1887

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Volume 68, Issue 6

Whole genome sequencing of NDM-1-producing serotype K1 ST23 hypervirulent Klebsiella pneumoniae in China Free

Abstract

Purpose. The emergence and spread of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) is causing worldwide concern, whereas NDM-producing hvKP is still rare. Here we report the complete genome sequence characteristics of an NDM-1-producing ST23 type clinical hvKP in PR China.

Methodology. Capsular polysaccharide serotyping was performed by PCR. The complete genome sequence of isolate 3214 was obtained using both the Illumina Hiseq platform and Pacbio RS platform. Multilocus sequence type was identified by submitting the genome sequence to mlst 2.0 and the antimicrobial resistance genes and plasmid replicons were identified using ResFinder and PlasmidFinder, respectively. Transferability of the bla NDM-1-bearing plasmid was determined by conjugation experiment, S1 pulsed-field gel electrophoresis and Southern hybridization.

Results. Isolate 3214 was classified to ST23 and belonged to the K1 capsular serotype. The isolate’s total genome size was 6 171 644 bp with a G+C content of 56.39 %, consisting of a 5 448 209 bp chromosome and seven plasmids. The resistome included 18 types of antibiotic resistance genes. Fourteen resistance genes including bla NDM-1 and bla CTX-M-14 were located on plasmids and five also including bla CTX-M-14 were in the chromosome. Plasmid pNDM_3214 carrying bla NDM-1 harboured six types of resistance genes surrounded by insertion sequences and was conjugative. The worldwide pLVPK-like virulence plasmid harbouring rmpA2 and rmpA was also found in this isolate.

Conclusion. This study provides basic information of phenotypic and genomic features of ST23 CR-hvKP isolate 3214. Our data highlights the potential risk of spread of NDM-1-producing ST23 hvKP.

  • Received:
  • Accepted:
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Keyword(s): Hypervirulent Klebsiella pneumoniae , NDM , ST23 and whole genome sequence
© 2019 The Authors
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2019-05-20
2024-04-23
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References

