Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 29, Number 11—November 2023
Research

Global Phylogeography and Genomic Epidemiology of Carbapenem-Resistant blaOXA-232–Carrying Klebsiella pneumoniae Sequence Type 15 Lineage

Yuye Wu, Tian Jiang, Xianhong He, Jiayu Shao, Chenghao Wu, Weifang Mao, Huiqiong Jia, Fang He, Yingying Kong, Jianyong Wu, Qingyang Sun, Long Sun, Mohamed S. Draz, Xinyou XieComments to Author , Jun ZhangComments to Author , and Zhi RuanComments to Author 
Author affiliations: Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China (Y. Wu, T. Jiang, X. He, J. Shao, C. Wu, W. Mao, Y. Kong, X. Xie, J. Zhang, Z. Ruan); Wenzhou Medical University Affiliated Wenling Hospital, Taizhou, China (T. Jiang); Third People's Hospital of Xiaoshan District, Hangzhou (X. He, J. Shao); Shaoxing University Affiliated Hospital, Shaoxing, China (W. Mao); Zhejiang University School of Medicine First Affiliated Hospital, Hangzhou (H. Jia); Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou (H. Jia); Zhejiang Provincial People's Hospital, Hangzhou (F. He); Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou (Y. Kong, X. Xie, J. Zhang, Z. Ruan); Zhejiang University School of Medicine Fourth Affiliated Hospital, Hangzhou (J. Wu); No. 903 Hospital of PLA Joint Logistic Support Force, Hangzhou (Q. Sun); Hangzhou Women's Hospital, Hangzhou (L. Sun); Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (M.S. Draz); Cleveland Clinic, Cleveland (M.S. Draz)

Main Article

Table 2

MICs for different antimicrobial drugs of 21 blaOXA-232–carrying sequence type 15 carbapenem-resistant Klebsiella pneumoniae isolates from patients in China*

Isolate MIC, mg/L
AMK ATM FOF FOX FEP CTX LVX IPM MEM CST TGC FDC CZA
KP3 >128 >128 >128 64 >64 >128 64 8 4 <0.0625 1 2 0.25/0.125
KP41 >128 >128 >128 16 >64 >128 16 4 2 <0.0625 0.25 2 0.5/0.25
KP105 >128 >128 >128 128 >64 >128 128 >128 >128 <0.0625 2 1 0.5/0.25
KP232 >128 >128 128 128 >64 >128 >128 8 4 0.0625 2 0.5 0.5/0.25
KP306 >128 >128 >128 64 >64 >128 64 4 4 <0.0625 1 4 0.25/0.125
KP5 >128 >128 >128 64 64 >128 32 2 4 0.5 2 0.25 2/1
KP441 >128 >128 >128 32 >64 >128 16 0.5 2 0.125 2 1 2/1
KP68 >128 >128 >128 64 >64 >128 32 32 32 0.5 1 1 4/2
KP76 >128 >128 >128 32 >64 >128 16 1 1 0.25 1 1 1/0.5
KP77 >128 >128 >128 32 >64 >128 16 0.5 1 0.5 2 0.5 2/1
KP79 >128 >128 >128 32 >64 >128 32 1 1 0.25 1 16 2/1
KP81 >128 >128 >128 128 >64 >128 128 16 32 0.125 4 1 2/1
KP85 >128 >128 >128 32 >64 >128 16 2 1 0.125 1 0.25 2/1
KP89 >128 >128 >128 32 >64 >128 32 1 2 0.125 2 0.25 2/1
KP91 >128 >128 >128 128 >64 >128 64 1 2 0.125 0.5 0.5 1/0.5
KP97 >128 >128 >128 64 >64 >128 128 16 32 0.0625 2 1 2/1
KP9112 >128 >128 >128 64 >64 >128 64 2 2 <0.0625 1 0.5 2/1
KP135 >128 >128 >128 64 64 >128 64 4 2 0.5 2 0.25 2/1
KP8474 >128 >128 >128 >128 >64 >128 64 1 2 0.0625 1 0.5 2/1
KP12339 >128 >128 >128 32 >64 >128 16 1 2 0.125 0.5 0.5 2/1
KP3295 >128 64 >128 >128 >64 >128 >128 32 32 0.25 0.25 0.5 0.25/0.125

