(22 days)
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No
The description details a standard Real-Time PCR assay based on Taqman chemistry, which relies on fluorescent signal thresholds for positive/negative determination, not AI/ML algorithms. There is no mention of AI, ML, or related concepts in the document.
No.
This device is an in vitro diagnostic test designed to detect and differentiate streptococcus nucleic acids, not to provide therapy or treatment.
Yes
The "Intended Use / Indications for Use" section explicitly states that "The Lyra Direct Strep Assay is a Real-Time PCR in vitro diagnostic test for the qualitative detection and differentiation of Group A ß-hemolytic Streptococcus (Streptococcus pvogenes) and pyogenic Group C and G B-hemolytic Streptococcus nucleic acids isolated from throat swab specimens..." This clearly indicates its function as a diagnostic tool.
No
The device description clearly outlines a Real-Time PCR in vitro diagnostic test that involves physical components like throat swabs, process buffer, master mix, and the use of an Applied Biosystems® 7500 Fast Dx instrument. This indicates it is a hardware-based system with associated reagents and software for analysis, not a software-only device.
Yes, this device is an IVD (In Vitro Diagnostic).
The "Intended Use / Indications for Use" section explicitly states: "The Lyra Direct Strep Assay is a Real-Time PCR in vitro diagnostic test for the qualitative detection and differentiation of Group A ß-hemolytic Streptococcus (Streptococcus pvogenes) and pyogenic Group C and G B-hemolytic Streptococcus nucleic acids isolated from throat swab specimens..."
This statement clearly identifies the device as an in vitro diagnostic test.
N/A
Intended Use / Indications for Use
The Lyra Direct Strep Assay is a Real-Time PCR in vitro diagnostic test for the qualitative detection and differentiation of Group A ß-hemolytic Streptococcus (Streptococcus pvogenes) and pyogenic Group C and G B-hemolytic Streptococcus nucleic acids isolated from throat swab specimens obtained from patients with signs and symptoms of pharvngitis, such as sore throat. The assay does not differentiate between pyogenic Groups C and G ß-hemolytic Streptococcus.
All negative test results should be confirmed by bacterial culture, because negative results do not preclude Group A, C or G Strep infection and should not be used as the sole basis for treatment.
The assay is intended for use in hospital, reference, or state laboratory settings. The device is not intended for point-of-care use.
Product codes (comma separated list FDA assigned to the subject device)
PGX, OOI
Device Description
The Lyra Direct Strep Assay detects nucleic acids isolated from throat swab specimens obtained from patients with signs and symptoms of pharyngitis. A multiplex Real-time PCR reaction is carried out under optimized conditions in a single tube generating amplicons for Group A B-hemolytic Streptococcus (Streptococcus pyogenes) and pyogenic Group C and G B-hemolytic Streptococcus, and the Process Control (PRC). Identification of Group A, pyogenic Group C/G, and the PRC occurs by the use of target-specific primers and fluorescent-labeled probes that hybridize to conserved regions in the genomes of Group A, pyogenic Group C/G, and the PRC. The assay does not differentiate between Group C and Group G streptococci.
A specimen from a patient's throat swab is transferred to the Process Buffer then heated to lyse the bacteria and expose the DNA. The lysed specimen is then added to a rehydrated Master Mix of targeted oligonucleotide primers, fluorophore and quencher-labeled probes is added to each plate. The plate is placed into the Applied Biosystems® 7500 Fast Dx instrument and the Quidel Molecular Direct Streptococci Assay protocol is initiated.
This assay is based on Taqman® chemistry, and uses an enzyme with DNA polymerase, and 5'-3' exonuclease activities. During DNA amplification, this enzyme cleaves the probe bound to the conserved complementary DNA sequence, separating the quencher dye from the reporter dye. This step generates an increase in fluorescent signal upon excitation by a light source of the appropriate wavelength. With each cycle, additional dye molecules are separated from their quenchers resulting in an increase in the fluorescent signal. If sufficient fluorescence is achieved, the sample is reported as positive for the detected nucleic acid.
Mentions image processing
Not Found
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
hospital, reference, or state laboratory settings. The device is not intended for point-of-care use.
Description of the training set, sample size, data source, and annotation protocol
Not Found
Description of the test set, sample size, data source, and annotation protocol
Not Found
Summary of Performance Studies (study type, sample size, AUC, MRMC, standalone performance, key results)
Precision/Reproducibility:
- Study Type: Precision/within laboratory repeatability
- Sample Size: Not explicitly stated, but 4-member panel tested twice a day for 12 days by 2 operators.
