(60 days)
The Great Basin Bordetella Direct Test is a qualitative in vitro diagnostic test for the detection of Bordetella pertussis DNA from nasopharyngeal swab specimens obtained from patients suspected of having a respiratory tract infection attributable to B. pertussis.
The Bordetella Direct Test is performed on the PA500 Portrait Analyzer and utilizes PCR amplification of the insertion sequence IS481. The IS481 sequence is also found in other organisms including Bordetella holmesii or Bordetella bronchiseptica. Respiratory infection with B. pertussis, B. holmesii ot B. bronchiseptica may yield positive test results with IS481 assays. B. holmesii infection may cause clinical illness similar to B. pertussis, and mixed outbreaks involving both B. pertussis and B. holmesii infection have been reported. Additional testing should be performed if necessary to differentiate B. holmesii and B. pertussis. B. bronchiseptica is a rare cause of infection in humans. When clinical factors suggest that B. pertussis may not be the cause of respiratory infection, other clinically appropriate investigation(s) should be carried out in accordance with published guidelines.
Negative results for the Great Basin Bordetella Direct Test do not preclude B. pertussis infection and positive results do not rule out co-infection with other respiratory pathogens. Results from the Great Basin Bordetella Direct Test should be used in conjunction with information obtained during the patient's clinical evaluation as an aid in diagnosis of Bordetella pertussis infection and should not be used as the sole basis for treatment or other patient management decisions.
The Great Basin Bordetella Direct Test on the PA500 Portrait™ Analyzer System utilizes automated hot-start PCR technology to target and amplify the IS481 insertion sequence of B. pertussis. Genomic DNA is extracted from microbial cells and diluted to reduce potential inhibitors of PCR. During PCR, double-stranded DNA is separated and the target nucleic acid sequence is amplified by thermal cycling using biotin-labeled primers that target the IS481 sequence for identification of B. pertussis. Following PCR, biotin-labeled amplicon is hybridized to sequence-specific capture probes immobilized on the silicon chip surface, then incubated with anti-biotin antibody conjugated to the horseradish peroxidase enzyme (HRP). The unbound conjugate is washed away and tetramethylbenzidine (TMB) is added to produce a visible precipitate at the location of the probe/target sequence complex. The resulting signal is detected by the automated Portrait™ Optical Reader within the PA500 Portrait™ Analyzer System. The Specimen Processing Control (SPC), undergoes the extraction, and detection steps to monitor for inhibitory substances as well as process inefficiency due to instrument or reagent failure. No operator intervention is necessary once the clinical sample is loaded into the sample port and the Bordetella Direct Test cartridge is loaded into the Portrait Analyzer.
The PA500 Portrait™ Analyzer System is a fully automated system that includes: The Portrait™ Analyzer, single-use Bordetella Direct Test Cartridges, and the Portrait™ Data Analysis Software Program. The Portrait™ System is designed to perform automated sample preparation, PCR, and optical chip-based detection with integrated data analysis in less than two hours.
This documentation describes acceptance criteria and the study that proves the Great Basin Bordetella Direct Test meets these criteria. The device is a qualitative in vitro diagnostic test for the detection of Bordetella pertussis DNA from nasopharyngeal swab specimens.
Here's the detailed breakdown of the acceptance criteria and study information:
1. Table of Acceptance Criteria and Reported Device Performance
The acceptance criteria for the Great Basin Bordetella Direct Test are implicitly defined by the performance observed in the analytical and clinical studies, which are designed to demonstrate the device's acceptable functioning for its intended use. While explicit numerical acceptance criteria (e.g., "PPA must be >X%") are not directly stated as pass/fail thresholds in the provided text, the reported performance metrics are presented as the results that demonstrate substantial equivalence.
| Performance Metric | Acceptance Criteria (Implied by Study Design & Comparison) | Reported Device Performance |
|---|---|---|
| Analytical Studies | ||
| Limit of Detection (LoD) | Lowest concentration of B. pertussis that can be reproducibly distinguished from negative samples with 95% confidence (19/20 replicates positive). | Between 1.6 x 10^3 and 3.3 x 10^3 CFU/mL, with an average LoD of 2.4 x 10^3 CFU/mL. Ranges for individual strains: |
- ATCC 8467: 3.3 x 10^3 CFU/mL (20/20 detected)
- ATCC 9797: 1.6 x 10^3 CFU/mL (20/20 detected)
- ATCC BAA-589: 2.3 x 10^3 CFU/mL (19/20 detected) |
| Analytical Reactivity (Inclusivity) | Correct detection of additional B. pertussis strains. | All 8 additional B. pertussis strains tested were correctly detected (3/3 positive for each strain). |
| Analytical Specificity (Exclusivity) | No cross-reactivity with non-target organisms commonly found in the human respiratory system, except for known IS481-positive Bordetella species, which should be noted as limitations. | Most non-target organisms (48 bacteria, 20 viruses, 2 yeast, 1 human genomic DNA) showed no cross-reactivity (100% expected negative results for all tested).
