(73 days)
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No
The description focuses on automated real-time PCR and internal controls, with no mention of AI or ML algorithms for data analysis or interpretation.
No
This device is described as an "in vitro diagnostic test" for the detection of a specific bacteria. It is used to diagnose a condition, not to treat or directly manage a patient's health.
Yes
The "Intended Use / Indications for Use" section explicitly states that it is a "qualitative in vitro diagnostic test for the detection of Streptoccus pyogenes". The "Device Description" also refers to it as an "in vitro diagnostic test". It aids in diagnosing pharyngitis by detecting Strep A.
No
The device is an in vitro diagnostic test that requires specific hardware components (GeneXpert Instrument Systems, single-use cartridges) to perform the assay. It is not solely software.
Yes, this device is an IVD (In Vitro Diagnostic).
Here's why:
- Explicitly Stated in Intended Use and Device Description: The document repeatedly and clearly states that the Xpert Xpress Strep A Assay is an "in vitro diagnostic test."
- Purpose: The test is designed to detect Streptococcus pyogenes in throat swab specimens from patients with symptoms of pharyngitis. This is a diagnostic purpose performed in vitro (outside the body) on a biological sample.
- Method: It utilizes automated real-time polymerase chain reaction (PCR), a common technique used in in vitro diagnostics to detect specific genetic material.
- Specimen Type: It uses throat swab specimens, which are biological samples collected from a patient.
- Intended Use/Indications for Use: The "Intended Use / Indications for Use" section explicitly defines the purpose of the device as a diagnostic test.
N/A
Intended Use / Indications for Use
The Xpert® Xpress Strep A Assay, performed on the GeneXpert Instrument Systems, is a rapid, qualitative in vitro diagnostic test for the detection of Streptoccus pyogenes (Group A beta-hemolytic Strep A) in throat swab specimens from patients with signs and symptoms of pharyngitis.
The Xpert Xpress Strep A Assay utilizes an automated real-time polymerase chain reaction (PCR) to detect Streptococcus pyogenes DNA.
Product codes (comma separated list FDA assigned to the subject device)
PGX, OOI
Device Description
The Xpert Xpress Strep A Assay 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 Assay is performed on the Cepheid GeneXpert® Instrument Systems (GeneXpert Dx, GeneXpert Infinity-48s, and GeneXpert Infinity-80 systems). The GeneXpert Instrument System platform automates sample preparation, amplification and real-time detection.
The GeneXpert Instrument Systems require 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 Assay includes primers and probes for the simultaneous detection and differentiation 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 Instrument 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 Instrument Systems, comprised of the GeneXpert Dx Systems and the GeneXpert Infinity Systems, have 1 to 80 randomly accessible modules. depending upon the instrument, that are each capable of performing separate sample preparation and real-time 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 Assay cartridge. The user initiates a test from the system user interface and places the cartridge into the GeneXpert 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.
Mentions image processing
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Mentions AI, DNN, or ML
Not Found
Input Imaging Modality
Not Found
Anatomical Site
throat swab specimens
Indicated Patient Age Range
Not Found
Intended User / Care Setting
Not Found
Description of the training set, sample size, data source, and annotation protocol
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Description of the test set, sample size, data source, and annotation protocol
Clinical Performance Study:
Clinical specimens were collected from two multi-center investigational studies using throat ESwab specimens (flocked swab in Liquid Amies medium) from patients presenting with signs and symptoms of pharyngitis. One study enrolled consented subjects from whom a second prospective throat swab specimen was collected following the collection of a standard of care (SOC) throat swab. Another study tested specimens from subjects for which leftover excess standard of care (SOC) throat swab specimens were available. Across the two studies, the Xpert Xpress Strep A assay was evaluated by 9 clinical sites from geographically diverse regions within the United States between December 2016 and March 2017.
Eight hundred and forty-four (844) specimens were initially enrolled in the two studies. Of these, 261 were excluded from the analysis of performance due to failure to comply with the inclusion criteria (19), reference culture procedural error (184), delay in reference culture inoculation (31), delay in shipment (26) or labeling error (1).
Among the 583 specimens included in the analysis of performance, 96.9 (565/583) were successful on the initial test and upon retest 99.0% (577/583) gave valid results.
