(177 days)
The Xpert Xpress Strep A test, performed on the GeneXpert Xpress System, is a rapid, qualitative in vitro diagnostic test for the detection of Streptococcus pyogenes (Group A B-hemolytic Strep A) in throat swab specimens from patients with signs and symptoms of pharyngitis. The Xpert Xpress Strep A test can be used as an aid in the diagnosis of Group A Streptococcal pharvngitis. The assay is not intended to monitor treatment for Group A Streptococus infections.
The Xpert Xpress Strep A test is an automated real-time polymerase chain reaction (PCR) in vitro diagnostic test for qualitative detection of Streptococcus pyogenes from throat swab specimens from patients with signs and symptoms of pharyngitis.
The Xpert Xpress Strep A test is performed on the Cepheid GeneXpert® Xpress System. The GeneXpert Xpress System platform automates sample preparation, amplification and real-time detection.
The GeneXpert Xpress System requires the use of single-use, disposable cartridges (the Xpert Xpress Strep A cartridges) that hold the PCR reagents and host the PCR process. Because the cartridges are self-contained and specimens never come into contact with working parts of the instrument modules, cross-contamination between samples is minimized.
The Xpress Strep A test includes primers and probes for the detection of a targeted sequence of the S. pyogenes genome allowing detection of Strep A directly from throat swab specimens collected from patients with signs and symptoms of pharyngitis. A Sample Processing Control (SPC) and a Probe Check Control (PCC) are internal controls utilized by the GeneXpert Xpress System platform. The SPC is present to control for adequate processing of the target bacteria and to monitor for the presence of inhibitor(s) in the PCR assay to avoid false-negative results. The Probe Check Control verifies reagent rehydration, real-time PCR tube filling in the cartridge, probe integrity, and dye stability.
The single-use, multi-chambered fluidic cartridges are designed to complete sample preparation and real-time PCR for the detection of genomic DNA S. pyogenes in ~24 minutes or less. The GeneXpert Xpress System, comprised of the GeneXpert Xpress II and GeneXpert Xpress IV, is capable of performing separate sample preparation and realtime PCR and RT-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 RT-PCR and detection.
Throat swab specimens are collected using the ESwab collection device and transported to the GeneXpert area and prepared according to package insert instructions. After mixing the specimen, the liquid sample is transferred to the Xpert Xpress Strep A cartridge. The user initiates a test from the system user interface and places the cartridge into the GeneXpert Xpress instrument platform, which performs hands-off real-time, multiplex PCR for detection of DNA. The results are automatically generated at the end of the process in a report that can be viewed and printed.
Here's a breakdown of the acceptance criteria and the study details for the Cepheid Xpert Xpress Strep A device, based on the provided FDA 510(k) summary:
1. Table of Acceptance Criteria and Reported Device Performance
The document does not explicitly state pre-defined "acceptance criteria" in a bulleted or numbered list with pass/fail thresholds. Instead, it presents the results of various studies and concludes substantial equivalence to a predicate device. For the purpose of this request, I will infer the acceptance criteria from the reported performance of the predicate device and the general regulatory expectations for such assays, then juxtapose it with the Xpert Xpress Strep A's performance.
| Acceptance Criterion (Inferred) | Xpert Xpress Strep A Reported Performance |
|---|---|
| Clinical Performance: | |
| Sensitivity (relative to culture) | 99.4% (95% CI: 96.5-99.9) |
| Specificity (relative to culture) | 94.1% (95% CI: 91.6-95.9) |
| Positive Predictive Value (PPV) | 85.3% (95% CI: 79.5-89.7) |
| Negative Predictive Value (NPV) | 99.8% (95% CI: 98.7-100.0) |
| Accuracy | 95.5% (95% CI: 93.5-96.8) |
| Indeterminate Rate (initial) | 5.3% (33/623) |
| Indeterminate Rate (after retest) | 0.8% (5/623) |
| Analytical Performance: | |
| Limit of Detection (LoD) - ATCC BAA-946 | 9 CFU/mL (3 CFU/test) |
| Limit of Detection (LoD) - ATCC 19615 | 18 CFU/mL (6 CFU/test) |
| Analytical Reactivity (Inclusivity) | 100% (24 S. pyogenes strains correctly detected at 3X LoD) |
| Analytical Specificity (Exclusivity) | 100% (70 potentially cross-reactive microorganisms reported as "Strep A NOT DETECTED") |
| Microbial Interference | No interference observed from 27 commensal microorganisms (with Strep A at 3X LoD) |
| Interfering Substances | No assay interference from 10 potentially interfering substances (e.g., blood, mucus, saliva) |
| Carry-Over Contamination | 0% (All 42 negative samples correctly reported as "Strep A NOT DETECTED" after high positive samples) |
| Reproducibility: | |
| Total Agreement (Negative) | 100% (90/90) |
| Total Agreement (Strep A High Neg) | 91% (82/90) |
| Total Agreement (Strep A Low Pos) | 97% (87/90) |
| Total Agreement (Strep A Moderate Pos) | 100% (90/90) |
| Initial Indeterminate Rate (reproducibility study) | 3.6% (13/360) (all resolved upon retesting) |
2. Sample Size and Data Provenance
- Clinical Study Test Set Sample Size: 618 specimens were included in the final analysis (initially 666, with 43 excluded).
