(89 days)
The Xpert® Carba-R Assay, performed on the GeneXpert® Instrument Systems, is a qualitative in vitro diagnostic test designed for the detection and differentiation of the blaker, blaNDM, blayIM, blackA-48, and blanny gene sequences associated with carbapenem-non-susceptibility. The test utilizes automated real-time polymerase chain reaction (PCR),
The Xpert Carba-R Assay is intended as an aid to infection of carbapenem-non- susceptible bacteria that colonize patients in healthcare settings. The Xpert Carba-R Assay is not intended to guide or monitor treatmannon-susceptible bacterial infections. A negative Xpert Carba-R Assay result does not preclude the presence of other resistance mechanisms.
The Xpert Carba-R Assay is for use with the following sample types:
Rectal Swab Specimens
The assay is performed on rectal swab specimens at risk for intestinal colonization with carbapenem-non-susceptible bacteria. Concomitant cultures are necessary to reanisms for epidemiological typing, antimicrobial susceptibility testing, and for further confirmatory bacterial identification.
Pure Colonies
The assay is performed on carbapenen-non-susceptible pure colonies of Enterobacter baumanni, or Pseudomonas aeruginosa, when grown on blood agar or MacConkey agar. For testing pure colonies, 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 an automated real-time polymerase chain reaction (PCR) in vitro diagnostic test for qualitative detection of the blaxpc, blaym, blaoxa-a8, and blamp gene sequences from rectal swab specimens. The Xpert Carba-R Assay is intended as an aid for infection control for monitoring the spread of carbapenem-nonsusceptible 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 blakec, blanDM, blaym, blaox 8-8, and blance 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 blaker, blanny, blaoxA-48. and blank gene sequences from rectal swab specimens 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 realtime 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.
Rectal swab specimens 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, blaypy, blaym, blaoxy-48, and blane 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 the study that proves the device meets them, based on the provided text:
Device: Xpert® Carba-R Assay
Indications for Use: Qualitative in vitro diagnostic test for the detection and differentiation of blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP gene sequences associated with carbapenem-non-susceptibility. Intended as an aid to infection control for detecting carbapenem-non-susceptible bacteria colonizing patients in healthcare settings (rectal swab specimens). Also for use with carbapenem-non-susceptible pure colonies of Enterobacteriaceae, Acinetobacter baumannii, or Pseudomonas aeruginosa.
1. Table of Acceptance Criteria and Reported Device Performance
The document does not explicitly state "acceptance criteria" for the clinical performance in a separate, clear table. However, the reported performance metrics in the clinical study can be considered as the evidence demonstrating the device meets an implicit acceptance level for regulatory approval. Regulatory bodies typically look for high Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA). Based on the "Prospective Specimen Results" section (Table 5-11), here are the key performance metrics:
| Target Gene | PPA (%) (95% CI) | NPA (%) (95% CI) |
|---|---|---|
| IMP | N/A (0 TP found) | 99.9% (99.3-100.0) |
| VIM | 60.0% (31.3-83.2) | 98.9% (97.9-99.5) |
| NDM | 100.0% (64.6-100.0) | 99.6% (98.8-99.9) |
| KPC | 100.0% (88.3-100.0) | 99.2% (98.2-99.6) |
| OXA-48 | 96.7% (83.3-99.4) | 98.6% (97.5-99.2) |
Note on IMP PPA: The PPA for IMP is "N/A" with 0 True Positives (TP) among the prospective specimens, which indicates a very low prevalence of this target in the prospective cohort.
Contrived Specimen Performance (Table 5-14):
| Target Gene | PPA (%) (95% CI) | NPA (%) (95% CI) |
|---|---|---|
| IMP | 95.0% (87.8-98.0) | 100.0% (98.9-100.0) |
| VIM | 98.8% (93.4-99.8) | 100.0% (98.9-100.0) |
| NDM | 100.0% (95.4-100.0) | 100.0% (98.9-100.0) |
| KPC | 100.0% (95.4-100.0) | 100.0% (98.9-100.0) |
| OXA-48 | 98.8% (93.3-99.8) | 100.0% (98.9-100.0) |
The reproducibility study (Table 5-15) shows high overall agreement, typically 100% for negative and moderate positive samples, and ranging from 86.1% to 97.2% for low positive samples, indicating consistent performance across sites and operators.
2. Sample Size Used for the Test Set and Data Provenance
- Prospective Clinical Study:
- Initial Enrollment: 802 rectal swab specimens.
- Eligible for Inclusion: 785 specimens.
- Final Dataset: 755 specimens after exclusions (including 16 Stenotrophomonas maltophilia due to intrinsic resistance).
- Provenance: Five geographically diverse sites (three across the United States and two in Europe). Data was collected prospectively from subjects hospitalized or in long-term care facilities.