The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the Xpert Xpress Strep A Assay were established relative to culture and latex agglutination for Strep A typing. Results of the first study (second swab specimens) and the second study (SOC throat swab, i.e., first swab) are presented separately.
Discordant results between Xpert Xpress Strep A and culture were investigated using an alternative PCR/bidirectional sequencing assay.
Reproducibility Study:
A three member reproducibility panel with varying concentrations of Streptococcus pyogenes was tested 4 times per day on six different days by two different operators at three sites. Three lots of Xpert Xpress Strep A Assay cartridges were used, with each representing two days of testing. The samples were prepared in simulated throat swab matrix at the different concentration levels.
Sample Panel:
- Negative
- Strep A Low Positive (~1X LoD)
- Strep A Moderate Positive (~3X LoD)
When the study was initially performed, there was an unexpectedly high rate of indeterminate results (47/432 = 10.8%), although no false positive or false negative results were observed. Upon retest of the indeterminate samples, the indeterminate rate was reduced to 2.8% (12/432). Following an investigation, the study was repeated with fresh panels and different lots of reagents.
Summary of Performance Studies (study type, sample size, AUC, MRMC, standalone performance, key results)
Non-Clinical Studies:
- Analytical Sensitivity (Limit of Detection - LoD): Studies were performed to determine the analytical sensitivity or LoD of the Xpert Xpress Strep A Assay using the ESwab collection kit. The LoD is the lowest concentration of sample (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. Two lots of reagents were tested across three testing days with two Streptococcus pyogenes strains: ATCC BAA-946 and ATCC 19615.
- Results:
- ATCC BAA-946: LoD (CFU/mL in ESwab transport medium) = 9, LoD (CFU/test) = 3
- ATCC 19615: LoD (CFU/mL in ESwab transport medium) = 18, LoD (CFU/test) = 6
- Results:
- Analytical Reactivity (Inclusivity): 24 Streptococcus pyogenes strains were tested at 3X LoD using the Xpert Xpress Strep A Assay in replicates of three. Strains included representative isolates of various emm-types.
- Results: All 24 strains were correctly reported as Strep A DETECTED.
- Analytical Specificity (Exclusivity): A panel of 70 potentially cross-reactive microorganisms (Gram-positive, Gram-negative, Gram-indeterminate, yeast, viruses, and other Streptococcus groups) was tested. 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.
- Results: All three replicates of all 70 organisms were reported as Strep A NOT DETECTED. Analytical specificity was 100%.
- 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 Assay. 27 microorganisms were tested at ≥10^6 CFU/mL in the presence of Strep A at 3X LoD concentration in ESwab medium containing simulated throat swab matrix.
- Results: The presence of the tested microorganisms did not interfere with the detection of Strep A target DNA.
- Potentially Interfering Substances Study: Ten potentially interfering substances (blood, mucus, human saliva, sugar-containing cold and flu remedies, cough medicine, antiseptic, salt-modifying remedies, pH-modifying remedies, antacids, and foods or drinks that increase salivary viscosity) were evaluated. Medically and/or physiologically relevant concentrations were tested in simulated throat swab matrix in the presence and absence of Strep A at 3X LoD.
- Results: There was no assay interference in the presence of the substances at the tested concentrations. All positive and negative samples were correctly identified.
- Carry-Over Contamination: Demonstrated that single-use, self-contained GeneXpert cartridges prevent specimen and amplicon carry-over contamination. A negative sample was processed in the same GeneXpert module immediately after processing a very high titer positive sample (≥ 1 X 10^7 CFU/mL). The testing scheme was repeated 40 times between 2 GeneXpert instruments.
- Results: All 42 negative samples were correctly reported as Strep A NOT DETECTED. All 40 positive samples were correctly reported as Strep A DETECTED. No evidence of carry-over contamination.
Clinical Studies:
- Clinical Performance:
- Study Type: Multi-site clinical study.
- Sample Size: 577 valid results out of 844 initially enrolled specimens (after exclusions).
- Standalone Performance: The Xpert Xpress Strep A Assay demonstrated performance relative to culture and latex agglutination for Strep A typing.