- Data Provenance: The clinical study was a prospective, multi-center investigational study conducted at nine clinical sites in geographically diverse regions within the United States between January 2017 and May 2017.
3. Number of Experts and Qualifications for Ground Truth (Clinical Study)
The document specifies that the Xpert Xpress Strep A clinical performance was established relative to culture and latex agglutination for Strep A typing. It also mentions "an alternative PCR/bidirectional sequencing assay" used to investigate discordant results.
- Number of Experts: Not explicitly stated for establishing the primary ground truth (culture and latex agglutination). These methods are standard laboratory procedures typically performed by trained medical technologists or microbiologists.
- Qualifications of Experts: Not explicitly described. However, the use of standard microbiology lab techniques implies performance by qualified laboratory personnel. The "alternative PCR/bidirectional sequencing assay" would also be performed by trained molecular diagnosticians or researchers.
4. Adjudication Method (Clinical Study)
- Primary Adjudication: The primary ground truth for the clinical study was established by culture and latex agglutination for Strep A typing. This acts as the "gold standard" against which the device was compared.
- Discordant Analysis: For specimens where the Xpert Xpress Strep A result differed from the culture result, an "alternative PCR/bidirectional sequencing assay" was used to investigate the discrepancy. This serves as a secondary adjudication method to verify the true status of discordant samples.
5. Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study
- No, an MRMC comparative effectiveness study was not done. The Xpert Xpress Strep A is an automated in vitro diagnostic (IVD) test, not an AI system designed to assist human readers in image interpretation or similar tasks. Its performance is evaluated independently against a reference method (culture).
6. Standalone Performance
- Yes, a standalone performance study was done. The entire clinical study, analytical sensitivity, specificity, interference, and reproducibility studies assess the performance of the algorithm and instrument (Xpert Xpress Strep A test on the GeneXpert Xpress System) directly against various reference standards and controlled conditions, without human interpretation of the final result. The device provides a "Strep A DETECTED" or "Strep A NOT DETECTED" result automatically.
7. Type of Ground Truth Used (Clinical Study)
- The primary ground truth used for the clinical study was bacterial culture and latex agglutination for Strep A typing.
- For discordant sample resolution, an alternative PCR/bidirectional sequencing assay was used.
8. Sample Size for the Training Set
The document describes pre-market validation studies typically conducted for IVD devices, not machine learning model development. Therefore, there is no explicit "training set" sample size mentioned as would be the case for an AI/ML device. The device's underlying PCR assay design and algorithm are developed based on established scientific principles and analytical verification, rather than being "trained" on a large dataset in the AI sense.
9. How Ground Truth for the Training Set Was Established
As mentioned above, the concept of a "training set" and its "ground truth" in the AI/ML context is not directly applicable here. The device is a PCR assay with a defined molecular target and detection algorithm. The closest analogue to "ground truth establishment" during development would be:
- Analytical Validation: Extensive analytical studies (e.g., Limit of Detection, Inclusivity, Exclusivity, Interference) using well-characterized bacterial strains, spiked samples, and clinical matrices to ensure the assay correctly identifies the target organism and differentiates it from non-targets under various conditions. These studies confirm the assay's fundamental ability to detect S. pyogenes DNA.
- Assay Design and Optimization: The design of the primers and probes for the S. pyogenes genome target would be based on known genetic sequences, and optimized empirically to ensure specificity and sensitivity.
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April 26, 2018
Cepheid Jim Kelly Executive Director, Regulatory Affairs 904 Caribbean Drive Sunnyvale, California 94089
Re: K173398
Trade/Device Name: Xpert Xpress Strep A Regulation Number: 21 CFR 866.2680 Regulation Name: Streptococcus spp. nucleic acid-based assay Regulatory Class: Class II Product Code: PGX, OOI Dated: October 28, 2017 Received: October 31, 2017
Dear Jim Kelly:
We have reviewed your Section 510(k) premarket notification of intent to market the device referenced above and have determined the device is substantially equivalent (for the indications for use stated in the enclosure) to legally marketed predicate devices marketed in interstate commerce prior to May 28, 1976, the enactment date of the Medical Device Amendments, or to devices that have been reclassified in accordance with the provisions of the Federal Food. Drug, and Cosmetic Act (Act) that do not require approval of a premarket approval application (PMA). You may, therefore, market the device, subject to the general controls provisions of the Act. The general controls provisions of the Act include requirements for annual registration, listing of devices, good manufacturing practice, labeling, and prohibitions against misbranding and adulteration. Please note: CDRH does not evaluate information related to contract liability warranties. We remind you, however, that device labeling must be truthful and not misleading.
If your device is classified (see above) into either class II (Special Controls) or class III (PMA), it may be subject to additional controls. Existing major regulations affecting your device can be found in the Code of Federal Regulations, Title 21, Parts 800 to 898. In addition, FDA may publish further announcements concerning your device in the Federal Register.
Please be advised that FDA's issuance of a substantial equivalence determination does not mean that FDA has made a determination that your device complies with other requirements of the Act or any Federal statutes and regulations administered by other Federal agencies. You must comply with all the Act's requirements, including, but not limited to: registration and listing (21 CFR Part 807); labeling (21 CFR Part 801 and Part 809); medical device reporting of medical device-related adverse events) (21 CFR 803); good manufacturing practice requirements as set forth in the quality systems (QS) regulation (21 CFR
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Part 820); and if applicable, the electronic product radiation control provisions (Sections 531-542 of the Act); 21 CFR 1000-1050.