- Key Results:
- Group A Strep: High Negative 100%, Low Positive 100%, Moderate Positive 45.8%, Negative 0%.
- Pyogenic Group C Strep: High Negative 100%, Low Positive 100%, Moderate Positive 75%, Negative 0%.
- Study Type: Reproducibility (evaluated at three laboratory sites)
- Sample Size: 90 results per level for each panel member (2 operators x 3 replicates x 5 days x 3 sites).
- Key Results:
- Group A Strep Low Pos: Site 1 (23%), Site 2 (53%), Site 3 (23%), Combined (33%).
- Group A Strep Low Pos: Site 1 (97%), Site 2 (100%), Site 3 (100%), Combined (99%).
- Group A Strep Mod Pos: Site 1 (100%), Site 2 (100%), Site 3 (100%), Combined (100%).
- Group A Strep Neg: Site 1 (0%), Site 2 (0%), Site 3 (0%), Combined (0%).
- Pyo Group C Strep Low Pos: Site 1 (7%), Site 2 (80%), Site 3 (7%), Combined (31%).
- Pyo Group C Strep Low Pos: Site 1 (100%), Site 2 (100%), Site 3 (100%), Combined (100%).
- Pyo Group C Strep Mod Pos: Site 1 (100%), Site 2 (100%), Site 3 (100%), Combined (100%).
- Pyo Group C Strep Neg: Site 1 (0%), Site 2 (0%), Site 3 (0%), Combined (0%).
Detection Limit (LoD):
- Study Type: LoD determination.
- Sample Size: Using 20 quantified contrived stocks for each of three strains of Group A streptococci, two strains of pyogenic Group C streptococci and two strains of pyogenic Group G streptococci.
- Key Results: Determined as the lowest concentration at which 95% of all replicates tested positive. Specific CFU/ml values for each strain provided in Table III.
Analytical Sensitivity (Inclusivity):
- Study Type: Inclusivity studies.
- Sample Size: 11 Group A ß-hemolytic Streptococcus strains, 10 Pyogenic Group C ß-hemolytic Streptococcus strains, and 13 Pyogenic Group G ß-hemolytic Streptococcus strains against 3 different reagent lots.
- Key Results: Strains detected at concentrations ranging from 0.1x LoD to 3.8x LoD (Tables IV-VI).
Co-infection Studies:
- Study Type: Competitive interference studies.
- Key Results: No competitive interference observed between Group A Streptococcus and pyogenic Group C/G Streptococcus when tested in combination at various concentrations.
Analytical Specificity:
- Study Type: In silico BLAST analysis (primers) and in vitro study (microorganisms).
- Sample Size: 60 potential interfering organisms for in silico, 44 microorganisms for in vitro.
- Key Results: No cross-reactivity observed with any of the tested microorganisms.
Clinical Studies:
- Study Type: Clinical Performance (comparison to composite culture).
- Sample Size: 1293 prospectively collected fresh throat specimens.
- Key Results:
- Group A ß-hemolytic Streptococcus (All Sites):
- Sensitivity: 96.5% (109/113) 95% CI (91.3%-98.6%)
- Specificity: 98.0% (1156/1180) 95% CI (97.0%-98.6%)
- Pyogenic Group C and G ß-hemolytic Streptococcus (All Sites):
- Sensitivity: 95.7% (67/70) 95% CI (88.1%-98.5%)
- Specificity: 98.3% (1202/1223) 95% CI (97.4%-98.9%)
- Group A ß-hemolytic Streptococcus (All Sites):
Key Metrics (Sensitivity, Specificity, PPV, NPV, etc.)
Group A ß-hemolytic Streptococcus (All Sites):
- Sensitivity: 96.5% (109/113) 95% CI (91.3%-98.6%)
- Specificity: 98.0% (1156/1180) 95% CI (97.0%-98.6%)
Pyogenic Group C and G ß-hemolytic Streptococcus (All Sites):
- Sensitivity: 95.7% (67/70) 95% CI (88.1%-98.5%)
- Specificity: 98.3% (1202/1223) 95% CI (97.4%-98.9%)
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.
Not Found
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.
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.
0
EVALUATION OF AUTOMATIC CLASS III DESIGNATION FOR Lyra Direct Strep Assay
DECISION SUMMARY
A. 510(k) Number:
B. Purpose for Submission:
De Novo request for evaluation of automatic class III designation for the Lyra Direct Strep Assay.
C. Measurand:
Group A B-hemolytic Streptococcus (Streptococcus pyogenes) and pyogenic Group C and G ß-hemolytic Streptococcus nucleic acids.
