(87 days)
The Xpert® MTB/RIF Assay, performed on the GeneXpert® Instrument Systems, is a qualitative, nested realtime polymerase chain reaction (PCR) in vitro diagnostic test for the detection of Mycobacterium tuberculosis complex DNA in raw sputum or concentrated sputum sediment prepared from induced or expectorated sputum. In specimens where Mycobacterium tuberculosis complex) is detected, the Xpert MTB/RIF Assay also detects the rifampin-resistance associated mutations of the rpoB gene.
The Xpert MTB/RIF Assay is intended for use with specimens for whom there is clinical suspicion of tuberculosis (TB) and who have received no antituberculosis therapy, or less than three days of therapy. This test is intended as an aid in the diagnosis of pulmonary tuberculosis when used in conjunction with clinical and other laboratory findings.
An Xpert MTB/RIF Assay result of "MTB NOT DETECTED" from either one or two sputum specimens is highly predictive of the absence of M. tuberculosis complex bacilli on serial fluorescent acid-fast sputum smears from patients with suspected active pulmonary tuberculosis and can be used as an aid in the decision of whether continued airborne infection isolation (AII) is warranted in patients with suspected pulmonary tuberculosis. The determination of whether testing of either one or two sputum specimens for decisions regarding removal from AII should be based on specific clinical circumstances and institutional guidelines. Clinical decisions regarding the need for continued AII should always occur in conjunction with other clinical and laboratory evaluations and Xpert MTB/RIF Assay results should not be the sole basis for infection control practices.
The Xpert MTB/RIF Assay must always be used in conjunction with mycobacterial culture to address the risk of false negative results and to recover organisms when MTB-complex is present for further characterization and drug susceptibility testing. However, decisions regarding the removal of patients from AII need not wait for culture results. Sputum specimens for TB culture, AFB smear microscopy, and Xpert MTB/RIF Assay testing should follow CDC recommendations with regard to collection methods and time frame between specimen collection.
The Xpert MTB/RIF Assay does not provide confirmation of rifampin susceptibility since mechanisms of rifampin resistance other than those detected by this device may exist that may be associated with a lack of clinical response to treatment.
Specimens that have both MTB-complex DNA and rifampin-resistance associated mutations of the rpoB gene detected by the Xpert MTB/RIF Assay must have results confirmed by a reference laboratory. If the presence of rifampin-resistance associated mutations of the rpoB gene is confirmed, specimens should also be tested for the presence of genetic mutations associated with resistance to other drugs.
The Xpert MTB/RIF Assay should only be performed in laboratories that follow safety practices in accordance with the CDC/NIH Biosafety in Microbiological and Biomedical Laboratories publication and applicable state or local regulations.
The Xpert MTB/RIF Assay is a qualitative, automated, in vitro diagnostic test for qualitative detection of Mycobacterium tuberculosis (MTB) complex DNA in raw sputum samples or in concentrated sputum sediments prepared from induced or expectorated sputa that are either acid-fast bacilli (AFB) smear positive or negative. The assay is performed on the Cepheid GeneXpert Instrument Systems. The Xpert MTB/RIF Assay on the GeneXpert Instrument System automates and integrates sample preparation, nucleic acid amplification, and detection of the target sequences in simple or complex samples using real-time PCR. The system consists of an instrument, personal computer, and preloaded software for running the tests and viewing the results. The system requires the use of single-use disposable cartridges that hold the PCR reagents and host the PCR process. Because the cartridges are self-contained, cross-contamination between samples is minimized.
The Xpert MTB/RIF Assay includes reagents for the detection of MTB and Rifampin (RIF) resistance from raw sputum samples and in prepared sputum sediments. A Sample Processing Control (SPC) and a Probe Check Control (PCC) are also included in the cartridge. The SPC is present to control for adequate processing of the target bacteria and to monitor for the presence of inhibitors in the PCR reaction. The Probe Check Control (PCC) verifies reagent rehydration, PCR tube filling in the cartridge, probe integrity, and dve stability.
The GeneXpert Instrument Systems, comprised of the GeneXpert Dx Systems, the GeneXpert Infinity-48 System, the GeneXpert Infinity-48s, and the GeneXpert Infinity-80 System, have 1 to 80 randomly accessible modules, depending upon the instrument, that are each capable of performing separate sample preparation and real-time 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 detection.
The provided document describes the Xpert® MTB/RIF Assay, an in vitro diagnostic test for the detection of Mycobacterium tuberculosis complex DNA and rifampin-resistance associated mutations. A clinical performance study (Study 2) was conducted to evaluate the device's effectiveness.
Here's a breakdown of the acceptance criteria and study information:
1. A table of acceptance criteria and the reported device performance
The document does not explicitly state pre-defined acceptance criteria in terms of specific performance metrics (e.g., "Sensitivity must be >= X%"). Instead, it presents the device's performance in a multi-center study and implicitly suggests that these results fulfill the requirements for substantial equivalence.