Observed cross-reactivity: - Bordetella bronchiseptica: 1 of 3 strains showed cross-reactivity (ATCC 4617).
- Bordetella holmesii: All 3 strains showed cross-reactivity.
- Bordetella hinzii: 1 of 2 strains showed cross-reactivity (ATCC 51784).
These noted cross-reactivities for Bordetella species are consistent with the presence of the IS481 insertion sequence also detected by the test. |
| Microbial Interference | No interference (i.e., correct detection of B. pertussis) when B. pertussis is present with high concentrations of other organisms. | 83 of 84 tested organisms (48 bacteria, 19 viruses, 2 yeast, 14 Bordetella non-B. pertussis strains, 1 human genomic DNA) showed no interference (100% expected positive results). One exception: 1 replicate for M. tuberculosis initially reported 'NOT DETECTED', but subsequent retesting confirmed no interference. |
| Interfering Substances | No interference with common chemical substances found in patients with upper respiratory conditions. | All 19 tested chemical substances showed no interference (100% expected positive and negative results). |
| Carry-over/Cross-Contamination | No false positives in negative samples following high positive samples. | No carry-over or cross-contamination observed (100% correct results for alternating high positive and negative samples). |
| Swab, Transport Media, Elution Buffer Equivalency | Device compatibility with various swab types, transport media, and elution buffers. | All tested swab types (Flocked Nylon, Polyester, Rayon), transport media (Remel M4/M4RT/M5/M6 VTM, BD Universal VTM, ESwab), and elution buffers (Molecular grade water, PBS, Saline, TE Buffer) showed no interference (3/3 expected results for each).
Equivalence study confirmed 100% agreement when using different combinations of swab types and transport/elution media. |
| Sample Stability and Storage | Specimen stability for specified storage conditions (room temperature and refrigerated). | 100% agreement with expected results for samples stored up to 72 hours at room temperature and up to 168 hours (7 days) at 2-8°C, supporting specimen storage claims of 48 hours at room temperature or ≤120 hours at 2-8°C. |
| Reproducibility | Consistent results across different sites, operators, and reagent lots. | 100% agreement observed across replicates, runs, operators (6), and sites (3 clinical sites) for low positive, moderate positive, and negative samples. |
| Clinical Studies | | |
| Positive Percent Agreement (PPA) | High agreement with the Reference NAAT for positive samples, demonstrating clinical sensitivity. (Implicitly, the confidence interval should be acceptable, likely meeting a lower bound, although not explicitly stated). | Prospective Study (Fresh): 85.7% (95% CI: 65.4% - 95.0%) (18/21 true positives)
Frozen Retrospective Study: 94.6% (95% CI: 86.1% - 98.3%) (56/59 true positives) |
| Negative Percent Agreement (NPA) | High agreement with the Reference NAAT for negative samples, demonstrating clinical specificity. (Implicitly, the confidence interval should be acceptable, likely meeting a lower bound, although not explicitly stated). | Prospective Study (Fresh): 99.6% (95% CI: 98.9% - 99.8%) (890/894 true negatives)
Frozen Retrospective Study: 100.0% (95% CI: 94.3% - 100.0%) (63/63 true negatives) |
2. Sample Size Used for the Test Set and Data Provenance
- Prospective Study (Fresh Samples):
- Sample Size: 915 samples (936 collected, 21 excluded due to improper storage or failed QC).
- Data Provenance: U.S. clinical study sites (four external, geographically-diverse sites: Northwest, Southwest, Midwest, West). Samples collected prospectively from July 2016 to January 2017. These were excess, de-identified nasopharyngeal (NP) swab specimens submitted for standard of care B. pertussis testing.
- Frozen Retrospective Study:
- Sample Size: 122 samples (124 initially, 2 excluded due to failed QC).
- Data Provenance: Archived frozen NP swab specimens from institutions across the U.S. (implied from the context of clinical studies and specimen collection methods), retrospective in nature. These were de-identified specimens previously characterized by a nucleic acid amplification test at their originating institution.
3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications of Those Experts
This document describes a diagnostic test for Bordetella pertussis using molecular methods (NAAT). The "ground truth" for the clinical test sets (both prospective and retrospective) was established by comparison to an FDA-cleared Nucleic Acid Amplification Test (Reference NAAT).
- No human experts (e.g., radiologists) were used to establish the ground truth for classification of positive/negative B. pertussis status in the clinical studies.
- The ground truth relies on the performance of the established Reference NAAT.
4. Adjudication Method for the Test Set
- For the clinical performance studies, discrepant results between the Great Basin Bordetella Direct Test and the initial Reference NAAT were investigated by testing in a second FDA-cleared NAAT (NAAT 2) which also detects Bordetella pertussis. This acts as an adjudication step.
