(162 days)
The Cepheid Xpert GBS LB Assay, performed on the GeneXpert® Instrument Systems, is a qualitative in vitro diagnostic test designed to detect Group B Streptococcus (GBS) DNA from enriched vaginal/rectal swab specimens, using fully automated real-time polymerase chain reaction (PCR) with fluorogenic detection of the amplified DNA. Xpert GBS LB Assay testing is indicated as an aid in determining GBS colonization status in antepartum women.
- The Xpert GBS LB Assay is used for antepartum testing on enriched Lim broth cultures of vaginal/rectal swabs after 18-24 hours of incubation.
- The Xpert GBS LB assay does not provide susceptibility results. Culture isolates are needed for performing susceptibility testing as recommended for penicillin-allergic women.
The Cepheid Xpert GBS LB Assay is an automated in vitro diagnostic DNA test for the qualitative detection of Group B Streptococcus (GBS) DNA from enriched vaginal/rectal swab specimens, using fully automated real-time polymerase chain reaction (PCR) with fluorogenic detection of the amplified DNA. Xpert GBS LB Assay testing is indicated for identification of antepartum GBS colonization with vaginal/rectal swab specimens prepared using an enrichment method in LB broth and then tested in the Xpert GBS LB Assay. The assay is performed on the Cepheid GeneXpert® Instrument Systems.
The GeneXpert Instrument Systems automate and integrate sample lysis, nucleic acid purification and amplification, and detection of the target sequence in complex samples using real-time PCR (Polymerase chain reaction) assays. The GeneXpert Instrument System family comprises a GeneXpert Dx instrument (GX-I, GX-IV, GX-XVI), the GeneXpert Dx XVI available with 4, 8, 12, or 16 modules; a GeneXpert Infinity-48. available with 16, 24, 32, 40 or 48 modules, or a GeneXpert Infinity-80 available with 16, 24, 32, 40, 48, 56, 64, 72, or 80 modules. The modules are identical for all instrument systems. The instrument systems also contain a computer, and preloaded software for running tests and viewing the results. The GeneXpert Infinity Systems contain robotic features for cartridge handling. Each module contains a syringe drive for dispensing fluids, an ultrasonic horn for lysing cells or spores, a valve drive for sample movement, and I-CORE® thermocycler for performing real-time PCR and detection.
The Xpert GBS LB Assay includes reagents pre-loaded in the Xpert GBS LB cartridge for the simultaneous detection of the target GBS DNA. A Sample Processing Control (SPC), an Internal Control (IC) and a Probe Check Control (PCC) are also included in the cartridge. The SPC is present to control for adequate processing of the target DNA; the IC is present to monitor the presence of inhibitors in the PCR reaction. The PCC verifies reagent rehydration, PCR-tube filling in the cartridge, probe integrity, and dye stability. The GBS primers and probe detect a target within a 3' DNA region adjacent to the cfb gene of S. agalactiae.
After collecting and transporting a swab sample to the laboratory, the swab is placed in Lim broth for enrichment overnight, after which a clean swab (Cepheid part number SDPS-120) dipped into the enrichment broth specimen is transferred to the designated chamber of the cartridge. The GeneXpert Instrument System performs sample preparation by eluting the specimen material from the swab, mixing the sample with the SPC (Bacillus globigii) in the form of a bead within the cartridge) and treatment reagent, capturing cellular material on a filter, lysing the cells, and eluting the DNA. The DNA solution is then mixed with dry PCR reagents and transferred into the integrated reaction tube for real-time PCR and detection. The results are interpolated by the GeneXpert Instrument Systems from measured fluorescent signals and embedded calculation algorithms. Results may be viewed and printed. The test process takes approximately 55 minutes. Sample preparation, amplification, and real-time detection are all fullyautomated and completely integrated.
Here's a breakdown of the acceptance criteria and study details for the Cepheid Xpert GBS LB Assay, based on the provided text:
Acceptance Criteria and Device Performance
| Acceptance Criterion | Reported Device Performance |
|---|---|
| Clinical Performance (Enriched Method): | Xpert GBS LB Assay: |
| Sensitivity | 99.0% (95% CI: 96.3-99.9) |
| Specificity | 92.4% (95% CI: 90.1-94.4) |
| Positive Predictive Value (PPV) | 79.7% (95% CI: 74.1-84.7) |
| Negative Predictive Value (NPV) | 99.7% (95% CI: 98.8-100) |
| Analytical Sensitivity (LoD) | Overall LoD for the assay: 333 CFU/mL (lowest concentration reproducibly distinguished from negative samples with 95% confidence, or 19/20 replicates positive). Specific LoDs for 11 GBS strains ranged from 67 CFU/mL to 333 CFU/mL. |
| Analytical Specificity (Exclusivity) | 100% (No false positives with 100 strains including 24 Streptococci, 76 other species, microflora, and human DNA at high concentrations). |
| Interfering Substances | None of the tested endogenous/exogenous substances (e.g., amniotic fluid, blood, urine, fecal sample, various medications, lubricants) had a statistically significant effect on assay performance. All positive samples reported correctly as GBS Positive, and all negative samples reported correctly as GBS Negative. |
| Carry-Over Contamination | 100% prevention of carry-over. All 48 negative samples processed immediately after very high GBS positive samples (1x10^6 CFU/swab) were correctly reported as GBS negative. |
| Reproducibility | Overall Agreement: |
- GBS strain 1 moderate positive: 100.0%
- GBS strain 1 low positive: 98.9%
- GBS strain 1 high negative: 72.2%
- GBS strain 2 moderate positive: 100.0%
- GBS strain 2 low positive: 100.0%
- GBS strain 2 high negative: 80.0%
- Negative: 100.0% (Except one instance due to retesting mistake) |
| Instrument Precision | Total Agreement by Sample (GeneXpert Dx & Infinity-80): - GBS strain 1 moderate positive: 100.0%
- GBS strain 1 low positive: 100.0%
- GBS strain 1 high negative: 76.6%
- GBS strain 2 moderate positive: 100.0%
- GBS strain 2 low positive: 98.4%
- GBS strain 2 high negative: 83.9%
- Negative: 100.0% |
| Linearity | The assay responds linearly over four to five logs, ranging from 1x10^8 CFU/swab to 10 CFU/swab, depending on the GBS serotype. |
Study Details
Clinical Performance Study
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Sample size used for the test set and the data provenance:
- Sample Size: 826 specimens were tested in the clinical performance study.
