(175 days)
The Xpert® Carba-R Assay, performed on the GeneXpert® Instrument Systems, is a qualitative in vitro diagnostic test for the detection and differentiation of the blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP gene sequences associated with carbapenem-non-susceptible pure colonies of Enterobacteriaceae, Acinetobacter baumannii, or Pseudomonas aeruginosa grown on blood agar or MacConkey agar. The test utilizes automated real-time polymerase chain reaction (PCR).
A negative Xpert Carba-R Assay result does not preclude the presence of other resistance mechanisms. The Xpert Carba-R Assay should be used in conjunction with other laboratory tests including phenotypic antimicrobial susceptibility testing. The Xpert Carba-R Assay is intended as an aid for infection control in detecting and differentiating genetic markers of resistance to monitor the spread of carbapenem-non-susceptible organisms in healthcare settings. The Xpert Carba-R Assay is not intended to guide or monitor treatment for carbapenem-non-susceptible bacterial infections.
The Xpert Carba-R Assay is an automated real-time polymerase chain reaction (PCR) in vitro diagnostic test for qualitative detection of the blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP gene sequences from isolates of pure cultures of carbapenem-non-susceptibility gram-negative bacteria. The Xpert Carba-R Assay is intended as an aid for infection control for monitoring the spread of carbapenem-non-susceptible organisms in healthcare settings.
The Xpert Carba-R Assay is performed on the Cepheid GeneXpert® Instrument Systems (GeneXpert Dx, GeneXpert Infinity-48, GeneXpert Infinity-48s, and GeneXpert Infinity-80 systems). The GeneXpert Instrument System platform automates sample preparation, amplification and real-time detection.
The GeneXpert Instrument Systems require the use of single-use, disposable cartridges (the Xpert Carba-R cartridges) that hold the PCR reagents and host the PCR process. Because the cartridges are self-contained and specimens never come into contact with working parts of the instrument modules, cross-contamination between samples is minimized.
The Xpert Carba-R Assay cartridges contain reagents for the detection of blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP gene sequences. A Sample Processing Control (SPC) and a Probe Check Control (PCC) are controls utilized by the GeneXpert Instrument System platform. The SPC is present to control for adequate processing of the target bacteria and to monitor the presence of inhibitors in the real-time PCR reaction to reduce the possibility of false negative results. The PCC verifies reagent rehydration, real-time PCR tube filling in the cartridge, probe integrity, and dye stability.
The single-use, multi-chambered fluidic cartridges are designed to complete sample preparation and real-time PCR for the detection of the blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP gene sequences from isolates of pure cultures of carbapenem-nonsusceptibility gram-negative bacteria in approximately 50 minutes. The GeneXpert Instrument Systems, comprised of the GeneXpert Dx Systems and the GeneXpert Infinity Systems, have 1 to 80 randomly accessible modules, depending upon the instrument, that are each capable of performing separate sample processing and real-time PCR and RT-PCR tests. Each module contains a syringe drive for dispensing fluids (i.e., the syringe drive activates the plunger that works in concert with the rotary valve in the cartridge to move fluids between chambers), an ultrasonic horn for lysing cells or spores, and a proprietary I-CORE® thermocycler for performing real-time PCR and RT-PCR and detection.
The bacterial isolates from culture are placed into a sample reagent. The sample is transferred to the sample chamber of the disposable fluidic cartridge (the Xpert Carba-R cartridge). The user initiates a test from the system user interface and places the cartridge into the GeneXpert instrument platform, which performs hands-off real-time, multiplex PCR for detection of the blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP gene sequences. The results are automatically generated at the end of the process in a report that can be viewed and printed.
Here's a summary of the acceptance criteria and study findings for the Xpert Carba-R Assay, based on the provided document:
1. Table of Acceptance Criteria and Reported Device Performance
The document does not explicitly state pre-defined acceptance criteria (e.g., "Sensitivity must be >90%"). Instead, it presents the results of the clinical study as evidence of the device's performance. For clarity, I will interpret the observed performance as the de facto acceptance criteria demonstrated by the study.
| Metric (Target) | Acceptance Criteria (from study results) | Reported Device Performance (Blood Agar) | Reported Device Performance (MacConkey Agar) |
|---|---|---|---|
| Overall Sensitivity (per isolate) | 100.0% (interpreted from 99.0-100% CI) | 100.0% (95% CI: 99.0-100) | 100% (95% CI: 99.0-100) |
| Overall Specificity (per isolate) | 98.1% (interpreted from 93.2-99.5% CI) | 98.1% (95% CI: 93.2-99.5) | 97.1% (95% CI: 91.8-99.0) |
| IMP Sensitivity (per target) | 100% (interpreted from 91.2-100% CI) | 100% (95% CI: 91.2-100) | 100% (95% CI: 91.2-100) |
| IMP Specificity (per target) | 99.8% (interpreted from 98.7-100% CI) | 99.8% (95% CI: 98.7-100) | 99.8% (95% CI: 98.7-100) |
| VIM Sensitivity (per target) | 100% (interpreted from 95.5-100% CI) | 100% (95% CI: 95.5-100) | 100% (95% CI: 95.5-100) |
| VIM Specificity (per target) | 99.7% (interpreted from 98.5-100% CI) | 99.7% (95% CI: 98.5-100) | 99.7% (95% CI: 98.5-100) |
| NDM Sensitivity (per target) | 100% (interpreted from 95.3-100% CI) | 100% (95% CI: 95.3-100) | 100% (95% CI: 95.3-100) |
| NDM Specificity (per target) | 100% (interpreted from 99.0-100% CI) | 100% (95% CI: 99.0-100) | 99.7% (95% CI: 98.6-100) |
| KPC Sensitivity (per target) | 100% (interpreted from 95.6-100% CI) | 100% (95% CI: 95.6-100) | 100% (95% CI: 95.6-100) |
| KPC Specificity (per target) | 99.7% (interpreted from 98.5-100% CI) | 99.7% (95% CI: 98.5-100) | 100% (95% CI: 99.0-100) |
| OXA-48 Sensitivity (per target) | 100% (interpreted from 95.9-100% CI) | 100% (95% CI: 95.9-100) | 100% (95% CI: 95.9-100) |
| OXA-48 Specificity (per target) | 100% (interpreted from 99.0-100% CI) | 100% (95% CI: 99.0-100) | 100% (95% CI: 99.0-100) |
| Analytical Specificity (Cross-reactivity) | 100% against non-target organisms | 100% | 100% |
| Valid Reporting Rate | 100% (interpreted from 934/934) | 100% (934/934) | 100% (934/934) |
| Reproducibility (Total Agreement by Sample) | Generally >98-100% | Ranges from 98.6% to 100% depending on the specific target/sample. | Ranges from 98.6% to 100% depending on the specific target/sample. |
2. Sample Size Used for the Test Set and Data Provenance
- Sample Size (Clinical Study Test Set): A total of 467 eligible isolates were included in the final dataset for clinical performance analysis. These consisted of 410 clinical stock isolates and 57 fresh isolates.
- Data Provenance: The isolates were sourced from a multi-site investigational study. The document does not specify the country of origin of the data, but the context of an FDA submission suggests it could be primarily US-based or from international sites participating in studies for FDA clearance. The study used both retrospective (clinical stock isolates) and prospective (fresh isolates) data.
3. Number of Experts Used to Establish the Ground Truth for the Test Set and the Qualifications of Those Experts
The document does not explicitly state the "number of experts" or their specific "qualifications" for establishing ground truth. Instead, the ground truth for the clinical study was established by reference bi-directional sequencing of the amplified DNA target, which is a highly standardized and objective molecular method. For discordant results, discrepant testing was performed using the same bi-directional sequencing method. This means the "ground truth" relies on robust analytical methods rather than subjective expert consensus.
4. Adjudication Method for the Test Set
The document describes the following adjudication method:
- For isolates with discordant results between the Xpert Carba-R Assay and initial reference sequencing (performed locally), discrepant testing was performed using bi-directional sequencing on isolates from MacConkey agar plates, and the results are footnoted in the performance tables.
- For the initial reference sequencing, if "no bands were shown on the Bioanalyzer for any of the five target genes," the isolate was "not sent for sequence analysis and the reference method result was considered negative for the five target genes." If bands were shown, the amplicon was sent to an independent laboratory for reference bi-directional sequencing analysis.
This implies a hierarchical adjudication where the primary reference method is bi-directional sequencing, with a secondary review/confirmation using the same method for discordant results.
5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done, If So, What Was the Effect Size of How Much Human Readers Improve with AI vs. Without AI Assistance
This question is not applicable to this device. The Xpert Carba-R Assay is an automated in vitro diagnostic test for detecting genetic sequences. It is a standalone algorithm (molecular assay) that provides a qualitative result (DETECTED/NOT DETECTED) and does not involve human readers interpreting images or data that an AI might assist with. Therefore, an MRMC comparative effectiveness study involving human readers and AI assistance was not performed.