D. Type of Test:
The Lyra Direct Strep Assay is a Real-Time PCR in vitro diagnostic test for the rapid and qualitative detection and differentiation of Group A B-hemolytic Streptococcus (Streptococcus pyogenes) and pyogenic Group C and G ß-hemolytic Streptococcus nucleic acids isolated from throat swab specimens obtained from patients with signs and symptoms of pharyngitis.
E. Applicant:
Quidel Corporation
F. Proprietary and Established Names:
Lyra Direct Strep Assay
G. Regulatory Information:
-
- Regulation section:
21 CFR 866.2680 - Streptococcus spp. nucleic acid-based assay
- Regulation section:
-
- Classification:
Class II
- Classification:
-
- Product code:
1
- PGX Group C and G Beta-Hemolytic Streptococcus Nucleic Acid Amplification System
- OOI Real-Time Nucleic Acid Amplification System
-
- Panel:
- 83- Microbiology
H. Intended Use:
-
- Intended use(s):
The Lyra Direct Strep Assay is a Real-Time PCR in vitro diagnostic test for the qualitative detection and differentiation of Group A ß-hemolytic Streptococcus (Streptococcus pvogenes) and pyogenic Group C and G B-hemolytic Streptococcus nucleic acids isolated from throat swab specimens obtained from patients with signs and symptoms of pharvngitis, such as sore throat. The assay does not differentiate between pyogenic Groups C and G ß-hemolytic Streptococcus.
- Intended use(s):
All negative test results should be confirmed by bacterial culture, because negative results do not preclude Group A, C or G Strep infection and should not be used as the sole basis for treatment.
The assay is intended for use in hospital, reference, or state laboratory settings. The device is not intended for point-of-care use.
-
- Indication(s) for use:
Same as intended use.
- Indication(s) for use:
-
- Special conditions for use statement(s):
For prescription use only in accordance with 21 CFR 801.109.
- Special conditions for use statement(s):
The device is not intended for point-of-care use.
-
- Special instrument requirements:
ABI 7500 Fast DX Thermocycler
- Special instrument requirements:
Plate centrifuge for ABI 96 well plate
Dry heating block, capable of heating 1.5 mL tubes at 95℃ for 10 minutes
I. Device Description:
2
The Lyra Direct Strep Assay detects nucleic acids isolated from throat swab specimens obtained from patients with signs and symptoms of pharyngitis. A multiplex Real-time PCR reaction is carried out under optimized conditions in a single tube generating amplicons for Group A B-hemolytic Streptococcus (Streptococcus pyogenes) and pyogenic Group C and G B-hemolytic Streptococcus, and the Process Control (PRC). Identification of Group A, pyogenic Group C/G, and the PRC occurs by the use of target-specific primers and fluorescent-labeled probes that hybridize to conserved regions in the genomes of Group A, pyogenic Group C/G, and the PRC. The assay does not differentiate between Group C and Group G streptococci.
A specimen from a patient's throat swab is transferred to the Process Buffer then heated to lyse the bacteria and expose the DNA. The lysed specimen is then added to a rehydrated Master Mix of targeted oligonucleotide primers, fluorophore and quencher-labeled probes is added to each plate. The plate is placed into the Applied Biosystems® 7500 Fast Dx instrument and the Quidel Molecular Direct Streptococci Assay protocol is initiated.
| Quidel Molecular Direct Probe Labels | |
|---|---|
| Target | Dye |
| Group A streptococci | FAM |
| Pyogenic group C and G streptococci | CAL Fluor Red® |
| Process Control (PRC) | Quaser® 670 |
This assay is based on Taqman® chemistry, and uses an enzyme with DNA polymerase, and 5'-3' exonuclease activities. During DNA amplification, this enzyme cleaves the probe bound to the conserved complementary DNA sequence, separating the quencher dye from the reporter dye. This step generates an increase in fluorescent signal upon excitation by a light source of the appropriate wavelength. With each cycle, additional dye molecules are separated from their quenchers resulting in an increase in the fluorescent signal. If sufficient fluorescence is achieved, the sample is reported as positive for the detected nucleic acid.
J. Standard/Guidance Document Referenced (if applicable):
Not applicable.
K. Test Principle:
The assay detects nucleic acids isolated from throat swab specimens obtained from patients with signs and symptoms of pharyngitis. A multiplex Real-Time PCR reaction is carried out under optimized conditions in a single tube generating amplicons for Group A ß-hemolytic Streptococcus (Streptococcus pyogenes) and pyogenic Group C and G ß-hemolytic Streptococcus, and the Process Control (PRC). Identification of Group A, pyogenic Group C/G streptococci, and the PRC occurs by the use of target-specific primers and fluorescentlabeled probes that hybridize to conserved regions in the genomes of Group A, pyogenic Group C/G, and the PRC. The assay does not differentiate between Group C and Group G streptococci.