  1. Zhang R, Liu L, Zhou H, Chan EW, Li J et al. Nationwide surveillance of clinical carbapenem-resistant Enterobacteriaceae (CRE) strains in China. EBioMedicine 2017; 19:98–106 [View Article]
     [Google Scholar]
  2. Singh-Moodley A, Perovic O. Antimicrobial susceptibility testing in predicting the presence of carbapenemase genes in Enterobacteriaceae in South Africa. BMC Infect Dis 2016; 16:536 [View Article]
     [Google Scholar]
  3. Lamba M, Graham DW, Ahammad SZ. Hospital wastewater releases of Carbapenem-Resistance pathogens and genes in urban India. Environ Sci Technol 2017; 51:13906–13912 [View Article]
     [Google Scholar]
  4. Liu B-T, Song FJ, Zou M, Zhang QD, Shan H. High Incidence of Escherichia coli strains coharboring mcr-1 and blaNDM from chickens. Antimicrob Agents Chemother 2017; 61: [View Article]
     [Google Scholar]
  5. Grundmann H, Glasner C, Albiger B, Aanensen DM, Tomlinson CT et al. Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study. Lancet Infect Dis 2017; 17:153–163 [View Article]
     [Google Scholar]
  6. Shon AS, Bajwa RP, Russo TA. Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: a new and dangerous breed. Virulence 2013; 4:107–118 [View Article]
     [Google Scholar]
  7. Lee CR, Lee JH, Park KS, Jeon JH, Kim YB et al. Antimicrobial resistance of hypervirulent Klebsiella pneumoniae: epidemiology, hypervirulence-associated determinants, and resistance mechanisms. Front Cell Infect Microbiol 2017; 7:483 [View Article]
     [Google Scholar]
  8. Tang HL, Chiang MK, Liou WJ, Chen YT, Peng HL et al. Correlation between Klebsiella pneumoniae carrying pLVPK-derived loci and abscess formation. Eur J Clin Microbiol Infect Dis 2010; 29:689–698 [View Article]
     [Google Scholar]
  9. Yeh KM, Kurup A, Siu LK, Koh YL, Fung CP et al. Capsular serotype K1 or K2, rather than magA and rmpA, is a major virulence determinant for Klebsiella pneumoniae liver abscess in Singapore and Taiwan. J Clin Microbiol 2007; 45:466–471 [View Article]
     [Google Scholar]
  10. Du P, Zhang Y, Chen C. Emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae. Lancet Infect Dis 2017
     [Google Scholar]
  11. Wong MHY, Shum HP, Chen JHK, Man MY, Wu A et al. Emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae. Lancet Infect Dis 2018; 18:24 [View Article]
     [Google Scholar]
  12. Zhang R, Lin D, Chan EW, Gu D, Chen GX et al. Emergence of carbapenem-resistant serotype K1 hypervirulent Klebsiella pneumoniae strains in China. Antimicrob Agents Chemother 2016; 60:709–711 [View Article]
     [Google Scholar]
  13. Gu D, Dong N, Zheng Z, Lin D, Huang M et al. A fatal outbreak of ST11 carbapenem-resistant hypervirulent Klebsiella pneumoniae in a Chinese hospital: a molecular epidemiological study. Lancet Infect Dis 2017; 18:37-46 [View Article]
     [Google Scholar]
  14. Compain F, Vandenberghe A, Gominet M, Genel N, Lebeaux D et al. Primary osteomyelitis caused by an NDM-1-producing K. pneumoniae strain of the highly virulent sequence type 23. Emerg Microbes Infect 2017; 6:e571–3 [View Article]
     [Google Scholar]
  15. Wei D-D, Wan LG, Liu Y. Draft genome sequence of an NDM-1- and KPC-2-coproducing hypervirulent carbapenem-resistant Klebsiella pneumoniae strain isolated from burn wound infections. Genome Announc 2018; 6: [View Article]
     [Google Scholar]
  16. Mei YF, Liu PP, Wan LG, Liu Y, Wang LH et al. Virulence and genomic feature of a virulent Klebsiella pneumoniae sequence type 14 strain of serotype K2 harboring blaNDM-5 in China. Front Microbiol 2017; 8:335 [View Article]
     [Google Scholar]
  17. Roulston KJ, Bharucha T, Turton JF, Hopkins KL, Mack DJF. A case of NDM-carbapenemase-producing hypervirulent Klebsiella pneumoniae sequence type 23 from the UK. JMM Case Rep 2018; 5:e005130 [View Article]
     [Google Scholar]
  18. Remya P, Shanthi M, Sekar U. Occurrence and characterization of hyperviscous K1 and K2 serotype in Klebsiella pneumoniae. J Lab Physicians 2018; 10:283–288 [View Article]
     [Google Scholar]
  19. Shankar C, Nabarro LE, Devanga Ragupathi NK, Muthuirulandi Sethuvel DP, Daniel JL et al. Draft Genome sequences of three hypervirulent carbapenem-resistant Klebsiella pneumoniae isolates from bacteremia. Genome Announc 2016; 4: [View Article]