- Key Results (Overall Performance - First and Second Swab Data Combined):
- Sensitivity: 100.0% (95% CI: 97.3-100.0)
- Specificity: 94.1% (95% CI: 91.5-95.9)
- PPV: 84.1% (95% CI: 77.8-88.9)
- NPV: 100.0% (95% CI: 99.1-100.0)
- Initial indeterminate rate: 3.1% (18/583), final indeterminate rate after retest: 0.9% (6/583).
- Discordant results investigated with alternative PCR/bidirectional sequencing: 21 of 26 discrepant negative samples were Strep A Positive by alternative PCR.
- Reproducibility Study:
- Study Type: Multi-site, multi-operator, multi-lot study.
- Sample Size: 432 data points (3 panel members x 4 times/day x 6 days x 2 operators x 3 sites).
- Key Results (Repeat Study):
- Negative samples: 100% agreement (144/144)
- Low Positive samples: 98.6% agreement (142/144)
- Moderate Positive samples: 100% agreement (144/144)
- Initial indeterminate rate: 2.5% (11/432); all expected results obtained upon retesting.
- Reproducibility of fluorescence signal (Ct values) evaluated by between-site, between-lot, between-day, between-operator, and within-assay variability (mean Ct, SD, CV reported).
Key Metrics (Sensitivity, Specificity, PPV, NPV, etc.)
Overall Performance of the Xpert Xpress Strep A Assay vs. Reference Method (First and Second Swab Data Combined):
- Sensitivity: 100.0% (95% CI: 97.3-100.0)
- Specificity: 94.1% (95% CI: 91.5-95.9)
- PPV: 84.1% (95% CI: 77.8-88.9)
- NPV: 100.0% (95% CI: 99.1-100.0)
Performance of the Xpert Xpress Strep A Assay vs. Reference Method (Data for First and Second Swab):
- First Swab:
- Sensitivity: 100% (95% CI: 94.4-100)
- Specificity: 96.4% (95% CI: 93.4-98.1)
- NPV: 100% (95% CI: 98.5-100)
- PPV: 87.8% (95% CI: 78.5-93.5)
- Second Swab:
- Sensitivity: 100% (95% CI: 95.0-100)
- Specificity: 90.9% (95% CI: 85.9-94.2)
- NPV: 100% (95% CI: 97.8-100)
- PPV: 81.1% (95% CI: 71.8-87.9)
Predicate Device(s): If the device was cleared using the 510(k) pathway, identify the Predicate Device(s) K/DEN number used to claim substantial equivalence and list them here in a comma separated list exactly as they appear in the text. List the primary predicate first in the list.
Reference Device(s): Identify the Reference Device(s) K/DEN number and list them here in a comma separated list exactly as they appear in the text.
Not Found
Predetermined Change Control Plan (PCCP) - All Relevant Information for the subject device only (e.g. presence / absence, what scope was granted / cleared under the PCCP, any restrictions, etc).
Not Found
§ 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.
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Image /page/0/Picture/1 description: The image shows the logo for the U.S. Department of Health & Human Services. The logo consists of a circular seal with the words "DEPARTMENT OF HEALTH & HUMAN SERVICES - USA" arranged around the perimeter. Inside the circle is a stylized image of three human profiles facing to the right, with flowing lines connecting them.
Food and Drug Administration 10903 New Hampshire Avenue Document Control Center - WO66-G609 Silver Spring, MD 20993-0002
September 25, 2017
CEPHEID JIM KELLY EXECUTIVE DIRECTOR, REGULATORY AFFAIRS 904 CARIBBEAN DRIVE SUNNYVALE CA 94089
Re: K172126
Trade/Device Name: Xpert Xpress Strep A Regulation Number: 21 CFR 866.2680 Regulation Name: Streptococcus spp. nucleic-acid based assay Regulatory Class: II Product Code: PGX, OOI Dated: July 13, 2017 Received: July 14, 2017
Dear Dr. 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 Parts 801 and 809); medical device reporting (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 Part 820); and if applicable, the electronic product radiation control provisions (Sections 531-542 of the Act); 21 CFR 1000-1050.