- Contrived Clinical Study:
- Sample Size: 432 contrived specimens prepared in rectal swab matrix.
- Provenance: This data is laboratory-generated, not from human subjects.
3. Number of Experts Used to Establish the Ground Truth for the Test Set and Their Qualifications
The document refers to a "reference culture laboratory" and an "independent laboratory for reference bi-directional sequencing analysis" for establishing ground truth. It does not explicitly state the number of experts or their specific qualifications (e.g., "radiologist with 10 years of experience"). However, the methodologies employed (culture, disk diffusion, CLSI document standards, PCR, and bi-directional DNA sequencing) imply the involvement of qualified laboratory professionals and molecular biologists.
4. Adjudication Method for the Test Set
For prospective specimens:
- The Xpert Carba-R Assay was evaluated against a reference method consisting of:
- Culture: MacConkey enrichment broth.
- Confirmation of carbapenem non-susceptibility: Disk diffusion method (per CLSI document M02 and M100) on isolated colonies.
- Molecular Confirmation: DNA extracted from non-susceptible isolates was purified, quantified, amplified with primers specific to the 5 target genes, and confirmed for appropriate amplicon size on an Agilent 2100 Bioanalyzer.
- Sequencing: If bands corresponded to expected amplicon sizes, the amplicon was sent to an independent laboratory for reference bi-directional sequencing analysis, which was validated for detecting the five targets.
- Discordant Analysis: For specimens where the Xpert Carba-R Assay was positive but a carbapenem-non-susceptible organism was not isolated by reference culture (False Positives based on initial reference), bi-directional sequencing on DNA extracted directly from the MacConkey enrichment broth was performed to confirm the presence of the gene sequences. This acts as an adjudication step.
5. Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study
No MRMC comparative effectiveness study was mentioned in this document. The device is an automated in vitro diagnostic test, so there is no "human reader" component in its direct output or interpretation in the way an imaging AI system would interact with a radiologist. Therefore, improvement of human readers with AI assistance is not applicable to this device.
6. Standalone (Algorithm Only) Performance Study
Yes, a standalone study was performed. The clinical studies (both prospective and contrived) directly evaluated the performance of the Xpert Carba-R Assay (the algorithm/device) against the reference method without human intervention in the interpretation of the Xpert Carba-R results. The reported PPA and NPA values represent the standalone performance of the device.
7. Type of Ground Truth Used
The ground truth for the test set was established using a multi-faceted approach:
- Expert Reference Method: A combination of culture (MacConkey enrichment broth followed by plating and disk diffusion based on CLSI standards) and molecular methods (PCR for specific gene amplification and bi-directional DNA sequence analysis).
- Outcomes Data: Not directly applicable here; the ground truth is based on the presence or absence of specific gene sequences and organism characteristics.
- Expert Consensus: While not explicitly stated as "expert consensus," the use of a multi-step reference method involving culture, phenotypic susceptibility testing, and sequencing performed by specialized laboratories implies a high standard of expert-driven verification. The discordant analysis further indicates a rigorous process to resolve discrepancies against the initial reference standard.
8. Sample Size for the Training Set
The document does not explicitly state the sample size of a "training set" for the Xpert Carba-R Assay. This is typical for in vitro diagnostic devices that are based on established molecular biology principles (like PCR) and analytical validation (LoD, reactivity, specificity) rather than machine learning models that require distinct training sets. The development process would involve extensive analytical testing to optimize primers and probes, which could be considered an iterative development phase but not a formal "training set" in the AI/ML sense.
9. How the Ground Truth for the Training Set Was Established
As no explicit "training set" is described in the context of an AI/ML model, the establishment of ground truth for a training set is not detailed. However, for a PCR-based assay, the development process would involve establishing the analytical robustness of the assay, including:
- Analytical Sensitivity (Limit of Detection - LoD): Determined by using carbapenemase-producing organisms seeded into negative human rectal swab matrix at varying concentrations and verified with known positive and negative replicates.
- Analytical Reactivity (Inclusivity): Evaluated against a panel of 72 well-characterized bacterial strains with known resistance markers in rectal swab matrix, tested at concentrations (e.g., 3x LoD).
- Analytical Specificity (Cross-reactivity): Evaluated against a panel of 62 carbapenem-susceptible bacteria with other resistance mechanisms, 24 commensal/enteric microorganisms, and human cells at defined concentrations.
These analytical studies use panels with known characteristics (verified through methods like individual PCR assays, DNA sequence analysis, or Check-Points array) to ensure the assay correctly identifies targets and avoids off-target detection. This rigorous analytical characterization serves a similar purpose to "ground truth establishment" for refining a diagnostic assay's performance.
§ 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).