Also, please note the regulation entitled, "Misbranding by reference to premarket notification" (21 CFR Part 807.97). For questions regarding the reporting of adverse events under the MDR regulation (21 CFR Part 803), please go to http://www.fda.gov/MedicalDevices/Safety/ReportaProblem/default.htm for the CDRH's Office of Surveillance and Biometrics/Division of Postmarket Surveillance.
For comprehensive regulatory information about mediation-emitting products, including information about labeling regulations, please see Device Advice (https://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/) and CDRH Learn (http://www.fda.gov/Training/CDRHLearn). Additionally, you may contact the Division of Industry and Consumer Education (DICE) to ask a question about a specific regulatory topic. See the DICE website (http://www.fda.gov/DICE) for more information or contact DICE by email (DICE@fda.hhs.gov) or phone (1-800-638-2041 or 301-796-7100).
Sincerely,
Ribhi Shawar -S
For
Uwe Scherf, M.Sc., Ph.D. Director Division of Microbiology Devices Office of In Vitro Diagnostics and Radiological Health Center for Devices and Radiological Health
Enclosure
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Indications for Use
510(k) Number (if known) K173398
Device Name
Xpert Xpress Strep A
Indications for Use (Describe)
The Xpert Xpress Strep A test, performed on the GeneXpert Xpress System, is a rapid, qualitative in vitro diagnostic test for the detection of Streptococcus pyogenes (Group A B-hemolytic Strep A) in throat swab specimens from patients with signs and symptoms of pharyngitis. The Xpert Xpress Strep A test can be used as an aid in the diagnosis of Group A Streptococcal pharvngitis. The assay is not intended to monitor treatment for Group A Streptococus infections.
The Xpert Xpress Strep A test utilizes an automated real-time polymerase chain reaction (PCR) to detect Streptococcus pyogenes DNA.
Type of Use (Select one or both, as applicable)
| Prescription Use (Part 21 CFR 801 Subpart D) |
|---|
| Over-The-Counter Use (21 CFR 801 Subpart C) |
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510(k) Summary
As required by 21 CFR Section 807.92(c).
| Submitted by: | Cepheid904 Caribbean DriveSunnyvale, CA 90489Phone number: (847) 228-3299Fax number: (847) 890-6589 |
|---|---|
| Contact: | Jim Kelly, Ph.D. |
| Date of Preparation: | April 23, 2018 |
| Device: | |
| Trade name: | Xpert® Xpress Strep A |
| Common name: | Xpert Xpress Strep A |
| Type of Test: | Real-time PCR assay for qualitative detection of Group AStreptococcus DNA in throat swab specimens. |
| Regulation number,Classification name, | 21 CFR 866.2690, Streptococcus spp. nucleic acid basedassay, PGX |
| Product code: | 21 CFR 862.2570, Instrumentation for clinical multiplex testsystems, OOI |
| ClassificationAdvisory Panel | Microbiology (83) |
| Prescription Use | Yes |
| Predicate DeviceAssay: | IQuum Roche Liat™ Strep A Assay[510(k) #K1413381] |
Device Description:
The Xpert Xpress Strep A test is an automated real-time polymerase chain reaction (PCR) in vitro diagnostic test for qualitative detection of Streptococcus pyogenes from throat swab specimens from patients with signs and symptoms of pharyngitis.
The Xpert Xpress Strep A test is performed on the Cepheid GeneXpert® Xpress System. The GeneXpert Xpress System platform automates sample preparation, amplification and real-time detection.
The GeneXpert Xpress System requires the use of single-use, disposable cartridges (the Xpert Xpress Strep A cartridges) that hold the PCR reagents and host the PCR process. Because the cartridges are self-contained and specimens never come into contact with working parts of the instrument modules, cross-contamination between samples is minimized.
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The Xpress Strep A test includes primers and probes for the detection of a targeted sequence of the S. pyogenes genome allowing detection of Strep A directly from throat swab specimens collected from patients with signs and symptoms of pharyngitis. A Sample Processing Control (SPC) and a Probe Check Control (PCC) are internal controls utilized by the GeneXpert Xpress System platform. The SPC is present to control for adequate processing of the target bacteria and to monitor for the presence of inhibitor(s) in the PCR assay to avoid false-negative results. The Probe Check Control verifies reagent rehydration, real-time PCR tube filling in the cartridge, probe integrity, and dye stability.
The single-use, multi-chambered fluidic cartridges are designed to complete sample preparation and real-time PCR for the detection of genomic DNA S. pyogenes in ~24 minutes or less. The GeneXpert Xpress System, comprised of the GeneXpert Xpress II and GeneXpert Xpress IV, is capable of performing separate sample preparation and realtime PCR and RT-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 RT-PCR and detection.
Throat swab specimens are collected using the ESwab collection device and transported to the GeneXpert area and prepared according to package insert instructions. After mixing the specimen, the liquid sample is transferred to the Xpert Xpress Strep A cartridge. The user initiates a test from the system user interface and places the cartridge into the GeneXpert Xpress instrument platform, which performs hands-off real-time, multiplex PCR for detection of DNA. The results are automatically generated at the end of the process in a report that can be viewed and printed.
