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.

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.

AI/ML Overview

Here's an analysis of the provided text to extract the acceptance criteria and study details:

1. Table of Acceptance Criteria and Reported Device Performance

The acceptance criteria for performance are not explicitly stated in a dedicated section with pre-defined numerical targets. However, based on the clinical study results and comparisons to the predicate, we can infer the demonstrated performance. The key performance metrics are Sensitivity, Specificity, Positive Predictive Value (PPV), and Negative Predictive Value (NPV) relative to culture and latex agglutination.

Inferred Acceptance Criteria (Based on demonstrating substantial equivalence to predicate) and Reported Device Performance (Combined First and Second Swab Data):

Performance Metric	Implied Acceptance Criterion (Likely for Substantial Equivalence)	Reported Device Performance	Comments
Sensitivity	High (e.g., comparable to or better than predicate)	100.0% (95% CI: 97.3-100.0)	Excellent sensitivity.
Specificity	High (e.g., comparable to or better than predicate)	94.1% (95% CI: 91.5-95.9)	Good specificity.
PPV	High (e.g., comparable to or better than predicate)	84.1% (95% CI: 77.8-88.9)
NPV	High (e.g., comparable to or better than predicate)	100.0% (95% CI: 99.1-100.0)	Excellent negative predictive value.
Indeterminate Rate	Low (e.g., <5%)	0.9% (6/583) after retest	Acceptable low rate.
Analytical Sensitivity (LoD)	Lowest concentration reproducibly distinguished 95% of the time	9 CFU/mL (ATCC BAA-946) & 18 CFU/mL (ATCC 19615)
Analytical Reactivity (Inclusivity)	100% detection of tested Streptococcus pyogenes strains	100% detection of 24 Strep A strains	All 24 strains correctly reported as DETECTED.
Analytical Specificity (Exclusivity)	100% non-detection of non-target organisms	100% non-detection of 70 potentially cross-reactive microorganisms	All 70 organisms correctly reported as NOT DETECTED.
Microbial Interference	No interference with Strep A detection	No interference from 27 tested microorganisms
Potentially Interfering Substances	No assay interference	No interference from 10 tested substances
Carry-Over Contamination	No evidence of carry-over	All 42 negative samples correctly reported as NOT DETECTED. All 40 positive samples correctly reported as DETECTED.
Reproducibility (Negative)	100% agreement expected	100% (144/144) agreement
Reproducibility (Low Positive)	High agreement expected (e.g., >95%)	98.6% (142/144) agreement
Reproducibility (Moderate Positive)	100% agreement expected	100% (144/144) agreement

Study Proving Acceptance Criteria (Clinical Performance):

Study Design: A multi-site clinical study that collected throat ESwab specimens from patients with signs and symptoms of pharyngitis. The study combined data from two approaches:
- One study collected a second prospective throat swab after a standard of care (SOC) swab.
- Another study used leftover excess SOC throat swab specimens.

2. Sample Sizes and Data Provenance for the Test Set:

Initial Enrolled Specimens: 844
Excluded Specimens: 261 (due to inclusion criteria failure, reference culture procedural error, delay in reference culture inoculation, delay in shipment, or labeling error).
Specimens Included in Performance Analysis (Test Set): 583
- Successful on initial test: 565/583 (96.9%)
- Valid results after retest (overall): 577/583 (99.0%)
Data Provenance: Geographically diverse regions within the United States. The study was conducted between December 2016 and March 2017, suggesting it was a prospective or mixed (prospective and retrospective for leftover samples) collection. The text states "one study enrolled consented subjects from whom a second prospective throat swab specimen was collected" and "another study tested specimens from subjects for which leftover excess standard of care (SOC) throat swab specimens were available."

3. Number of Experts and Qualifications for Ground Truth for the Test Set:

The document does not specify the number of experts or their qualifications for establishing the initial ground truth (culture and latex agglutination). These are standard laboratory procedures, but details about expert reviewers for discordant results are mentioned.

4. Adjudication Method for the Test Set:

Discordant results between the Xpert Xpress Strep A Assay and the reference method (culture) were investigated.
Method: An alternative PCR/bidirectional sequencing assay was used for adjudication. The results of this alternative PCR were footnoted in the performance tables (e.g., for 26 discrepant samples in Table 8-7, 21 were confirmed positive by alternative PCR, 4 negative, and 1 not tested). This indicates an independent molecular method was used to resolve discrepancies.

5. Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study:

No, a MRMC comparative effectiveness study was not done. This device is an in vitro diagnostic (IVD) assay, not an imaging device or one that involves human "readers" interpreting results in a variable way that MRMC studies are designed for. Its performance is evaluated biochemically against a reference standard.

6. Standalone Performance Study (Algorithm only without human-in-the-loop):

Yes, a standalone study was performed. The clinical performance data presented (Sensitivity, Specificity, PPV, NPV) represents the performance of the Xpert Xpress Strep A Assay (the "algorithm/device") functioning independently relative to a microbiological reference method (culture). The results are automatically generated by the GeneXpert Instrument Systems.