Based on the provided tables, we can extrapolate the reported device performance metrics:
| Metric | Acceptance Criteria (Implied) | Reported Device Performance (Xpert MTB/RIF Assay) |
|---|---|---|
| For Smear Positive Cases: | (Not explicitly stated, but high sensitivity/specificity desirable) | Sensitivity: 98.5% (129/131); 95% CI: 94.6%, 99.6% |
| Specificity: 94.4% (17/18); 95% CI: 74.2%, 99.0% | ||
| For Smear Negative Cases: | (Not explicitly stated, but good sensitivity/specificity desirable) | Sensitivity: 54.8% (46/84); 95% CI: 44.1%, 65.0% |
| Specificity: 98.8% (718/727); 95% CI: 97.7%, 99.4% | ||
| Overall (One Xpert MTB/RIF Assay vs. MTB Culture): | (Not explicitly stated, but good sensitivity/specificity desirable) | Sensitivity: 81.4% (95% CI: 75.7%, 86.0%) |
| Specificity: 98.7% (95% CI: 97.5%, 99.3%) | ||
| Negative Predictive Value (NPV) for Single Test (U.S. Subjects, for AII removal): | (High NPV for ruling out AFB smear-positive TB for AII removal) | NPV: 97.6% (95% CI: 95.9%, 98.6%) |
| Difference in NPV (Xpert vs. Two AFB Smears, U.S. Subjects): | (Improvement over AFB smears indicated) | Difference in NPV: 2.6% (95% CI: 1.2%, 4.2%), indicating better performance for Xpert for U.S. subjects compared to two AFB smears |
2. Sample size used for the test set and the data provenance
- Sample Size for Clinical Performance Study (Study 2): 960 subjects.
- Data Provenance: The study was a prospective multi-center study conducted at multiple sites in the United States, as well as South Africa and Brazil.
3. Number of experts used to establish the ground truth for the test set and the qualifications of those experts
The document does not specify the number of experts or their qualifications for establishing the ground truth. It states that the ground truth for MTB detection was based on mycobacterial culture (stated in Table 5.5). For rifampin resistance, it is stated that "Specimens that have both MTB-complex DNA and rifampin-resistance associated mutations of the rpoB gene detected by the Xpert MTB/RIF Assay must have results confirmed by a reference laboratory."
4. Adjudication method for the test set
The document does not describe a formal adjudication method (like 2+1 or 3+1) for resolving discrepancies in the ground truth. The ground truth for MTB detection was based on mycobacterial culture, an objective laboratory method. For rifampin resistance, a reference laboratory confirmation is required for positive 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 is not a MRMC study involving human readers or AI assistance in the traditional sense of image interpretation. The device is an automated, in vitro diagnostic test. However, the study does compare the performance of the Xpert MTB/RIF Assay (the device) against AFB smear microscopy which involves human interpretation (laboratory technicians reading smears).
- Comparison between device and AFB smears: The document notes: "One Xpert MTB/RIF Assay was associated with a sensitivity of 81.4% (95% CI: 75.7%, 86.0%) for identifying MTB culture-positive subjects compared to a sensitivity of 60.9% (95% CI: 54.3%, 67.2%) for two AFB smears."
- Effect Size (implicitly an improvement over human-read smears): For U.S. subjects, the NPV for one Xpert MTB/RIF Assay result was 97.6% compared to 95.0% for two AFB smears results. The difference in NPVs was 2.6% (95% CI: 1.2%, 4.2%). This suggests that the device performs better than two AFB smears in ruling out active pulmonary TB for decisions on airborne infection isolation in the U.S. context.
6. If a standalone (i.e. algorithm only without human-in-the loop performance) was done
Yes, the primary clinical performance study (Study 2) evaluated the standalone performance of the Xpert MTB/RIF Assay. The assay is an automated in vitro diagnostic test that processes the sample and provides a result without direct human interpretation of the PCR data. Human involvement is primarily in sample collection, preparation, loading the cartridge, and interpreting the output from the instrument system.
7. The type of ground truth used
The primary ground truth for MTB detection was mycobacterial culture. For cases where MTB complex DNA and rifampin-resistance associated mutations were detected, confirmation by a reference laboratory served as the ground truth for rifampin resistance.
8. The sample size for the training set
The document does not explicitly mention the size of a "training set" for the device's development. This is typical for a diagnostic assay where algorithms are often based on well-established molecular biology principles and analytical validation rather than machine learning on a large training set in the same way an imaging AI algorithm would. Previous FDA-cleared 510(k) K131706 references are made for analytical sensitivity, reactivity, specificity, interfering substances, carry-over contamination, RIF resistance study, reproducibility, and instrument system precision. These earlier studies would have involved extensive analytical testing to establish the device's performance characteristics.