1
If you desire specific advice for your device on our labeling regulations (21 CFR Parts 801 and 809), please contact the Division of Industry and Consumer Education at its toll-free number (800) 638 2041 or (301) 796-7100 or at its Internet address
http://www.fda.gov/MedicalDevices/Resourcesfor You/Industry/default.htm. 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.
You may obtain other general information on your responsibilities under the Act from the Division of Industry and Consumer Education at its toll-free number (800) 638-2041 or (301) 796-7100 or at its Internet address
http://www.fda.gov/MedicalDevices/ResourcesforYou/Industry/default.htm.
Sincerely yours,
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
2
Indications for Use
510(k) Number (if known) K172126
Device Name Xpert Xpress Strep A
Indications for Use (Describe)
The Xpert Xpress Strep A Assay, performed on the GeneXpert Instrument Systems, is a rapid, qualitative in vitro diagnostic test for the detection of Streptoccus pyogenes (Group A beta-hemolytic Strep A) in throat swab specimens from patients with signs and symptoms of pharyngitis.
The Xpert Xpress Strep A Assay 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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3
510(k) Summary
As required by 21 CFR Section 807.92(c).
| Submitted by: | Cepheid
904 Caribbean Drive
Sunnyvale, CA 90489
Phone number: (847) 228-3299
Fax number: (847) 890-6589 |
|-------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|
| Contact: | Jim Kelly, Ph.D. |
| Date of Preparation: | September 19, 2017 |
| Device: | |
| Trade name: | Xpert® Xpress Strep A |
| Common name: | Xpert Xpress Strep A Assay |
| Type of Test: | Real-time PCR assay for qualitative detection of Group A
Streptococcus DNA in throat swab specimens. |
| Regulation number,
Classification name,
Product code: | 21 CFR 866.2690, Streptococcus spp. nucleic acid based
assay, PGX
21 CFR 862.2570, Instrumentation for clinical multiplex test
systems, OOI |
| Classification
Advisory Panel | Microbiology (83) |
| Prescription Use | Yes |
| Predicate Device
Assay: | IQuum Roche Liat™ Strep A Assay
[510(k) #K141338] |
4
Device Description:
The Xpert Xpress Strep A Assay 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 Assay is performed on the Cepheid GeneXpert® Instrument Systems (GeneXpert Dx, GeneXpert Infinity-48s, and GeneXpert Infinity-80 systems). The GeneXpert Instrument System platform automates sample preparation, amplification and real-time detection.
The GeneXpert Instrument Systems require 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 Assay includes primers and probes for the simultaneous detection and differentiation 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 Instrument 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 Instrument Systems, comprised of the GeneXpert Dx Systems and the GeneXpert Infinity Systems, have 1 to 80 randomly accessible modules. depending upon the instrument, that are each capable of performing separate sample preparation and real-time 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 Assay cartridge. The user initiates a test from the system user interface and places the cartridge into the GeneXpert 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.
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Device Intended Use:
The Xpert® Xpress Strep A Assay, performed on the GeneXpert Instrument Systems, is a rapid, qualitative in vitro diagnostic test for the detection of Streptococcus pyogenes (Group A B-hemolytic Streptococcus, Strep A) in throat swab specimens from patients with signs and symptoms of pharyngitis.
The Xpert Xpress Strep A Assay utilizes an automated real-time polymerase chain reaction (PCR) to detect Streptococcus pyogenes DNA.
Substantial Equivalence:
The Xpert Xpress Strep A Assay is substantially equivalent to the Roche Liat Strep A Assay [510(k) # K141338]. The performance of the Xpert Xpress Strep A Assay was evaluated in a multi-site clinical study in which the performance of the Xpert Xpress Strep A Assay was determined relative to culture. The results of the study demonstrated that the performance of the Xpert Xpress Strep A Assay is substantially equivalent to that of the predicate device.