*By broth microdilution method for amikacin, aztreonam, fosfomycin, cefoxitin, cefepime, cefotaxime, cefiderocol, levofloxacin, imipenem, meropenem, polymyxin, tigecycline, and ceftazidime/avibactam; iron-depleted cation-adjusted Mueller-Hinton broth in custom-prepared MIC panels (14) method for cefiderocol. Breakpoints are according to Clinical and Laboratory Standards Institute 2020 (https://clsi.org) and EUCAST 10.0 (https://www.eucast.org/clinical_breakpoints) guidelines. Escherichia coli ATCC 25922 was the quality control strain. AMK, amikacin; ATM, aztreonam; FOF, fosfomycin; FOX, cefoxitin; FEP, cefepime; CTX, cefotaxime; LVX, levofloxacin; IPM, imipenem; MEM, meropenem; CST, colistin; TGC, tigecycline; FDC, cefiderocol; CZA, ceftazidime/avibactam.

Main Article

References
  1. Zhang  Y, Wang  Q, Yin  Y, Chen  H, Jin  L, Gu  B, et al. Epidemiology of carbapenem-resistant Enterobacteriaceae infections: report from the China CRE network. Antimicrob Agents Chemother. 2018;62:e0188217. DOIPubMedGoogle Scholar
  2. Nordmann  P, Cuzon  G, Naas  T. The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria. Lancet Infect Dis. 2009;9:22836. DOIPubMedGoogle Scholar
  3. Karlowsky  JA, Lob  SH, Kazmierczak  KM, Badal  RE, Young  K, Motyl  MR, et al. In vitro activity of imipenem against carbapenemase-positive Enterobacteriaceae isolates collected by the SMART Global Surveillance Program from 2008 to 2014. J Clin Microbiol. 2017;55:163849. DOIPubMedGoogle Scholar
  4. Tian  D, Pan  F, Wang  C, Sun  Y, Zhang  H. Resistance phenotype and clinical molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae among pediatric patients in Shanghai. Infect Drug Resist. 2018;11:193543. DOIPubMedGoogle Scholar
  5. Li  X, Ma  W, Qin  Q, Liu  S, Ye  L, Yang  J, et al. Nosocomial spread of OXA-232-producing Klebsiella pneumoniae ST15 in a teaching hospital, Shanghai, China. BMC Microbiol. 2019;19:235. DOIPubMedGoogle Scholar
  6. Han  X, Chen  Y, Zhou  J, Shi  Q, Jiang  Y, Wu  X, et al. Epidemiological characteristics of OXA-232–producing carbapenem-resistant Klebsiella pneumoniae strains isolated during nosocomial clonal spread associated with environmental colonization. Microbiol Spectr. 2022;10:e0257221. DOIPubMedGoogle Scholar
  7. Potron  A, Rondinaud  E, Poirel  L, Belmonte  O, Boyer  S, Camiade  S, et al. Genetic and biochemical characterisation of OXA-232, a carbapenem-hydrolysing class D β-lactamase from Enterobacteriaceae. Int J Antimicrob Agents. 2013;41:3259. DOIPubMedGoogle Scholar
  8. Lutgring  JD, Zhu  W, de Man  TJB, Avillan  JJ, Anderson  KF, Lonsway  DR, et al. Phenotypic and genotypic characterization of Enterobacteriaceae producing oxacillinase-48–like carbapenemases, United States. Emerg Infect Dis. 2018;24:7009. DOIPubMedGoogle Scholar
  9. Jia  H, Zhang  Y, Ye  J, Xu  W, Xu  Y, Zeng  W, et al. Outbreak of multidrug-resistant OXA-232-producing ST15 Klebsiella pneumoniae in a teaching hospital in Wenzhou, China. Infect Drug Resist. 2021;14:4395407. DOIPubMedGoogle Scholar
