Abstract
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.
GENOME ANNOUNCEMENT
Klebsiella 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), macrolides (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.
Footnotes
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.
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