Table 8-1 shows the similarities and differences between the Xpert Xpress Strep A Assay and the predicate device.
| Similarities | ||
|---|---|---|
| Item | Device | Predicate Device |
| Cepheid Xpert Xpress Strep | ||
| A Assay | IQuum Inc. (Roche) Liat | |
| Strep A Assay | ||
| 510(k) Number | K172126 | K141338 |
| Regulation | Same | 866.2680 |
| Product Code | Same | PGX |
| Device Class | Same | II |
| Similarities | ||
| Item | Device | |
| Cepheid Xpert Xpress Strep A Assay | Predicate Device | |
| IQuum Inc. (Roche) Liat Strep A Assay | ||
| Intended Use | The Xpert® Xpress Strep A | |
| Assay, performed on the | ||
| GeneXpert Instrument | ||
| Systems, 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 | ||
| Assay 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 ß- | ||
| 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 |
| Specimen Type | Same | Throat swab |
| Assay Controls | Yes | Yes |
| Strep A Target | Same | Conserved sequence within the |
| genome of S. pyogenes | ||
| Assay Method | Same | PCR for detecting the presence |
| / absence of bacterial DNA in | ||
| clinical 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 | ||
| New Device | Predicate Device | |
| Item | Cepheid Xpert Xpress Strep | |
| A Assay | IQuum Inc. (Roche) Liat | |
| Strep A Assay | ||
| Equipment Required | Cepheid GeneXpert® Dx, | |
| GeneXpert Infinity-48s, and | ||
| GeneXpert Infinity-80 | Liat™ Analyzer | |
| Early assay | ||
| termination function | Yes | |
| (for positive samples) | No | |
| Time-to-result | ~24 minutes without early | |
| assay termination; | ||
| ~18 minutes with early assay | ||
| termination for positive | ||
| samples | ~15 minutes |
Table 8-1: Comparison of Similarities and Differences of the Xpert Xpress Strep A Assay with the Predicate Device
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7
The Xpert Xpress Strep A Assay has the same general intended use as the predicate device and has the same technological characteristics as the predicate device. The differences between the Xpert Xpress Strep A Assay and the predicate device do not raise different questions of safety and effectiveness. The clinical study demonstrates that the Xpert Xpress Strep A Assay is acceptable for its intended use with inexperienced lab users and is substantially equivalent to the predicate device described above.
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 Assay using the ESwab collection kit (Copan P/N 480CE or 480C referred to as the "ESwab"). 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 Assay.
The analytical sensitivity of the Xpert Xpress Strep A Assay 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.
8
| Strep A Strain | emm type | LoD
(CFU/mL in
ESwab
transport
medium) | LoD
(CFU/test) |
|----------------|----------|----------------------------------------------------|-------------------|
| ATCC BAA-946 | 6 | 9 | 3 |
| ATCC 19615 | 80 | 18 | 6 |
Table 8-2: Strep A LoD and Confidence Intervals
Analytical Reactivity (Inclusivity)
Twenty-four Streptococcus pyogenes strains were tested at 3X LoD using the Xpert Xpress Strep A Assay 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 Assay.
| 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 |
| 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 |
Table 8-3: Analytical Reactivity (Inclusivity) of the Xpert Xpress Strep A Assay
9
Analytical Specificity (Exclusivity)
The analytical specificity of the Xpert Xpress Strep A Assay 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 Veillonella parvula |
| a. Although all samples were reported appropriately
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 Assay were evaluated. The potentially interfering substances included blood, mucus, human saliva, sugar-containing cold and flu remedies, cough medicine, antiseptic, salt-modifying remedies, pH-modifying 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 Assay.
| Substance/Class | Description/Active Ingredient | Concentration Tested |
|---|---|---|
| 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-containing | ||
| cold and flu | ||
| remedies | Acetaminophen 650 mg, | |
| Dextromethorphan HBr 20 mg, | ||
| Doxylamine Succinate 12.5 mg, | ||
| Phenylephrine HCl 10 mg | 6.5% (v/v) | |
| Salt-modifying | ||
| remedies | Sodium Chloride (0.65%) | 6.5% (v/v) |
Table 8-6: Potential Interfering Substances Tested
13
| Substance/Class | Description/Active Ingredient | Concentration
Tested |
|-----------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------|
| Foods/drinks that
increase salivary
viscosity | Milk | 6.5% (v/v) |
| pH Modifying
Remedies | 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) |
a. Although all samples were reported appropriately as positive or negative, 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 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 Assay is a qualitative assay.
