Identification of gram-negative bacteria and genetic resistance determinants from positive blood culture broths by use of the verigene gram-negative blood culture multiplex microarray-based molecular assay

Nathan A. Ledeboer, Bert K. Lopansri, Neelam Dhiman, Robert Cavagnolo, Karen C. Carroll, Paul Granato, Richard Thomson, Susan M. Butler-Wu, Heather Berger, Linoj Samuel, Preeti Pancholi, Lettie Swyers, Glen T. Hansen, Nam Tran, Christopher R Polage, Kenneth S. Thomson, Nancy D. Hanson, Richard Winegar, Blake W. Buchan

Research output: Contribution to journalArticlepeer-review

77 Scopus citations

Abstract

Bloodstream infection is a serious condition associated with significant morbidity and mortality. The outcome of these infections can be positively affected by the early implementation of effective antibiotic therapy based on the identification of the infecting organism and genetic markers associated with antibiotic resistance. In this study, we evaluated the microarray-based Verigene Gram-negative blood culture (BC-GN) assay in the identification of 8 genus or species targets and 6 genetic resistance determinants in positive blood culture broths. A total of 1,847 blood cultures containing Gram-negative organisms were tested using the BC-GN assay. This comprised 729 prospective fresh, 781 prospective or retrospective frozen, and 337 simulated cultures representing 7 types of aerobic culture media. The results were compared to those with standard bacterial culture and biochemical identification with nucleic acid sequence confirmation of the resistance determinants. Among monomicrobial cultures, the positive percent agreement (PPA) of the BC-GN assay with the reference method was as follows; Escherichia coli, 100%; Klebsiella pneumoniae, 92.9%; Klebsiella oxytoca, 95.5%; Enterobacter spp., 99.3%; Pseudomonas aeruginosa, 98.9%; Proteus spp., 100%; Acinetobacter spp., 98.4%; and Citrobacter spp., 100%. All organism identification targets demonstrated>99.5% negative percent agreement (NPA) with the reference method. Of note, 25/26 cultures containing K. pneumoniae that were reported as not detected by the BC-GN assay were subsequently identified as Klebsiella variicola. The PPA for identification of resistance determinants was as follows; blaCTX-M, 98.9%; blaKPC, 100%; blaNDM, 96.2%; blaOXA, 94.3%; blaVIM, 100%; and blaIMP, 100%. All resistance determinant targets demonstrated>99.9% NPA. Among polymicrobial specimens, the BC-GN assay correctly identified at least one organism in 95.4% of the broths and correctly identified all organisms present in 54.5% of the broths. The sample-to-result processing and automated reading of the detection microarray results enables results within 2 h of culture positivity.

Original languageEnglish (US)
Pages (from-to)2460-2472
Number of pages13
JournalJournal of Clinical Microbiology
Volume53
Issue number8
DOIs
StatePublished - Aug 1 2015

ASJC Scopus subject areas

  • Microbiology (medical)

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