(183 days)
The Cepheid Xpert MRSA/SA Skin and Soft Tissues Infection Assay (Xpert MRSA/SA SSTI Assay) performed in the GeneXpert® Dx System is a qualitative in vitro diagnostic test intended for the detection of Staphylococcus aureus (SA) and methicillin-resistant Staphylococcus aureus (MRSA) from skin and soft tissue infection swabs. The test utilizes automated real-time polymerase chain reaction (PCR) to detect MRSA/SA DNA. The Xpert MRSA/SA SSTI Assay is indicated for use in conjunction with other laboratory tests such as microbiology culture, and clinical data available to the clinician as an aid in the detection of MRSA/SA from skin and soft tissue infections. The Xpert MRSA/SA SSTI Assay is not intended to monitor treatment for MRSA/SA infections. Concomitant cultures for SA and MRSA are necessary to recover organisms for susceptibility testing or epidemiological typing. In a mixed culture containing MRSA/SA and other organisms (e.g. Gram negative bacilli, yeast), results can be false negative or variable depending on the concentration of MRSA/SA present, particularly if the concentration of MRSA/SA is close to the LoD of the assay.
The Cepheid Xpert MRSA/SA Skin and Soft Tissue Infection Assay (Xpert MRSA/SA SSTI Assay) is a rapid, automated DNA test for simultaneously detecting MRSA and SA directly from skin and soft tissue specimen is collected on a double swab, which is placed in a tube containing elution reagent. Following brief vortexing, the eluted matcrial and two single-use reagents (Reagent 1 and Reagent 2) that are provided with the assay are transferred to different, uniquely-labeled chambers of the disposable fluidic cartridge (the Xpert MRSA/SA cartridge). The user initiates a test from the system user interface and places the cartridge into the GeneXpert® Dx System instrument platform, which performs hands-off real-time, multiplex polymerase chain reaction (PCR) for detection of DNA. In this platform, additional sample preparation, amplification, and real-time detection are all fully-automated and completely integrated. The GeneXpert® System consists of a GeneXpert instrument, personal computer, and the multi-chambered fluidic cartridges that are designed to complete sample preparation and real-time PCR for detection of MRSA and SA in approximately 50 minutes. Each system has 1 to 16 randomly accessible modules that are each capable of performing separate sample preparation and real-time PCR tests. Each module contains a syringe drive for dispensing fluids, an ultrasonic horn for lysing cells or spores, and a proprietary I-CORE® thermocycler for performing real-time PCR and detection. The Xpert MRSA/SA Assay includes reagents for the simultaneous detection of the target organisms, SA and MRSA. The primers and probes in the Xpert MRSA/SA Assay detect nucleic acid sequences of the staphylococcal protein A (spa), the gene for MecA-Mediated Oxacillin resistance (mecA), and staphylococcal cassette chromosome (SCCmec) inserted in the SA chromosomal attB site. The test includes a sample processing control (SPC) to control for adequate processing of the target bacteria and to monitor the presence of inhibitor(s) in the PCR assay. The Probe Check Control (PCC) verifies reagent rehydration, PCR tube filling in the cartridge, probe integrity, and dye stability.
Here's a breakdown of the acceptance criteria and study details for the Cepheid Xpert MRSA/SA SSTI Assay, based on the provided text:
1. Table of Acceptance Criteria and Reported Device Performance
The document doesn't explicitly state "acceptance criteria" numerical targets in a table format. Instead, it presents performance data (Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA)) in comparison to a reference culture method. These performance metrics implicitly serve as the acceptance criteria for regulatory approval.