     [Google Scholar]
  20. Liu Z, Gu Y, Li X, Liu Y, Ye Y et al. Identification and characterization of NDM-1-producing hypervirulent (hypermucoviscous) Klebsiella pneumoniae in China. Ann Lab Med 2019; 39:167–175 [View Article]
     [Google Scholar]
  21. Mollet C, Drancourt M, Raoult D. rpoB sequence analysis as a novel basis for bacterial identification. Mol Microbiol 1997; 26:1005–1011 [View Article]
     [Google Scholar]
  22. Zhan L, Wang S, Guo Y, Jin Y, Duan J et al. Outbreak by hypermucoviscous Klebsiella pneumoniae ST11 isolates with carbapenem resistance in a tertiary hospital in China. Front Cell Infect Microbiol 2017; 7:182 [View Article]
     [Google Scholar]
  23. Fang CT, Lai SY, Yi WC, Hsueh PR, Liu KL et al. Klebsiella pneumoniae genotype K1: an emerging pathogen that causes septic ocular or central nervous system complications from pyogenic liver abscess. Clin Infect Dis 2007; 45:284–293 [View Article]
     [Google Scholar]
  24. CLSI Performance Standards for Antimicrobial Susceptibility Testing, Twenty-Fifth informational supplement. CLSI document M100-S25. Wayne, PA: 2015
     [Google Scholar]
  25. Pournaras S, Zarkotou O, Poulou A, Kristo I, Vrioni G et al. A combined disk test for direct differentiation of carbapenemase-producing Enterobacteriaceae in surveillance rectal swabs. J Clin Microbiol 2013; 51:2986–2990 [View Article]
     [Google Scholar]
  26. Poirel L, Walsh TR, Cuvillier V, Nordmann P. Multiplex PCR for detection of acquired carbapenemase genes. Diagn Microbiol Infect Dis 2011; 70:119–123 [View Article]
     [Google Scholar]
  27. Chaisson MJ, Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 2012; 13:238 [View Article]
     [Google Scholar]
  28. Liu BT, Song FJ, Zou M. Characterization of highly prevalent plasmids coharboring mcr-1, oqxAB, and blaCTX-M and plasmids harboring oqxAB and blaCTX-M in Escherichia coli isolates from food-producing animals in China. Microb Drug Resist 2019; 25:108–119 [View Article]
     [Google Scholar]
  29. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H et al. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 2012; 50:1355–1361 [View Article]
     [Google Scholar]
  30. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [View Article]
     [Google Scholar]
  31. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article]
     [Google Scholar]
  32. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. blast ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011; 12:402 [View Article]
     [Google Scholar]
  33. Chen L, Chen ZL, Liu JH, Zeng ZL, Ma JY et al. Emergence of RmtB methylase-producing Escherichia coli and Enterobacter cloacae isolates from pigs in China. J Antimicrob Chemother 2007; 59:880–885 [View Article]
     [Google Scholar]
  34. Versalovic J, Koeuth T, Lupski JR. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 1991; 19:6823–6831 [View Article]
     [Google Scholar]
  35. Lee CR, Lee JH, Park KS, Kim YB, Jeong BC et al. Global dissemination of carbapenemase-producing Klebsiella pneumoniae: epidemiology, genetic context, treatment options, and detection methods. Front Microbiol 2016; 7:895 [View Article]
     [Google Scholar]
  36. Siu LK, Yeh KM, Lin JC, Fung CP, Chang FY. Klebsiella pneumoniae liver abscess: a new invasive syndrome. Lancet Infect Dis 2012; 12:881–887 [View Article]
     [Google Scholar]
  37. Shankar C, Veeraraghavan B, Nabarro LEB, Ravi R, Ragupathi NKD et al. Whole genome analysis of hypervirulent Klebsiella pneumoniae isolates from community and hospital acquired bloodstream infection. BMC Microbiol 2018; 18:6 [View Article]
     [Google Scholar]
  38. Liu YM, Li BB, Zhang YY, Zhang W, Shen H et al. Clinical and molecular characteristics of emerging hypervirulent Klebsiella pneumoniae bloodstream infections in mainland China. Antimicrob Agents Chemother 2014; 58:5379–5385 [View Article]
     [Google Scholar]
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Whole genome sequencing of NDM-1-producing serotype K1 ST23 hypervirulent Klebsiella pneumoniae in China
J. Med. Microbiol. 68, 866 (2019); https://doi.org/10.1099/jmm.0.000996
/content/journal/jmm/10.1099/jmm.0.000996
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