments on this manuscript. We also thank the team of curators of the Institut Pasteur MLST and whole-genome MLST databases for curating the data and making them publicly available at http://bigsdb.web.pasteur.fr/.

This study was supported by grant MOST 104-2320-B-006-018-MY3 from the Ministry of Science and Technology, Taiwan and by grant NCKUH-10301002 from the National Cheng Kung University Hospital, Tainan, Taiwan.

Footnotes

Citation Kao C-Y, Yan J-J, Lin Y-C, Zheng P-X, Wu J-J. 2017. Complete genome sequence of carbapenem-resistant Klebsiella pneumoniae strain 1756, isolated from a pus specimen. Genome Announc 5:e00066-17. https://doi.org/10.1128/genomeA.00066-17.

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Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)