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Volume 70, Issue 9

Molecular characterization of rectal isolates of carbapenemase-negative carbapenem-resistant enterobacterales obtained from ICU patients in Kuwait by whole-genome sequencing No Access

Abstract

Carbapenem-resistant enterobacterales (CRE) are listed among the most urgent antibiotic resistance threats.

Previous studies on the mechanisms of CRE in Kuwait have focused on carbapenemases. There have been no studies on non-carbapenemase-producing CRE in Kuwait.

The aim of this study was to investigate the genetic characteristics of non-carbapenemase-producing carbapenem-resistant enterobacterales (NCPE) isolates using whole-genome sequencing (WGS).

Fourteen confirmed NCPE isolates that were negative for genes encoding carbapenemase production by polymerase chain reaction (PCR) assays using rectal swabs from intensive care unit patients were characterized using phenotypic, PCR and WGS methods. Susceptibility testing was performed via Etest and clonality via multi-locus sequence typing (MLST).

All of the isolates were resistant to ertapenem; 78.6 % were resistant to imipenem, meropenem and trimethoprim–sulfamethoxazole. Resistance to the other antibiotics was variable, ranging from 28.5 (colistin) through 50 (tigecycline) and 64.3 (amikacin) up to 85.7 % against both amoxicillin–clavulanic acid and ciprofloxacin. WGS detected several resistance genes mediating the production of β-lactamases, genes encoding an outer-membrane porin permeability mutation resulting in reduced susceptibility to β-lactams, including carbapenems, and genes for multidrug-resistant (MDR) efflux pumps. The isolates also possessed global activator protein MarA, which mediated reduced permeability to β-lactams. The existence of β-lactamase genes, overexpression of MDR efflux pumps and reduced permeability mediated by the porin genes were responsible for carbapenem resistance.

This finding reflects the superior detection capabilities offered by WGS analysis, which can be used to complement traditional methods and overcome their limited resolution in clinical settings.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): CRE , ICU and WGS
Funding
This study was supported by the:
  • college of graduate studies, kuwait university (Award YM 07/17)
    • Principle Award Recipient: AmaniH Al Fadhli
© 2021 The Authors
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/content/journal/jmm/10.1099/jmm.0.001409
2021-09-03
2024-04-24
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References

