Volume 20, Number 11—November 2014
Research
Genomic Definition of Hypervirulent and Multidrug-Resistant Klebsiella pneumoniae Clonal Groups
Figure 1
![Phylogenetic network of the 167 Klebsiella pneumoniae genomes as determined on the basis of the allelic profiles of the 694 core genome multilocus sequence typing (cgMLST) genes. The network was constructed by using the neighbor-net method implemented in SplitsTree v4.13.1 (18). Nodes are colored according to the clonal group (CG). Only the 10 most relevant CGs are highlighted; note that ST35 was subdivided into 2 CGs (CG35-A and CG35-B). Gray shading indicates CG258. Gray dots indicate phylogro](/eid/images/14-0206-F1.jpg)
Figure 1. Phylogenetic network of the 167 Klebsiella pneumoniae genomes as determined on the basis of the allelic profiles of the 694 core genome multilocus sequence typing (cgMLST) genes. The network was constructed by using the neighbor-net method implemented in SplitsTree v4.13.1 (18). Nodes are colored according to the clonal group (CG). Only the 10 most relevant CGs are highlighted; note that ST35 was subdivided into 2 CGs (CG35-A and CG35-B). Gray shading indicates CG258. Gray dots indicate phylogroups KpII-B and KpIII (K. variicola). Bold indicates reference strains. Scale bar represents 100 allelic mismatches. ATCC, American Type Culture Collection; ST, sequence type.
References
- Podschun R, Ullmann U. Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev. 1998;11:589–603.PubMedGoogle Scholar
- Shon AS, Bajwa RP, Russo TA. Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: a new and dangerous breed. Virulence. 2013;4:107–18. DOIPubMedGoogle Scholar
- Rice LB. Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no ESKAPE. J Infect Dis. 2008;197:1079–81. DOIPubMedGoogle Scholar
- Woodford N, Turton JF, Livermore DM. Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance. FEMS Microbiol Rev. 2011;35:736–55. DOIPubMedGoogle Scholar
- Breurec S, Guessennd N, Timinouni M, Le TA, Cao V, Ngandjio A, Klebsiella pneumoniae resistant to third-generation cephalosporins in five African and two Vietnamese major towns: multiclonal population structure with two major international clonal groups, CG15 and CG258. Clin Microbiol Infect. 2013;19:349–55. DOIPubMedGoogle Scholar
- Baraniak A, Izdebski R, Fiett J, Sadowy E, Adler A, Kazma M, Comparative population analysis of Klebsiella pneumoniae strains with extended-spectrum β-lactamases colonizing patients in rehabilitation centers in four countries. Antimicrob Agents Chemother. 2013;57:1992–7. DOIPubMedGoogle Scholar
- Turton JF, Englender H, Gabriel SN, Turton SE, Kaufmann ME, Pitt TL. Genetically similar isolates of Klebsiella pneumoniae serotype K1 causing liver abscesses in three continents. J Med Microbiol. 2007;56:593–7. DOIPubMedGoogle Scholar
- Brisse S, Fevre C, Passet V, Issenhuth-Jeanjean S, Tournebize R, Diancourt L, Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS ONE. 2009;4:e4982. DOIPubMedGoogle Scholar
- Decré D, Verdet C, Emirian A, Le Gourrierec T, Petit JC, Offenstadt G, Emerging severe and fatal infections due to Klebsiella pneumoniae in two university hospitals in France. J Clin Microbiol. 2011;49:3012–4. DOIPubMedGoogle Scholar
- Jung SW, Chae HJ, Park YJ, Yu JK, Kim SY, Lee HK, Microbiological and clinical characteristics of bacteraemia caused by the hypermucoviscosity phenotype of Klebsiella pneumoniae in Korea. Epidemiol Infect. 2013;141:334–40. DOIPubMedGoogle Scholar
- Merlet A, Cazanave C, Dutronc H, de Barbeyrac B, Brisse S, Dupon M. Primary liver abscess due to CC23-K1 virulent clone of Klebsiella pneumoniae in France. Clin Microbiol Infect. 2012;18:E338–9. DOIPubMedGoogle Scholar
- Diancourt L, Passet V, Verhoef J, Grimont PA, Brisse S. Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol. 2005;43:4178–82. DOIPubMedGoogle Scholar
- Köser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, Farrington M, Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog. 2012;8:e1002824. DOIPubMedGoogle Scholar
- Struelens MJ, Brisse S. From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases. Euro Surveill. 2013;18:20386.PubMedGoogle Scholar
- Fang CT, Lai SY, Yi WC, Hsueh PR, Liu KL, Chang SC. Klebsiella pneumoniae genotype K1: an emerging pathogen that causes septic ocular or central nervous system complications from pyogenic liver abscess. Clin Infect Dis. 2007;45:284–93. DOIPubMedGoogle Scholar
- Jolley KA, Maiden MC. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010;11:595. DOIPubMedGoogle Scholar
- Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology. 2012;158:1005–15. DOIPubMedGoogle Scholar
- Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23:254–67. DOIPubMedGoogle Scholar
- Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, MicroScope–an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res. 2013;41:D636–47. DOIPubMedGoogle Scholar
- Bialek-Davenet S, Nicolas-Chanoine MH, Decre D, Brisse S. Microbiological and clinical characteristics of bacteraemia caused by the hypermucoviscosity phenotype of Klebsiella pneumoniae in Korea [letter]. Epidemiol Infect. 2013;141:188. DOIPubMedGoogle Scholar
- Samuelsen Ø, Naseer U, Tofteland S, Skutlaberg DH, Onken A, Hjetland R, Emergence of clonally related Klebsiella pneumoniae isolates of sequence type 258 producing plasmid-mediated KPC carbapenemase in Norway and Sweden. J Antimicrob Chemother. 2009;63:654–8. DOIPubMedGoogle Scholar
- Warburg G, Hidalgo-Grass C, Partridge SR, Tolmasky ME, Temper V, Moses AE, A carbapenem-resistant Klebsiella pneumoniae epidemic clone in Jerusalem: sequence type 512 carrying a plasmid encoding aac(6')-Ib. J Antimicrob Chemother. 2012;67:898–901. DOIPubMedGoogle Scholar
- Broberg CA, Palacios M, Miller VL. Whole-genome draft sequences of three multidrug-resistant Klebsiella pneumoniae strains available from the American Type Culture Collection. Genome Announc. 2013;1:e00312–3.
