(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.
§ 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).