6. If a Standalone (i.e., algorithm only without human-in-the-loop performance) Was Done
Yes, a standalone study was done. The entire clinical performance evaluation described compares the Xpert Carba-R Assay's automated results directly against the reference standard (bi-directional sequencing). The device itself is designed for "hands-off real-time, multiplex PCR" with "results automatically generated." This inherently means its performance was evaluated as a standalone algorithm without human intervention in the result generation or interpretation phase beyond the initial sample preparation.
7. The Type of Ground Truth Used (Expert Consensus, Pathology, Outcomes Data, etc.)
The primary type of ground truth used for the clinical performance study was molecular reference sequencing (bi-directional DNA sequencing) of the amplified DNA target. This is a highly objective and analytical method to determine the presence or absence of the target gene sequences.
8. The Sample Size for the Training Set
The document does not explicitly describe a separate "training set" for an algorithm in the way machine learning algorithms typically use them. This is a molecular diagnostic assay, not an AI/machine learning model. The initial development and optimization of the assay would have involved various analytical studies (e.g., analytical reactivity, analytical specificity, limit of detection, etc.) using numerous characterized strains, but these are not typically referred to as a "training set" in the context of molecular assays as they are for AI algorithms. The "Analytical Reactivity (Inclusivity)" study used a panel of 71 well-characterized bacterial strains.
9. How the Ground Truth for the Training Set Was Established
As noted above, a traditional "training set" in the AI sense is not applicable here. For the analytical studies and assay development:
- Analytical Reactivity (Inclusivity): The ground truth for the 71 bacterial strains tested was established by their "well-characterized" nature and "variant information," likely through prior molecular characterization (e.g., sequencing) to confirm the presence and type of resistance markers.
- Analytical Specificity (Cross-reactivity): The ground truth for the 62 non-target bacterial strains and 24 commensal/enteric microorganisms was established by "Confirmed Resistance Mechanisms" (determined by individual PCR assays, DNA sequence analysis, or Check-Points array version CT102) or their known carbapenem susceptibility/resistance profiles.
These methods ensure the accurate molecular identification of the strains used in the analytical performance evaluations during the assay's development and validation.
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Food and Drug Administration 10903 New Hampshire Avenue Document Control Center - WO66-G609 Silver Spring, MD 20993-0002
March 7, 2016
CEPHEID JIM KELLY, Ph.D. EXECUTIVE DIRECTOR, REGULATORY AFFAIRS 904 CARIBBEAN DRIVE SUNNYVALE CA 94089-1189
Re: K152614
Trade/Device Name: Xpert® Carba-R Regulation Number: 21 CFR 866.1640 Regulation Name: Antimicrobial susceptibility test powder Regulatory Class: II Product Code: PMY, OOI Dated: February 5, 2016 Received: February 8, 2016
Dear Dr. Kelly:
We have reviewed your Section 510(k) premarket notification of intent to market the device referenced above and have determined the device is substantially equivalent (for the indications for use stated in the enclosure) to legally marketed predicate devices marketed in interstate commerce prior to May 28, 1976, the enactment date of the Medical Device Amendments, or to devices that have been reclassified in accordance with the provisions of the Federal Food. Drug. and Cosmetic Act (Act) that do not require approval of a premarket approval application (PMA). You may, therefore, market the device, subject to the general controls provisions of the Act. The general controls provisions of the Act include requirements for annual registration, listing of devices, good manufacturing practice, labeling, and prohibitions against misbranding and adulteration. Please note: CDRH does not evaluate information related to contract liability warranties. We remind you, however, that device labeling must be truthful and not misleading.
If your device is classified (see above) into either class II (Special Controls) or class III (PMA), it may be subject to additional controls. Existing major regulations affecting your device can be found in the Code of Federal Regulations, Title 21. Parts 800 to 898. In addition, FDA may publish further announcements concerning your device in the Federal Register.
Please be advised that FDA's issuance of a substantial equivalence determination does not mean that FDA has made a determination that your device complies with other requirements of the Act or any Federal statutes and regulations administered by other Federal agencies. You must comply with all the Act's requirements, including, but not limited to: registration and listing (21 CFR Part 807); labeling (21 CFR Parts 801 and 809); medical device reporting (reporting of medical device-related adverse events) (21 CFR 803); good manufacturing practice requirements as set forth in the quality systems (QS) regulation (21 CFR Part 820); and if applicable, the electronic product radiation control provisions (Sections 531-542 of the Act); 21 CFR 1000-1050.
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If you desire specific advice for your device on our labeling regulations (21 CFR Parts 801 and 809), please contact the Division of Industry and Consumer Education at its toll-free number (800) 638 2041 or (301) 796-7100 or at its Internet address
http://www.fda.gov/MedicalDevices/Resourcesfor You/Industry/default.htm. Also, please note the regulation entitled, "Misbranding by reference to premarket notification" (21 CFR Part 807.97). For questions regarding the reporting of adverse events under the MDR regulation (21 CFR Part 803), please go to
http://www.fda.gov/MedicalDevices/Safety/ReportaProblem/default.htm for the CDRH's Office of Surveillance and Biometrics/Division of Postmarket Surveillance.
You may obtain other general information on your responsibilities under the Act from the Division of Industry and Consumer Education at its toll-free number (800) 638-2041 or (301) 796-7100 or at its Internet address
http://www.fda.gov/MedicalDevices/ResourcesforYou/Industry/default.htm.
Sincerely yours,
Ribhi Shawar -S
For Uwe Scherf, M.Sc., Ph.D. Director Division of Microbiology Devices Office of In Vitro Diagnostics and Radiological Health Center for Devices and Radiological Health
Enclosure
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Indications for Use
510(k) Number (if known)
K152614
Device Name
Xpert Carba-R
Indications for Use (Describe)
The Xpert® Carba-R Assay, performed on the GeneXpert® Instrument Systems, is a qualitative in vitro diagnostic test for the detection and differentiation of the blaχρι, blaკγι blaკγൂ and blânup gene sequences associated with carbapenem-non-susceptible pure colonies of Enterobacteriaceae, Acinetobacter baumannii, or Pseudomonas aeruginosa grown on blood agar or MacConkey agar. The test utilizes automated real-time polymerase chain reaction (PCR).
A negative Xpert Carba-R Assay result does not presence of other resistance mechanisms. The Xpert Carba-R Assay should be used in conjunction with other laboratory tests including phenotypic antimicrobial susceptibility testing. The Xpert Carba-R Assay is intended as an aid for infection control in detecting and differentiating genetic markers of resistance to monitor the spread of carbapenem-non-susceptible organisms in healthcare settings. The Xpert Carba-R Assay is not intended to quide or monitor treatment for carbapenem-non-susceptible bacterial infections.
| Type of Use (Select one or both, as applicable) | |
|---|---|
| Prescription Use (Part 21 CFR 801 Subpart D) | Over-The-Counter Use (21 CFR 801 Subpart C) |
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510(k) Summary
As required by 21 CFR Section 807.92(c).
| Submitted by: | Cepheid904 Caribbean DriveSunnyvale, CA 90489Phone number: (847) 228-3299Fax number: (847) 890-6589 |
|---|---|
| Contact: | Scott A. Campbell, PhD, MBA |
| Date of Preparation: | March 2, 2016 |
| Device: | |
| 510(k) Number: | K152614 |
| Trade name: | Xpert® Carba-R |
| Common name: | Xpert Carba-R Assay |
| Type of Test: | Qualitative nucleic acid amplification test of the blaKPC, blaNDM,blaVIM, blaOXA-48, and blaIMP gene sequences from isolates ofpure cultures of carbapenem-non-susceptibility gram-negativebacteria |
| Classification: | II |
| Regulation number | 866.1640 |
| Classification name:Product code: | Antimicrobial susceptibility test powderPMY, OOI |
| ClassificationAdvisory Panel | Microbiology (83) |
| Prescription Use | Yes |
| Predicate DeviceAssay: | Cepheid Xpert® vanA[510(k) #K092953] |
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Device Description:
The Xpert Carba-R Assay is an automated real-time polymerase chain reaction (PCR) in vitro diagnostic test for qualitative detection of the blaker, blaym, blaym, blagxa-a8, and blang gene sequences from isolates of pure cultures of carbapenem-non-susceptibility gram-negative bacteria. The Xpert Carba-R Assay is intended as an aid for infection control for monitoring the spread of carbapenem-non-susceptible organisms in healthcare settings.
The Xpert Carba-R Assay is performed on the Cepheid GeneXpert® Instrument Systems (GeneXpert Dx, GeneXpert Infinity-48, GeneXpert Infinity-48s, and GeneXpert Infinity-80 systems). The GeneXpert Instrument System platform automates sample preparation, amplification and real-time detection.
