Failure to detect carbapenem-resistant Escherichia coli producing OXA-48-like using the Xpert Carba-R assay®

Decousser, Jean‐Winoc; Poirel, Laurent; Desroches, Marine; Jayol, Aurélie; Denamur, Erick; Nordmann, Patrice

doi:10.1016/j.cmi.2014.09.006

Cited by 30 publications

(20 citation statements)

References 6 publications

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“…Similarly, it is possible to imagine the emergence of a novel carbapenem resistance gene that is not detected by the Xpert Carba-R. This is more than theoretical, as both our in-house PCR and the first iteration of the Xpert Carba-R were unable to detect the OXA-181 and OXA-232 variants of the OXA-48 genes (26,27). In contrast, the CIM method should detect any carbapenemase that hydrolyzes meropenem.…”

Section: Discussionmentioning

confidence: 97%

Use of Ancillary Carbapenemase Tests To Improve Specificity of Phenotypic Definitions for Carbapenemase-Producing Enterobacteriaceae

2017

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Carbapenemase-producing Enterobacteriaceae (CPE) are a significant threat to public health. In 2015, CDC revised the surveillance definition for CPE to include all Enterobacteriaceae resistant to any carbapenem tested. However, this definition is associated with poor specificity. We evaluated the performance of this definition, compared to carbapenemase PCR, for a collection of 125 Enterobacteriaceae. We also investigated the impact of ancillary testing for carbapenemase of isolates that met the CDC CPE surveillance definition. The two ancillary tests evaluated were the Xpert Carba-R assay, a molecular test, and the carbapenem inactivation method (CIM). Two variables were evaluated for the CIM: suspension of organisms in double-distilled water (ddH 2 O) versus tryptic soy broth (TSB) to incubate disks, and incubation of plates for 6 h versus 18 to 20 h. The sensitivity and specificity of the Carba-R assay were 100% compared to the results of in-house PCR. The sensitivities of the CIM performed with TSB were 94.6% when read at 6 h and 97.7% when read at 18 to 20 h; the sensitivities with ddH 2 O were 88.0% when read at 6 h and 93.0% when incubated for 18 to 20 h. The specificity was 100% for all variables tested. Without ancillary testing, the sensitivity of the CDC definition was 98.9% for CPE, and the specificity was 6.1%. Testing isolates that screened positive by the CDC definition with the Xpert Carba-R did not change the sensitivity, and it improved the specificity to 100%. Similarly, the use of the CIM (TSB and 18 to 20 h of incubation) to confirm screen-positive isolates resulted in a sensitivity of 95.6% and specificity of 100%.KEYWORDS Carba-R, Enterobacteriaceae, carbapenamase, carbapenem inactivation method C arbapenem-resistant Enterobacteriaceae (CRE), particularly those that are resistant due to carbapenemase production, are a significant threat to public health. Infections caused by CRE are associated with a high attributable mortality (1), and U.S. surveillance data have demonstrated a steady increase in the burden of disease caused by CRE since 2000 (2). The U.S. CRE epidemic is driven, in part, by Klebsiella pneumoniae isolates of sequence type (ST) 258 that express the K. pneumoniae carbapenemase (KPC) (3). Transfer of patients colonized or infected with this organism between health care institutions is thought to have led to the dissemination of ST 258 K. pneumoniae across the country. One particularly well documented outbreak described by the Centers for Disease Control and Prevention Epicenter Program demonstrated that patient transfers between 26 health care facilities across four counties lead to the spread of KPCproducing CRE to 40 patients over a 1-year period (4). Subsequent studies in this region documented that nearly 1 in 3 residents of long-term acute care facilities were colonized with KPC-producing CRE (5). CRE harboring other carbapenem-hydrolyzing enzymes, such as NDM, VIM, IMP, or the OXA-48 type, common in other areas of the world (6), are also spreading in the Unite...

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Section: Discussionmentioning

confidence: 97%

Use of Ancillary Carbapenemase Tests To Improve Specificity of Phenotypic Definitions for Carbapenemase-Producing Enterobacteriaceae

2017

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“…A modification of this assay, the immediate predicate device to the test evaluated in this study, added bla IMP and bla and was CE-IVD-cleared for use in the European markets (17). According to Tato et al, the revised assay demonstrated sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) that were all above 95% (17), but that study and other reports failed to detect bla (18,19) and bla (20), both of which have emerged as important variants of bla (19,21).…”

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Rapid Identification of Five Classes of Carbapenem Resistance Genes Directly from Rectal Swabs by Use of the Xpert Carba-R Assay