Device Intended Use:
The Xpert® Xpress Strep A test, performed on the GeneXpert Xpress System, is a rapid, qualitative in vitro diagnostic test for the detection of Streptococcus pyogenes (Group A ß-hemolytic Streptococcus, Strep A) in throat swab specimens from patients with signs and symptoms of pharyngitis. The Xpert Xpress Strep A test can be used as an aid in the diagnosis of Group A Streptoccal pharyngitis. The assay is not intended to monitor treatment for Group A Streptococcus infections.
The Xpert Xpress Strep A test utilizes an automated real-time polymerase chain reaction (PCR) to detect Streptococcus pyogenes DNA.
Substantial Equivalence:
The Xpert Xpress Strep A test is substantially equivalent to the Roche Liat Strep A Assay [510(k) # K141338]. The performance of the Xpert Xpress Strep A test was evaluated in a multi-site clinical study in which the performance of Xpert Xpress Strep A was determined relative to culture. The results of the study demonstrated that the performance of Xpert Xpress Strep A is substantially equivalent to the predicate device.
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Table 8-1 shows the similarities and differences between Xpert Xpress Strep A and the predicate device.
| Similarities | ||
|---|---|---|
| Item | Device | Predicate Device |
| Cepheid Xpert Xpress Strep A | IQuum Inc. (Roche) Liat Strep A Assay | |
| 510(k) Number | To be assigned | K141338 |
| Regulation | Same | 866.2680 |
| Product Code | Same | PGX |
| Device Class | Same | II |
| Intended Use | The Xpert® Xpress Strep A test, performed on the GeneXpert Xpress System, is a rapid, qualitative in vitro diagnostic test for the detection of Streptococcus pyogenes (Group A β-hemolytic Streptococcus , Strep A) in throat swab specimens from patients with signs and symptoms of pharyngitis. The Xpert Xpress Strep A test can be used as an aid in the diagnosis of Group A Streptococcal pharyngitis. The assay is not intended to monitor treatment for Group A Streptococcus infections. The Xpert Xpress Strep A test utilizes an automated real-time polymerase chain reaction (PCR) to detect Streptococcus pyogenes DNA. | The Liat™ Strep A Assay, performed on the Liat™ Analyzer, is a qualitative in vitro diagnostic test for the detection of Streptococcus pyogenes (Group A β-hemolytic Streptococcus ) in throat swab specimens from patients with signs and symptoms of pharyngitis. The Liat™ Strep A Assay utilizes nucleic acid purification and polymerase chain reaction (PCR) technology to detect Streptococcus pyogenes by targeting a segment of the Streptococcus pyogenes genome. |
| Assay Target | Same | Streptococcus A |
| Table 8-1: Comparison of Similarities and Differences | ||
|---|---|---|
| of Xpert Xpress Strep A with the Predicate Device |
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| Similarities | ||
|---|---|---|
| Item | DeviceCepheid Xpert Xpress Strep A | Predicate DeviceIQuum Inc. (Roche) Liat Strep A Assay |
| Specimen Type | Same | Throat swab |
| Assay Controls | Yes | Yes |
| Strep A Target | Same | Conserved sequence within thegenome of S. pyogenes |
| Assay Method | Same | PCR for detecting the presence / absence of bacterial DNA inclinical specimens |
| Extraction Method | Same | Automated nucleic acid extraction and purification |
| Detection Technique | Same | Different reporter dyes for target and Internal Control |
| Assay Result | Same | Qualitative |
| Differences | ||
| Item | New DeviceCepheid Xpert Xpress Strep A | Predicate DeviceIQuum Inc. (Roche) Liat Strep A Assay |
| Equipment Required | Cepheid GeneXpert® Dx,GeneXpert Infinity-48s,GeneXpert Infinity-80, andGeneXpert Xpress System | Liat™ Analyzer |
| Early assaytermination function | Yes(for positive samples) | No |
| Time-to-result | ~24 minutes without earlyassay termination;~18 minutes with early assaytermination for positivesamples | ~15 minutes |
The Xpert Xpress Strep A test has the same general intended use as the predicate device and has the same technological characteristics as the predicate device. The differences between Xpert Xpress Strep A and the predicate device do not raise different questions of safety and effectiveness. The clinical study demonstrates that the Xpert Xpress Strep A test is acceptable for its intended use with inexperienced lab users and is substantially equivalent to the predicate device described above.
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Non-Clinical Studies:
Analytical Sensitivity (Limit of Detection)
Studies were performed to determine the analytical sensitivity or Limit of Detection (LoD) of the Xpert Xpress Strep A using the ESwab collection kit. The limit of detection is the lowest concentration of sample (reported as CFU/mL in ESwab transport medium or CFU/test) that can be reproducibly distinguished from negative samples 95% of the time, or the lowest concentration of organisms at which 19 of 20 replicates were positive. This study determined the lowest concentration of Streptococcus pyogenes cells diluted into pooled clinical throat swab matrix that can be detected using the Xpert Xpress Strep A.
The analytical sensitivity of the Xpert Xpress Strep A was performed using two lots of reagents tested across three testing days with two Streptococcus pyogenes strains: ATCC BAA-946 and ATCC 19615.