Implicit Acceptance Criteria (Performance Targets) and Reported Device Performance
| Metric (Relative to Reference Culture) | Performance Target (Implicit) | Reported Device Performance (No Antibiotic Use, n=441) | Reported Device Performance (Unknown Antibiotic Use, n=200) | Reported Device Performance (Known Antibiotic Use, n=207) |
|---|---|---|---|---|
| MRSA Detection: | ||||
| Positive Percent Agreement (MRSA+) | High agreement expected for detecting MRSA | 93.8% (95% CI: 88.6-97.1) | 94.0% (95% CI: 83.5-98.7) | 88.0% (95% CI: 75.7-95.5) |
| Negative Percent Agreement (MRSA+) | High agreement expected for correctly identifying absence of MRSA | 97.3% (95% CI: 94.7-98.8) | 97.3% (95% CI: 93.3-99.3) | 92.4% (95% CI: 87.0-96.0) |
| SA Detection: | ||||
| Positive Percent Agreement (SA+/MRSA+) | High agreement expected for detecting SA (including MRSA, as MRSA is a type of SA) | 95.7% (95% CI: 92.2-97.9) | 96.9% (95% CI: 91.2-99.4) | 95.2% (95% CI: 88.3-98.7) |
| Negative Percent Agreement (SA+/MRSA+) | High agreement expected for correctly identifying absence of SA (and MRSA) | 89.5% (95% CI: 84.6-93.3) | 88.3% (95% CI: 80.5-93.8) | 76.4% (95% CI: 67.9-83.6) |
| Analytical Performance: | ||||
| Analytical Specificity (Cross-reactivity) | 100% (No detection of non-target organisms) | 100% (All 105 tested isolates reported MRSA negative and SA negative) | N/A | N/A |
| Limit of Detection (LoD) - SA | Lowest CFU/swab at which 95% of replicates are positive (e.g., ≤ 150 CFU/swab) | 51 CFU/swab (N7129, USA900) to 123 CFU/swab (29213, unknown PFGE) | N/A | N/A |
| Limit of Detection (LoD) - MRSA | Lowest CFU/swab at which 95% of replicates are positive (e.g., ≤ 350 CFU/swab) | 82 CFU/swab (MW2, USA400) to 242 CFU/swab (ST59-MRSA-V, USA1000) | N/A | N/A |
| Reproducibility (Total Agreement) | High agreement across sites and days (e.g., ≥ 95%) | 94.2% (565/600, 1st study); 99.6% (239/240, 2nd study) | N/A | N/A |
| Carry-Over Contamination | No evidence of carry-over contamination (0 false positives after high positives) | 0% (All 21 negative samples correctly reported negative after 21 high positives) | N/A | N/A |
Note: The document states "The test results showed the Xpert MRSA/SA SSTI to be substantially equivalent to the current standard of care" and explicitly lists performance data, which are interpreted as meeting implicit acceptance criteria for regulatory clearance.
2. Sample Size Used for the Test Set and the Data Provenance
- Clinical Test Set Sample Size: A total of 848 specimens were collected from patients.
- No Antibiotic Use (within 3 weeks): 441 subjects
- Unknown Antibiotic Use (within 3 weeks): 200 subjects
- Known Antibiotic Use (within 3 weeks): 207 subjects
- Data Provenance: The study was a multi-site prospective investigation conducted at four US institutions. This means the data was collected specifically for this study in a forward-looking manner, and from within the United States.
3. Number of Experts Used to Establish the Ground Truth for the Test Set and the Qualifications of Those Experts
The document states that the reference culture method involved "confirmation of presumptive positive colonies was performed with catalase, tube coagulase, and Gram stain. MecA-Mediated Oxacillin resistance was tested by disk diffusion test using a 30 µg cefoxitin disk and cutoff of 21/22 mm." This implies standard microbiology laboratory procedures were followed by trained laboratory personnel.
- Number of Experts: Not explicitly stated as a specific number of individual "experts."
- Qualifications of Experts: Implied to be trained microbiologists or clinical laboratory technologists experienced in performing and interpreting standard microbiology culture, identification (catalase, coagulase, Gram stain), and susceptibility testing (cefoxitin disk diffusion). The reference culture was performed at a "centralized laboratory," suggesting specialized expertise.