The GeneXpert Instrument Systems require the use of single-use, disposable cartridges (the Xpert Carba-R cartridges) that hold the PCR reagents and host the PCR process. Because the cartridges are self-contained and specimens never come into contact with working parts of the instrument modules, cross-contamination between samples is minimized.
The Xpert Carba-R Assay cartridges contain reagents for the detection of blaker, blayDM. blaym, blaoxa-as, and blansp gene sequences. A Sample Processing Control (SPC) and a Probe Check Control (PCC) are controls utilized by the GeneXpert Instrument System platform. The SPC is present to control for adequate processing of the target bacteria and to monitor the presence of inhibitors in the real-time PCR reaction to reduce the possibility of false negative results. The PCC verifies reagent rehydration, real-time PCR tube filling in the cartridge, probe integrity, and dye stability.
The single-use, multi-chambered fluidic cartridges are designed to complete sample preparation and real-time PCR for the detection of the blakpc, blaNDM, blaviM, blaoxA-48, and blamp gene sequences from isolates of pure cultures of carbapenem-nonsusceptibility gram-negative bacteria in approximately 50 minutes. The GeneXpert Instrument Systems, comprised of the GeneXpert Dx Systems and the GeneXpert Infinity Systems, have 1 to 80 randomly accessible modules, depending upon the instrument, that are each capable of performing separate sample processing and real-time PCR and RT-PCR tests. Each module contains a svringe drive for dispensing fluids (i.e., the syringe drive activates the plunger that works in concert with the rotary valve in the cartridge to move fluids between chambers), an ultrasonic horn for lysing cells or spores, and a proprietary I-CORE® thermocycler for performing real-time PCR and RT-PCR and detection.
The bacterial isolates from culture are placed into a sample reagent. The sample is transferred to the sample chamber of the disposable fluidic cartridge (the Xpert Carba-R cartridge). The user initiates a test from the system user interface and places the cartridge into the GeneXpert instrument platform, which performs hands-off real-time, multiplex PCR for detection of the blaker, bland, blaym, blagx,-48, and blange gene sequences. The results are automatically generated at the end of the process in a report that can be viewed and printed.
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Device Intended Use:
The Xpert® Carba-R Assay, performed on the GeneXpert® Instrument Systems, is a qualitative in vitro diagnostic test for the detection and differentiation of the blakpor blands blayms blacks and bland gene sequences associated with carbapenem-nonsusceptible pure colonies of Enterobacteriaceae, Acinetobacter baumannii, or Pseudomonas aeruginosa grown on blood agar or MacConkey agar. The test utilizes automated real-time polymerase chain reaction (PCR).
A negative Xpert Carba-R Assay result does not preclude the presence of other resistance mechanisms. The Xpert Carba-R Assay should be used in conjunction with other laboratory tests including phenotypic antimicrobial susceptibility testing. The Xpert Carba-R Assay is intended as an aid for infection control in detecting and differentiating genetic markers of resistance to monitor the spread of carbapenem-nonsusceptible organisms in healthcare settings. The Xpert Carba-R Assay is not intended to guide or monitor treatment for carbapenem-non-susceptible bacterial infections.
Substantial Equivalence:
The Cepheid Xpert Carba-R Assay is substantially equivalent to the Xpert® vanA, 510(k) #K092953. The Xpert Carba-R Assay and the Xpert vanA Assay both detect target gene sequences from antibiotic-resistant bacteria and use real-time PCR amplification and fluorogenic target-specific hybridization detection. The performance of the Xpert Carba-R Assay was determined in a multi-site clinical study in which the performance of the Xpert Carba-R Assay was evaluated relative to reference DNA sequence analysis. The results of the study demonstrated that the performance of the Xpert Carba-R Assay is substantially equivalent to the predicate device.
Table 5-1 shows the similarities and differences between the Xpert Carba-R Assay and the predicate device.
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| Similarities | ||
|---|---|---|
| Item | Device | Predicate Device |
| Cepheid Xpert Carba-R Assay | Cepheid Xpert vanA AssayK092953 | |
| General IntendedUse | The Xpert® Carba-R Assay,performed on the GeneXpert®Instrument Systems, is aqualitative in vitro diagnostictest for the detection anddifferentiation of the bla KPC,bla NDM, bla VIM, bla OXA-48, andbla IMP gene sequencesassociated with carbapenem-non-susceptible pure colonies ofEnterobacteriaceae ,Acinetobacter baumannii , orPseudomonas aeruginosagrown on blood agar orMacConkey agar. The testutilizes automated real-timepolymerase chain reaction(PCR) .A negative Xpert Carba-RAssay result does not precludethe presence of other resistancemechanisms. The Xpert®Carba-R Assay should be usedin conjunction with otherlaboratory tests includingphenotypic antimicrobialsusceptibility testing. The XpertCarba-R Assay is intended asan aid for infection control indetecting and differentiatinggenetic markers of resistanceto monitor the spread ofcarbapenem-non-susceptibleorganisms in healthcaresettings. The Xpert Carba-RAssay is not intended to guideor monitor treatment forcarbapenem-non-susceptiblebacterial infections. | The Cepheid Xpert® vanA Assayperformed in the GeneXpert® DxSystem is a qualitative in vitrodiagnostic test designed for rapiddetection of the vanA genesequence associated withvancomycin resistance inbacteria obtained from rectalswab specimens from patients atrisk for intestinal colonizationwith vancomycin-resistantbacteria . The test utilizesautomated real-timepolymerase chain reaction(PCR) to detect the vanA genethat is frequently associated withvancomycin-resistant enterococci(VRE). The Xpert vanA Assay isintended to aid in the recognition,prevention, and control ofvancomycin resistant organismsthat colonize patients inhealthcare settings. The XpertvanA Assay is not intended todiagnose infections caused byvancomycin-resistant bacterianor to guide or monitor treatmentfor vancomycin-resistantbacterial infections. Concomitantcultures are necessary to recoverorganisms for confirmatoryidentification of vancomycin-resistant bacteria, antimicrobialsusceptibility testing, and forepidemiological typing. |
| Similarities | ||
| Item | Device | Predicate Device |
| Cepheid Xpert Carba-R Assay | Cepheid Xpert vanA AssayK092953 | |
| Type of test | Same | Qualitative |
| TechnologicalPrinciples | Same | Fully-automated nucleic acidamplification (DNA); real-timePCR |
| Test Cartridge | Same | Disposable single-use, multi-chambered fluidic cartridge |
| Probes | Same | TaqMan® Probes |
| Controls | Same | Internal sample processingcontrol (SPC) and probecheck control (PCC)External controls available |
| InstrumentSystem | GeneXpert Instrument System(includes GeneXpert Dx,Infinity-48, Infinity-48s, andInfinity-80) | GeneXpert Dx |
| Time to obtaintest results | Approximately 50 minutes toresults | Approximately 45 minutes toresults |
| Interpretation oftest results | Diagnostic software of theGeneXpert Instrument System | Diagnostic software of theGeneXpert Dx |
| Laboratory Users | Operators in CLIA Moderate orHigh Complexity labs | Operators in CLIA Moderate orHigh Complexity labs |
| Differences | ||
| Item | New Device | Predicate Device |
| Cepheid Xpert Carba-R Assay | Cepheid Xpert vanA AssayK092953 | |
| Sample Type | Bacterial isolates from culture | Rectal swabs |
| Assay Targets | Detects blaKPC, blaNDM, blaVIM,blaOXA-48, and blaIMP genesequences | Detects gene sequences for thevanA encoded resistance tovancomycin/teicoplanin |
| Similarities | ||
| Item | Device | Predicate Device |
| Cepheid Xpert Carba-R Assay | Cepheid Xpert vanA AssayK092953 | |
| InstrumentSystem | GeneXpert Instrument System(includes GeneXpert Dx,Infinity-48, Infinity-48s, andInfinity-80) | GeneXpert Dx |
Table 5-1: Comparison of Similarities and Differences of the
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The Xpert Carba-R Assay has the same general intended use as the predicate device and has the same technological characteristics as the predicate device. The differences between the Xpert Carba-R Assay and the predicate device do not raise questions of safety and effectiveness. The clinical study demonstrates that the Xpert Carba-R Assay is acceptable for its intended use with inexperienced laboratory users and is substantially equivalent to the predicate device described above.
