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Abstract

Carbapenem-resistant Klebsiella pneumoniae (CRKP) increasingly cause high-mortality outbreaks in hospital settings globally. Following a patient fatality at a hospital in Beijing due to a bla KPC-2-positive CRKP infection, close monitoring was put in place over the course of 14 months to characterize all bla KPC-2-positive CRKP in circulation in the hospital. Whole genome sequences were generated for 100 isolates from bla KPC-2-positive isolates from infected patients, carriers and the hospital environment. Phylogenetic analyses identified a closely related cluster of 82 sequence type 11 (ST11) isolates circulating in the hospital for at least a year prior to admission of the index patient. The majority of inferred transmissions for these isolates involved patients in intensive care units. Whilst the 82 ST11 isolates collected during the surveillance effort all had closely related chromosomes, we observed extensive diversity in their antimicrobial resistance (AMR) phenotypes. We were able to reconstruct the major genomic changes underpinning this variation in AMR profiles, including multiple gains and losses of entire plasmids and recombination events between plasmids, including transposition of bla KPC-2. We also identified specific cases where variation in plasmid copy number correlated with the level of phenotypic resistance to drugs, suggesting that the number of resistance elements carried by a strain may play a role in determining the level of AMR. Our findings highlight the epidemiological value of whole genome sequencing for investigating multi-drug-resistant hospital infections and illustrate that standard typing schemes cannot capture the extraordinarily fast genome evolution of CRKP isolates.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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2019-04-02
2024-03-28
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References

  1. Bradley P, Gordon NC, Walker TM, Dunn L, Heys S et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun 2015; 6:10063 [View Article][PubMed]
    [Google Scholar]
  2. Tyson GH, Mcdermott PF, Li C, Chen Y, Tadesse DA et al. WGS accurately predicts antimicrobial resistance in Escherichia coli. J Antimicrob Chemother 2015; 70:2763–2769 [View Article][PubMed]
    [Google Scholar]
  3. Gordon NC, Price JR, Cole K, Everitt R, Morgan M et al. Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J Clin Microbiol 2014; 52:1182–1191 [View Article][PubMed]
    [Google Scholar]
  4. Balloux F, Brønstad Brynildsrud O, van Dorp L, Shaw LP, Chen H et al. From theory to practice: translating whole-genome sequencing (WGS) into the clinic. Trends Microbiol 2018; 26:1035–1048 [View Article][PubMed]
    [Google Scholar]
  5. Tacconelli E, Carrara E, Savoldi A, Harbarth S, Mendelson M et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis 2018; 18:318–327 [View Article][PubMed]
    [Google Scholar]
  6. Hauck C, Cober E, Richter SS, Perez F, Salata RA et al. Spectrum of excess mortality due to carbapenem-resistant Klebsiella pneumoniae infections. Clin Microbiol Infect 2016; 22:513–519 [View Article][PubMed]
    [Google Scholar]
  7. Hussein K, Raz-Pasteur A, Finkelstein R, Neuberger A, Shachor-Meyouhas Y et al. Impact of carbapenem resistance on the outcome of patients' hospital-acquired bacteraemia caused by Klebsiella pneumoniae. J Hosp Infect 2013; 83:307–313 [View Article][PubMed]
    [Google Scholar]
  8. Munoz-Price LS, Poirel L, Bonomo RA, Schwaber MJ, Daikos GL et al. Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet Infect Dis 2013; 13:785–796 [View Article][PubMed]
    [Google Scholar]
  9. Wei ZQ, du XX, Yu YS, Shen P, Chen YG et al. Plasmid-mediated KPC-2 in a Klebsiella pneumoniae isolate from China. Antimicrob Agents Chemother 2007; 51:763–765 [View Article][PubMed]
    [Google Scholar]
  10. Nordmann P, Cuzon G, Naas T. The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria. Lancet Infect Dis 2009; 9:228–236 [View Article][PubMed]
    [Google Scholar]
  11. Huang W, Wang G, Sebra R, Zhuge J, Yin C et al. Emergence and evolution of multidrug-resistant Klebsiella pneumoniae with both blaKPC and blaCTX-M integrated in the chromosome. Antimicrob Agents Chemother 2017; 61:AAC.00076-17 [View Article][PubMed]
    [Google Scholar]
  12. Mathers AJ, Stoesser N, Chai W, Carroll J, Barry K et al. Chromosomal integration of the Klebsiella pneumoniae Carbapenemase Gene, bla kpc in Klebsiella Species Is Elusive but Not Rare. Antimicrob Agents Chemother 2017; 61:e0182316 [View Article][PubMed]
    [Google Scholar]