  10. Shu  L, Dong  N, Lu  J, Zheng  Z, Hu  J, Zeng  W, et al. Emergence of OXA-232 Carbapenemase-producing Klebsiella pneumoniae that carries a pLVPK-like virulence plasmid among elderly patients in China. Antimicrob Agents Chemother. 2019;63:e0224618. DOIPubMedGoogle Scholar
  11. Ruan  Z, Yu  Y, Feng  Y. The global dissemination of bacterial infections necessitates the study of reverse genomic epidemiology. Brief Bioinform. 2020;21:74150. DOIPubMedGoogle Scholar
  12. Shi  Q, Han  R, Guo  Y, Zheng  Y, Yang  Y, Yin  D, et al. Emergence of ST15 Klebsiella pneumoniae clinical isolates producing plasmids-mediated RmtF and OXA-232 in China. Infect Drug Resist. 2020;13:31259. DOIPubMedGoogle Scholar
  13. Poirel  L, Héritier  C, Tolün  V, Nordmann  P. Emergence of oxacillinase-mediated resistance to imipenem in Klebsiella pneumoniae. Antimicrob Agents Chemother. 2004;48:1522. DOIPubMedGoogle Scholar
  14. Hackel  MA, Tsuji  M, Yamano  Y, Echols  R, Karlowsky  JA, Sahm  DF. Reproducibility of broth microdilution MICs for the novel siderophore cephalosporin, cefiderocol, determined using iron-depleted cation-adjusted Mueller-Hinton broth. Diagn Microbiol Infect Dis. 2019;94:3215. DOIPubMedGoogle Scholar
  15. 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. DOIPubMedGoogle Scholar
  16. Feldgarden  M, Brover  V, Haft  DH, Prasad  AB, Slotta  DJ, Tolstoy  I, et al. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother. 2019;63:e0048319. DOIPubMedGoogle Scholar
  17. Carattoli  A, Zankari  E, García-Fernández  A, Voldby Larsen  M, Lund  O, Villa  L, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58:3895903. DOIPubMedGoogle Scholar
  18. Lam  MMC, Wick  RR, Watts  SC, Cerdeira  LT, Wyres  KL, Holt  KE. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun. 2021;12:4188. DOIPubMedGoogle Scholar
  19. Liu  B, Zheng  D, Zhou  S, Chen  L, Yang  J. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 2022;50(D1):D9127. DOIPubMedGoogle Scholar
  20. Feng  Y, Zou  S, Chen  H, Yu  Y, Ruan  Z. BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking. Nucleic Acids Res. 2021;49(D1):D64450. DOIPubMedGoogle Scholar
  21. Sullivan  MJ, Petty  NK, Beatson  SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27:100910. DOIPubMedGoogle Scholar
  22. Alikhan  NF, Petty  NK, Ben Zakour  NL, Beatson  SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011;12:402. DOIPubMedGoogle Scholar
  23. Deneke  C, Uelze  L, Brendebach  H, Tausch  SH, Malorny  B. Decentralized investigation of bacterial outbreaks based on hashed cgMLST. Front Microbiol. 2021;12:649517. DOIPubMedGoogle Scholar
  24. Zhou  Z, Alikhan  NF, Sergeant  MJ, Luhmann  N, Vaz  C, Francisco  AP, et al. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res. 2018;28:1395404. DOIPubMedGoogle Scholar
  25. Bouckaert  R, Vaughan  TG, Barido-Sottani  J, Duchêne  S, Fourment  M, Gavryushkina  A, et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLOS Comput Biol. 2019;15:e1006650. DOIPubMedGoogle Scholar
  26. Tonkin-Hill  G, Lees  JA, Bentley  SD, Frost  SDW, Corander  J. RhierBAPS: An R implementation of the population clustering algorithm hierBAPS. Wellcome Open Res. 2018;3:93. DOIPubMedGoogle Scholar
  27. Letunic  I, Bork  P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49(W1):W2936. DOIPubMedGoogle Scholar