Non-Clinical Studies:
Analytical Reactivity (Inclusivity)
The analytical sensitivity of the Xpert Carba-R Assay was evaluated by testing a panel of 71 samples consisting of 11 blakec (KPC), 13 blandy (NDM), 11 blavm (VIM), 8 blaoxa-48 (OXA-48), 5 blaNDM/OXA-181 (NDM/OXA-181), 5 blaoxA-181 (OXA-181), 17 blann (IMP), and one blakecym (KPC/VIM) well-characterized bacterial strains (Table 5-2). Organisms were tested in replicates of four that were prepared by diluting 10 µL of 0.5 McFarland cell suspension for each bacterial strain in 5 mL of Xpert Carba-R Sample Reagent. Testing was performed using both blood agar and MacConkey plates. Xpert Carba-R Assay target genes were detected in 68 of 71 bacterial strains from both plates (Table 5-2). Xpert Carba-R Assay target DNA sequences were not detected in three bacterial strains as shown in Table 5-2. In one of the three bacterial strains, the IMP-13 gene was not detected by the assay, although it was predicted to be detected by in silico analysis. In two of the three bacterial strains, theIMP-7 and IMP-14 genes that were not detected by the assay were also not predicted to be detected by in silico analysis. See the Limitations section in the package insert.
The variants detected, and predictions for detecting other subtypes of each resistance gene based on in silico analysis, are presented in Table 5-3.
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| Strain ID | Organism | Resistance Markerwith variantinformation |
|---|---|---|
| NCTC 13438 | Klebsiella pneumoniae | KPC-3 |
| 31551 | Klebsiella pneumoniae | KPC-4 |
| ATCC BAA-1705 | Klebsiella pneumoniae | KPC-2 |
| CFVL | Enterobacter cloacae | KPC-2 |
| KBM18 | Enterobacter aerogenes | KPC-2 |
| COL | Escherichia coli | KPC-2 |
| BM9 | Klebsiella pneumoniae | KPC-3 |
| CGNC | Serratia marcescens | KPC-2 |
| PA3 | Pseudomonas aeruginosa | KPC-2 |
| COL | Pseudomonas aeruginosa | KPC-2 |
| GR-04/KP-69 | Klebsiella pneumoniae | KPC-2, VIM |
| 164-3 | Klebsiella oxytoca | KPC |
| NCTC 13437 | Pseudomonas aeruginosa | VIM-10 |
| NCTC 13439 | Klebsiella pneumoniae | VIM-1 |
| NCTC 13440 | Klebsiella pneumoniae | VIM-1 |
| 758 | Pseudomonas aeruginosa | VIM |
| N/A | Klebsiella pneumoniae | VIM |
| N/A | Pseudomonas aeruginosa | VIM |
| Col 1 | Pseudomonas aeruginosa | VIM-2 |
| BM19 | Serratia marcescens | VIM-2 |
| KOW7 | Escherichia coli | VIM-4 |
| DIH | Klebsiella pneumoniae | VIM-19 |
| MSH2014-3 | Enterobacter cloacae | VIM |
| NCTC 13443 | Klebsiella pneumoniae | NDM-1 |
| ATCC BAA-2146 | Klebsiella pneumoniae | NDM-1 |
| 34262 | Klebsiella pneumoniae | NDM |
| GEN | Acinetobacter baumannii | NDM-1 |
| 3047 | Enterobacter cloacae | NDM-1 |
| 7892 | Proteus mirabilis | NDM-1 |
| CAN | Salmonella spp. | NDM-1 |
| EGY | Acinetobacter baumannii | NDM-2 |
| I5 | Escherichia coli | NDM-4 |
| 405 | Escherichia coli | NDM-5 |
| CF-ABE | Citrobacter freundii | NDM |
| 73999 | Pseudomonas aeruginosa | NDM |
| 39365 | Providencia rettgeri | NDM-1 |
Table 5-2: Analytical Reactivity of the Xpert Carba-R Assay
{10}------------------------------------------------
| Strain ID | Organism | Resistance Marker with variant information |
|---|---|---|
| NCTC 13442 | Klebsiella pneumoniae | OXA-48 |
| OM11 | Klebsiella pneumoniae | OXA-48 |
| 501 | Enterobacter cloacae | OXA-48 |
| DUW | Klebsiella pneumoniae | OXA-48 |
| OM22 | Escherichia coli | OXA-48 |
| BOU | Enterobacter cloacae | OXA-48 |
| TUR | Enterobacter cloacae | OXA-48 |
| 11670 | Escherichia coli | OXA-48 |
| MSH2014-64 | Klebsiella pneumoniae | OXA-181 |
| MSH2014-72 | Escherichia coli | OXA-181 |
| B108A | Klebsiella pneumoniae | NDM, OXA-181 |
| C10192-DISCS | Enterobacter aerogenes | NDM, OXA-181 |
| KP-OMA3 | Klebsiella pneumoniae | NDM-1, OXA-181 |
| 166643 | Klebsiella pneumoniae | OXA-181 |
| 42194 | Klebsiella pneumoniae | OXA-181 |
| 1300920 | Klebsiella pneumoniae | NDM, OXA-181 |
| MSH2014-69 | Klebsiella pneumoniae | NDM, OXA-181 |
| 74 | Escherichia coli | OXA-181 |
| NCTC 13476 | Escherichia coli | IMP-1 |
| 695 | Acinetobacter baumannii | IMP-1 |
| 2340 | Enterobacter cloacae | IMP-1 |
| IMPBMI | Klebsiella pneumoniae | IMP-1 |
| 6852 | Klebsiella pneumoniae | IMP-1 |
| Yonsei_1 | Acinetobacter baumannii | IMP-1 |
| Yonsei_2 | Acinetobacter baumannii | IMP-1 |
| 70450-1 | Pseudomonas aeruginosa | IMP-1 |
| 3994 | Pseudomonas | IMP-10 |
| MKAM | Pseudomonas aeruginosa | IMP-1 |
| 5344 | Pseudomonas aeruginosa | IMP-2 |
| G029 | Salmonella spp | IMP-4 |
| 3985 | Pseudomonas aeruginosa | IMP-11 |
| 4032 | Pseudomonas aeruginosa | IMP-6 |
| 3424 | Pseudomonas aeruginosa | IMP-7 a,b |
| 32443 | Klebsiella pneumoniae | IMP-13 a |
| 92 | Pseudomonas aeruginosa | IMP-14 a, b |
a. Not detected by Xpert Carba-R (see Limitations in package insert).
b. IMP-7 and IMP-14 genes were not detected by the assay and were not predicted to be
detected by in silico analysis (see Limitations in package insert).
{11}------------------------------------------------
| Marker | Wet testing | Not tested but predicted tobe detected based on | |||
|---|---|---|---|---|---|
| (or TraditionalSubgroup) | No. ofSamples | Type(s)Detected | Type(s) notDetected | in silico analysis | |
| KPC | 12 | KPC-2, 3, 4 | -- | KPC-5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16 | |
| NDM | 18 | NDM-1, 2, 4,5 | -- | NDM-3, 6, 7, 8, 9 | |
| VIM | 12 | VIM-1, 2, 4,10, 19 | -- | VIM-5, 6, 7, 8, 9, 11, 12, 13,14, 15, 16, 17, 18, 20, 23, 24,25, 26, 27, 28, 29, 30, 31, 32,33, 34, 35, 36, 37, 38 | |
| OXA-48 | 18 | OXA-48,181(OXA-48variant) | -- | OXA-162, 163, 204, 232, 244,245, 247 | |
| IMP | 17 | IMP-1 (9strains), IMP-2, 4, 6, 10, 11 | IMP-7a,13b, 14a | IMP-3, 8, 9, 13b, 19, 20, 21,22, 24, 25, 27, 28, 30, 31, 33,37, 40, 42 |
Table 5-3: Summary of Variants Detected by Wet Testing or Predicted to be Detected Based on In Silico Analysis
a. IMP-7 and IMP-14 genes (Pseudomonas aeruginosa) were not detected by the assay and were not predicted to be detected by in silico analysis (see Limitations in package insert).
b. IMP-13 gene (Klebsiella pneumoniae): although predicted to be detected by in silico analysis, the IMP-13 gene was not detected by the assay (see Limitations in package insert).
Analytical Specificity (Cross-reactivity)
The analytical specificity of the Xpert Carba-R Assay was evaluated by testing a panel of 62 well-characterized bacterial strains of carbapenem-susceptible bacteria or bacteria with carbapenem non-susceptibility due to genes or mechanisms other than the Xpert Carba-R target genes (Table 5-4 and Table 5-5). Twenty-four commensal bacterial strains and other enteric microorganisms were also evaluated in the study (Table 5-6). Resistance mechanisms were determined by individual PCR assays, DNA sequence analysis, or Check-Points array version CT102.
Organisms were grown aerobically on blood agar and MacConkey agar plates or chocolate agar plates. Two cell suspensions equivalent to a 0.5 McFarland cell suspension were prepared from isolated colonies on each type of agar plate. Each organism was tested a total of four times (two replicates from each of two 0.5 McFarland cell suspensions per organism) from each plate.