Clinical Studies
Clinical Performance
Clinical specimens were collected from two multi-center investigational studies using throat ESwab specimens (flocked swab in Liquid Amies medium) from patients presenting with signs and symptoms of pharyngitis. One study enrolled consented subjects from whom a second prospective throat swab specimen was collected following the collection of a standard of care (SOC) throat swab. Another study tested specimens from subjects for which leftover excess standard of care (SOC) throat swab specimens were available. Across the two studies, the Xpert Xpress Strep A assay was evaluated by 9 clinical sites from geographically diverse regions within the United States between December 2016 and March 2017.
14
Eight hundred and forty-four (844) specimens were initially enrolled in the two studies. Of these, 261 were excluded from the analysis of performance due to failure to comply with the inclusion criteria (19), reference culture procedural error (184), delay in reference culture inoculation (31), delay in shipment (26) or labeling error (1).
Among the 583 specimens included in the analysis of performance, 96.9 (565/583) were successful on the initial test and upon retest 99.0% (577/583) gave valid results.
The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the Xpert Xpress Strep A Assay were established relative to culture and latex agglutination for Strep A typing. The overall performance of the Xpert Xpress Strep Assay from both studies combined is presented in Table 8-7. Results of the first study (second swab specimens) and the second study (SOC throat swab, i.e., first swab) are presented separately in Table 8-8. Discordant results between Xpert Xpress Strep A and culture were investigated using an alternative PCR/bidirectional sequencing assay and results, the results of which are footnoted in Table 8-7 and Table 8-8.
| Table 8-7: Overall Performance of the Xpert Xpress Strep A Assay vs. Reference | |
|---|---|
| Method (First and Second Swab Data Combined) |
| Reference Method | ||||
|---|---|---|---|---|
| Xpert Xpress | ||||
| Strep A Assay | Strep A | Positive | Negative | Total |
| Positive | 138 | 26a | 164 | |
| Negative | 0 | 413 | 413 | |
| Total | 138 | 439 | 577b | |
| Sensitivity | 100.0% (95% CI: 97.3-100.0) | |||
| Specificity | 94.1% (95% CI: 91.5-95.9) | |||
| PPV | 84.1% (95% CI: 77.8-88.9) | |||
| NPV | 100.0% (95% CI: 99.1-100.0) |
a. Results from alternative PCR with bidirectional sequencing: 21 of 26 were Strep A Positive; 4 of 26 were Strep A Negative; 1 of 26 samples was not tested.
b. On initial testing, 18/583 specimens (3.1%) produced indeterminate results; 16/18 were retested, of which 12 produced valid results that were included in the analysis of performance for a final indeterminate rate of 6/583 (0.9%)
15
| First Swaba | Second Swabb | |||
|---|---|---|---|---|
| N | % (95% CI) | N | % (95% CI) | |
| Sensitivity | 65/65 | 100% | ||
| (94.4-100) | 73/73 | 100% | ||
| (95.0-100) | ||||
| Specificity | 244/253c | 96.4% | ||
| (93.4-98.1) | 169/186d | 90.9% | ||
| (85.9-94.2) | ||||
| NPV | 244/244 | 100% | ||
| (98.5-100) | 169/169 | 100% | ||
| (97.8-100) | ||||
| PPV | 65/74 | 87.8% | ||
| (78.5-93.5) | 73/90 | 81.1% | ||
| (71.8-87.9) |
Table 8-8: Performance of the Xpert Xpress Strep A Assay vs. Reference Method (Data for First and Second Swab)
a. On initial testing, 9/321 specimens (2.8%) produced indeterminate results; 7/9 were retested, of which 6 produced valid results that were included in the analysis of performance for a final indeterminate rate of 3/321 (0.9%)
b. On initial testing, 9/262 specimens (3.4%) produced indeterminate results; all 9 were retested, of which 6 produced valid results that were included in the analysis of performance for a final indeterminate rate of 3/262 (1.1%)
c. Results from alternative PCR with bidirectional sequencing: 7 of 9 were Strep A Positive; 1 of 9 was Strep A Negative; 1 of 9 samples was not sequenced.
d. Results from alternative PCR with bidirectional sequencing: 14 of 17 were Strep A Positive: 3 of 17 were Strep A Negative.