The claimed LoD for each Strep A strain tested is summarized in Table 8-2.
| Strep A Strain | emm type | LoD(CFU/mL in ESwabtransport medium) | LoD(CFU/test) |
|---|---|---|---|
| ATCC BAA-946 | 6 | 9 | 3 |
| ATCC 19615 | 80 | 18 | 6 |
Table 8-2: Strep A LoD
Analytical Reactivity (Inclusivity)
Twenty-four Streptococcus pyogenes strains were tested at 3X LoD using the Xpert Xpress Strep A in replicates of three. The strains tested included representative isolates of emm types 1, 3, 4, 6, 11, 12, 18, 22, 25, 27, 38, 75, 77, 89, 94, 95. The list of strains tested in ESwab medium containing simulated throat swab matrix is shown in Table 8-3. All 24 strains were correctly reported as Strep A DETECTED with the Xpert Xpress Strep A.
Table 8-3: Analytical Reactivity (Inclusivity) of Xpert Xpress Strep A
| Strep A Strain ID | emm type | Strain |
|---|---|---|
| ATCC 12202 | 1 | NCTC 8370 |
| ATCC 12344 | 1 | T1 |
| ATCC 700294 | 1 | SF370 |
| ATCC 12383 | 3 | D58X |
| ATCC 12384 | 3 | C203 |
| ATCC 12385 | 4 | J17A4 |
| ATCC 12203 | 6 | NCTC 8709 |
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| Strep A Strain ID | emm type | Strain |
|---|---|---|
| ATCC 12352 | 11 | T11 |
| ATCC BAA-1065 | 12 | MGAS 2096 |
| ATCC BAA-1315 | 12 | MGAS9429 |
| ATCC 12357 | 18 | J17C |
| ATCC 10403 | 22 | T22 |
| ATCC 12204 | 25 | A25 |
| ATCC 8135 | 27 | T27 |
| ATCC 12365 | 38 | C107 |
| ATCC 12370 | 38 | C94 |
| ATCC 700497 | 75 | CDC-SS-1147 |
| ATCC 700499 | 77 | CDC-SS-1149 |
| ATCC 700949 | 89 | CDC-SS-1397 |
| ATCC BAA-355 | 94 | N/A |
| ATCC BAA-356 | 95 | N/A |
| ATCC 14289 | M protein-deficient S.pyogenes | C203 S |
| ATCC 49399 | emm type not available | QC A62 |
| ATCC 51339 | emm type not available | 1805 |
Analytical Specificity (Exclusivity)
The analytical specificity of the Xpert Xpress Strep A was evaluated by testing a panel of 70 potentially cross-reactive microorganisms, including species that are phylogenetically related to Streptococcus pyogenes and members of the throat commensal microflora (e.g., other bacteria, viruses, and yeast). The 70 organisms tested were identified as either Gram-positive (27), Gram-negative (33), or Gram-indeterminate (3), yeast (1), and viruses (6). Streptococcus Group B, Streptococcus Group C, and Streptococcus Group G strains were also included in this study. All strains were tested in triplicate in ESwab transport medium containing simulated throat swab matrix at ≥10 CFU/mL for bacteria and yeast and ≥10 TCID </mL for viruses. All three replicates of all 70 organisms were reported as Strep A NOT DETECTED by the Xpert Xpress Strep A (Table 8-4). The analytical specificity of the Xpert Xpress Strep A was 100%.
| Organism | Results |
|---|---|
| Acinetobacter baumannii | Strep A NOT DETECTED |
| Arcanobacterium haemolyticum | Strep A NOT DETECTED |
| Adenovirus, Type 1 | Strep A NOT DETECTED |
| Adenovirus, Type 7 | Strep A NOT DETECTED |
| Bacillus cereus | Strep A NOT DETECTED |
| Bordetella bronchiseptica | Strep A NOT DETECTED |
| Bordetella parapertussis | Strep A NOT DETECTED |
| Bordetella pertussis | Strep A NOT DETECTED |
| Organism | Results |
| Burkholderia cepacia | Strep A NOT DETECTED |
| Campylobacter rectus | Strep A NOT DETECTED |
| Candida albicans | Strep A NOT DETECTED |
| Corynebacterium diphtheriae | Strep A NOT DETECTED |
| Corynebacterium | Strep A NOT DETECTED |
| Cytomegalovirus AD-169 | Strep A NOT DETECTED |
| Enterococcus faecalis | Strep A NOT DETECTED |
| Enterococcus faecium | Strep A NOT DETECTED |
| Epstein-Barr Virus 4 | Strep A NOT DETECTED |
| Escherichia coli | Strep A NOT DETECTED |
| Fusobacterium necrophorum | Strep A NOT DETECTED |
| Haemophilus influenzae type A | Strep A NOT DETECTED |
| Haemophilus parahaemolyticus | Strep A NOT DETECTED |
| Haemophilus parainfluenzae | Strep A NOT DETECTED |
| Hepatitis B Virus | Strep A NOT DETECTED |
| Herpes Simplex Virus | Strep A NOT DETECTED |
| Klebsiella pneumoniae | Strep A NOT DETECTED |
| Lactobacillus acidophilus | Strep A NOT DETECTED |
| Lactococcus lactis subsp. lactis | Strep A NOT DETECTED |
| Legionella jordanis | Strep A NOT DETECTED |
| Legionella micdadei | Strep A NOT DETECTED |
| Legionella pneumophila | Strep A NOT DETECTED |
| Listeria monocytogenes | Strep A NOT DETECTED |
| Moraxella catarrhalis (two strains) | Strep A NOT DETECTED |
| Moraxella lacunata | Strep A NOT DETECTED |
| Mycoplasma pneumoniae | Strep A NOT DETECTED |