During DNA amplification, the Taq polymerase with 5'-3' exonuclease activity cleaves the probe bound to the complementary DNA sequence, separating the quencher dye from the
3
reporter dye. This step generates an increase in fluorescent signal upon excitation by a light source of the appropriate wavelength. With each cycle, additional dye molecules are separated from their quenchers resulting in an increase in the fluorescent signal. If sufficient fluorescence is achieved, the sample is reported as positive for the detected nucleic acid, otherwise the sample is determined to be negative or invalid, based on the internal PRC control.
L. Performance Characteristics (if/when applicable):
1. Analytical performance:
a. Precision/Reproducibility:
Precision/within laboratory repeatability was demonstrated with a contrived four (4) member panel consisting of moderate positive (3 x LoD), low positive (2 x LoD), high negative (0.3 x LoD) Group A Streptococcus and pyogenic Group C Streptococcus, and negative samples (negative matrix) tested by two (2) operators, twice a day (2X) for twelve (12) days. The precision study results are acceptable. The results are shown in Table I.
| Table I: Precision | |||||
|---|---|---|---|---|---|
| Panel ID | High | ||||
| Negative | Low | ||||
| Positive | Moderate | ||||
| Positive | Negative | ||||
| Group A Strep | |||||
| (% Detection) | 100% | 100% | 45.8% | 0% | |
| Pyogenic Group C Strep | |||||
| (% Detection) | 100% | 100% | 75% | 0% |
The reproducibility of the Lyra Direct Strep Assay was evaluated at three (3) laboratory sites (two external, one in-house). Reproducibility was assessed using a panel of four (4) simulated samples that include moderate positive and low positive, high negative and negative (as defined in the precision study above) Group A Streptococcus (Streptococcus pyogenes) and pyogenic Group C Streptococcus (Streptococcus equi subsp. zooepidemicus) samples. The panels and controls were processed and tested on the Applied Biosystems® 7500 Fast Dx. Panels and controls were tested at each site by 2 operators for 5 non-consecutive days (2 operators x 3 replicates x 5 days x 3 sites = 90 results per level for each panel member). The LoD values were based on the values obtained in the LoD study. The reproducibility study results are acceptable. The results are shown in Table II.
4
| Table II: Reproducibility | ||||||||
|---|---|---|---|---|---|---|---|---|
| Panel ID | Site 1 | Site 2 | Site 3 | Combined | ||||
| Detected | ||||||||
| Pos/Total | % Pos | Detected | ||||||
| Pos/Total | % Pos | Detected | ||||||
| Pos/Total | % Pos | Detected | ||||||
| Pos/Total | % Pos | |||||||
| Group | ||||||||
| A | ||||||||
| Strep | 7/30 | 23% | 16/30 | 53% | 7/30 | 23% | 30/90 | 33% |
| Low Pos | 29/30 | 97% | 30/30 | 100% | 30/30 | 100% | 89/89 | 99% |
| Mod Pos | 30/30 | 100% | 30/30 | 100% | 30/30 | 100% | 90/90 | 100% |
| Neg | 0/30 | 0% | 0/30 | 0% | 0/30 | 0% | 0/90 | 0% |
| Pyo | ||||||||
| Group | ||||||||
| C | ||||||||
| Strep | 2/30 | 7% | 24/30 | 80% | 2/30 | 7% | 28/90 | 31% |
| Low Pos | 30/30 | 100% | 30/30 | 100% | 29/29* | 100% | 89/90 | 100% |
| Mod Pos | 30/30 | 100% | 30/30 | 100% | 30/30 | 100% | 90/90 | 100% |
| Neg | 0/30 | 0% | 0/30 | 0% | 0/30 | 0% | 0/90 | 0% |
- 1 replicate removed due to invalid control
b. Linearity/assay reportable range:
Not applicable.
Traceability, Stability, Expected values (controls, calibrators, or methods): C.
Reagents, transport media, specimen storage and hold time studies were performed to characterize the Lyra Direct Strep Assay. Validation studies were performed in house on swabs dipped in contrived negative matrix spiked with Group A Streptococcus and pyogenic Groups C and G Streptococcus at 3x LoD.
Studies using 4 different swabs (Liquid Amies Single Plastic Applicator, Liquid Stuart Single Plastic Applicator, Puritan Liquid Amies Transport System, and Sterile Puritan Rayon Throat Swabs) demonstrated that samples stored at 2-8 ℃ and 20-25 °C produced expected results for up to 13-days.
