Comparison of clinical methods for detecting carbapenem-resistant Enterobacteriaceae

Abstract

We evaluated detection of carbapenem-resistant <i>Enterobacteriaceae</i> (CRE) by routine minimal inhibitory concentration (MIC) testing, polymerase chain reaction (PCR) using Xpert® Carba-R assay, hydrolysis of ertapenem and imipenem detected by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS), and hydrolysis by colorimetry using the EPI-CRE assay. Ninety-six <i>Enterobacteriaceae</i> isolates possessing carbapenemase genes and 29 carbapenem-susceptible <i>Enterobacteriaceae</i> were available for testing. The sensitivity and specificity of each assay was determined. For sensitivity, discrepant results from each assay compared to reference genotype were arbitrated with MIC and/ or PCR testing to assess loss of plasmid-mediated resistance. Xpert Carba-R was evaluated for resistance genes in their FDA claim (i.e., the genes encoding KPC; NDM; VIM; IMP; and OXA-48). The sensitivity for the assays was: MIC (N=96), 96.8%, (discrepant analysis to 98.9% [2 cured plasmids]); Xpert Carba-R (N=85), 97.6% (discrepant analysis to 100% % [2 cured plasmids]); EPI-CRE (N=96), 91.7% (discrepant analysis to 91.7%); MALDI-TOF MS (N=96) ertapenem hydrolysis using Compass software for interpretation (2 h incubation), 92.7% (discrepant analysis to 94.7% % [2 cured plasmids]); MALDI-TOF MS (N=96) imipenem hydrolysis (1 h incubation), 97.9% (discrepant analysis to 98.9% % [1 cured plasmid]). The specificity for each assay was: MIC (N=29), 100%; EPI-CRE (N=29), 96.6%; MALDI-TOF MS ertapenem hydrolysis (N=29), 100%; MALDI-TOF MS imipenem hydrolysis (N=29), 96.6%. All isolates tested to ensure specificity demonstrated susceptible MIC results for carbapenems and did not qualify for testing with Xpert Carba-R. No single assay detected all of the known genetic markers of carbapenem hydrolysis.