| Neisseria gonorrhoeae | Strep A NOT DETECTED |
| Neisseria lactamica | Strep A NOT DETECTED |
| Neisseria meningitidis | Strep A NOT DETECTED |
| Neisseria mucosa | Strep A NOT DETECTED |
| Neisseria sicca | Strep A NOT DETECTED |
| Neisseria subflava | Strep A NOT DETECTED |
| Peptostreptococcus micros | Strep A NOT DETECTED |
| Prevotella (Bacteroides) oralis | Strep A NOT DETECTED |
| Proteus mirabilis | Strep A NOT DETECTED |
| Proteus vulgaris | Strep A NOT DETECTED |
| Pseudomonas aeruginosa | Strep A NOT DETECTED |
| Pseudomonas fluorescens | Strep A NOT DETECTED |
| Serratia marcescens | Strep A NOT DETECTED |
| Staphylococcus aureus | Strep A NOT DETECTED |
| Staphylococcus epidermidis | Strep A NOT DETECTED |
| Organism | Results |
| Staphylococcus haemolyticus | Strep A NOT DETECTED |
| Stenotrophomonas maltophilia | Strep A NOT DETECTED |
| Streptococcus agalactiae | Strep A NOT DETECTED |
| Streptococcus anginosus | Strep A NOT DETECTED |
| Streptococcus bovis | Strep A NOT DETECTED |
| Streptococcus canis | Strep A NOT DETECTED |
| Streptococcus constellatus | Strep A NOT DETECTED |
| Streptococcus dysgalactiae | Strep A NOT DETECTED |
| Streptococcus equi | Strep A NOT DETECTED |
| Streptococcus gallolyticus | Strep A NOT DETECTED |
| Streptococcus intermedius | Strep A NOT DETECTED |
| Streptococcus mitis | Strep A NOT DETECTED |
| Streptococcus mutans | Strep A NOT DETECTED |
| Streptococcus oralis | Strep A NOT DETECTED |
| Streptococcus pneumoniae | Strep A NOT DETECTED |
| Streptococcus salivarius | Strep A NOT DETECTED |
| Streptococcus sanguinus | Strep A NOT DETECTED |
| Treponema denticola | Strep A NOT DETECTED |
| Veillonella parvula | Strep A NOT DETECTED |
| Yersinia enterocolitica | Strep A NOT DETECTED |
Table 8-4: Analytical Specificity of Xpert Xpress Strep A
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Microbial Interference
An interfering microorganism study was performed to assess the inhibitory effects of commensal microorganisms in throat swab samples on the performance of the Xpert Xpress Strep A. Twenty-seven microorganisms were tested for potential interference with Strep A detection (Table 8-5). The microorganisms were tested at ≥10° CFU/mL in the presence of Strep A at 3X LoD concentration in ESwab medium containing simulated throat swab matrix. The results showed that the presence of the tested microorganisms did not interfere with the detection of Strep A target DNA.
Table 8-5: Commensal Microorganisms Tested
| Organism |
|---|
| Acinetobacter baumannii |
| Candida albicans |
| Enterococcus faecalis |
| Fusobacterium necrophorum |
| Haemophilus influenzae type A |
| Lactobacillus acidophilus |
| Neisseria lactamicaa |
| Peptostreptococcus micros |
| Prevotella (Bacteroides) oralis |
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| Staphylococcus epidermidis |
|---|
| Streptococcus agalactiae |
| Streptococcus anginosus |
| Streptococcus bovis |
| Streptococcus canis |
| Streptococcus constellatus |
| Streptococcus dysgalactiae |
| Streptococcus equi |
| Streptococcus gallolyticus |
| Streptococcus intermedius |
| Streptococcus mitis |
| Streptococcus mutans |
| Streptococcus oralis |
| Streptococcus pneumoniae |
| Streptococcus salivarius |
| Streptococcus sanguinus |
| Treponema denticola |
| Veillonella parvula |
| a. Although all samples were reported appropriate |
as positive, reduced fluorescent signal was observed for the S. pyogenes target in the presence of high concentrations of N. lactamica.
Potentially Interfering Substances Study
Ten potentially interfering substances that may be present in clinical throat specimens with the potential to interfere with the performance of the Xpert Xpress Strep A were evaluated. The potentially interfering substances included blood, mucus, human saliva, sugarcontaining cold and flu remedies, cough medicine, antiseptic, salt-modifying remedies, pHmodifying remedies, antacids, and foods or drinks that increase salivary viscosity. The substances, active ingredients, and concentrations tested are listed in Table 8-6. Medically and/or physiologically relevant concentrations of potential interferents were tested in simulated throat swab matrix in the presence and absence of Strep A at 3X LoD.
There was no assay interference in the presence of the substances at the concentrations tested in this study. All positive and negative samples were correctly identified using the Xpert Xpress Strep A.