9. How the ground truth for the training set was established
As there isn't a clearly defined "training set" in the context of machine learning, the establishment of ground truth would refer to the methods used during the development and analytical validation of the assay. This would involve:
- Known positive and negative samples: Using characterized bacterial strains (e.g., M. tuberculosis complex, non-tuberculous mycobacteria) and samples with known resistance profiles.
- Sequencing and other molecular methods: To confirm the presence of M. tuberculosis DNA and specific rpoB gene mutations associated with rifampin resistance.
- Culture results: As the gold standard for viability and identification of M. tuberculosis.
§ 866.3373 Nucleic acid-based in vitro diagnostic devices for the detection of Mycobacterium tuberculosis complex (MTB-complex) and the genetic mutations associated with MTB-complex antibiotic resistance in respiratory specimens.
(a)
Identification. Nucleic acid-based in vitro diagnostic devices for the detection ofMycobacterium tuberculosis complex (MTB-complex) and the genetic mutations associated with MTB-complex antibiotic resistance in respiratory specimens are qualitative nucleic acid-based devices that detect the presence of MTB-complex-associated nucleic acid sequences in respiratory samples. These devices are intended to aid in the diagnosis of pulmonary tuberculosis and the selection of an initial treatment regimen when used in conjunction with clinical findings and other laboratory results. These devices do not provide confirmation of antibiotic susceptibility since other mechanisms of resistance may exist that may be associated with a lack of clinical response to treatment other than those detected by the device.(b)
Classification. Class II (special controls). The special controls for this device are:(1) The FDA document entitled “Class II Special Controls Guideline: Nucleic Acid-Based In Vitro Diagnostic Devices for the Detection of
Mycobacterium tuberculosis Complex and Genetic Mutations Associated with Antibiotic Resistance in Respiratory Specimens,” which addresses the mitigation of risks specific to the detection of MTB-complex. For availability of the document, see § 866.1(e).(2) The following items, which address the mitigation of risks specific to the detection of the genetic mutations associated with antibiotic resistance of MTB-complex:
(i) The device must include an external positive assay control as appropriate. Acceptable positive assay controls include MTB-complex isolates containing one or more antibiotic-resistance associated target sequences detected by the device.
(ii) The device must include internal controls as appropriate. An acceptable internal control may include human nucleic acid co-extracted with MTB-complex containing nucleic acid sequences associated with antibiotic resistance and primers amplifying human housekeeping genes (e.g., RNaseP, β-actin).
(iii) The device's intended use must include a description of the scope of antibiotic resistance targeted by the assay, i.e., the specific drugs and/or drug classes.
(iv) The specific performance characteristics section of the device's labeling must include information regarding the specificity of the assay oligonucleotides for detecting mutations associated with antibiotic resistance of MTB-complex, and any information indicating the potential for non-specific binding (e.g., BLAST search).
(v) In demonstrating device performance you must perform:
(A) Pre-analytical studies that evaluate:
(
1 )Frozen samples. If there is use of any frozen samples in the device performance studies, or if there is a device claim for the use of frozen samples for testing, the effect of freezing samples prior to testing and the effect of multiple freeze/thaw cycles on both antibiotic susceptible and antibiotic resistant strains of MTB-complex.(
2 )Nucleic acid extraction methods. Extraction methods must parallel those used in devices for the detection of MTB-complex nucleic acid and confirm that the detection of the genetic mutations associated with antibiotic resistance is not affected.(B) Analytical studies that analyze:
(
1 )Limit of Detection. Limit of Detection must be determined in the most challenging matrix (e.g., sputum) claimed for use with the device. The Limit of Detection must be determined using both antibiotic susceptible and antibiotic resistant strains of MTB-complex. The antibiotic resistant strains must be those with well characterized genetic mutations associated with antibiotic resistance.(
2 )Analytical Reactivity (Inclusivity). Testing must be conducted to evaluate the ability of the device to detect genetic mutations associated with antibiotic resistance in a diversity of MTB-complex strains. Isolates used in testing must be well characterized. Isolate strain characterization must be determined using standardized reference methods recognized by a reputable scientific body and appropriate to the strain lineage.(
3 )Within-Laboratory (Repeatability) Precision Testing. Within-laboratory precision studies, if appropriate, must include at least one antibiotic resistant and one antibiotic susceptible strain of MTB-complex.(
4) Between Laboratory Reproducibility Testing. The protocol for the reproducibility study may vary slightly depending on the assay format; however, the panel must include at least one antibiotic resistant and one antibiotic susceptible strain of MTB-complex.(C) Clinical Studies. Clinical performance of the device must be established by conducting prospective clinical studies that include subjects with culture confirmed active tuberculosis. Studies must attempt to enroll subjects at risk for antibiotic-resistant MTB-complex; however, it may be necessary to include supplemental antibiotic resistant retrospective and contrived samples. Clinical studies must compare device results to both phenotypic drug susceptibility testing and genotypic reference methods. The genotypic reference method must be a polymerase chain reaction based method that uses primers different from those in the experimental device and confirmed by bidirectional sequencing.