- The document states: "In total, there were six (6) false negative and four (4) false positive results. Two (2) of the six (6) false negatives were also negative by a second FDA cleared NAAT and two (2) of the four (4) false positives were also positive by the second FDA cleared NAAT." This indicates the NAAT 2 was used to help understand the nature of the discrepancies, but it does not specify if the NAAT 2 result was definitively taken as the final "truth" for the agreement calculations in all cases. Typically, in diagnostic studies, a third, independent method or a consensus of multiple reference methods is used for resolving discrepancies, but the exact arbitration rule (e.g., 2-out-of-3, or specific tie-breaking rules) is not detailed for the final truth determination for PPA/NPA beyond the investigation by NAAT 2.
5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study was done
- No, an MRMC comparative effectiveness study was not done. This device is an in vitro diagnostic (IVD) test, specifically a nucleic acid amplification test (NAAT). The performance is measured by its ability to detect specific DNA directly from a patient sample, not by a human interpreting images or data to make a diagnosis. Therefore, comparative effectiveness with human readers (e.g., radiologists, pathologists) is not relevant for this type of device. The studies focused on its analytical performance and its agreement with a reference molecular diagnostic test.
6. If a Standalone (i.e., algorithm only without human-in-the-loop performance) was done
- Yes, the primary performance evaluation of the Great Basin Bordetella Direct Test is effectively "standalone" performance. This means the device itself, the automated PA500 Portrait Analyzer and its associated assay, is evaluated for its ability to produce positive or negative results. There is no human interpretation or intervention in the diagnostic output generation described beyond loading the sample into the automated system. The results are generated by the instrument's automated software.
7. The Type of Ground Truth Used
- For the clinical studies, the ground truth for classifying samples as positive or negative for B. pertussis was established by a Reference FDA-cleared Nucleic Acid Amplification Test (NAAT). Discrepancies were investigated by a second FDA-cleared NAAT.
- For the analytical studies (LoD, inclusivity, exclusivity, interference), the ground truth was established by known concentrations of cultured bacterial strains (CFU/mL) or genomic copies/TCID50 for viruses and other microbes, which were spiked into negative clinical matrix.
8. The Sample Size for the Training Set
- The provided document is a 510(k) premarket notification summary for a test that is likely based on traditional molecular biology techniques (PCR) rather than a machine learning/AI algorithm that requires a separate training set.
- Therefore, the concept of a "training set" in the context of machine learning, where an algorithm learns patterns from data, does not directly apply to the development and validation of this specific in vitro diagnostic device. Its "training" is more akin to traditional assay development and optimization to ensure primers, probes, and reaction conditions are specific and sensitive.
- The document does not mention a machine learning component or a distinct "training set" data size.
9. How the Ground Truth for the Training Set was Established
- As explained in point 8, the concept of a "training set" for a machine learning algorithm is not applicable here. The device's underlying technology is PCR amplification, which is based on established biological and chemical principles rather than machine learning from a specific training dataset. Development and optimization of such assays involve
- Designing and testing primers/probes: Based on known genetic sequences of B. pertussis.
- Optimizing reaction conditions: To achieve desired sensitivity and specificity using known positive and negative controls/samples.
- Analytical validation: As described in the document (LoD, inclusivity, exclusivity) using characterized bacterial strains and other microbes.
- The "ground truth" during the development and optimization phases would have been established by precisely characterized biological materials, such as pure cultures of B. pertussis at known concentrations, or panels of well-characterized positive and negative patient samples.
§ 866.3980 Respiratory viral panel multiplex nucleic acid assay.
(a)
Identification. A respiratory viral panel multiplex nucleic acid assay is a qualitative in vitro diagnostic device intended to simultaneously detect and identify multiple viral nucleic acids extracted from human respiratory specimens or viral culture. The detection and identification of a specific viral nucleic acid from individuals exhibiting signs and symptoms of respiratory infection aids in the diagnosis of respiratory viral infection when used in conjunction with other clinical and laboratory findings. The device is intended for detection and identification of a combination of the following viruses:(1) Influenza A and Influenza B;
(2) Influenza A subtype H1 and Influenza A subtype H3;
(3) Respiratory Syncytial Virus subtype A and Respiratory Syncytial Virus subtype B;
(4) Parainfluenza 1, Parainfluenza 2, and Parainfluenza 3 virus;
(5) Human Metapneumovirus;
(6) Rhinovirus; and
(7) Adenovirus.
(b)
Classification. Class II (special controls). The special controls are:(1) FDA's guidance document entitled “Class II Special Controls Guidance Document: Respiratory Viral Panel Multiplex Nucleic Acid Assay;”
(2) For a device that detects and identifies Human Metapneumovirus, FDA's guidance document entitled “Class II Special Controls Guidance Document: Testing for Human Metapneumovirus (hMPV) Using Nucleic Acid Assays;” and
(3) For a device that detects and differentiates Influenza A subtype H1 and subtype H3, FDA's guidance document entitled “Class II Special Controls Guidance Document: Testing for Detection and Differentiation of Influenza A Virus Subtypes Using Multiplex Nucleic Acid Assays.” See § 866.1(e) for the availability of these guidance documents.