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Volume 68, Issue 3

Utilizing genomic analyses to investigate the first outbreak of van A vancomycin-resistant Enterococcus in Australia with emergence of daptomycin non-susceptibility Free

Abstract

Introduction. The majority of vancomycin-resistant Enterococcus faecium (VREfm) in Australia is of the vanB genotype. An outbreak of vanA VREfm emerged in our haematology/oncology unit between November 2014 and May 2015. The first case of daptomycin non-susceptible E. faecium (DNSEfm) detected was a patient with vanA VREfm bacteraemia who showed clinical failure of daptomycin therapy, prompting microbiologic testing confirming daptomycin non-susceptibility.

Objectives. To describe the patient profiles, antibiotic susceptibility and genetic relatedness of vanA VREfm isolates in the outbreak.

Methods. Chart review of vanA VREfm colonized and infected patients was undertaken to describe the demographics, clinical features and outcomes of therapy. Whole genome sequencing of vanA VREfm isolates involved in the outbreak was conducted to assess clonality.

Results. In total, 29 samples from 24 patients tested positive for vanA VREfm (21 screening swabs and 8 clinical isolates). Five isolates were DNSEfm (four patients colonized, one patient with bacteraemia), with only one patient exposed to daptomycin previously. In silico multi-locus sequence typing of the isolates identified 25/26 as ST203, and 1/26 as ST796. Comparative genomic analysis revealed limited core genome diversity amongst the ST203 isolates, consistent with an outbreak of a single clone of vanA VREfm.

Conclusions. Here we describe an outbreak of vanA VREfm in a haematology/oncology unit. Genomic analysis supports transmission of an ST203 vanA VRE clone within this unit. Daptomycin non-susceptibility in 5/24 patients left linezolid as the only treatment option. Daptomycin susceptibility cannot be assumed in vanA VREfm isolates and confirmatory testing is recommended.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): daptomycin non-susceptible , outbreak , Vancomycin-resistant Enterococcus and whole genome sequencing
© 2019 The Authors
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2019-01-21
2024-04-24
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References