7. Type of Ground Truth Used:

For the clinical performance study (test set), the primary ground truth reference method was culture and latex agglutination for Strep A typing.
For resolving discordant results, an alternative PCR/bidirectional sequencing assay was used.

8. Sample Size for the Training Set:

The document does not specify the sample size for a "training set" in the context of an algorithm. For IVDs, the development process typically involves various internal testing and optimization (which could be considered analogous to training) but not usually a distinct "training set" of patient specimens in the same way an AI model would have. The document focuses on analytical and clinical validation studies.

9. How Ground Truth for the Training Set Was Established:

As a training set is not explicitly defined in the context of this IVD device's approval process in this document, the method for establishing its ground truth is not applicable/not provided. The analytical and clinical validation studies use established reference methods as ground truth.

Summary

{0}------------------------------------------------

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 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)

CONTINUE ON A SEPARATE PAGE IF NEEDED.

This section applies only to requirements of the Paperwork Reduction Act of 1995.

DO NOT SEND YOUR COMPLETED FORM TO THE PRA STAFF EMAIL ADDRESS BELOW.

The burden time for this collection of information is estimated to average 79 hours per response, including the time to review instructions, search existing data sources, gather and maintain the data needed and complete and review the collection of information. Send comments regarding this burden estimate or any other aspect of this information collection, including suggestions for reducing this burden, to:

Department of Health and Human Services Food and Drug Administration Office of Chief Information Officer Paperwork Reduction Act (PRA) Staff PRAStaff@fda.hhs.gov

"An agency may not conduct or sponsor, and a person is not required to respond to, a collection of information unless it displays a currently valid OMB number."

{3}------------------------------------------------

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:	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 AStreptococcus DNA in throat swab specimens.
Regulation number,Classification name,Product code:	21 CFR 866.2690, Streptococcus spp. nucleic acid basedassay, PGX21 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) #K141338]

{4}------------------------------------------------

Device Description:

{5}------------------------------------------------

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 StrepA Assay	IQuum Inc. (Roche) LiatStrep A Assay
510(k) Number	K172126	K141338
Regulation	Same	866.2680
Product Code	Same	PGX
Device Class	Same	II
Similarities
Item	DeviceCepheid Xpert Xpress Strep A Assay	Predicate DeviceIQuum Inc. (Roche) Liat Strep A Assay
Intended Use	The Xpert® Xpress Strep AAssay, performed on theGeneXpert InstrumentSystems, is a rapid, qualitativein vitro diagnostic test for thedetection of Streptococcuspyogenes (Group A ß-hemolytic Streptococcus ,Strep A) in throat swabspecimens from patients withsigns and symptoms ofpharyngitis.The Xpert Xpress Strep AAssay utilizes an automatedreal-time polymerase chainreaction (PCR) to detectStreptococcus pyogenesDNA.	The Liat™ Strep A Assay,performed on the Liat™Analyzer, is a qualitative invitro diagnostic test for thedetection of Streptococcuspyogenes (Group A ß-hemolytic Streptococcus ) inthroat swab specimens frompatients with signs andsymptoms of pharyngitis.The Liat™ Strep A Assayutilizes nucleic acidpurification and polymerasechain reaction (PCR)technology to detectStreptococcus pyogenes bytargeting a segment of theStreptococcus pyogenesgenome.
Assay Target	Same	Streptococcus A
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 acidextraction and purification
Detection Technique	Same	Different reporter dyes fortarget and Internal Control
Assay Result	Same	Qualitative
	Differences
	New Device	Predicate Device
Item	Cepheid Xpert Xpress StrepA Assay	IQuum Inc. (Roche) LiatStrep A Assay
Equipment Required	Cepheid GeneXpert® Dx,GeneXpert Infinity-48s, andGeneXpert Infinity-80	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

Table 8-1: Comparison of Similarities and Differences of the Xpert Xpress Strep A Assay with the Predicate Device

{6}------------------------------------------------

{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 inESwabtransportmedium)	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 </mL for viruses. All three replicates of all 70 organisms were reported as Strep A NOT DETECTED by the Xpert Xpress Strep A Assay (Table 8-4). The analytical specificity of the Xpert Xpress Strep A Assay 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
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 pseudodiphtheriticum	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
Organism	Results
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
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
Organism	Results
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 the Xpert Xpress Strep A Assay

{10}------------------------------------------------

{11}------------------------------------------------

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. 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.

Organism
Acinetobacter baumannii
Candida albicans
Enterococcus faecalis
Fusobacterium necrophorum
Haemophilus influenzae type A
Lactobacillus acidophilus
Neisseria lactamicaa
Peptostreptococcus micros
Prevotella (Bacteroides) oralis
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

Table 8-5: Commensal Microorganisms Tested

{12}------------------------------------------------

Organism
Veillonella parvula
a. Although all samples were reported appropriatelyas positive, reduced fluorescent signal wasobserved for the S. pyogenes target in thepresence 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-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)

Table 8-6: Potential Interfering Substances Tested

{13}------------------------------------------------

Substance/Class	Description/Active Ingredient	ConcentrationTested
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)

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 XpressStrep 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			% TotalAgreement bySample 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	AssayChannel(Analyte)	Na	MeanCt	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.

Regulation Number and Section

§ 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.