{12}------------------------------------------------
The Xpert Carba-R Assay did not cross react with any of the organisms tested (Table 5-5, and Table 5-6). The analytical specificity of the assay was 100%.
| Ertapenem | Imipenem | Meropenem | |
|---|---|---|---|
| Susceptible | 19 | 30 | 24 |
| Intermediate | 0 | 8 | 4 |
| Resistant | 43 | 24 | 34 |
Table 5-4: Number of Carbapenem-susceptible and Non-susceptible Organisms for each Antibiotic
| Organism | Strain ID | Confirmed ResistanceMechanisms | Carbapenemsusceptibility (S/I/R)a | ||
|---|---|---|---|---|---|
| ETPa | IMPa | MEMa | |||
| Escherichia coli | NCTC 13441 | CTX-M (15) | S | S | S |
| Klebsiella pneumoniae | NCTC 13465 | CTX-M (25) | S | S | S |
| Enterobacter cloacae | Clinical isolate | OmpC/OmpF deficient | R | R | R |
| Citrobacter freundii | Clinical isolate | TEM (WT+164S) | S | S | S |
| Enterobacter cloacae | Clinical isolate | AmpC (ACT/MIR) | R | R | R |
| Klebsiella pneumoniae | kpn5 | CTX-M-2 | R | S | R |
| Klebsiella pneumoniae | kpn12 | TEM; SHV; CTX-M | R | R | R |
| Escherichia coli | eco1 | TEM; CTX-M-2 | R | R | R |
| Escherichia coli | Clinical isolate | CTX-M (2); TEM | R | S | S |
| Enterobacter cloacae | Clinical isolate | CTX-M (2); TEM | R | R | R |
| Serratia marcescens | Clinical isolate | CTX-M (2); TEM | S | S | S |
| Morganella morganii | fer29 | CTX-M (2); TEM | S | R | S |
| Proteus mirabilis | gut25 | CTX-M (2); TEM | S | R | S |
| Salmonella spp. | Clinical isolate | CTX-M (2); TEM | S | S | S |
| Shigella flexnerii | Clinical isolate | CTX-M (2); TEM | S | S | S |
| Enterobacter cloacae | PA_3 | AmpC; CTX-M-15; TEM | S | S | S |
| Klebsiella pneumoniae | Clinical isolate | SHV | S | S | S |
| Klebsiella pneumoniae | Clinical isolate | CTX-M (1, -type 15like); SHV | S | S | S |
| Klebsiella pneumoniae | 32598 | CTX-M (-1, -type 15like); SHV; TEM | R | I | R |
| Klebsiella pneumoniae | 33560 | CTX-M (15); SHV-11;TEM-1 | S | S | S |
| Organism | Strain ID | Confirmed ResistanceMechanisms | Carbapenemsusceptibility (S/I/R)a | ||
| ETPa | IMPa | MEMa | |||
| Klebsiella pneumoniae | 33603 | SHV-2 | R | I | R |
| Klebsiella pneumoniae | Clinical isolate | SHV-27 | S | S | S |
| Klebsiella pneumoniae | Clinical isolate | SHV (-5, -55); TEM | S | S | S |
| Klebsiella pneumoniae | 34430 | SHV; TEM; CTX-M-15 | S | S | S |
| Klebsiella pneumoniae | 34680 | TEM; CTX-M-2 | R | S | R |
| Klebsiella pneumoniae | 34732 | CTX-M (15); SHV; TEM | R | S | S |
| Enterobacter cloacae | PA_174 | GX-/Culture+; SHV; TEM | S | S | S |
| Enterobacter aerogenes | Clinical isolate | SHV (WT+238S+240K) | R | S | R |
| Enterobacter aerogenes | STU 669 | SHV (WT+238S+240K) | R | R | R |
| Escherichia coli | C3015 | AmpC (CMY II); TEM | R | R | R |
| Enterobacter aerogenes | RI_100 | AmpC (DHA); SHV | R | R | R |
| Klebsiella pneumoniae | B4A | SHV (WT + 238S +240K) | R | R | R |
| Klebsiella pneumoniae | B13A | SHV (WT + 238S +240K) | R | S | S |
| Enterobacter cloacae | RI_474 | AmpC (ACT/MIR) | R | I | I |
| Enterobacter amnigenus | B71 | AmpC (ACT/MIR) | R | R | R |
| Klebsiella pneumoniae | DD82A | SHV (WT + 238S + 240K) | R | S | R |
| Klebsiella pneumoniae | B100 | CTX-M (-1, type-15 like); SHV (WT+238S); TEM | R | S | R |
| Enterobacter cloacae | 135B | TEM | S | S | S |
| Klebsiella pneumoniae | B157 | SHV; TEM | R | R | R |
| Escherichia coli | T2914280 | CTX-M (-1, -15); TEM | R | S | R |
| Providencia stuartii | DD188 | TEM (104K + 164S) | R | I | I |
| Enterobacter cloacae | DD189 | AmpC (ACT/MIR) | R | S | S |
| Escherichia coli | B198B | CTX-M (-1, type -15 like); TEM | R | S | R |
| Klebsiella pneumoniae | T3019989-1 | CTX-M (-1, type-15 like); SHV | R | I | R |
| Klebsiella pneumoniae | T3019989-2 | CTX-M (-1, type-15 like); SHV | R | S | R |
| Enterobacter cloacae | ENC-THAI14 | VEB-1, TEM | S | S | S |
| Escherichia coli | CB154006 | CTX-M (9); TEM | R | I | I |
| Enterobacter cloacae | S35766 | AmpC(ACT/MIR) | S | S | S |
| Enterobacter cloacae | X1856910 | AmpC (ACT/MIR); TEM | R | I | I |
| Organism | Strain ID | Confirmed Resistance | Carbapenemsusceptibility (S/I/R)ª | ||
| Mechanisms | ETPa | IMPa | MEMª | ||
| Klebsiella pneumoniae | W3758164 | CTX-M (-1, -15 like);SHV; TEM. | R | I | R |
| Klebsiella pneumoniae | X2135758 | CTX-M (-1, -15 like);SHV | R | S | S |
| Klebsiella pneumoniae | W3809535 | CTX-M (-1, -15 like);SHV | R | R | R |
| Pseudomonas aeruginosa | CDC0064 | SPM | R | R | R |
| Serratia marcescens | CDC0099 | SME | R | R | R |
| Serratia marcescens | CDC0121 | SME | R | R | R |
| Serratia marcescens | CDC0122 | SME | R | R | R |
| Serratia marcescens | CDC0123 | SME | R | R | R |
| Serratia marcescens | CDC0124 | SME | R | R | R |
| Serratia marcescens | CDC0130 | SME | R | R | R |
| Serratia marcescens | CDC0131 | SME | R | R | R |
| Enterobacter cloacaegroup | CDC0132 | IMI | R | R | R |
| Enterobacter cloacaecomplex | CDC0164 | IMI | R | R | R |
Table 5-5: Cross-Reactivity Panel
{13}------------------------------------------------
{14}------------------------------------------------
S/I/R = Susceptible/Intermediate/Resistant, ETP = Ertapenem, IMP = Imipenem, MEM = Meropenem a.
| Organism | Strain ID |
|---|---|
| Escherichia coli | ATCC 25922 |
| Enterococcus faecalis | ATCC 29212 |
| Klebsiella pneumoniae | ATCC 700603 |
| Escherichia coli | ATCC 35218 |
| Staphylococcus aureus | ATCC 25923 |
| Pseudomonas aeruginosa | ATCC 27853 |
| Enterobacter cloacae | ATCC 700621 |
| Enterococcus faecium | ATCC 9756 |
| Klebsiella oxytoca | ATCC 13182 |
| Acinetobacter baumannii | ATCC BAA-747 |
| Citrobacter freundii | ATCC 33128 |
| Morganella morganii | ATCC 49948 |
| Stenotrophomonas maltophilia | ATCC 51331 |
| Citrobacter koseri | ATCC 27028 |
| Providencia stuartii | ATCC 49809 |
| Streptococcus agalactiae | CCUG 29780 / ATCC12401 |
{15}------------------------------------------------
| Organism | Strain ID |
|---|---|
| Enterobacter aerogenes | ATCC 51697 |
| Proteus mirabilis | ATCC 43071 |
| Acinetobacter spp. | CCUG 34787 |
| Citrobacter freundii | CCUG 418 |
| Corynebacterium diphtheriae | CCUG 33629 |
| Helicobacter pylori | CCUG 17874 |
| Listeria monocytogenes | CCUG 33548 |
| Providencia alcalifaciens | CCUG 6325 |
Carry-Over Contamination
A study was conducted to demonstrate that single-use, self-contained GeneXpert cartridges prevent carry-over contamination in negative samples run following very high positive samples. The study consisted of a negative sample processed in the same GeneXpert module immediately following a very high positive sample. The high positive sample is composed of inactivated E. coli cells containing a plasmid with an insert consisting of a synthetic oligonucleotide of the amplicon sequences from the five Xpert Carba-R target analyte genes (KPC, NDM, VIM, IMP and OXA-48 targets). Positive cells were diluted in Sample Reagent to a concentration of 1 x 100 CFU/mL. The testing scheme was repeated 50 times on two GeneXpert modules for a total of 102 tests (25 high positive samples per module and 26 negative samples per module). All 50 positive samples correctly reported all Xpert Carba-R targets as DETECTED. All 52 negative samples correctly reported all Xpert Carba-R targets as NOT DETECTED.