  1. Magill SS, Edwards JR, Bamberg W, Beldavs ZG, Dumyati G et al. Multistate point-prevalence survey of health care-associated infections. N Engl J Med 2014; 370:1198–1208 [View Article]
     [Google Scholar]
  2. Zarb P, Coignard B, Griskeviciene J, Muller A, Vankerckhoven V et al. The European Centre for Disease Prevention and Control (ECDC) pilot point prevalence survey of healthcare-associated infections and antimicrobial use. Euro Surveill 2012; 17:20316 [View Article]
     [Google Scholar]
  3. Prematunge C, MacDougall C, Johnstone J, Adomako K, Lam F et al. VRE and VSE bacteremia outcomes in the era of effective VRE therapy: a systematic review and meta-analysis. Infect Control Hosp Epidemiol 2016; 37:26–35 [View Article]
     [Google Scholar]
  4. Zasowski EJ, Claeys KC, Lagnf AM, Davis SL, Rybak MJ. Time is of the essence: the impact of delayed antibiotic therapy on patient outcomes in hospital-onset enterococcal bloodstream infections. Clin Infect Dis 2016; 62:1242–1250 [View Article]
     [Google Scholar]
  5. Worth LJ, Spelman T, Bull AL, Brett JA, Richards MJ. Central line-associated bloodstream infections in Australian intensive care units: time-trends in infection rates, etiology, and antimicrobial resistance using a comprehensive Victorian surveillance program, 2009-2013. Am J Infect Control 2015; 43:848–852 [View Article]
     [Google Scholar]
  6. Kamarulzaman A, Tosolini FA, Boquest AL, Geddes JE, Richards MJ. Vancomycin-resistant Enterococcus faecium in a liver transplant patient: in proceedings of the annual scientific meeting of the Australasian Society of infectious diseases. Aust N Z J Med 1995; 25:555
     [Google Scholar]
  7. Johnson PD, Ballard SA, Grabsch EA, Stinear TP, Seemann T et al. A sustained hospital outbreak of vancomycin-resistant Enterococcus faecium bacteremia due to emergence of vanB E. faecium sequence type 203. J Infect Dis 2010; 202:1278–1286 [View Article]
     [Google Scholar]
  8. Worth LJ, Thursky KA, Seymour JF, Slavin MA. Vancomycin-resistant Enterococcus faecium infection in patients with hematologic malignancy: patients with acute myeloid leukemia are at high-risk. Eur J Haematol 2007; 79:226–233 [View Article]
     [Google Scholar]
  9. Karki S, Houston L, Land G, Bass P, Kehoe R et al. Prevalence and risk factors for VRE colonisation in a tertiary hospital in Melbourne, Australia: a cross sectional study. Antimicrob Resist Infect Control 2012; 1:31 [View Article]
     [Google Scholar]
  10. Edelsberg J, Weycker D, Barron R, Li X, Wu H et al. Prevalence of antibiotic resistance in US hospitals. Diagn Microbiol Infect Dis 2014; 78:255–262 [View Article]
     [Google Scholar]
  11. Coombs GW, Pearson JC, Daly DA, Le TT, Robinson JO et al. Australian Enterococcal Sepsis Outcome Programme annual report, 2013. Commun Dis Intell Q Rep 2014; 38:E320–326
     [Google Scholar]
  12. Coombs GW, Daley DA, Thin Lee Y, Pearson JC, Robinson JO et al. Australian Group on antimicrobial resistance Australian Staphylococcus aureus sepsis outcome programme annual report, 2014. Commun Dis Intell Q Rep 2016; 40:E244–254
     [Google Scholar]
  13. The Australian Group on Antimicrobial Resistance Australian Enterococcal Sepsis Outcome Program (AESOP) 2016 final report; 2017 [updated 23/6/2017] http://agargroup.org.au/wp-content/uploads/2017/08/AESOP-2016-Final-Report-2017.pdf
  14. Long JK, Choueiri TK, Hall GS, Avery RK, Sekeres MA. Daptomycin-resistant Enterococcus faecium in a patient with acute myeloid leukemia. Mayo Clin Proc 2005; 80:1215–1216 [View Article]
     [Google Scholar]
  15. Menon V, Davis R, Shackel N, Espedido BA, Beukers AG et al. Failure of daptomycin β-Lactam combination therapy to prevent resistance emergence in Enterococcus faecium. Diagn Microbiol Infect Dis 2018; 90:120–122 [View Article]
     [Google Scholar]
  16. Bell JM, Turnidge JD, Sader HS, Jones RN. Antimicrobial activity and spectrum of daptomycin: results from the surveillance program in Australia and New Zealand (2008). Pathology 2010; 42:470–473 [View Article]
     [Google Scholar]
  17. Chitnis S, Katara G, Hemvani N, Pareek S, Chitnis DS. In vitro activity of daptomycin & linezolid against methicillin resistant Staphylococcus aureus & vancomycin resistant enterococci isolated from hospitalized cases in Central India. Indian J Med Res 2013; 137:191–196
     [Google Scholar]
  18. Sader HS, Flamm RK, Jones RN. Antimicrobial activity of daptomycin tested against Gram-positive pathogens collected in Europe, Latin America, and selected countries in the Asia-Pacific Region (2011). Diagn Microbiol Infect Dis 2013; 75:417–422 [View Article]
     [Google Scholar]
  19. Wang JT, Chang SC, Wang HY, Chen PC, Shiau YR et al. High rates of multidrug resistance in Enterococcus faecalis and E. faecium isolated from inpatients and outpatients in Taiwan. Diagn Microbiol Infect Dis 2013; 75:406–411 [View Article]
     [Google Scholar]
  20. Ballester F, Pujol I, Cueto P, Rovira C, Iftimie S et al. Emergence of daptomycin-resistant Enterococcus faecium in a critically ill patient with postoperative intra-abdominal sepsis. Rev Esp Quimioter 2015; 28:109–110
     [Google Scholar]
  21. Egli A, Schmid H, Kuenzli E, Widmer AF, Battegay M et al. Association of daptomycin use with resistance development in Enterococcus faecium bacteraemia-a 7-year individual and population-based analysis. Clin Microbiol Infect 2017; 23:118.e1–11118 [View Article]
     [Google Scholar]
  22. Lellek H, Franke GC, Ruckert C, Wolters M, Wolschke C et al. Emergence of daptomycin non-susceptibility in colonizing vancomycin-resistant Enterococcus faecium isolates during daptomycin therapy. Int J Med Microbiol 2015; 305:902–909 [View Article]
     [Google Scholar]
  23. Sorlózano A, Panesso D, Navarro-Marí JM, Arias CA, Gutiérrez-Fernández J. Characterization of daptomycin non-susceptible Enterococcus faecium producing urinary tract infection in a renal transplant recipient. Rev Esp Quimioter 2015; 28:207–209
     [Google Scholar]
  24. 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]
     [Google Scholar]
  25. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
     [Google Scholar]
  26. Lee RS, Gonçalves da Silva A, Baines SL, Strachan J, Ballard S et al. The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study. J Antimicrob Chemother 2018; 73:3268–3278 [View Article]
     [Google Scholar]
  27. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article]
     [Google Scholar]
  28. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006; 23:254–267 [View Article]
     [Google Scholar]
  29. Sinel C, Cosquer T, Auzou M, Goux D, Giard JC et al. Sequential steps of daptomycin resistance in Enterococcus faecium and reversion to hypersusceptibility through IS-mediated inactivation of the liaFSR operon. J Antimicrob Chemother 2016; 71:2793–2797 [View Article]
     [Google Scholar]
  30. Vydra J, Shanley RM, George I, Ustun C, Smith AR et al. Enterococcal bacteremia is associated with increased risk of mortality in recipients of allogeneic hematopoietic stem cell transplantation. Clin Infect Dis 2012; 55:764–770 [View Article]
     [Google Scholar]
  31. Green SL, Maddox JC, Huttenbach ED. Linezolid and reversible myelosuppression. JAMA 2001; 285:1291 [View Article]
     [Google Scholar]
  32. Averbuch D, Cordonnier C, Livermore DM, Mikulska M, Orasch C et al. Targeted therapy against multi-resistant bacteria in leukemic and hematopoietic stem cell transplant recipients: guidelines of the 4th European Conference on Infections in Leukemia (ECIL-4, 2011). Haematologica 2013; 98:1836–1847 [View Article]
     [Google Scholar]
  33. Bryant KA, Roberts AL, Rupp ME, Anderson JR, Lyden ER et al. Susceptibility of enterococci to daptomycin is dependent upon testing methodology. Diagn Microbiol Infect Dis 2013; 76:497–501 [View Article]
     [Google Scholar]
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Utilizing genomic analyses to investigate the first outbreak of vanA vancomycin-resistant Enterococcus in Australia with emergence of daptomycin non-susceptibility
J. Med. Microbiol. 68, 303 (2019); https://doi.org/10.1099/jmm.0.000916
/content/journal/jmm/10.1099/jmm.0.000916
/content/journal/jmm/10.1099/jmm.0.000916
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