Study results demonstrated that the rehydrated master mix was stable for 2h at 20-25 °C, 8 days at 2-8 °C, and 8 days at -20 °C.
Study results demonstrated that the Lyra Direct Strep Assay processed samples are stable up to 13 days at 2-8 ℃, ambient room temperature, -20 ℃, or -70 ℃.
The Lyra Direct Strep Assay incorporates a process control which is used to monitor sample processing and evaluate the presence of inhibitory substances. The process control confirms the integrity of assay reagents and detection. Additional controls are performed in accordance with end user laboratory guidelines and requirements.
d. Detection Limit:
The limit of detection (LoD) of the Lyra Direct Strep Assay was determined using 20 quantified (CFU/mL) contrived stocks for each of three strains of Group A streptococci, two strains of pyogenic Group C streptococci and two strains of pyogenic Group G streptococci diluted in a negative matrix (see table below). The
5
| Table III: LoD for Group A β-hemolytic Streptococcus and Pyogenic Group C
| and G β-hemolytic Streptococcus | ||
|---|---|---|
| Strain | Strain ID | CFU/ml |
| Group A Streptococcal strain 1 | ||
| (Streptococcus pyogenes) | ATCC 19615 | 6.0E+02 |
| Group A Streptococcal strain 2 | ||
| (Streptococcus pyogenes) | ATCC 700942 | 2.2E+03 |
| Group A Streptococcal strain 3 | ||
| (Streptococcus pyogenes) | CCUG 33061 | 1.5E+03 |
| Pyogenic Group C Streptococcal strain 1 | ||
| (Streptococcus equi subsp. zooepidemicus) | ATCC 700400 | 1.7E+04 |
| Pyogenic Group C Streptococcal strain 2 | ||
| (Streptococcus dysgalactiae subsp. equisimilis) | CCUG 1483 | 1.8E+04 |
| Pyogenic Group G Streptococcal strain 1 | ||
| (Streptococcus dysgalactiae subsp. equisimilis) | ATCC 12394 | 1.6E+04 |
| Pyogenic Group G Streptococcal strain 2 | CCUG 27477 | 1.6E+04 |
LoD is defined as the lowest concentration at which 95% of all replicates tested positive. The LoD study results are shown in Table III.
These study results are acceptable.
- e. Analytical Sensitivity:
Inclusivity studies were conducted with 11 Group A ß-hemolytic Streptococcus strains, 10 Pyogenic Group C ß-hemolytic Streptococcus strains and 13 Pyogenic Group G ß-hemolytic Streptococcus strains against 3 different reagent lots. The strains were cultured, serial diluted in contrived negative matrix and titered to determine the CFU/ml. A rayon swab was twirled in the stock and run with the Lyra Direct Strep Assay. The inclusivity study results and the final organism concentrations tested are shown in Tables IV-VI.
| Table IV: Group A β-hemolytic Streptococcus Inclusivity | ||
|---|---|---|
| Strain | Strain ID | Conc (x LoD) |
| Group A Streptococcal strain 1 | ATCC 19615 | 1.1x |
| Group A Streptococcal strain 2 | ATCC 700942 | 3.8x |
| Group A Streptococcal strain 3 | ATCC 700952 | 2.6x |
| Group A Streptococcal strain 4 | ATCC 12344 | 1.2x |
| Group A Streptococcal strain 5 | ATCC 12384 | 0.7x |
| Group A Streptococcal strain 6 | ATCC 49399 | 0.4x |
| Group A Streptococcal strain 7 | NCIMB 13285 | 1.8x |
6
| Table IV: Group A ß-hemolytic Streptococcus Inclusivity | ||||
|---|---|---|---|---|
| Strain | Strain ID | Conc (x LoD) | ||
| Group A Streptococcal strain 8 | CCUG 33061 | 1.4x | ||
| Group A Streptococcal strain 9 | CCUG 33409 | 0.4x | ||
| Group A Streptococcal strain 10 | CCUG 39158 | 0.5x | ||
| Group A Streptococcal strain 11 | CCUG 53553 | 0.6x |
| Table V: Pyogenic Group C β-hemolytic Streptococcus Inclusivity | ||
|---|---|---|
| Strain | Strain ID | Conc (x LoD) |
| Streptococcus dysgalactiae subsp. | ||
| equisimilis | ATCC 12388 | 1.4x |
| Streptococcus equi subsp. zooepidemicus | ATCC 700400 | 1.3x |
| Streptococcus dysgalactiae subsp. | CCUG 1483 | 2.2x |
| Pyogenic Group C Streptococcal strain | ||
| (Specific species not identified) | CCUG 27479 | 2.1x |
| Pyogenic Group C Streptococcal strain | ||
| (Specific species not identified) | CCUG 27664 | 1.2x |