Clinical Studies
Clinical Performance
Performance characteristics of the Xpert Carba-R Assay with bacterial isolates were determined in a multi-site investigational study by comparing the Xpert Carba-R Assay to reference bi-directionalsequencing of the amplified DNA target. Study sampless included bacterial isolates grown from both blood agar and MacConkey agar.
To be included in the study, isolates must have been previously identified as Enterobacteriaceae, Pseudomonas aeruginosa, or Acinetobacter baumannii. For determination of sensitivity, isolates must have been either intermediate or resistant to meropenem, ertapenem and/or imipenem per CLSI M100-S24. Isolates of Pseudomonas aeruginosa or Acinetobacter baumannii must have been intermediate or resistant to either imipenem or meropenem. These organisms are intrinsically resistant to ertapenem. For evaluation of specificity, isolates may have been susceptible or resistant to meropenem, ertapenem, and imipenem per CLSI M100-S24. Pseudomonas aeruginosa and Acinetobacter baumannii isolates should have been susceptible to both imipenem and meropenem. Isolates were tested only once in the study.
A total of 489 isolates (431 clinical stock isolates and 58 fresh isolates) were initially enrolled in this clinical study, of which 485 were eligible for inclusion. The ineligible isolates included four isolates previously enrolled in the study.
{16}------------------------------------------------
From the 485 eligible isolates, 467 isolates (410 clinical stock isolates and 57 fresh isolates) were included in the final dataset used for the analyses presented in this report; two isolates were excluded because reference testing was not performed; and sixteen isolates were excluded because they were not identified as Enterobacteriaceae, A. baumannii, or P. aeruginosa.
For Xpert Carba-R Assay testing, well-isolated colonies that grew on each of the agar types were diluted to a 0.5 McFarland standard equivalent suspension using the direct colony suspension method per CLSI M07-A9.
For reference sequencing, DNA from culture isolates was purified, quantified, and amplified using primers specific to all 5 target genes that amplify larger regions than the assay targets and include the Xpert Carba-R primer sequences. The production of the appropriate size of amplification product was confirmed on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
If bands shown on the Bioanalyzer corresponded to the expected size of the amplicon from any of the five target genes detected by the Xpert Carba-R Assay, the amplicon for the isolate was sent to an independent laboratory for reference bi-directional sequencing analysis, validated for detection of the five targets in the Xpert Carba-R Assay. If no bands were shown on the Bioanalyzer for any of the five target genes, the isolate was not sent for sequence analysis and the reference method result was considered negative for the five target genes.
Multiple targets were detected by the Xpert Carba-R Assay in samples from ten isolates. The details are provided in Table 5-7, along with the reference sequencing result.
| Table 5-7. Isolates with Multiple Targets Detected | |||
|---|---|---|---|
| Isolate | AgarTypea | Targets Detected byXpert Carba-R Assay | Targets Detected byReference Sequencing |
| 1 | BA, MC | NDM, OXA-48 | NDM, OXA-48 |
| 2 | BA | VIM, KPC | VIM |
| 3 | BA, MC | NDM, OXA-48 | NDM, OXA-48 |
| 4 | BA, MC | NDM, OXA-48 | NDM, OXA-48 |
| 5 | BA, MC | NDM, OXA-48 | NDM, OXA-48 |
| 6 | BA, MC | NDM, OXA-48 | NDM, OXA-48 |
| 7 | BA, MC | NDM, OXA-48 | NDM, OXA-48 |
| 8 | BA, MC | NDM, OXA-48 | NDM, OXA-48 |
| 9 | BA, MC | NDM, OXA-48 | NDM, OXA-48 |
| 10 | BA, MC | NDM, OXA-48 | NDM, OXA-48 |
Table 5-7 Isolates with Multiple Targets Detected
a. BA=blood agar, MC=MacConkey agar
When tested with isolates from blood agar, the Xpert Carba-R Assay demonstrated an overall sensitivity and specificity of 100.0% (95% CI: 99.0-100) and 98.1% (95% CI: 93.2-99.5), respectively, relative to reference sequencing performed from the blood agar isolates (Table 5-8). The combined result was defined as positive for the Xpert Carba-R Assay if any of the targets were positive, and negative for the Xpert Carba-R Assay if all of the targets were negative.
{17}------------------------------------------------
Table 5-8: Xpert Carba-R (blood agar) vs. Reference Sequencing (isolate grown on blood agar) - Combined
| Target | N | TP | FP | TN | FN | Sensitivity %(95 CI) | Specificity %(95 CI) |
|---|---|---|---|---|---|---|---|
| Overall | 467 | 364a | 2a | 101 | 0 | 100.0%(99.0-100) | 98.1%(93.2-99.5) |
a. Combined results represent results by isolate. Multiple target results were observed for some isolates.
When tested with isolates from blood agar, the Xpert Carba-R Assay demonstrated a sensitivity and specificity of >99% for each of the five assay targets, relative to reference sequencing performed from the blood agar isolates (Table 5-9).
For isolates with discordant results between the Xpert Carba-R Assay and reference sequencing, discrepant testing was performed using bi-directional sequencing on isolates from MacConkey agar plates. Discrepant testing results are footnoted in Table 5-9 and Table 5-11.
Table 5-9: Xpert Carba-R (blood agar) vs. Reference Sequencing (isolate grown on blood agar) -
| Target | N | TP | FP | TN | FN | Sensitivity %(95 CI) | Specificity %(95 CI) |
|---|---|---|---|---|---|---|---|
| IMP | 467 | 40 | 1 a | 426 | 0 | 100%(91.2-100) | 99.8%(98.7-100) |
| VIM | 467 | 82 | 1 b | 384 | 0 | 100%(95.5-100) | 99.7%(98.5-100) |
| NDM | 467 | 78 | 0 | 389 | 0 | 100%(95.3-100) | 100%(99.0-100) |
| KPC | 467 | 84 | 1 c | 382 | 0 | 100%(95.6-100) | 99.7%(98.5-100) |
| OXA-48 | 467 | 89 | 0 | 378 | 0 | 100%(95.9-100) | 100%(99.0-100) |
By Target
a. The bi-directional DNA sequencing result for this false positive IMP isolate exhibited 92.95% sequence homology which was slightly below the 95% cutoff criteria. Discrepant testing was not performed.
b. Discrepant testing results: 1 of 1 was VIM positive.
c. This false positive isolate is likely due to KPC cross-contamination at the level of sample preparation. Discrepant testing did not produce a sequence match with the KPC target. Discrepant testing produced a sequence match for the VIM target, therefore this isolate is classified as a TP in the Combined" assessment presented in Table 5-8, above.
When tested with isolates from MacConkey agar, the Xpert Carba-R Assay demonstrated an overall sensitivity and specificity of 100% (95% CI: 99.0-100) and 97.1% (95% CI: 91.8-99.0), respectively, relative to reference sequencing performed from the blood agar isolates (Table 5-10). The combined result was defined as positive for the Xpert Carba-R Assay if any of the targets were positive, and negative for the Xpert Carba-R Assay if all of the targets were negative.
{18}------------------------------------------------
| Target | N | TP | FP | TN | FN | Sensitivity %(95 CI) | Specificity %(95 CI) |
|---|---|---|---|---|---|---|---|
| Combined | 467 | 364a | 3 | 100 | 0 | 100%(99.0-100) | 97.1%(91.8-99.0) |
Table 5-10. Xpert Carba-R (MacConkey agar) vs. Reference Sequencing (isolate grown on blood agar) - Combined
Combined results represent results by isolate. Multiple target results were observed for some a. isolates.
When tested with isolates from MacConkey agar, the Xpert Carba-R Assay demonstrated a sensitivity and specificity of >99% for each of the five assay targets, relative to reference sequencing performed from the blood agar isolates (Table 5-11).