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| Substance/Class | Description/Active Ingredient | ConcentrationTested |
|---|---|---|
| Saliva | 100% Human Saliva | 6.5% (v/v) |
| Mucin | Bound sialic acid, 0.5-1.5% | 2.5% (w/v) |
| Blood | Whole human blood | 5.0% (v/v) |
| Antiseptic | 0.092% Eucalyptol,0.042% menthol,0.060% methyl salicylate,0.064% thymol | 6.5% (v/v)a |
| Cough Medicine | Dextromethorphan HBr USP 10 mg,Guaifenesin USP 200 mg | 5 mg/mL |
| Sugar-containingcold and fluremedies | Acetaminophen 650 mg,Dextromethorphan HBr 20 mg,Doxylamine Succinate 12.5 mg,Phenylephrine HCl 10 mg | 6.5% (v/v) |
| Salt-modifyingremedies | Sodium Chloride (0.65%) | 6.5% (v/v) |
| Foods/drinks thatincrease salivaryviscosity | Milk | 6.5% (v/v) |
| pH ModifyingRemedies | 100% Orange juice | 6.5% (v/v) |
| Antacids | Aluminum Hydroxide 400 mg(equivalent to dried gel, USP) - antacid,Magnesium Hydroxide 400 mg - antacid,Simethicone 40 mg - antigas | 6.5% (v/v) |
Table 8-6: Potential Interfering Substances Tested
a. Although all samples were reported appropriately as positive, reduced fluorescent signal for the S. pyogenes target was observed in the presence of antiseptic mouthwash at 6.5% v/v.
Carry-Over Contamination
A study was conducted to demonstrate that single-use, self-contained GeneXpert cartridges prevent specimen and amplicon carry-over contamination from very high titer positive samples (S. pyogenes) into successively run negative samples when processed in the same GeneXpert module. The study consisted of a negative sample processed in the same GeneXpert module immediately after processing a very high titer positive sample at a concentration ≥ 1 X 10° CFU/mL in ESwab transport medium containing simulated throat swab matrix. The testing scheme was repeated 40 times between 2 GeneXpert instruments (one module per instrument) for a total of 41 runs per instrument (20 high positive samples per instrument and 21 negative samples per instrument). There was no evidence of any carry-over contamination. All 42 negative samples were correctly
{13}------------------------------------------------
reported as Strep A NOT DETECTED. All 40 positive samples were correctly reported as Strep A DETECTED.
Linearity
Not applicable, the Xpert Xpress Strep A test is a qualitative assay.
Clinical Studies
Clinical Performance
A prospective, multi-center investigational study was conducted to evaluate the clinical performance of the Xpert Xpress Strep A. An initial throat swab was collected for the standard of care method and a second throat swab was collected from consented subjects for testing by the Xpert Xpress Strep A and reference method. The specimens were collected using ESwabs (flocked swab in Liquid Amies medium) from patients presenting with signs and symptoms of pharyngitis. The Xpert Xpress Strep A test was evaluated at nine clinical sites from geographically diverse regions within the United States between January 2017 and May 2017.
Six hundred sixty-six (666) specimens were initially enrolled in the study. Of these, 43 were excluded from the analysis due to failure to comply with the inclusion criteria (11), delay in shipment (27), reference method indeterminate (4) or incorrect specimen type (1).
Among the 623 specimens included in the analysis, 94.7% (590/623) were successful on the initial test and 99.2% (618/623) upon retest.
The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the Xpert Xpress Strep A were established relative to culture and latex agglutination for Strep A typing. The overall performance of the Xpert Xpress Strep A is presented in Table 8-7. Discordant results between Xpert Xpress Strep A and culture were investigated using an alternative PCR/bidirectional sequencing assay; the results of which are footnoted in Table 8-7.
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| Reference Method | ||||
|---|---|---|---|---|
| Pos | Neg | Total | ||
| Xpert XpressStrep A | Pos | 157 | 27a | 184 |
| Neg | 1b | 433 | 434 | |
| Total | 158 | 460 | 618c | |
| Sensitivity | 99.4% (95%CI: 96.5-99.9) | |||
| Specificity | 94.1% (95%CI: 91.6-95.9) | |||
| PPV | 85.3% (95%CI: 79.5-89.7) | |||
| NPV | 99.8% (95%CI: 98.7-100.0) | |||
| Accuracy | 95.5% (95%CI: 93.5-96.8) | |||
| Prevalence | 25.6% (95% CI: 22.3-29.1) |
Table 8-7: Performance of Xpert Xpress Strep A vs. Reference Method
a. Results from alternative PCR with bidirectional sequencing: 10 of 27 were Strep A Positive; 13 of 27 were Strep A Negative; 4 of 27 were inconclusive.
b. Results from alternative PCR with bidirectional sequencing: 1 of 1 was Strep A Negative.
On initial testing, 33/623 specimens (5.3%) produced indeterminate C. results; 31/33 were retested, of which 28 produced valid results that were included in the analysis of performance for a final indeterminate rate of 5/623 (0.8%).