| Pyogenic Group C Streptococcal strain | ||
| (Specific species not identified) | CCUG 6713 | 0.1x |
| Pyogenic Group C Streptococcal strain | ||
| (Specific species not identified) | CCUG 21557 | 0.7x |
| Pyogenic Group C Streptococcal strain | ||
| (Specific species not identified) | CCUG 27478 | 2.6x |
| Pyogenic Group C Streptococcal strain | ||
| (Specific species not identified) | CCUG 27480 | 1.6x |
| Pyogenic Group C Streptococcal strain | ||
| (Specific species not identified) | CCUG 28238 | 1.6x |
| Table VI: Pyogenic Group G β-hemolytic Streptococcus Inclusivity | ||
|---|---|---|
| Strain | Strain ID | Conc (x LoD) |
| Streptococcus dysgalactiae subsp. | ||
| equisimilis | ATCC 12394 | 0.5x |
| Streptococcus canis | ATCC 43497 | 0.6x |
| Streptococcus dysgalactiae subsp. | ||
| equisimilis | CCUG 502 | 0.6x |
| Streptococcus dysgalactiae subsp. | ||
| equisimilis | CCUG 24070 | 0.4x |
| Streptococcus dysgalactiae subsp. | ||
| equisimilis | CCUG 27482 | 0.3x |
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| Table VI: Pyogenic Group G β-hemolytic Streptococcus Inclusivity | ||
|---|---|---|
| Strain | Strain ID | Conc (x LoD) |
| Streptococcus dysgalactiae subsp. equisimilis | CCUG 27483 | 2.8x |
| Streptococcus dysgalactiae subsp. equisimilis | CCUG 33645 | 1.2x |
| Streptococcus dysgalactiae subsp. equisimilis | CCUG 33802 | 1.0x |
| Pyogenic Group G Streptococcal strain (Specific species not identified) | CCUG 1859 | N/A* |
| Pyogenic Group G Streptococcal strain (Specific species not identified) | CCUG 15679 | 0.3x |
| Pyogenic Group G Streptococcal strain (Specific species not identified) | CCUG 15680 | 1.0x |
| Pyogenic Group G Streptococcal strain (Specific species not identified) | CCUG 26147 | 0.3x |
| Pyogenic Group G Streptococcal strain (Specific species not identified) | CCUG 27477 | 2.3x |
- The concentration of the glycerol stock of the CCUG 1859 strain was below detectable levels and therefore could not be titered, therefore it was tested at the neat concentration.
These study results are acceptable.
Co-infection Studies:
Competitive interference studies with the Lyra Direct Strep Assay were conducted to ensure that both Group A Streptococcus and pyogenic Group C/G Streptococcus could be detected in the same reaction in cases of co-infection. Group A Streptococcus and pyogenic Group C Streptococcus stocks at 2 to 3 x LoD concentrations in contrived negative matrix were tested in the presence of varying amounts of the other analyte.
No competitive interference was observed with 2 to 3 x LoD concentrations of Group A Streptococcus when tested with high concentrations (2E05, 1E06, 1E07 and 1E08 CFU/ml) of pyogenic Group C Streptococcus in the same reaction. No competitive interference was observed with 2 to 3 x LoD concentrations of pyogenic Group C Streptococcus when tested with high concentrations (2E03, 1E04, 1E05 and 1E06 CFU/ml) of Group A Streptococcus in the same reaction. These study results are acceptable.
f. Analytical Specificity:
8
An in silico BLAST analysis of primers used in the Lyra Direct Strep Assay against the NCBI database against sixty (60) potential interfering organisms did not show evidence of cross-reactivity.
A study was performed on the Applied Biosystems® 7500 Fast Dx to evaluate the performance of the Lyra Direct Strep Assay in the presence of forty-four (44) other microorganisms commonly found in throat specimens. Each potentially interfering microorganism was tested in the presence of 2 x LoD Group A Streptococcus (2 strains), a pyogenic Group C Streptococcus strain and a pyogenic Group G streptococcus strain in the presence of clinically relevant levels of viruses (10 pfu/ml) and bacteria (10°cfu/mL) or higher. All strain combinations were spiked into contrived negative matrix. The strains included in the cross-reactivity study are shown in Tables VII.