Reproducibility Study
A three member reproducibility panel with varying concentrations of Streptococcus pyogenes was tested 4 times per day on six different days by two different operators at three sites (3 specimens x 4 times/day x 6 days x 2 operators x 3 sites). Three lots of Xpert Xpress Strep A Assay cartridges were used, with each representing two days of testing. The samples were prepared in simulated throat swab matrix at the different concentration levels and are presented in Table 8-9. When the study was initially performed, there was an unexpectedly high rate of indeterminate results (47/432 = 10.8%), although no false positive or false negative results were observed. Upon retest of the indeterminate samples, the indeterminate rate was reduced to 2.8% (12/432). Despite the high indeterminate rate, the analytical performance of the assay was acceptable in the initial reproducibility study; the percent concordance met the acceptance criteria for the negative, Strep A low positive, and Strep A moderate positive samples at 100% (144/144), 100% (138/138), and 100% (138/138), respectively. Following an investigation, the study was repeated with fresh panels and different lots of reagents. Results of the repeat reproducibility study are summarized in Table 8-10 by site/operator.
16
| Strain | Panel Member |
|---|---|
| Not applicable | Negative |
| ATCC BAA-946 (Streptococcus pyogenes) | Low Positive (~1X LoD) |
| ATCC BAA-946 (Streptococcus pyogenes) | Moderate Positive (~3X LoD) |
Table 8-10: Summary of Reproducibility Results: % Agreement by Study Site/Operator
| Sample | Site 1 | | | Site 2 | | | Site 3 | | | % Total
Agreement by
Sample a |
|---------|-----------------|-----------------|-----------------|-----------------|-----------------|-----------------|-----------------|-----------------|-----------------|-------------------------------------|
| | Op 1 | Op 2 | Site | Op 1 | Op 2 | Site | Op 1 | Op 2 | Site | |
| Neg | 100%
(24/24) | 100%
(24/24) | 100%
(48/48) | 100%
(24/24) | 100%
(24/24) | 100%
(48/48) | 100%
(24/24) | 100%
(24/24) | 100%
(48/48) | 100%
(144/144) |
| Low Pos | 92%
(22/24) | 100%
(24/24) | 96%
(46/48) | 100%
(24/24) | 100%
(24/24) | 100%
(48/48) | 100%
(24/24) | 100%
(24/24) | 100%
(48/48) | 98.6%
(142/144) |
| Mod Pos | 100%
(24/24) | 100%
(24/24) | 100%
(48/48) | 100%
(24/24) | 100%
(24/24) | 100%
(48/48) | 100%
(24/24) | 100%
(24/24) | 100%
(48/48) | 100%
(144/144) |
a. Eleven (11) indeterminate results were obtained over the course of the repeat study for an initial indeterminate rate of 2.5% (11/432). In all cases, the expected results were obtained upon retesting
The reproducibility of the Xpert Xpress Strep A Assay 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 8-11.
| Sample | Assay
Channel
(Analyte) | Na | Mean
Ct | Between-
Site | | Between-
Lot | | Between-
Day | | Between-
Operator | | Within-
Assay | | Total | |
|-----------------|-------------------------------|-----|------------|------------------|-----|-----------------|-----|-----------------|-----|----------------------|-----|------------------|-----|-------|-----|
| | | | | SD | CV | SD | CV | SD | CV | SD | CV | SD | CV | SD | CV |
| Neg | SPC | 144 | 34.7 | 0 | 0 | 1.9 | 5.3 | 0.3 | 1.0 | 0 | 0 | 1.3 | 3.7 | 2.3 | 6.6 |
| Strep A Low Pos | SA | 142 | 37.8 | 0.2 | 0.6 | 0 | 0 | 0.1 | 0.4 | 0.1 | 0.2 | 1.0 | 2.7 | 1.1 | 2.8 |
| Strep A Mod Pos | SA | 144 | 36.5 | 0 | 0 | 0.3 | 0.8 | 0 | 0 | 0.1 | 0.3 | 0.9 | 2.3 | 0.9 | 2.5 |
Table 8-11: Summary of Reproducibility Data
a. Results with non-zero Ct values out of 144.
Conclusions
The results of the nonclinical analytical and clinical performance studies summarized above demonstrate that the Xpert Xpress Strep A Assay is substantially equivalent to the predicate device.