  28. Bielejec  F, Baele  G, Vrancken  B, Suchard  MA, Rambaut  A, Lemey  P. SpreaD3: interactive visualization of spatiotemporal history and trait evolutionary processes. Mol Biol Evol. 2016;33:21679. DOIPubMedGoogle Scholar
  29. Agyeman  AA, Bergen  PJ, Rao  GG, Nation  RL, Landersdorfer  CB. A systematic review and meta-analysis of treatment outcomes following antibiotic therapy among patients with carbapenem-resistant Klebsiella pneumoniae infections. Int J Antimicrob Agents. 2020;55:105833. DOIPubMedGoogle Scholar
  30. Xu  L, Sun  X, Ma  X. Systematic review and meta-analysis of mortality of patients infected with carbapenem-resistant Klebsiella pneumoniae. Ann Clin Microbiol Antimicrob. 2017;16:18. DOIPubMedGoogle Scholar
  31. Yin  D, Dong  D, Li  K, Zhang  L, Liang  J, Yang  Y, et al. Clonal dissemination of OXA-232 carbapenemase-producing Klebsiella pneumoniae in neonates. Antimicrob Agents Chemother. 2017;61:e0038517. DOIPubMedGoogle Scholar
  32. Yamamoto  S, Nakano  M, Kitagawa  W, Tanaka  M, Sone  T, Hirai  K, et al. Characterization of multi-antibiotic-resistant Escherichia coli Isolated from beef cattle in Japan. Microbes Environ. 2014;29:13644. DOIPubMedGoogle Scholar
  33. Villa  L, Poirel  L, Nordmann  P, Carta  C, Carattoli  A. Complete sequencing of an IncH plasmid carrying the blaNDM-1, blaCTX-M-15 and qnrB1 genes. J Antimicrob Chemother. 2012;67:164550. DOIPubMedGoogle Scholar
  34. Palavecino  E, Ramirez  K, Greene  SR, Kilic  A. Co-existence of VIM-2-producing Pseudomonas aeruginosa and KPC-2 and OXA-232-co-producing Klebsiella pneumoniae in the United States. Ann Lab Med. 2020;40:2679. DOIPubMedGoogle Scholar
  35. Docquier  JD, Calderone  V, De Luca  F, Benvenuti  M, Giuliani  F, Bellucci  L, et al. Crystal structure of the OXA-48 beta-lactamase reveals mechanistic diversity among class D carbapenemases. Chem Biol. 2009;16:5407. DOIPubMedGoogle Scholar
  36. Rodrigues  C, Desai  S, Passet  V, Gajjar  D, Brisse  S. Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147. Microb Genom. 2022;8:000737. DOIPubMedGoogle Scholar
  37. Gaiarsa  S, Comandatore  F, Gaibani  P, Corbella  M, Dalla Valle  C, Epis  S, et al. Genomic epidemiology of Klebsiella pneumoniae in Italy and novel insights into the origin and global evolution of its resistance to carbapenem antibiotics. Antimicrob Agents Chemother. 2015;59:38996. DOIPubMedGoogle Scholar
  38. Long  TE, Williams  JT. Cephalosporins currently in early clinical trials for the treatment of bacterial infections. Expert Opin Investig Drugs. 2014;23:137587. DOIPubMedGoogle Scholar
  39. Zaffiri  L, Gardner  J, Toledo-Pereyra  LH. History of antibiotics. From salvarsan to cephalosporins. J Invest Surg. 2012;25:6777. DOIPubMedGoogle Scholar
  40. Lima  LM, Silva  BNMD, Barbosa  G, Barreiro  EJ. β-lactam antibiotics: An overview from a medicinal chemistry perspective. Eur J Med Chem. 2020;208:112829. DOIPubMedGoogle Scholar

Main Article

Page created: September 05, 2023
Page updated: October 23, 2023
Page reviewed: October 23, 2023
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.
file_external