| Table VII: Strains Included in Cross-Reactivity | ||
|---|---|---|
| Strain | ||
| Acinetobacter lwoffii | Moraxella catarrhalis | Streptococcus oralis |
| Arcanobacterium | ||
| haemolyticum | Neisseria gonorrhoeae | Streptococcus pneumoniae |
| Bacillus cereus | Neisseria subflava | Streptococcus salivarius |
| Bordetella pertussis | Pseudomonas aeruginosa | Streptococcus sanguinis |
| Burkholderia cepacia | Serratia marcescens | Streptococcus suis |
| Corynebacterium diphtheria | Staphylococcus aureus | Veillonella parvula |
| Enterococcus faecalis vanB | Staphylococcus epidermidis | Candida albicans |
| Escherichia coli | Stenotrophomonas maltophilia | Adenovirus Type 1 |
| Fusobacterium necrophorum | Streptococcus agalactiae | Adenovirus Type 11 (Slobitski) |
| Haemophilus influenza | Streptococcus anginosus | Influenza A/ Victoria/ 3/75/ |
| H3N2 | ||
| Klebsiella pneumonia | Streptococcus bovis | Influenza B/Panama/45/90 |
| Lactococcus lactis | Streptococcus gordonii | |
| (Virdans type) | Influenza C/Taylor/1233/47 | |
| Legionella jordanis | Streptococcus intermedius | Parainfluenza virus 4a |
| Legionella micdadei | Streptococcus mitis | Rhinovirus Type 15 (1734) |
| Legionella pneumophila | Streptococcus mutans |
None of the forty-four (44) microorganisms tested that might be found in throat specimens cross-react with the assay.
These study results are acceptable.
- g. Assay Cut-off:
9
The Lyra Direct Strep Assay has fixed cut-offs based on fluorescence values attained for each fluorophore associated with each analyte. Ct cut-off values were determined after testing Group A streptococci and pyogenic Group C and G streptococci at the limit of detection (contrived specimens spiked in negative matrix) and a set of clinical specimens in the Lyra Direct Strep Assay on the Applied Biosystems® 7500 Fast Dx instrument. The Ct value cut-offs were selected to fall above the highest true positive Ct value observed for an analyte in both the analytical sensitivity and clinical specimen testing study and to minimize cycle time. A Ct cut-off of 40 cycles was recommended for both analytes and the PRC.
The baseline, threshold, and Ct cut-off settings for the Lyra Direct Strep Assay on the Applied Biosystems® 7500 Fast Dx are described in Table VIII:
| Table VIII: Lyra™ Direct Strep Assay ABI 7500 Fast Dx Baseline, | |||
|---|---|---|---|
| Threshold and Ct Cut-off | |||
| Analyte | Fluorescence | ||
| Threshold | Baseline | Ct | |
| Cut-off | |||
| Group A Streptococcus | 8.00E+04 | ||
| Pyogenic Group C/G Streptococcus | 1.00E+05 | Auto | |
| Baseline | 40 | ||
| Cycles | |||
| Process Control (PRC) | 1.90E+04 |
2. Comparison studies:
-
a. Method comparison with predicate device:
Clinical performance was based on comparison of the Lyra Direct Strep Assay results to those obtained by a composite culture of directly plated patients' throat swabs and culture of the transport fluid material at a central location. -
b. Matrix comparison:
A comparison study was conducted between negative clinical matrix and a contrived negative matrix in order to validate the use of the contrived negative matrix in place of a clinical negative matrix for the analytic studies in section M1 above. Contrived negative matrix was constructed to mimic challenging clinical specimens, and consisting of Porcine Gastric Mucin (PGM), Phosphate Buffered Saline (PBS), Bovine Serum Albumin and sodium azide. The matrix comparison study results are shown in Table IX.
| Table IX: Matrix Comparison Study | |||||
|---|---|---|---|---|---|
| Panel ID | Contrived | ||||
| Negative Matrix | Pooled Negative | ||||
| Clinical Matrix | |||||
| Detected | % Pos | Detected | % Pos | ||
| Group A | |||||
| Streptococcus | 3 x LoD | 20/20 | 100% | 20/20 | 100% |
| 1 x LoD | 19/20 | 95% | 20/20 | 100% |
10
| Table IX: Matrix Comparison Study | ||||
|---|---|---|---|---|
| Panel ID | Contrived Negative Matrix | Pooled Negative Clinical Matrix | ||
| Detected | % Pos | Detected | % Pos | |
| Pyo Group C | ||||
| Streptococcus 3 x LoD | 20/20 | 100% | 20/20 | 100% |
| Streptococcus 1 x LoD | 19/20 | 95% | 20/20 | 100% |
| Pyo Group G | ||||
| Streptococcus 3 x LoD | 20/20 | 100% | 20/20 | 100% |
| Streptococcus 1 x LoD | 20/20 | 100% | 20/20 | 100% |
These studies demonstrate that the contrived negative matrix is equivalent to a clinical matrix.