4. Adjudication Method for the Test Set
The document does not describe a formal adjudication method (like 2+1 or 3+1 consensus) for the ground truth of the clinical test set. The "reference culture" is treated as the definitive ground truth, performed at a centralized laboratory following established protocols. Implicitly, any discrepancies would be resolved by the standard operating procedures of that centralized laboratory, but a multi-reader adjudication process is not detailed.
5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study was Done
No, an MRMC comparative effectiveness study involving human readers with and without AI assistance was not done. This device is an automated in vitro diagnostic test (Nucleic Acid Amplification Test) performed on a GeneXpert Dx System, designed to provide results directly without requiring human interpretation of complex images or data that AI might otherwise augment for human readers. Its comparison is against a reference culture method.
6. If a standalone (i.e. algorithm only without human-in-the loop performance) was done
Yes, a standalone performance study was done. The Xpert MRSA/SA SSTI Assay is an automated system (algorithm only without human interpretation in the loop beyond sample preparation and loading). The "Performance Characteristics" and "Clinical Performance" sections detail the direct comparison of the Xpert MRSA/SA SSTI Assay's results against the reference culture method, making it a standalone evaluation.
7. The Type of Ground Truth Used
The primary ground truth used for the clinical performance study was reference microbiology culture and susceptibility testing. This involved:
- Enrichment in trypticase soy broth.
- Streaking onto plates with and without cefoxitin.
- Sub-culturing presumptive colonies onto blood agar.
- Confirmation of positive colonies with catalase, tube coagulase, and Gram stain for Staphylococcus aureus (SA) identification.
- MecA-Mediated Oxacillin resistance tested by disk diffusion using a 30 µg cefoxitin disk and a cutoff of 21/22 mm for MRSA identification.
8. The Sample Size for the Training Set
The document does not explicitly state a sample size for a "training set" in the context of machine learning (AI). This device is a real-time PCR assay, which is a molecular diagnostic method based on known biological reactions, not typically developed using machine learning algorithms that require distinct training sets.
However, if "training set" is interpreted more broadly as data used for analytical development and optimization, the document mentions extensive analytical studies:
- Analytical Inclusivity Study on CDC Staphylococcus aureus Specimens: 21 MRSA strains and 3 MSSA strains (total 24 strains).
- Analytical Inclusivity Study on Expanded Panel of Staphylococcus aureus Specimens: 121 additional Staphylococcus aureus strains (78 MRSA, 43 SA).
- Evaluation of Empty Cassette Variants: 22 isolates.
- Limit of Detection Studies: Multiple individual isolates (6 MRSA, 3 SA) each tested with 20 replicates at various concentrations.
- Linearity Studies: SA and MRSA isolates tested across ten-fold serial dilutions.
- Cross-reactivity Study: 105 strains (various bacteria and yeast).
- Evaluation of BORSA Strains: 7 BORSA strains.
These analytical tests provide the data and parameters for the assay's design and demonstrate its performance characteristics, which is analogous to the role of a training set for algorithm development, even though it's a traditional molecular test.
9. How the Ground Truth for the Training Set Was Established
For the analytical studies (which can be considered analogous to a training/development phase for a molecular assay), the ground truth was established through:
- Confirmed Identification: Using CDC-reported strains, phylogenetically characterized strains, ATCC cultures, and NARSA strains.
- Phenotypic Testing: Catalase, tube coagulase, Gram stain, and cefoxitin disk diffusion (for oxacillin resistance) were used to characterize discrepant results and confirm the identity and resistance profile of isolates.
- Genetic Characterization: PFGE for USA types and SCCmec typing for MRSA strains provided detailed genetic ground truth.
- Known Concentrations: For LoD and linearity studies, bacterial concentrations were carefully quantified (CFU/sample) to establish precise analytical ground truth.
§ 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).