(124 days)
The Great Basin Toxigenic C. difficile Direct Test, performed on the Great Basin PA500 Analyzer, is a qualitative in vitro diagnostic test for the detection of toxigenic Clostridioides difficile in unformed (liquid or soft) stool samples collected from patients suspected of having C. difficile infection (CDI). The automated assay utilizes polymerase chain reaction (PCR) to detect a conserved region of the toxin gene (tcdB) associated with toxin-producing C. difficile.
The Toxigenic C. difficile Direct Test is intended for use as an aid in the diagnosis of CDI in conjunction with clinical and epidemiological risk factors.
The Great Basin Toxigenic C. difficile Direct Test (CDF2) performed on the PA500 Analyzer utilizes automated, hot-start PCR amplification technology to amplify specific nucleic acid sequences that are then detected using hybridization probes immobilized on a modified silicon chip surface, in a single-use, self-contained test cartridge.
A swab volume of the specimen (raw stool) is first processed using the Sample Preparation Device (SPD). During processing through the SPD the specimen is infused with a synthetic bacterial sample processing control (SPC). An aliquot (250 µL) of the eluate obtained from the SPD, containing diluted specimen mixed with SPC, is loaded into the sample port of the CDF2 Test Cartridge.
Genomic DNA is extracted from microbial cells and diluted to reduce potential inhibitors of PCR. During the PCR process, biotin-labeled primers direct the amplification of specific nucleic acid sequences within a conserved region of the C. difficile Toxin B (tcdB) gene.
Following PCR, biotin-labeled, amplified target DNA sequences are hybridized to sequence specific probes immobilized on the silicon chip surface and incubated with antibody conjugated to the horseradish peroxidase enzyme (HRP). The unbound conjugate is washed away, and then tetramethylbenzidine (TMB) is added to produce a colored precipitate at the location of the probe/target sequence complex.
The resulting signal is detected by the automated PA500 Optical Reader within the PA500 Analyzer System. The SPC undergoes the same extraction, and detection steps as the sample in order to monitor for inhibitory substances, as well as process inefficiency due to instrument or reagent failure. No operator intervention is required once the sample is loaded into the sample port and the Toxigenic C. difficile Direct Test cartridge is loaded into the PA500 Analyzer.
The Great Basin System is a fully automated in vitro diagnostic system that includes: the PA500 Analyzer, single-use SPDs, single-use Toxigenic C. difficile Direct Test Cartridges, and the PA500 Data Analysis Software Program. The PA500 Analyzer is designed to perform automated sample preparation, target amplification via PCR, chip-based (optical) target detection, and integrated data analysis in less than two hours.
The Great Basin Toxigenic C. difficile Direct Test (CDF2) is a qualitative in vitro diagnostic test designed to detect toxigenic Clostridioides difficile in unformed stool samples from patients suspected of CDI. The device utilizes PCR to detect a conserved region of the toxin B gene (tcdB).
The study that proves the device meets the acceptance criteria is a prospective multi-center method comparison study (section H. Performance Data - Clinical Studies, page 12).
Here's a breakdown of the requested information:
1. Table of Acceptance Criteria and Reported Device Performance
The acceptance criteria are not explicitly stated as numerical targets in the provided text. However, the study aims to demonstrate "acceptable performance" and states that the "information submitted...supports substantial equivalence." Based on the clinical performance, the implicit acceptance criteria would involve high positive and negative percent agreements with an FDA-cleared molecular reference.
| Metric | Acceptance Criteria (Implicit) | Reported Device Performance (All Sites Combined) |
|---|---|---|
| Positive Percent Agreement (PPA) | High agreement with reference | 95.8% (91.2% - 98.5% CI) |
| Negative Percent Agreement (NPA) | High agreement with reference | 98.5% (97.3% - 99.3% CI) |
2. Sample Size Used for the Test Set and Data Provenance
- Sample Size (Clinical Test Set): A total of 829 specimens were included in the final dataset (page 12).
- Data Provenance: The study was conducted at three geographically diverse U.S. clinical study sites (Midwest, West). The data is prospective, as specimens were collected from symptomatic individuals suspected of CDI between June 2022 and February 2023 (page 12). The specimens were "excess remnants of unpreserved stool specimens...processed according to routine standard of care testing, and would have otherwise been discarded" (page 12).
3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications
The ground truth for the clinical test set was established using an FDA-cleared molecular reference (page 12), not human experts. Discrepant results were investigated by testing on a third molecular test (page 14). Therefore, no human experts were directly involved in establishing the primary ground truth for the clinical samples.
4. Adjudication Method for the Test Set
The adjudication method for discrepant results was comparison to a third FDA-cleared molecular C. difficile test (page 14). If the CDF2 test result differed from the initial molecular comparator, the specimen was re-tested using a third molecular test to resolve the discrepancy.
5. If a Multi Reader Multi Case (MRMC) Comparative Effectiveness Study was done
No, an MRMC comparative effectiveness study was not done. The study compares the device performance against a molecular reference, not human readers.
6. If a Standalone Study (algorithm only without human-in-the-loop performance) was done
Yes, this was a standalone study. The device is an automated in vitro diagnostic test where "No operator intervention is required once the sample is loaded into the sample port and the Toxigenic C. difficile Direct Test cartridge is loaded into the PA500 Analyzer" (page 4). The performance metrics (PPA, NPA) directly reflect the device's accuracy against a molecular comparator without human interpretation of the results.
7. The Type of Ground Truth Used
The primary ground truth for the clinical study was an FDA-cleared molecular reference (page 12). For discrepant samples, a third FDA-cleared molecular C. difficile test was used for resolution (page 14).
8. The Sample Size for the Training Set
The document does not explicitly state a separate training set or its size for the algorithm itself. The studies described are primarily analytical (LoD, inclusivity, exclusivity, interference, reproducibility) and a clinical validation study. These types of in vitro diagnostic device submissions typically focus on analytical and clinical performance rather than a distinct "training set" for an AI algorithm in the same sense as image recognition or similar machine learning applications. The device's "automated data analysis software program" (page 4) is part of its design, and its performance is evaluated through the described analytical and clinical studies.
9. How the Ground Truth for the Training Set Was Established
As no specific "training set" is described for an AI algorithm, the method for establishing its ground truth is not detailed. However, the performance is established through rigorous analytical studies using characterized microbial strains and spiked samples (e.g., cell cultures with known CFU/mL) and clinical specimens compared to a molecular reference.
§ 866.3130 Clostridium difficile toxin gene amplification assay.
(a)
Identification. AClostridium difficile toxin gene amplification assay is a device that consists of reagents for the amplification and detection of target sequences inClostridium difficile toxin genes in fecal specimens from patients suspected of havingClostridium difficile infection (CDI). The detection of clostridial toxin genes, in conjunction with other laboratory tests, aids in the clinical laboratory diagnosis of CDI caused byClostridium difficile. (b)
Classification. Class II (special controls). The special controls are set forth in FDA's guideline document entitled: “Class II Special Controls Guideline: Toxin Gene Amplification Assays for the Detection ofClostridium difficile; Guideline for Industry and Food and Drug Administration Staff.” See § 866.1(e) for information on obtaining this document.