  1. World Health Organization Antimicrobial resistance: global report on surveillance; 2014 https://apps.who.int/iris/handle/10665/112642
  2. Centers for Disease Control and Prevention Antibiotic resistance threats in the United States, 2013; 2013 http://www.cdc.gov/drugresistance/threat-report-2013/pdf/ar-threats-2013-508.pdf
  3. Sheu CC, Chang YT, Lin SY, Chen YH, Hsueh PR. Infections caused by carbapenem-resistant Enterobacteriaceae: an update therapeutic options. Front Microbiol 2019; 10:80 [View Article] [PubMed]
     [Google Scholar]
  4. Nordmann P, Poirel L. Epidemiology and diagnostics of carbapenem resistance in Gram-negative bacteria. Clin Infect Dis 2019; 69:S521–S528 [View Article] [PubMed]
     [Google Scholar]
  5. Capone A, Giannella M, Fortini D, Giordano A, Meledandri M et al. High rate of colistin resistance among patients with carbapenem-resistant Klebsiella pneumoniae infection accounts for an excess of mortality. Clin Microbiol Infect 2013; 19:E23–E30 [View Article] [PubMed]
     [Google Scholar]
  6. Jamal W, Rotimi VO, Albert MJ, Khodakhast F, Udo EE et al. Emergence of nosocomial New Delhi metallo-β-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae in patients admitted to a tertiary care hospital in Kuwait. Int J Antimicrob Agents 2012; 39:183–184 [View Article] [PubMed]
     [Google Scholar]
  7. Jamal W, Rotimi VO, Albert MJ, Khadakhast F, Nordmann P et al. High Prevalence of VIM-4 and NDM-1 metallo-β-lactamase among carbapenem–resistant Enterobacteriaceae. J Med Microbiol 2013; 62:1239–1244 [View Article] [PubMed]
     [Google Scholar]
  8. Jamal WY, Albert MJ, Khodakhast F, Poirel L, Rotimi VO. Emergence of new sequence type OXA-48 carbapenemase-producing Enterobacteriaceae in Kuwait. Microb Drug Resist 2015; 21:329–334 [View Article] [PubMed]
     [Google Scholar]
  9. CLSI Performance standards for antimicrobial susceptibility testing. In 30th Informational Supplement-Clinical and Laboratory Standards Institute Document Wayne, PA, USA: 2020
     [Google Scholar]
  10. Bogaerts P, Rezende de Castro R, de Mendonça R, Huang TD, Denis O et al. Validation of carbapenemase and extended-spectrum β-lactamase multiplex endpoint PCR assays according to ISO 15189. J Antimicrob Chemother 2013; 68:1576–1582 [View Article] [PubMed]
     [Google Scholar]
  11. The European Committee on Antimicrobial Susceptibility Testing Breakpoint tables for interpretation of MICs and zone diameters. Version 8.0; 2018 http://www.eucast.org
  12. Center for Genomic epidemiology DTU, Kemitorvet, Building 204, 2800 Kgs Lyngby, Denmark:
     [Google Scholar]
  13. Joensen KG, Scheutz F, Lund O. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol 2014; 52:1501–1510 [View Article] [PubMed]
     [Google Scholar]
  14. Carattoli A, García-Fernández A. 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]
  15. Zankari E, Hasman H, Cosentino S. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [View Article] [PubMed]
     [Google Scholar]
  16. Larsen MV, Cosentino S, Rasmussen S. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 2012; 50:1355–1361 [View Article] [PubMed]
     [Google Scholar]
  17. Pournaras S, Koumaki V, Spanakis N, Gennimata V, Tsakris A. Current perspectives on tigecycline resistance in Enterobacteriaceae: susceptibility testing issues and mechanisms of resistance. Int J Antimicrob Agents 2016; 48:11–18 [View Article] [PubMed]
     [Google Scholar]
  18. Doménech-Sánchez A, Hernández-Allés S, Martínez-Martínez L, Benedí VJ, Albertí S. Identification and characterization of a new porin gene of Klebsiella pneumoniae: its role in beta-lactam antibiotic resistance. J Bacteriol 1999; 181:2726–2732 [View Article] [PubMed]
     [Google Scholar]
  19. Rimoldi SG, Gentile B, Pagani C. Whole genome sequencing for the molecular characterization of carbapenem-resistant Klebsiella pneumoniae strains isolated at the Italian ASST Fatebenefratelli Sacco Hospital, 2012-2014. BMC Infect Dis 2017; 17:666 [View Article] [PubMed]
     [Google Scholar]
  20. Lin TL, Pan YJ, Hsieh PF, Hsu CR, Wu M-C et al. Imipenem represses CRISPR-Cas interference of DNA acquisition through H-NS stimulation in Klebsiella pneumoniae. . Sci Rep 2016; 6:31644 [View Article] [PubMed]
     [Google Scholar]
  21. Li X-Z, Plésiat P, Nikaido H. The challenge of efflux-mediated antibiotic resistance in gram-negative bacteria.Clin. Microbiol Rev 2015; 28:337–418
     [Google Scholar]
  22. Hirata T, Saito A, Nishino K, Tamura N, Yamaguchi A. Effects of efflux transporter genes on susceptibility of Escherichia coli to tigecycline (GAR-936. Antimicrob Agents Chemother 2004; 48:2179–2184 [View Article] [PubMed]
     [Google Scholar]
  23. Ramirez MS, Traglia GM, Lin DL, Tran T, Tolmasky ME. Plasmid-mediated antibiotic resistance and virulence in Gram-negatives: Klebsiella pneumoniae paradim. Microbiol Spectr 2014; 2:1–15 [View Article] [PubMed]
     [Google Scholar]
  24. Giani T, Arena F, Vaggelli G. Large nosocomial outbreak of colistin-resistant, carbapenemase-producing Klebsiella pneumoniae traced to clonal expansion of an mgrB deletion mutant. J Clin Microbiol 2015; 53:3341–3344 [View Article] [PubMed]
     [Google Scholar]
  25. Pitout JDD, Peirano G, Kock MM, Strydom KA, Matsumura Y. The global ascendency of oxa-48-type carbapenemases. Clin Microbiol Rev 2019; 33:e00102 [View Article]
     [Google Scholar]
  26. Campos ACC, Andrade NL, Ferdous M. Comprehensive molecular characterization of Escherichia coli isolates from urine samples of hospitalized patients in Rio de Janeiro. Front Microbiol 2018; 9:243 [View Article] [PubMed]
     [Google Scholar]
  27. Potron A, Nordmann P, Lafeuille E, Al Maskari Z, Al Rashdi F et al. Characterization of OXA-181, a carbapenem-hydrolyzing class D beta-lactamase from Klebsiella pneumoniae. Antimicrob Agents Chemother 2011; 55:4896–4899 [View Article] [PubMed]
     [Google Scholar]
  28. Teo JW, Kurup A, Lin RT, Hsien KT. Emergence of clinical Klebsiella pneumoniae producing OXA-232 carbapenemase in Singapore. New Microbes New Infect 2013; 1:13–15 [View Article] [PubMed]
     [Google Scholar]
  29. Mancini S, Poirel L, Tritten ML, Lienhard R, Bassi C et al. Emergence of an MDR Klebsiella pneumoniae ST231 producing oxa-232 and RMTF in Switzerland. J Microbiol Immunol Infect 2018; 73:821–823
     [Google Scholar]
  30. Randall LP, Woodward MJ. The multiple antibiotic resistance (mar) locus and its significance. Res Vet Sci 2002; 72:87–93 [View Article] [PubMed]
     [Google Scholar]
  31. Webber M, Buckley AM, Randall LP, Woodward MJ, Piddock LJV. Overexpression of marA, soxS and acrB in veterinary isolates of Salmonella enterica rarely correlates with cyclohexane tolerance. J Antimicrob Chemother 2006; 57:673–679 [View Article] [PubMed]
     [Google Scholar]
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Molecular characterization of rectal isolates of carbapenemase-negative carbapenem-resistant enterobacterales obtained from ICU patients in Kuwait by whole-genome sequencing
J. Med. Microbiol. 70, 001409 (2021); https://doi.org/10.1099/jmm.0.001409
/content/journal/jmm/10.1099/jmm.0.001409
/content/journal/jmm/10.1099/jmm.0.001409
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