Table 5-11. Xpert Carba-R (MacConkey agar) vs. Reference Sequencing (isolate grown on blood agar) - By Target
| Target | N | TP | FP | TN | FN | Sensitivity %(95 CI) | Specificity %(95 CI) |
|---|---|---|---|---|---|---|---|
| IMP | 467 | 40 | 1 a | 426 | 0 | 100%(91.2-100) | 99.8%(98.7-100) |
| VIM | 467 | 82 | 1 b | 384 | 0 | 100%(95.5-100) | 99.7%(98.5-100) |
| NDM | 467 | 78 | 1 c | 388 | 0 | 100%(95.3-100) | 99.7%(98.6-100) |
| KPC | 467 | 84 | 0 | 383 | 0 | 100%(95.6-100) | 100%(99.0-100) |
| OXA-48 | 467 | 89 | 0 | 378 | 0 | 100%(95.9-100) | 100%(99.0-100) |
The bi-directional DNA sequencing result for this false positive IMP isolate exhibited 92.95% a. sequence homology which was slightly below the 95% cutoff criteria. Discrepant testing was not performed.
Discrepant testing results: 1 of 1 was VIM positive. b.
The clinical site reported that in-house characterization of this false positive isolate prior to study C. testing resulted in a positive NDM gene target. Discrepant testing did not produce a sequence match for any of the 5 gene targets.
The Xpert Carba-R Assay performance by specific organism group is shown in Table 5-12 for both blood agar and MacConkey Agar medium. The overall result was defined as positive for the Xpert Carba-R Assay if any of the targets were positive, and negative for the Xpert Carba-R Assay if all of the targets were negative.
{19}------------------------------------------------
| Medium | Organisms | Target | N | TP | FP | TN | FN | Sensitivity %(95 CI) | Specificity%(95 CI) |
|---|---|---|---|---|---|---|---|---|---|
| Blood Agar | Enterobacteriaceae | IMP | 343 | 4 | 0 | 339 | 0 | 100%(51.0-100) | 100%(98.9-100) |
| VIM | 343 | 51 | 1 | 291 | 0 | 100%(93.0-100) | 99.7%(98.1-99.9) | ||
| NDM | 343 | 73 | 0 | 270 | 0 | 100%(95.0-100) | 100%(98.6-100) | ||
| KPC | 343 | 83 | 1 | 259 | 0 | 100%(95.6-100) | 99.6%(97.9-99.9) | ||
| OXA-48 | 343 | 89 | 0 | 254 | 0 | 100%(95.9-100) | 100%(98.5-100) | ||
| Overall | 343 | 291a | 1a | 51 | 0 | 0 | 100%(98.7-100) | ||
| Pseudomonasaeruginosa | IMP | 80 | 16 | 1 | 63 | 0 | 100%(80.6-100) | 98.4%(91.7-99.7) | |
| VIM | 80 | 31 | 0 | 49 | 0 | 100%(89.0-100) | 100%(92.7-100) | ||
| NDM | 80 | 0 | 0 | 80 | 0 | NA | 100%(95.4-100) | ||
| KPC | 80 | 1 | 0 | 79 | 0 | 100%(20.7-100) | 100%(95.4-100) | ||
| OXA-48 | 80 | 0 | 0 | 80 | 0 | NA | 100%(95.4-100) | ||
| Overall | 80 | 48 | 1 | 31 | 0 | 100%(92.6-100) | 96.9%(84.3-99.5) | ||
| Acinetobacterbaumannii | IMP | 44 | 20 | 0 | 24 | 0 | 100%(83.9-100) | 100%(86.2-100) | |
| VIM | 44 | 0 | 0 | 44 | 0 | NA | 100%(92.0-100) | ||
| NDM | 44 | 5 | 0 | 39 | 0 | 100%(56.6-100) | 100%(91.0-100) | ||
| KPC | 44 | 0 | 0 | 44 | 0 | NA | 100%(92.0-100) | ||
| OXA-48 | 44 | 0 | 0 | 44 | 0 | NA | 100%(92.0-100) | ||
| Overall | 44 | 25 | 0 | 19 | 0 | 100%(86.7-100) | 100%(83.2-100) | ||
| MacConkeyAgar | Enterobacteriaceae | IMP | 343 | 4 | 0 | 339 | 0 | 100%(51.0-100) | 100%(98.9-100) |
| VIM | 343 | 51 | 1 | 291 | 0 | 100%(93.0-100) | 99.7%(98.1-99.9) | ||
| NDM | 343 | 73 | 1 | 269 | 0 | 100%(95.0-100) | 99.6%(97.9-99.9) | ||
| KPC | 343 | 83 | 0 | 260 | 0 | 100%(95.6-100) | 100%(98.5-100) | ||
| OXA-48 | 343 | 89 | 0 | 254 | 0 | 100%(95.9-100) | 100%(98.5-100) | ||
| Overall | 343 | 291a | 2 | 50 | 0 | 0 | 100%(98.7-100) | ||
| Pseudomonasaeruginosa | IMP | 80 | 16 | 1 | 63 | 0 | 100%(80.6-100) | 98.4%(91.7-99.7) | |
| VIM | 80 | 31 | 0 | 49 | 0 | 100%(89.0-100) | 100%(92.7-100) | ||
| Medium | Organisms | Target | N | TP | FP | TN | FN | Sensitivity %(95 CI) | Specificity %(95 CI) |
| NDM | 80 | 0 | 0 | 80 | 0 | NA | 100%(95.4-100) | ||
| KPC | 80 | 1 | 0 | 79 | 0 | 100%(20.7-100) | 100%(95.4-100) | ||
| OXA-48 | 80 | 0 | 0 | 80 | 0 | NA | 100%(95.4-100) | ||
| Overall | 80 | 48 | 1 | 31 | 0 | 100%(92.6-100) | 96.9%(84.3-99.5) | ||
| Acinetobacterbaumannii | IMP | 44 | 20 | 0 | 24 | 0 | 100%(83.9-100) | 100%(86.2-100) | |
| VIM | 44 | 0 | 0 | 44 | 0 | NA | 100%(92.0-100) | ||
| NDM | 44 | 5 | 0 | 39 | 0 | 100%(56.6-100) | 100%(91.0-100) | ||
| КРС | 44 | 0 | 0 | 44 | 0 | NA | 100%(92.0-100) | ||
| OXA-48 | 44 | 0 | 0 | 44 | 0 | NA | 100%(92.0-100) | ||
| Overall | 44 | 25 | 0 | 19 | 0 | 100%(86.7-100) | 100%(83.2-100) |
Table 5-12: Xpert Carba-R vs. Reference Sequencing
{20}------------------------------------------------
a.Overall results represent results by isolate. Multiple target results were observed for some isolates.
Xpert Carba-R Assay results by phenotype are presented in Table 5-13 and Table 5-14 below. Phenotypic results were based on the organism identification and susceptibility results for each of the isolates. The combined result was defined as positive for the Xpert Carba-R Assay if any of the five assay targets were positive, and negative for the Xpert Carba-R Assay if all five of the assay targets were negative. A non-susceptible phenotype means the isolate was intermediate or resistant to at least one carbapenem. A susceptible phenotype means the isolate was susceptible to imipenem, meropenem, and ertapenem.
| Phenotypic Results | ||||
|---|---|---|---|---|
| Non-susceptible | Susceptible | Total | ||
| Xpert Carba-R | Gene Detected | 356 | 10 | 366 |
| Gene Not Detected | 95 | 6 | 101 | |
| Total | 451 | 16 | 467 |
Table 5-13. Xpert Carba-R (blood agar) vs. Phenotype – Combined
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| Phenotypic Results | ||||
|---|---|---|---|---|
| Non-susceptible | Susceptible | Total | ||
| Xpert Carba-R | Gene Detected | 357 | 10b | 367 |
| Gene Not Detected | 94a | 6 | 100 | |
| Total | 451 | 16 | 467 |
Table 5-14. Xpert Carba-R (MacConkey agar) vs. Phenotype - Combined
a. The 94 isolates that are phenotypically carbapenem non-susceptible but negative by the Xpert Carba-R Assay may contain other mechamisms of carbapenem resistance, such as AmpC betalactamases or extended spectrum beta-lactamases in combination with porin mutations, or potentially other carbapenem resistance genes that are not detected by the Xpert Carba-R Assay.
b. The 10 isolates that are phenotypically carbapenem susceptible but positive by the Xpert Carba-R assay may contain mutations that inactivate or down regulate expression of the carbapenem resistance gene detected by the Xpert Carba-R Assay.
Among the 934 tests performed (467 isolates x 2 agar types), one had an initial NO RESULT outcome (0.10%, 95% CI 0.00-0.58). The isolate vielded valid results upon repeat assay. The overall valid reporting rate of the assay was 100% (934/934).
