Abstract
Here, we present the draft genome sequence of Klebsiella pneumoniae subsp. pneumoniae sequence type 512 (ST512) isolated during a KPC-producer outbreak. This strain is resistant to β-lactams, cephalosporins, fluoroquinolones, aminoglycosides, macrolides, tetracyclines, and carbapenems but susceptible to colistin. The ST512-K30BO genome is composed of 289 contigs for 5,392,844 bp with 56.9% G+C content.
GENOME ANNOUNCEMENT
Klebsiella pneumoniae is responsible for an increasing number of healthcare-related infections, mostly in patients with impaired immunity, including bloodstream and wound infections, pneumonia, and abscesses. The rapid diffusion of this pathogen is due mainly to the emergence of a number of multidrug-resistant strains (1). In particular, the first report of carbapenem-resistant K. pneumoniae in 2001 was followed by a worldwide spread of different types of carbapenemase producers, including the most widespread, K. pneumoniae carbapenemase (KPC) and New Delhi metallo-β-lactamase (NDM) (2). The first Italian outbreak of K. pneumoniae KPC producers was reported recently (3).
The K. pneumoniae isolate ST512-K30BO was isolated using a central venous catheter from a hospitalized patient at the St. Orsola Malpighi University Hospital in Bologna, Italy. Antimicrobial susceptibility testing was performed according to the European Committee on Antimicrobial Susceptibility Testing guidelines (4). The isolate ST512-K30BO showed multiple resistances to clinically used antibiotics, including β-lactams, cephalosporins, carbapenems, fluoroquinolones, macrolides, aminoglycosides, and tigecycline. The strain was susceptible to colistin. Whole DNA was extracted using the Qiagen DNeasy kit and subjected to quality controls. Next-generation sequencing was performed on an Illumina HiSeq 2000 platform (5) with 300-base distant paired ends. Overall, 29,008,494 paired sequences were generated, for a total of more than 5.7 gigabases and a mean length of 199 bases per pair.
The genome assembly was performed using MIRA 3.4 (6) after quality selection and trimming via a specifically designed PerlScript. The assembly was manually checked using the Gap4 software of the Staden package (7). The resulting assembly consists of 289 contigs, with a G+C content of 56.9% for a total of 5,392,844 bp. Multilocus sequence type (MLST) analysis was performed using the Center for Biological Sequence Analysis (CBS) server online tool (http://www.cbs.dtu.dk/services/MLST/). The sequenced genome was of strain 512. This strain, which is highly similar to the most widespread multidrug-resistant ST258 strain (8), has been reported previously as carbapenem-resistant and epidemic in Israel (9).
Genome annotation was performed automatically on the Rapid Annotation using Subsystem Technology (RAST) server (10) using Glimmer for base calling. Additionally, all open reading frames obtained from the RAST annotation were subjected to BLAST analysis against the Antibiotic Resistance Database (ARDB) (11) and the Comprehensive Antibiotic Resistance Database (CARD) (http://arpcard.mcmaster.ca). All of the genes indicated by at least one database as being implicated in antibiotic resistance were manually controlled. This approach highlighted the presence of 164 genes related to antibiotic resistance, including blaCTX-M9, blaTEM-33, blaSHV-2, blaKPC-3, ant(3″)-Ia, ant(2″)-Ia, marA, macA, macB, and tetR. Comparative genomic analyses will be performed to highlight similarities and differences between ST512 and other K. pneumoniae strains with different antimicrobial susceptibility patterns.
Nucleotide sequence accession number.
The genome sequence was deposited in the European Bioinformatics Institute (EBI) under accession no. CAJM01000000.
ACKNOWLEDGMENTS
This study was supported by Grants RFO 2010 and RFO 2011 from the University of Bologna to V.S. and by funds from the Fondazione IRCCS Policlinico San Matteo to P.M.
Footnotes
Citation Comandatore F, Gaibani P, Ambretti S, Landini MP, Daffonchio D, Marone P, Sambri V, Bandi C, Sassera D. 2013. Draft genome of Klebsiella pneumoniae sequence type 512, a multidrug-resistant strain isolated during a recent KPC outbreak in Italy. Genome Announc. 1(1):e00035-12. doi:10.1128/genomeA.00035-12.
REFERENCES
- 1. Chong Y, Ito Y, Kamimura T. 2011. Genetic evolution and clinical impact in extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae. Infect. Genet. Evol. 11:1499–1504 [DOI] [PubMed] [Google Scholar]
- 2. Nordmann P, Gniadkowski M, Giske CG, Poirel L, Woodford N, Miriagou V. on Carbapenemases. 2012. The European network on carbapenemases. Identification and screening of carbapenemase-producing Enterobacteriaceae. Clin. Microbiol. Infect. 18:432–438 [DOI] [PubMed] [Google Scholar]
- 3. Gaibani P, Ambretti S, Berlingeri A, Gelsomino F, Bielli A, Landini MP, Sambri V. 2010. Rapid increase of carbapenemase-producing Klebsiella pneumoniae strains in a large Italian hospital: surveillance period 1 March –30 September 2010. Euro Surveill. 16:, 19800. [PubMed] [Google Scholar]
- 4. European Committee on Antimicrobial Susceptibility Testing 2011. Breakpoint tables for interpretation of MICs and zone diameters. Version 1.3. EUCAST, Basel, Switzerland [Google Scholar]
- 5. Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433–438 [DOI] [PubMed] [Google Scholar]
- 6. Chevreux B, Wetter T, Suhai S. 1999. Genome sequence assembly using trace signals and additional sequence information, p 45–56, In Proceedings of the German Conference on Bioinformatics, Hanover, Germany [Google Scholar]
- 7. Staden R, Beal KF, Bonfield JK. 2000. The Staden package. Methods Mol. Biol. 1998:132:115–130 [DOI] [PubMed] [Google Scholar]
- 8. Woodford N, Turton JF, Livermore DM. 2011. Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance. FEMS Microbiol. Rev. 35:736–755 [DOI] [PubMed] [Google Scholar]
- 9. Warburg G, Hidalgo-Grass C, Partridge SR, Tolmasky ME, Temper V, Moses AE, Block C, Strahilevitz J. 2012. A carbapenem-resistant Klebsiella pneumoniae epidemic clone in Jerusalem: sequence type 512 carrying a plasmid encoding aac(6′)-lb. J. Antimicrob. Chemother. 67:898–901 [DOI] [PubMed] [Google Scholar]
- 10. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 8:75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Liu B, Pop M. 2009. ARDB—Antibiotic Resistance Genes Database. Nucleic Acids Res. 37:D443–D447 [DOI] [PMC free article] [PubMed] [Google Scholar]