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Volume 20, Number 11—November 2014
Research

Genomic Definition of Hypervirulent and Multidrug-Resistant Klebsiella pneumoniae Clonal Groups

Suzanne Bialek-Davenet1, Alexis Criscuolo1, Florent Ailloud, Virginie Passet, Louis Jones, Anne-Sophie Delannoy-Vieillard, Benoit Garin, Simon Le Hello, Guillaume Arlet, Marie-Hélène Nicolas-Chanoine, Dominique Decré, and Sylvain BrisseComments to Author 
Author affiliations: Institut Pasteur, Paris, France (S. Bialek-Davenet, A. Criscuolo, F. Ailloud, V. Passet, L. Jones, A.-S. Delannoy-Vieillard, S. Le Hello, S. Brisse); Centre National de la Recherche Scientifique (CNRS), Paris (S. Bialek-Davenet, A. Criscuolo, V. Passet, S. Brisse); Hôpital Beaujon, Clichy, France (S. Bialek-Davenet, M.-H. Nicolas-Chanoine); Institut Pasteur, Antananarivo, Madagascar (B. Garin); Sorbonne Université, Paris (G. Arlet, D. Decré); Institut National de la Santé et de la Recherche Médicale (INSERM), Paris (G. Arlet, M.-H. Nicolas-Chanoine, D. Decré); Hôpitaux de l’Est Parisien, Paris (G. Arlet, D. Decré); Faculté de Médecine, Université Paris Diderot, Paris (M.-H. Nicolas-Chanoine)

Main Article

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

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.

Main Article

References
  1. Podschun  R, Ullmann  U. Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev. 1998;11:589603.PubMedGoogle Scholar
  2. Shon  AS, Bajwa  RP, Russo  TA. Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: a new and dangerous breed. Virulence. 2013;4:10718. DOIPubMedGoogle Scholar
  3. Rice  LB. Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no ESKAPE. J Infect Dis. 2008;197:107981. DOIPubMedGoogle Scholar
  4. 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;35:73655. DOIPubMedGoogle Scholar
  5. 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;19:34955. DOIPubMedGoogle Scholar
  6. 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;57:19927. DOIPubMedGoogle Scholar
  7. 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;56:5937. DOIPubMedGoogle Scholar
  8. 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
  9. 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;49:30124. DOIPubMedGoogle Scholar
  10. 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;141:33440. DOIPubMedGoogle Scholar
  11. 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:E3389. DOIPubMedGoogle Scholar
  12. Diancourt  L, Passet  V, Verhoef  J, Grimont  PA, Brisse  S. Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol. 2005;43:417882. DOIPubMedGoogle Scholar
  13. 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
  14. Struelens  MJ, Brisse  S. From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases. Euro Surveill. 2013;18:20386.PubMedGoogle Scholar
  15. 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;45:28493. DOIPubMedGoogle Scholar
  16. Jolley  KA, Maiden  MC. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010;11:595. DOIPubMedGoogle Scholar
  17. 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;158:100515. DOIPubMedGoogle Scholar
  18. Huson  DH, Bryant  D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23:25467. DOIPubMedGoogle Scholar
  19. 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:D63647. DOIPubMedGoogle Scholar
  20. 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
  21. 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;63:6548. DOIPubMedGoogle Scholar
  22. 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;67:898901. DOIPubMedGoogle Scholar
  23. 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.
  24. 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.
  25. 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;337:18998. DOIPubMedGoogle Scholar
  26. 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;49:37615. DOIPubMedGoogle Scholar
  27. 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;48:24008. DOIPubMedGoogle Scholar
  28. 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;49:514952. DOIPubMedGoogle Scholar
  29. Leski  T, Vora  GJ, Taitt  CR. Multidrug resistance determinants from NDM-1-producing Klebsiella pneumoniae in the USA. Int J Antimicrob Agents. 2012;40:2824. DOIPubMedGoogle Scholar
  30. 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;55:426776. DOIPubMedGoogle Scholar
  31. 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;48:33327. DOIPubMedGoogle Scholar
  32. 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;57:46023. DOIPubMedGoogle Scholar
  33. 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;56:40245. DOIPubMedGoogle Scholar
  34. Hu  FP, Xu  XG, Zhu  DM, Wang  MG. Coexistence of qnrB4 and qnrS1 in a clinical strain of Klebsiella pneumoniae. Acta Pharmacol Sin. 2008;29:3204. DOIPubMedGoogle Scholar
  35. 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;57:10736. DOIPubMedGoogle Scholar
  36. 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
  37. 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;50:304653. DOIPubMedGoogle Scholar
  38. 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.
  39. Shin  J, Soo Ko  K. Single origin of three plasmids bearing blaCTX-M-15 from different Klebsiella pneumoniae clones. J Antimicrob Chemother. 2014;69:96972. DOIPubMedGoogle Scholar
  40. 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;58:22532. DOIPubMedGoogle Scholar

Main Article

1These first authors contributed equally to this article.

Page created: October 17, 2014
Page updated: October 17, 2014
Page reviewed: October 17, 2014
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