Reproducibility Study
A four member reproducibility panel with varying concentrations of Streptococcus pvogenes was tested two times per day on five different days by three different operators at three sites (4 specimens x 2 times/day x 5 days x 3 operators x 3 sites). Three lots of Xpert Xpress Strep A cartridges were used. The samples were prepared in simulated throat swab matrix at the different concentration levels and are presented in Table 8-8. Results of the reproducibility study are summarized in Table 8-9 by study site/operator.
| Strain | Panel Member |
|---|---|
| Not applicable | Negative |
| ATCC BAA-946 (Streptococcus pyogenes) | High Negative (~0.05X LoD) |
| ATCC BAA-946 (Streptococcus pyogenes) | Low Positive (~1X LoD) |
| ATCC BAA-946 (Streptococcus pyogenes) | Moderate Positive (~3X LoD) |
Table 8-8: Reproducibility Panel
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| Sample | Site 1 | Site 2 | Site 3 | % TotalAgreementby Samplea,b | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Op 1 | Op 2 | Op 3 | Site | Op 1 | Op 2 | Op 3 | Site | Op 1 | Op 2 | Op 3 | Site | ||
| Neg | 100%(10/10) | 100%(10/10) | 100%(10/10) | 100%(30/30) | 100%(10/10) | 100%(10/10) | 100%(10/10) | 100%(30/30) | 100%(10/10) | 100%(10/10) | 100%(10/10) | 100%(30/30) | 100%(90/90) |
| Strep AHigh Neg | 70%(7/10) | 100%(10/10) | 100%(10/10) | 90%(27/30) | 80%(8/10) | 100%(10/10) | 100%(10/10) | 93%(28/30) | 90%(9/10) | 100%(10/10) | 80%(8/10) | 90%(27/30) | 91%(82/90) |
| Strep ALow Pos | 100%(10/10) | 100%(10/10) | 90%(9/10) | 97%(29/30) | 100%(10/10) | 90%(9/10) | 100%(10/10) | 97%(29/30) | 100%(10/10) | 100%(10/10) | 90%(9/10) | 97%(29/30) | 97%(87/90) |
| Strep AMod Pos | 100%(10/10) | 100%(10/10) | 100%(10/10) | 100%(30/30) | 100%(10/10) | 100%(10/10) | 100%(10/10) | 100%(30/30) | 100%(10/10) | 100%(10/10) | 100%(10/10) | 100%(30/30) | 100%(90/90) |
Table 8-9: Summary of Reproducibility Results: % Agreement by Study Site/Operator
a. Agreement based on expected result: Neg and High Neg=expected negative; Low Pos and Mod Pos=expected positive
b. Thirteen (13) indeterminate results were obtained over the course of the study for an initial indeterminate rate of 3.6% (13/360). In all cases, the expected results were obtained upon retesting.
The reproducibility of the Xpert Xpress Strep A was also evaluated in terms of the fluorescence signal expressed in Ct values for each target detected. The mean, standard deviation (SD), and coefficient of variation (CV) between-sites, between-lots, betweendays, between-operators and within-assay for each panel member are presented in Table 8-10.
| AssayChannel(Analyte) | Nᵃ | MeanCt | Between-Site | Between-Lot | Between-Day | Between-Operator | Within-Assay | Total | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample | SD | CV | SD | CV | SD | CV | SD | CV | SD | CV | SD | CV | |||
| Neg | SPC | 90 | 33.5 | 0.3 | 0.9 | 1.0 | 3.0 | 0.3 | 0.9 | 0 | 0 | 1.5 | 4.5 | 1.9 | 5.5 |
| Strep A High Neg | SPC | 82 | 33.6 | 0.4 | 1.2 | 1.1 | 3.2 | 0 | 0 | 0 | 0 | 1.3 | 3.9 | 1.7 | 5.2 |
| Strep A Low Pos | SAᵇ | 87 | 38.6 | 0 | 0 | 0.4 | 0.9 | 0 | 0 | 0 | 0 | 1.3 | 3.4 | 1.3 | 3.5 |
| Strep A Mod Pos | SAᵇ | 90 | 37.2 | 0 | 0 | 0.1 | 0.3 | 0.2 | 0.5 | 0.2 | 0.5 | 0.9 | 2.4 | 1.0 | 2.6 |
Table 8-10: Summary of Reproducibility Data
a. Results with non-zero Ct values out of 90.
b. SA = Strep A
Conclusions
The results of the nonclinical analytical and clinical performance studies summarized above demonstrate that the Xpert Xpress Strep A test is substantially equivalent to the predicate device.
§ 866.2680
Streptococcus spp. nucleic acid-based assay.(a)
Identification. AStreptococcus spp. nucleic acid-based assay is a qualitative in vitro diagnostic device intended to simultaneously detect and identify variousStreptococcus spp. nucleic acids extracted directly from clinical specimens. The device detects specific nucleic acid sequences for organism identification. 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 II (special controls). The special controls for this device are:(1) Premarket notification submissions must include detailed device description documentation, including the device components, ancillary reagents required but not provided, and a detailed explanation of the methodology including primer/probe sequence, design, and rationale for sequence selection.
(2) Premarket notification submissions must include detailed documentation from the following analytical and clinical performance studies: Analytical sensitivity (Limit of Detection), reactivity, inclusivity, precision, reproducibility, interference, cross reactivity, carry-over, and cross contamination.
(3) Premarket notification submissions must include detailed documentation from a clinical study. The study, performed on a study population consistent with the intended use population, must compare the device performance to results obtained from well-accepted reference methods.
(4) Premarket notification submissions must include detailed documentation for device software, including, but not limited to, software applications and hardware-based devices that incorporate software.
(5) Premarket notification submissions must include database implementation methodology, construction parameters, and quality assurance protocols, as appropriate.
(6) The device labeling must include limitations regarding the need for culture confirmation of negative specimens, as appropriate.
(7) A detailed explanation of the interpretation of results and acceptance criteria must be included in the device's 21 CFR 809.10(b)(9) compliant labeling.
(8) Premarket notification submissions must include details on an end user device training program that will be offered while marketing the device, as appropriate.