  13. Mathers AJ, Cox HL, Kitchel B, Bonatti H, Brassinga AK et al. Molecular dissection of an outbreak of carbapenem-resistant enterobacteriaceae reveals Intergenus KPC carbapenemase transmission through a promiscuous plasmid. MBio 2011; 2:e0020400211 [View Article][PubMed]
    [Google Scholar]
  14. Conlan S, Thomas PJ, Deming C, Park M, Lau AF et al. Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med 2014; 6:254ra126 [View Article][PubMed]
    [Google Scholar]
  15. Hardiman CA, Weingarten RA, Conlan S, Khil P, Dekker JP et al. Horizontal Transfer of Carbapenemase-Encoding Plasmids and Comparison with Hospital Epidemiology Data. Antimicrob Agents Chemother 2016; 60:4910–4919 [View Article][PubMed]
    [Google Scholar]
  16. Sheppard AE, Stoesser N, Wilson DJ, Sebra R, Kasarskis A et al. Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC. Antimicrob Agents Chemother 2016; 60:3767–3778 [View Article][PubMed]
    [Google Scholar]
  17. Stoesser N, Sheppard AE, Peirano G, Anson LW, Pankhurst L et al. Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli. Sci Rep 2017; 7:5917 [View Article][PubMed]
    [Google Scholar]
  18. Feng J, Yin Z, Zhao Q, Zhao Y, Zhang D et al. Genomic characterization of novel IncFII-type multidrug resistant plasmids p0716-KPC and p12181-KPC from Klebsiella pneumoniae. Sci Rep 2017; 7:5830 [View Article][PubMed]
    [Google Scholar]
  19. Shi L, Feng J, Zhan Z, Zhao Y, Zhou H et al. Comparative analysis of blaKPC-2- and rmtB-carrying IncFII-family pKPC-LK30/pHN7A8 hybrid plasmids from Klebsiella pneumoniae CG258 strains disseminated among multiple Chinese hospitals. Infect Drug Resist 2018; 11:1783–1793 [View Article][PubMed]
    [Google Scholar]
  20. Moland ES, Hong SG, Thomson KS, Larone DH, Hanson ND. Klebsiella pneumoniae isolate producing at least eight different beta-lactamases, including AmpC and KPC beta-lactamases. Antimicrob Agents Chemother 2007; 51:800–801 [View Article][PubMed]
    [Google Scholar]
  21. Dong N, Lin D, Zhang R, Chan EW, Chen S. Carriage of blaKPC-2 by a virulence plasmid in hypervirulent Klebsiella pneumoniae. J Antimicrob Chemother 2018; 73:3317–3321 [View Article][PubMed]
    [Google Scholar]
  22. Wyres KL, Nguyen TN, Lam MM, Judd LM, Chau N et al. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia. bioRxiv 2019557785
    [Google Scholar]
  23. Yang J, Ye L, Guo L, Zhao Q, Chen R et al. A nosocomial outbreak of KPC-2-producing Klebsiella pneumoniae in a Chinese hospital: dissemination of ST11 and emergence of ST37, ST392 and ST395. Clin Microbiol Infect 2013; 19:E509E515 [View Article][PubMed]
    [Google Scholar]
  24. Shen P, Zhang Y, Li G, Jiang X. Characterization of the genetic environment of the blaKPC-2 gene among Klebsiella pneumoniae isolates from a Chinese Hospital. Braz J Infect Dis 2016; 20:384–388 [View Article][PubMed]
    [Google Scholar]
  25. Rasheed JK, Biddle JW, Anderson KF, Washer L, Chenoweth C et al. Detection of the Klebsiella pneumoniae carbapenemase type 2 Carbapenem-hydrolyzing enzyme in clinical isolates of Citrobacter freundii and K. oxytoca carrying a common plasmid. J Clin Microbiol 2008; 46:2066–2069 [View Article][PubMed]
    [Google Scholar]
  26. Martin J, Phan HTT, Findlay J, Stoesser N, Pankhurst L et al. Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission. J Antimicrob Chemother 2017; 72:3025–3034 [View Article][PubMed]
    [Google Scholar]
  27. Weingarten RA, Johnson RC, Conlan S, Ramsburg AM, Dekker JP et al. Genomic analysis of hospital plumbing reveals diverse reservoir of bacterial plasmids conferring carbapenem resistance. MBio 2018; 9:e0201102017 [View Article][PubMed]
    [Google Scholar]
  28. Cerqueira GC, Earl AM, Ernst CM, Grad YH, Dekker JP et al. Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proc Natl Acad Sci USA 2017; 114:1135–1140 [View Article][PubMed]
    [Google Scholar]
  29. Kanamori H, Parobek CM, Juliano JJ, van Duin D, Cairns BA et al. A Prolonged Outbreak of KPC-3-Producing Enterobacter cloacae and Klebsiella pneumoniae Driven by Multiple Mechanisms of Resistance Transmission at a Large Academic Burn Center. Antimicrob Agents Chemother 2017; 61:e0151616 [View Article][PubMed]
    [Google Scholar]
  30. Mathers AJ, Stoesser N, Sheppard AE, Pankhurst L, Giess A et al. Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing. Antimicrob Agents Chemother 2015; 59:1656–1663 [View Article][PubMed]
    [Google Scholar]
  31. Kwong JC, Lane CR, Romanes F, Gonçalves da Silva A, Easton M et al. Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak. PeerJ 2018; 6:e4210 [View Article][PubMed]
    [Google Scholar]
