Draft Genome Sequence of an Extremely Drug-Resistant KPC-Producing Klebsiella pneumoniae ST258 Epidemic Strain

Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae has spread widely and become a major clinical and public health threat. Among extremely drug-resistant (XDR) KPC-producing K. pneumoniae clones, sequence type 258 (ST258) is the most commonly identified in various parts of the world. Since its first appearance in 2001 in the United States and in 2006 in Israel, this clone had spread extensively and become an epidemic clone (3). We report here the draft sequence of KPC-producing ST258 isolate 490 from Israel.

(This work was performed in partial fulfillment of the requirements for L. Naparstek's Ph.D. degree [third year] at Mina and Everard Goodman Faculty of Life Sciences, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel, 2012.)

Total DNA of K. pneumoniae isolated from a patient with urinary tract infection and belonging to epidemic clone ST258 was sequenced by using the Illumina HiSeq 2000 sequencer at the Technion High Throughput Sequencing Unit, Haifa, Israel. We obtained 31.02 million 50-bp single-end reads. Using CLC Genomics Workbench 5.1 (CLC bio, Aarhus, Denmark), 569 contigs were assembled de novo; 286 of them were contigs of greater than 500 bp. The average coverage across most of the contigs was about 250 times. The draft genome contains 5.8 Mb of assembled contigs, and the G+C-content was determined to be 57%, as expected for Klebsiella species (7). In addition to the de novo assembly, we mapped the reads to the three plasmids of an Italian ST258 strain (accession no. JN233704, JN247852, and JN247853) (2) using SMALT v0.5.8 (http://www.sanger.ac.uk/resources/software/smalt/). The average coverages across the three plasmids were 389, 344, and 1,409 times, respectively. The high coverage for JN247853 might indicate regions that are repeated or a higher plasmid copy number. The fourth plasmid, which was previously published (accession no. NC_014016) (4), had 289 times coverage.

Twenty-eight tRNA genes were predicted by the tRNA-SCAN v1.23 program (5). The coverage of the rRNA molecules containing contigs was significantly higher than average (2,440 versus 250 times), suggesting multiple rRNA operon copies, as expected for rRNA operons.

For open reading frame (ORF) identification, Glimmer v3.02 was used (1, 6). In total, 5,669 ORFs, with lengths ranging from 114 to 4,950 bp and an average length of 850 bp, were identified. A total of 2,813 ORFs were found on one strand, and 2,856 were found on the other strand.

This work was supported by a European Commission Research FP7 grant, SATURN—Impact of Specific Antibiotic Therapies on the Prevalence of Human Host Resistant Bacteria—grant 241796.