- Data Provenance: The study was a "prospective multi-center study at three sites." The text does not specify the country of origin but implies it was conducted in the U.S., as it references "three institutions in the U.S."
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Number of experts used to establish the ground truth for the test set and the qualifications of those experts:
- The ground truth for the clinical performance study was established by reference culture. The text does not mention the number or qualifications of experts for interpreting these cultures or establishing a ground truth based on expert consensus. It refers to "culture" as the standard of care without detailing expert involvement for that specific ground truth method.
- However, for the specific cases where the Xpert GBS LB Assay results disagreed with the culture (48 false positives, 2 false negatives), sequencing was used for further investigation. The text doesn't specify if experts were involved in sequencing interpretation, but it is a laboratory technique rather than expert clinical judgment for the primary ground truth.
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Adjudication method for the test set:
- The primary comparison was against "reference culture." For discrepant results between the Xpert GBS LB Assay and the reference culture, sequencing was used to resolve discrepancies.
- 47 of 48 Xpert GBS positive / Culture negative specimens were sequenced. Of these, 42 were GBS positive by sequencing, and 5 were GBS negative by sequencing. One Lim broth was not sequenced.
- Both of the 2 Xpert GBS negative / Culture positive specimens were sequenced and both were GBS negative by sequencing.
- This suggests a form of tiered adjudication where culture was the initial ground truth, and sequencing was used to investigate discrepancies.
- The primary comparison was against "reference culture." For discrepant results between the Xpert GBS LB Assay and the reference culture, sequencing was used to resolve discrepancies.
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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:
- No, a multi-reader multi-case (MRMC) comparative effectiveness study was not explicitly mentioned or presented in the provided text. This device is an automated in vitro diagnostic (IVD) test (a lab test), not an AI-assisted diagnostic imaging or interpretation tool for human readers. Therefore, the concept of human readers improving with AI assistance is not applicable here.
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If a standalone (i.e. algorithm only without human-in-the-loop performance) was done:
- Yes, the Cepheid Xpert GBS LB Assay is explicitly described as a standalone algorithm. It is "fully automated real-time polymerase chain reaction (PCR) with fluorogenic detection" and "The GeneXpert Instrument System performs sample preparation by eluting the specimen material... The results are interpolated by the GeneXpert Instrument Systems from measured fluorescent signals and embedded calculation algorithms." This indicates a fully automated, standalone performance.
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The type of ground truth used (expert consensus, pathology, outcomes data, etc):
- The primary ground truth used for the clinical performance study was reference culture. For discrepant samples, sequencing was used as a confirmatory method.
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The sample size for the training set:
- The document describes a clinical performance study using 826 specimens, which serves as the test set. It does not explicitly mention a separate "training set" for the clinical performance characteristics. For an IVD like this, the "training" (development and optimization) of the embedded algorithms typically happens during the assay development phase, using internal validation samples, rather than a separate, formally documented "training set" comparable to machine learning models. The document focuses on the validation of the device against established methods.
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How the ground truth for the training set was established:
- As a formal "training set" for the clinical performance study is not described, the method for establishing its ground truth is not applicable or detailed in this document. The assay's internal algorithms and parameters were likely developed and refined using laboratory-controlled samples and reference strains (e.g., those used for analytical sensitivity, specificity, and linearity studies) during the product development process.
§ 866.3740
Streptococcus spp. serological reagents.(a)
Identification. Streptococcus spp. serological reagents are devices that consist of antigens and antisera (excluding streptococcal exoenzyme reagents made from enzymes secreted by streptococci) used in serological tests to identifyStreptococcus spp. from cultured isolates derived from clinical specimens. The identification aids in the diagnosis of diseases caused by bacteria belonging to the genusStreptococcus and provides epidemiological information on these diseases. Pathogenic streptococci are associated with infections, such as sore throat, impetigo (an infection characterized by small pustules on the skin), urinary tract infections, rheumatic fever, and kidney disease.(b)
Classification. Class I (general controls). The device is exempt from the premarket notification procedures in subpart E of part 807 of this chapter subject to § 866.9.