  32. Conlan S, Park M, Deming C, Thomas PJ, Young AC et al. Plasmid dynamics in KPC-Positive Klebsiella pneumoniae during long-term patient colonization. MBio 2016; 7:e0074216 [View Article][PubMed]
    [Google Scholar]
  33. Hu L, Liu Y, Deng L, Zhong Q, Hang Y et al. Outbreak by ventilator-associated ST11 K. pneumoniae with Co-production of CTX-M-24 and KPC-2 in a SICU of a tertiary teaching hospital in central China. Front Microbiol 2016; 7:1190 [View Article][PubMed]
    [Google Scholar]
  34. 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][PubMed]
    [Google Scholar]
  35. 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 2018; 18:37–46 [View Article][PubMed]
    [Google Scholar]
  36. Li J, Zou MX, Wang HC, Dou QY, Hu YM et al. An outbreak of infections caused by a Klebsiella pneumoniae ST11 Clone Coproducing Klebsiella pneumoniae Carbapenemase-2 and RmtB in a Chinese Teaching Hospital. Chin Med J 2016; 129:2033–2039 [View Article][PubMed]
    [Google Scholar]
  37. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:132 [View Article][PubMed]
    [Google Scholar]
  38. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM; 2013
  39. Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing; 2012
  40. Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol 2015; 11:e1004041 [View Article][PubMed]
    [Google Scholar]
  41. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  42. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2014; 10:e1003537 [View Article][PubMed]
    [Google Scholar]
  43. Bouckaert RR, Drummond AJ. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evol Biol 2017; 17:42 [View Article][PubMed]
    [Google Scholar]
  44. Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y. ggtree: an package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 2017; 8:28–36 [View Article]
    [Google Scholar]
  45. Didelot X, Fraser C, Gardy J, Colijn C. Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks. Mol Biol Evol 2017; 34:msw075 [View Article][PubMed]
    [Google Scholar]
  46. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  47. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:btu153 [View Article][PubMed]
    [Google Scholar]
  48. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article][PubMed]
    [Google Scholar]
  49. 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][PubMed]
    [Google Scholar]
  50. Lam MMC, Wick RR, Wyres KL, Gorrie CL, Judd LM et al. Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. Microb Genom 2018; 4: [View Article][PubMed]
    [Google Scholar]
  51. 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][PubMed]
    [Google Scholar]
  52. Siguier P. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34:D32–D36 [View Article]
    [Google Scholar]
  53. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357–359 [View Article][PubMed]
    [Google Scholar]
  54. Anders S, Pyl PT, Huber W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 2015; 31:166–169 [View Article][PubMed]
    [Google Scholar]
  55. Wagner GP, Kin K, Lynch VJ. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci 2012; 131:281–285 [View Article][PubMed]
    [Google Scholar]
  56. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article][PubMed]
    [Google Scholar]
  57. Qi Y, Wei Z, Ji S, du X, Shen P et al. ST11, the dominant clone of KPC-producing Klebsiella pneumoniae in China. J Antimicrob Chemother 2011; 66:307–312 [View Article][PubMed]
    [Google Scholar]
  58. Rieux A, Balloux F. Inferences from tip-calibrated phylogenies: a review and a practical guide. Mol Ecol 2016; 25:1911–1924 [View Article][PubMed]
    [Google Scholar]
  59. Konopka K, Bindereif A, Neilands JB. Aerobactin-mediated utilization of transferrin iron. Biochemistry 1982; 21:6503–6508 [View Article][PubMed]
    [Google Scholar]
  60. Nassif X, Honoré N, Vasselon T, Cole ST, Sansonetti PJ. Positive control of colanic acid synthesis in Escherichia coli by rmpA and rmpB, two virulence-plasmid genes of Klebsiella pneumoniae. Mol Microbiol 1989; 3:1349–1359 [View Article][PubMed]
    [Google Scholar]
  61. Wacharotayankun R, Arakawa Y, Ohta M, Tanaka K, Akashi T et al. Enhancement of extracapsular polysaccharide synthesis in Klebsiella pneumoniae by RmpA2, which shows homology to NtrC and FixJ. Infect Immun 1993; 61:3164–3174[PubMed]
    [Google Scholar]
  62. Wang L, Fang H, Feng J, Yin Z, Xie X et al. Complete sequences of KPC-2-encoding plasmid p628-KPC and CTX-M-55-encoding p628-CTXM coexisted in Klebsiella pneumoniae. Front Microbiol 2015; 6:838 [View Article][PubMed]
    [Google Scholar]
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