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. 2014 Jun 19;2(3):e00558-14. doi: 10.1128/genomeA.00558-14

Genome Sequences of Two Carbapenemase-Resistant Klebsiella pneumoniae ST258 Isolates

Maria Soledad Ramirez a,b,a,b, Gang Xie c, Shannon Johnson c, Karen Davenport c, David van Duin f, Federico Perez d, Robert A Bonomo d,e,d,e, Patrick Chain c, Marcelo E Tolmasky a,✉
PMCID: PMC4064024  PMID: 24948759

Abstract

Klebsiella pneumoniae, an ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogen, has acquired multiple antibiotic resistance genes and is becoming a serious public health threat. Here, we report the genome sequences of two representative strains of K. pneumoniae from the emerging K. pneumoniae carbapenemase (KPC) outbreak in northeast Ohio belonging to sequence type 258 (ST258) (isolates Kb140 and Kb677, which were isolated from blood and urine, respectively). Both isolates harbor a blaKPC gene, and strain Kb140 carries blaKPC-2, while Kb677 carries blaKPC-3.

GENOME ANNOUNCEMENT

Klebsiella pneumoniae, a bacterium belonging to the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, K. pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species), is responsible for serious community- and hospital-acquired infections (1–5). The difficulty in treating infections caused by K. pneumoniae is increasing due to its ability to acquire antibiotic resistance genes (6–8), including carbapenemases (9).

Despite the clinical importance of this bacterium, the number of identified and characterized virulence factors has remained relatively low (10–13). Nucleotide and whole-genome mapping comparisons among several strains led to the identification of a high heterogeneity zone (HHZ) (14), which includes the capsular polysaccharide biosynthesis gene cluster (HHZ subregion 4) and a hot spot (HHZ subregion 3), which in strain K. pneumoniae NTUH-K2044 is the point of insertion of a fragment that includes a pathogenicity island related to that found in Yersinia species. This fragment includes the genes coding for the yersiniabactin siderophore system, a region previously identified in a Klebsiella plasmid, and genes coding for conjugation functions (10, 14, 15).

K. pneumoniae strains harboring carbapenem resistance genes, such as blaKPC or blaNDM-1, are becoming more frequent and extremely problematic. K. pneumoniae Kb140 and Kb677, two representative strains from an emerging KPC outbreak in northeast Ohio, were isolated in 2012. Kb140 was isolated from a patient with fatal bloodstream infection and pneumonia, while Kb677 was isolated from a patient with urinary tract colonization. Both strains were draft sequenced using Illumina (353× and 293× genome coverage for Kb140 and Kb677, respectively) and PacBio RS II (100× and 105× genome coverage, respectively). The submitted de novo assemblies utilized Velvet (version 1.2.08), Newbler (version 2.6), AllPaths (version 44837), HGAP (version 2.1.1), and parallel Phrap (SPS-4.24), along with manual review and curation. The draft genomes of Kb140 and Kb677 consist of 5,677,714-bp and 5,894,762-bp sequences, respectively.

There are 5,420 and 5,499 predicted protein-coding genes within the genomes of K. pneumoniae isolates Kb140 and Kb677, respectively. Of these, 20.7% and 21.9% of the protein-coding genes, respectively, are annotated as hypothetical or conserved hypothetical proteins. Of those with functional predictions, 31 (Kb140) and 68 (Kb677) are associated with phages/prophages, while 103 (Kb140) and 126 (Kb677) are associated with resistance to antibiotics or toxic compounds. The blaKPC genes are likely located within the sequence with accession no. AQRD01000007 of the Kb140 assembly (positions 1431915 to 1432775) and the sequence with accession no. AQPG01000002 of the Kb677 assembly (positions 7281 to 8240), respectively. The strain Kb140 and Kb677 genomes have 86 and 85 tRNA genes, respectively, as well as 24 rRNA genes.

K. pneumoniae strains usually harbor several plasmids (4, 6, 16). Analysis of the nucleotide sequences of strains Kb140 and Kb677 showed homology to the IncFIIk-FIB-like plasmids pKPN- and pKpQIL-type (17, 18), pIncX-SHV (17), and pKP1780-kpc (accession no. KF874497), pNJST258C1, pNJST258C2 (19), pBK31551, pBK15692 (20), p1 (accession no. CP006657), pR55 (21), and the K. pneumoniae subsp. rhinoscleromatis pKRH (22).

Nucleotide sequence accession numbers.

The GenBank accession no. for K. pneumoniae Kb140 and Kb677 are AQRD01000001 to AQRD01000008 and AQPG01000001 to AQPG01000012, respectively.

ACKNOWLEDGMENTS

This work was supported by Public Health Service grants 2R15AI047115 (to M.E.T.), the U.S. Department of Energy Joint Genome Institute through the Office of Science of the U.S. Department of Energy under contract DE-AC02-05CH11231, the Cleveland Department of Veterans Affairs, the Veterans Affairs Merit Review Program award 1I01BX001974, and the Geriatric Research Education and Clinical Center VISN 10. This work was also supported by funds from the National Institute of Allergy and Infectious Diseases of the National Institutes of Health, under award numbers R01AI063517 and R01AI10056 (to R.A.B.), and through the Antibiotic Resistance Leadership Group under National Institutes of Health award UM1AI104681 (to D.v.D.) and the Clinical and Translational Science Collaborative of Cleveland, UL1TR000439 from the National Center for Advancing Translational Sciences (NCATS) component of the National Institutes of Health (to D.v.D. and F.P.).

The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Footnotes

Citation Ramirez MS, Xie G, Johnson S, Davenport K, van Duin D, Perez F, Bonomo RA, Chain P, Tolmasky ME. 2014. Genome sequences of two carbapenemase-resistant Klebsiella pneumoniae ST258 isolates. Genome Announc. 2(3):e00558-14. doi:10.1128/genomeA.00558-14.

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