Reproducibility Study
Reproducibility of the Xpert Carba-R Assay was evaluated using a panel of 13 bacterial samples that included: two different organisms per each of the five resistance gene targets detected by the Xpert Carba-R Assay; two stock samples that included two gene targets; and one stock sample negative for all five gene targets. Two operators at each of the three study sites tested one panel of 13 samples in replicates of four per day. Each sample was used to make two 0.5 McFarland equivalent suspensions from which two replicates were tested over six testing days (13 samples x 2 times/day x 6 days x 2 operators x 3 sites). Three lots of Xpert Carba-R Assay cartridges were used at each of the 3 testing sites. The Xpert Carba-R Assay was performed according to the Xpert Carba-R Assay procedure. Upon completion of the testing, 25 tests run on one instrument module were excluded resulting in a total of 1847 samples included in the analyses. Results are summarized in Table 5-15.
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| ResistanceGene | Site 1 | Site 2 | Site 3 | % TotalAgreement | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| (Sample #) | Op 1 | Op 2 | Site | Op 1 | Op 2 | Site | Op 1 | Op 2 | Site | by Sample |
| KPC (1) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
| (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (144/144) | |
| KPC (2) | 100% | 100% | 100% | 95.8% | 100% | 97.9% | 100% | 100% | 100% | 99.3% |
| (23/23) | (22/22) | (45/45) | (23/24) | (24/24) | (47/48) | (24/24) | (24/24) | (48/48) | (140/141) | |
| VIM (1) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
| (22/22) | (23/23) | (45/45) | (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (141/141) | |
| VIM (2) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
| (22/22) | (24/24) | (46/46) | (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (142/142) | |
| IMP (1) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
| (23/23) | (24/24) | (47/47) | (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (143/143) | |
| IMP (2) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
| (23/23) | (23/23) | (46/46) | (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (142/142) | |
| OXA (1) | 100% | 100% | 100% | 100% | 91.7% | 95.8% | 100% | 100% | 100% | 98.6% |
| (23/23) | (23/23) | (46/46) | (24/24) | (22/24) | (46/48) | (24/24) | (24/24) | (48/48) | (140/142) | |
| OXA (2) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
| (23/23) | (22/22) | (45/45) | (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (141/141) | |
| NDM (1) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
| (22/22) | (21/21) | (43/43) | (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (139/139) | |
| NDM (2) | 100% | 100% | 100% | 91.7% | 100% | 95.8% | 100% | 100% | 100% | 98.6% |
| (23/23) | (23/23) | (46/46) | (22/24) | (24/24) | (46/48) | (24/24) | (24/24) | (48/48) | (140/142) | |
| OXA,NDM (1) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
| (24/24) | (23/23) | (47/47) | (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (143/143) | |
| OXA,NDM (2) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
| (23/23) | (24/24) | (47/47) | (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (143/143) | |
| NEG | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
| (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (24/24) | (24/24) | (48/48) | (144/144) |
Table 5-15: Summary of Reproducibility Results
The reproducibility of the Xpert Carba-R Assay was also evaluated in terms of the fluorescence signal expressed in Ct values for each target detected. The mean, standard deviation (SD), and coefficient of variation (CV) between-sites, between-lots, betweendays, between-operators, and within-assays for each panel member are presented in Table 5-16.
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| ResistanceGene(Sample #) | AssayChannel(Analyte) | Na | Between-Site | Between-Lot | Between-Day | Between-Operator | Within-Assay | Total | ||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SD | CV | SD | CV | SD | CV | SD | CV | SD | CV | SD | CV | |||||||||||||||||||||||||||||||||||||||||||||
| KPC (1) | KPC | 144 | 1.1 | 4.4 | 0 | 0 | 0 | 0 | 0.6 | 2.6 | 0.6 | 2.6 | 1.4 | 5.8 | ||||||||||||||||||||||||||||||||||||||||||
| KPC (2) | KPC | 143 | 0.8 | 3.1 | 0.1 | 0.2 | 0.2 | 0.9 | 0.5 | 2.0 | 0.8 | 3.1 | 1.2 | 4.9 | ||||||||||||||||||||||||||||||||||||||||||
| VIM (1) | VIM | 141 | 1.1 | 5.1 | 0 | 0 | 0 | 0 | 0.5 | 2.3 | 0.8 | 3.7 | 1.5 | 6.7 | ||||||||||||||||||||||||||||||||||||||||||
| VIM (2) | VIM | 142 | 0.3 | 1.3 | 0.2 | 0.8 | 0 | 0 | 0.8 | 3.8 | 0.7 | 3.1 | 1.1 | 5.1 | ||||||||||||||||||||||||||||||||||||||||||
| IMP (1) | IMP1 | 143 | 0.3 | 1.0 | 0 | 0 | 0.3 | 1.2 | 0.6 | 2.3 | 0.8 | 3.1 | 1.0 | 4.2 | ||||||||||||||||||||||||||||||||||||||||||
| IMP (2) | IMP1 | 142 | 1.4 | 6.3 | 0.1 | 0.5 | 0 | 0 | 0.6 | 2.8 | 0.7 | 3.2 | 1.7 | 7.6 | ||||||||||||||||||||||||||||||||||||||||||
| OXA (1) | OXA48 | 140 | 0.6 | 2.6 | 0 | 0 | 0 | 0 | 0.7 | 2.8 | 0.8 | 3.5 | 1.2 | 5.2 | ||||||||||||||||||||||||||||||||||||||||||
| OXA (2) | OXA48 | 141 | 1.1 | 4.9 | 0.3 | 1.5 | 0 | 0 | 0.5 | 2.0 | 0.7 | 3.3 | 1.5 | 6.4 | ||||||||||||||||||||||||||||||||||||||||||
| NDM (1) | NDM | 139 | 1.2 | 5.3 | 0 | 0 | 0 | 0 | 0.6 | 2.4 | 0.7 | 3.1 | 1.5 | 6.6 | ||||||||||||||||||||||||||||||||||||||||||
| NDM (2) | NDM | 140 | 0.9 | 4.0 | 0.3 | 1.4 | 0 | 0 | 0.8 | 3.3 | 0.8 | 3.3 | 1.5 | 6.3 | ||||||||||||||||||||||||||||||||||||||||||
| NDM/OXA (1) | NDM | 143 | 1.3 | 5.4 | 0.2 | 0.8 | 0 | 0 | 0.6 | 2.5 | 0.7 | 3.1 | 1.6 | 6.8 | ||||||||||||||||||||||||||||||||||||||||||
| OXA48 | 143 | 1.2 | 6.2 | 0.3 | 1.4 | 0 | 0 | 0.5 | 2.4 | 0.7 | 3.7 | 1.5 | 7.7 | NDM/OXA (2) | NDM | 143 | 1.2 | 5.3 | 0.2 | 1.1 | 0 | 0 | 0.5 | 2.4 | 0.8 | 3.5 | 1.6 | 6.9 | OXA48 | 143 | 1.2 | 6.0 | 0.2 | 1.2 | 0 | 0 | 0.5 | 2.5 | 0.7 | 3.8 | 1.5 | 7.6 | NEG | SPC | 144 | 0.1 | 0.3 | 0.1 | 0.3 | 0 | 0 | 0.2 | 0.5 | 0.4 | 1.3 | |
| OXA48 | 143 | 1.2 | 6.2 | 0.3 | 1.4 | 0 | 0 | 0.5 | 2.4 | 0.7 | 3.7 | 1.5 | 7.7 | |||||||||||||||||||||||||||||||||||||||||||
| NDM/OXA (2) | NDM | 143 | 1.2 | 5.3 | 0.2 | 1.1 | 0 | 0 | 0.5 | 2.4 | 0.8 | 3.5 | 1.6 | 6.9 | ||||||||||||||||||||||||||||||||||||||||||
| OXA48 | 143 | 1.2 | 6.0 | 0.2 | 1.2 | 0 | 0 | 0.5 | 2.5 | 0.7 | 3.8 | 1.5 | 7.6 | |||||||||||||||||||||||||||||||||||||||||||
| NEG | SPC | 144 | 0.1 | 0.3 | 0.1 | 0.3 | 0 | 0 | 0.2 | 0.5 | 0.4 | 1.3 | 0.5 | 1.5 |
Table 5-16. Summary of Reproducibility Data
a. Results with non-zero Ct values out of 144.
Conclusions
The results of the nonclinical analytical and clinical performance studies summarized above demonstrate that the Xpert Carba-R Assay is safe and effective for its intended use and is substantially equivalent to the predicate device.
§ 866.1640 Antimicrobial susceptibility test powder.
(a)
Identification. An antimicrobial susceptibility test powder is a device that consists of an antimicrobial drug powder packaged in vials in specified amounts and intended for use in clinical laboratories for determining in vitro susceptibility of bacterial pathogens to these therapeutic agents. Test results are used to determine the antimicrobial agent of choice in the treatment of bacterial diseases.(b)
Classification. Class II (performance standards).