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Draft Genome Sequence of a Klebsiella pneumoniae Strain (New Sequence Type 2357) Carrying Tn3926 Xing-bei Weng,a Zu-huang Mi,b Chun-xin Wang,c Jian-ming Zhud Department of Medical Laboratory, Ningbo First Hospital, Ningbo, Chinaa; Department of Bioinformation, Wuxi Clon-Gen Technology Institute, Wuxi, Chinab; Department of Medical Laboratory, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, Chinac; Department of Medical Laboratory, Hangzhou Yuhang Hospital of Traditional Chinese Medicine, Hangzhou, Chinad

We present the draft genome sequence of a Klebsiella pneumoniae carbapenemase–producing sequence type 2357 (ST2357) strain, NB60, which contains drug-resistant genes encoding resistance to beta-lactams, fluoroquinolones, aminoglycosides, trimethoprim-sulfamethoxazole, colistin, macrolides, and tetracycline. Strain NB60 was isolated from human blood, making it an important tool for studying K. pneumoniae pathogenesis. Received 23 July 2016 Accepted 8 August 2016 Published 22 September 2016 Citation Weng X-B, Mi Z-H, Wang C-X, Zhu J-M. 2016. Draft genome sequence of a Klebsiella pneumoniae strain (new sequence type 2357) carrying Tn3926. Genome Announc 4(5):e00986-16. doi:10.1128/genomeA.00986-16. Copyright © 2016 Weng et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Xing-bei Weng, [email protected].

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lebsiella pneumoniae carbapenemase (KPC)–producing Enterobacteriaceae have spread worldwide and pose a significant threat in nosocomial infections, such as septicemia, pneumonia, and urinary tract infections (1). K. pneumoniae strain NB60 was isolated from the blood of a patient in Ningbo First Hospital, People’s Republic of China, in 2012. The strain belongs to the new multilocus sequence type 2357 (ST2357). The variety of virulence genes and resistant genes in the genome sequence of NB60 will thus serve as a useful resource for future studies into bacterial survival and antibiotic resistance of this important human pathogen. NB60 was resistant to multiple antibiotics used clinically, including beta-lactams, fluoroquinolones, aminoglycosides, trimethoprim-sulfamethoxazole, colistin, macrolides, and tetracycline. Next-generation sequencing was performed using an Illumina MiSeq instrument with 150-bp paired-end reads and ~500-fold coverage. De novo assembly was performed with Edena version 3 (2), ABySS version 1.3.1 (3), and Velvet version 1.2 (4). Reads were also aligned to Klebsiella pneumoniae NTUH_K2044 (GenBank accession no. NC_012731). The de novo assemblies and alignment-based contigs were merged using Gap4 (5) and scaffolded with SSPACE version 2.0 (6), and gaps were PCR-amplified and sequenced by Sanger sequencing. The assembly of the pseudochromosome resulted in 42 contigs, and 15 unmapped contigs, which were annotated via the NCBI Prokaryotic Genome Annotation Pipeline (PGAAP) (7). The pseudochromosome is 5.07 Mb and its G⫹C content is 57.43%. The unmapped contigs comprise 0.73 Mb with a G⫹C content of 48.39%. NB8 provides a total of 6,197 genes, 9 rRNAs (5S, 16S, 23S), and 78 tRNAs. In silico genome analysis identified 17 antimicrobial resistance genes encoding resistance to beta-lactams (blaKPC-2, blaCTX-M-14, blaCTX-M-15, blaOXA-1, blaSHV-2), aminoglycosides [ant(3=’)-Ia, aac(6=)-Ib, aph(3=)-II, ksga], fluoroquinolones (qnrS1), macro-

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lides (mphA), sulfonamide-trimethoprim (sul1, dfrA12), colistin (arnA), and tetracycline (tetA, 2 copies of tetC). In addition, NB60 carried a Tn21-like transposon, Tn3926, which was also isolated from a strain of K. pneumoniae in Taiwan (8). And the genome encodes numerous transposases and insertion sequences, highlighting the importance of genomic exchange in creating the NB60 pathogenic phenotype. The draft genome sequence of K. pneumoniae strain NB60 will aid in precise genetic manipulation and thereby further improve the study of KPC-producing K. pneumoniae virulence. Accession number(s). The draft genome sequence of Klebsiella pneumoniae strain NB60 has been included in the GenBank whole-genome shotgun database under the accession number AZAP00000000. ACKNOWLEDGMENTS We thank the team of curators of the Institut Pasteur multilocus sequence type (MLST) and whole-genome databases for curating the data and making them publicly available at http://bigsdb.web.pasteur.fr.

FUNDING INFORMATION This work, including the efforts of Xing-bei WENG, was funded by Zhejiang Traditional Chinese Medical Bureau (2011ZB126). This work, including the efforts of Xing-bei WENG, was funded by Ningbo Municipal Bureau of Science and Technology (2012A610186).

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ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117–1123. http://dx.doi.org/10.1101/gr.089532.108. 4. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821– 829. http:// dx.doi.org/10.1101/gr.074492.107. 5. Bonfield JK, Smith KF, Staden R. 1995. A new DNA sequence assembly program. Nucleic Acids Res 23:4992– 4999. 6. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaf-

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folding pre-assembled contigs using SSPACE. Bioinformatics 27:578 –579. http://dx.doi.org/10.1093/bioinformatics/btq683. 7. Daraselia N, Dernovoy D, Tian Y, Borodovsky M, Tatusov R, Tatusova T. 2003. Reannotation of Shewanella oneidensis genome. Omics 7:171–175. http://dx.doi.org/10.1089/153623103322246566. 8. Lai YC, Yang SL, Peng HL, Chang HY. 2000. Identification of genes present specifically in a virulent strain of Klebsiella pneumoniae. Infect Immun 68:7149 –7151. http://dx.doi.org/10.1128/IAI.68.12.7149-7151.2000.

Genome Announcements

September/October 2016 Volume 4 Issue 5 e00986-16

Draft Genome Sequence of a Klebsiella pneumoniae Strain (New Sequence Type 2357) Carrying Tn3926.

We present the draft genome sequence of a Klebsiella pneumoniae carbapenemase-producing sequence type 2357 (ST2357) strain, NB60, which contains drug-...
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