et al. 2017

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Carbapenemase-producing organisms (CPO) have been identified by global health leaders as an urgent threat. Detection of patients with gastrointestinal carriage of CPO is necessary to interrupt their spread within health care facilities. In this multisite study, we assessed the performance of the Xpert Carba-R test, a rapid real-time quantitative PCR (qPCR) assay that detects five families of carbapenemase genes (bla IMP , bla KPC , bla NDM , bla , and bla VIM ) directly from rectal swab specimens. Using dual swabs, specimens from 755 patients were collected and tested prospectively. An additional 432 contrived specimens were prepared by seeding well-characterized carbapenem-susceptible and -nonsusceptible strains into a rectal swab matrix and inoculating them onto swabs prior to testing. Antimicrobial susceptibility testing, broth enriched culture, and DNA sequencing were performed by a central laboratory blind to the Xpert Carba-R results. The Xpert Carba-R assay demonstrated a positive percentage of agreement (PPA) between 60 and 100% for four targets (bla KPC , bla NDM , bla VIM , and bla ) and a negative percentage of agreement (NPA) ranging between 98.9 and 99.9% relative to the reference method (culture and sequencing of any carbapenem-nonsusceptible isolate). There were no prospective bla IMP -positive samples. Contrived specimens demonstrated a PPA between 95 and 100% and an NPA of 100% for all targets. Testing of rectal swabs directly using the Xpert Carba-R assay is effective for rapid detection and identification of CPO from hospitalized patients.KEYWORDS Gram-negative bacteria, multidrug resistance, public health, surveillance studies T he rapid dissemination of carbapenemase-producing organisms (CPOs) throughout the world has raised concerns globally. Bacteria harboring these enzymes represent an infection control challenge for health care facilities and have proven to be a major public health threat (1-3).In the United States, most clinical infections due to CPOs have been attributed to organisms containing the Klebsiella pneumoniae carbapenemase (KPC) or the New Delhi metallo-␤-lactamase (NDM) (2). More recently, however, outbreaks due to organisms containing oxacillinase enzymes (e.g., OXA-48) have been reported, particularly in some European countries (4, 5). KPC-containing organisms have reached endemic levels in parts of Europe and Israel (6, 7), and NDM-containing organisms have been recovered throughout the Indian subcontinent (8) from clinical samples as well as from the

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“…Although still rare in France, the identification of these two variants rose from 0.8% in 2012 (8) to 3.4% in 2014 and 6.7% by mid-2015 of the total CPEs received at the French National Reference Centre for Antibiotic Resistance (L. Dortet, unpublished data). Accordingly, the use of the Xpert Carba-R kit as a unique screening method for CPE carriage led to the reports of several outbreaks caused by OXA-181-producing Enterobacteriaceae in France (9,10).…”

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confidence: 99%

Improvement of the Xpert Carba-R Kit for the Detection of Carbapenemase-Producing Enterobacteriaceae

Dortet

Fusaro

Naas

2016

Antimicrob Agents Chemother

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The Xpert Carba-R kit, version 2 (v2), which has been improved for the efficient detection of bla OXA-181 and bla OXA-232 genes, was tested on a collection of 150 well-characterized enterobacterial isolates that had a reduced susceptibility to carbapenems. The performance of the Xpert Carba-R v2 was high, as it was able to detect the five major carbapenemases (NDM, VIM, IMP, KPC, and OXA-48). Thus, it is now well adapted to the carbapenemase-producing Enterobacteriaceae epidemiology of many countries worldwide. Carbapenemase-producing Enterobacteriaceae (CPEs) have been increasingly reported worldwide (1). The most clinically relevant carbapenemases encountered in Enterobacteriaceae belong to Ambler class A (KPC type); Ambler class B or metallo-␤-lactamases (MBLs), such as IMP, VIM, and NDM types; or Ambler class D (OXA-48-like) (1). In the United States and Europe, a mixture of KPC, NDM, VIM, and OXA-48-like carbapenemases dominates (1), while IMP-producing Enterobacteriaceae are more prevalent in the Far East (2). Carbapenem resistance may be the result of combined mechanisms of outer-membrane permeability defect (e.g., porin defect) and noncarbapenemase ␤-lactamases (e.g., acquired or overexpressed chromosome-encoded cephalosporinase and extended-spectrum ␤-lactamases) (1). However, it was recently demonstrated that despite having identical MICs for carbapenems, carbapenemase-producing Klebsiella pneumoniae exhibit a marked inoculum effect and were more resistant to the bactericidal effect of meropenem than were non-carbapenemase-producing K. pneumoniae (3). The finding suggested that MIC measurements alone are not sufficient to predict therapeutic efficacy of carbapenems against CPE and that the rapid detection of carbapenemase production is essential for the guidance of antimicrobial treatment (3). Finally, CPEs are known to be highly proficient in disseminating and causing outbreaks through highrisk lineages (e.g., KPC-producing K. pneumoniae ST258), and successful plasmids (e.g., IncL OXA-48 plasmid) (4, 5). Therefore, rapid confirmation of carbapenemase production is essential not only for effective therapy but also for the prompt implementation of infection control measures capable of preventing CPE dissemination (6).Molecular diagnostic assays have been increasingly used for the rapid screening of patients for carbapenemase producers directly from rectal swabs (7). Most of them can detect the four main carbapenemases (KPC, NDM, VIM, and OXA-48-like), which represent Ͼ95% of the carbapenemases produced by Enterobacteriaceae. The Xpert Carba-R kit (Cepheid, Sunnyvale, CA, USA) is the only commercially available assay that can also detect IMP-1 group producers (7). However, the Xpert Carba-R kit did not detect some OXA-48 variants, e.g., OXA-181 and OXA-232. Although still rare in France, the identification of these two variants rose from 0.8% in 2012 (8) to 3.4% in 2014 and 6.7% by mid-2015 of the total CPEs received at the French National Reference Centre for Antibiotic Resistance (L. Dortet, unpublishe...

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Failure to detect carbapenem-resistant Escherichia coli producing OXA-48-like using the Xpert Carba-R assay®

Cited by 30 publications

References 6 publications

Use of Ancillary Carbapenemase Tests To Improve Specificity of Phenotypic Definitions for Carbapenemase-Producing Enterobacteriaceae

Use of Ancillary Carbapenemase Tests To Improve Specificity of Phenotypic Definitions for Carbapenemase-Producing Enterobacteriaceae

Rapid Identification of Five Classes of Carbapenem Resistance Genes Directly from Rectal Swabs by Use of the Xpert Carba-R Assay

Improvement of the Xpert Carba-R Kit for the Detection of Carbapenemase-Producing Enterobacteriaceae

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