- Snitkin ES, Zelazny AM, Thomas PJ, Stock F, Henderson DK, Palmore TN, Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med. 2012;4:148ra16.
- Chen YT, Chang HY, Lai YC, Pan CC, Tsai SF, Peng HL. Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43. Gene. 2004;337:189–98. DOIPubMedGoogle Scholar
- Siu LK, Fung CP, Chang FY, Lee N, Yeh KM, Koh TH, Molecular typing and virulence analysis of serotype K1 Klebsiella pneumoniae strains isolated from liver abscess patients and stool samples from noninfectious subjects in Hong Kong, Singapore, and Taiwan. J Clin Microbiol. 2011;49:3761–5. DOIPubMedGoogle Scholar
- Haeggman S, Lofdahl S, Paauw A, Verhoef J, Brisse S. Diversity and evolution of the class A chromosomal beta-lactamase gene in Klebsiella pneumoniae. Antimicrob Agents Chemother. 2004;48:2400–8. DOIPubMedGoogle Scholar
- Fevre C, Passet V, Weill FX, Grimont PA, Brisse S. Variants of the Klebsiella pneumoniae OKP chromosomal beta-lactamase are divided into two main groups, OKP-A and OKP-B. Antimicrob Agents Chemother. 2005;49:5149–52. DOIPubMedGoogle Scholar
- Leski T, Vora GJ, Taitt CR. Multidrug resistance determinants from NDM-1-producing Klebsiella pneumoniae in the USA. Int J Antimicrob Agents. 2012;40:282–4. DOIPubMedGoogle Scholar
- Kumar V, Sun P, Vamathevan J, Li Y, Ingraham K, Palmer L, Comparative genomics of Klebsiella pneumoniae strains with different antibiotic resistance profiles. Antimicrob Agents Chemother. 2011;55:4267–76. DOIPubMedGoogle Scholar
- Hansen LH, Johannesen E, Burmolle M, Sørensen AH, Sørensen SJ. Plasmid-encoded multidrug efflux pump conferring resistance to olaquindox in Escherichia coli. Antimicrob Agents Chemother. 2004;48:3332–7. DOIPubMedGoogle Scholar
- Perez F, Rudin SD, Marshall SH, Coakley P, Chen L, Kreiswirth BN, OqxAB, a quinolone and olaquindox efflux pump, is widely distributed among multidrug-resistant Klebsiella pneumoniae isolates of human origin. Antimicrob Agents Chemother. 2013;57:4602–3. DOIPubMedGoogle Scholar
- Papagiannitsis CC, Miriagou V, Kotsakis SD, Tzelepi E, Vatopoulos AC, Petinaki E, Characterization of a transmissible plasmid encoding VEB-1 and VIM-1 in Proteus mirabilis. Antimicrob Agents Chemother. 2012;56:4024–5. DOIPubMedGoogle Scholar
- Hu FP, Xu XG, Zhu DM, Wang MG. Coexistence of qnrB4 and qnrS1 in a clinical strain of Klebsiella pneumoniae. Acta Pharmacol Sin. 2008;29:320–4. DOIPubMedGoogle Scholar
- Dolejska M, Villa L, Dobiasova H, Fortini D, Feudi C, Carattoli A. Plasmid content of a clinically relevant Klebsiella pneumoniae clone from the Czech Republic producing CTX-M-15 and QnrB1. Antimicrob Agents Chemother. 2013;57:1073–6. DOIPubMedGoogle Scholar
- Huang TW, Chen TL, Chen YT, Lauderdale TL, Liao TL, Lee YT, Copy number change of the NDM-1 sequence in a multidrug-resistant Klebsiella pneumoniae clinical isolate. PLoS ONE. 2013;8:e62774. DOIPubMedGoogle Scholar
- Jolley KA, Hill DM, Bratcher HB, Harrison OB, Feavers IM, Parkhill J, Resolution of a meningococcal disease outbreak from whole-genome sequence data with rapid web-based analysis methods. J Clin Microbiol. 2012;50:3046–53. DOIPubMedGoogle Scholar
- Sheppard SK, Jolley KA, Maiden MC. A gene-by-gene approach to bacterial population genomics: whole genome MLST of Campylobacter. Genes (Basel). 2012;3:261–77.
- Shin J, Soo Ko K. Single origin of three plasmids bearing blaCTX-M-15 from different Klebsiella pneumoniae clones. J Antimicrob Chemother. 2014;69:969–72. DOIPubMedGoogle Scholar
- Li W, Sun G, Yu Y, Li N, Chen M, Jin R, Increasing occurrence of antimicrobial-resistant hypervirulent (hypermucoviscous) Klebsiella pneumoniae isolates in China. Clin Infect Dis. 2014;58:225–32. DOIPubMedGoogle Scholar
1These first authors contributed equally to this article.
Page created: October 17, 2014
Page updated: October 17, 2014
Page reviewed: October 17, 2014
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.