3. Clinical studies:
a. Clinical Sensitivity:
The clinical performance of the Lyra Direct Strep Assay was demonstrated with one thousand two hundred ninety three (1293) prospectively collected fresh throat specimens at three (3) sites across the United States. The assay was evaluated for the qualitative detection and differentiation of Group A B-hemolytic Streptococcus and pyogenic Group C and G B-hemolytic Streptococcus using nucleic acids isolated from the patients' throat swabs. A single specimen was collected per patient. Samples were collected using Polyester or Rayon Swab with liquid Amie's or Polyester Swab or Rayon with liquid Stuart's.
All one thousand two hundred ninety three (1293) fresh throat specimens were cultured for Group A B-hemolytic Streptococcus (GAS), pyogenic Group C and G Bhemolytic Streptococcus (GCS/GGS) and tested with the Lyra Direct Strep Assay. The specimens were cultured at the testing sites and the transport fluid was cultured at a central location. The specimen was considered positive if culture from either the swab or the transport fluid was positive for Group A β-hemolytic Streptococcus and/or pyogenic Group C and G 8-hemolytic Streptococcus, as appropriate. Cultured isolates were typed by latex agglutination. B-hemolytic isolates that were typed as Group C or G were subcultured and the species were determined using MALDI TOF.
The breakdown of performance by analyte is summarized in Tables X and XI:
11
| Table X: Clinical Performance Data for the Lyra Direct
Strep Assay vs. Composite Cultures for Group A β-
| hemolytic Streptococcus | |||
|---|---|---|---|
| All Sites | |||
| Lyra | Composite Culture | ||
| GAS | Negative | Total | |
| GAS | 109 | 24 | 133 |
| Negative | 4 | 1156 | 1160 |
| Total | 113 | 1180 | 1293 |
| Sensitivity: 96.5% (109/113) 95% CI (91.3%-98.6%) | |||
| Specificity: 98.0% (1156/1180) 95% CI (97.0%-98.6%) | |||
| Site 1 | |||
| Lyra | Composite Culture | ||
| GAS | Negative | Total | |
| GAS | 18 | 1 | 19 |
| Negative | 0 | 246 | 246 |
| Total | 18 | 247 | 265 |
| Sensitivity: 96.5% (18/18) 95% CI (82.4%-100.0%) | |||
| Specificity: 99.6% (246/247) 95% CI (97.7%-99.9%) | |||
| Site 2 | |||
| Lyra | Composite Culture | ||
| GAS | Negative | Total | |
| GAS | 54 | 17 | 71 |
| Negative | 2 | 556 | 558 |
| Total | 56 | 573 | 629 |
| Sensitivity: 96.4% (54/56) 95% CI (87.9%-99.0%) | |||
| Specificity: 97.0% (556/573) 95% CI (95.3%-98.1%) | |||
| Site 3 | |||
| Lyra | Composite Culture | ||
| GAS | Negative | Total | |
| GAS | 37 | 6 | 43 |
| Negative | 2 | 354 | 356 |
| Total | 39 | 360 | 399 |
| Sensitivity: 94.9% (37/39) 95% CI (83.1%-98.6%) | |||
| Specificity: 98.3% (354/360) 95% CI (96.4%-99.2%) |
These study results are acceptable.
12
| Table XI: Clinical Performance Data for the Lyra Direct
| Strep Assay vs. Composite Cultures for Pyogenic Group | |||
|---|---|---|---|
| C and G β-hemolytic Streptococcus | |||
| All Sites | |||
| Lyra | Composite Culture | ||
| GCS/GGS | Negative | Total | |
| GCS/GGS | 67 | 21 | 88 |
| Negative | 3 | 1202 | 1205 |
| Total | 70 | 1223 | 1293 |
| Sensitivity: 95.7% (67/70) 95% CI (88.1%-98.5%) | |||
| Specificity: 98.3% (1202/1223) 95% CI (97.4%-98.9%) | |||
| Site 1 | |||
| Lyra | Composite Culture | ||
| GCS/GGS | Negative | Total | |
| GCS/GGS | 29 | 8 | 37 |
| Negative | 0 | 228 | 228 |
| Total | 29 | 236 | 265 |
| Sensitivity: 100.0% (29/29) 95% CI (88.3%-100.0%) | |||
| Specificity: 96.6% (228/236) 95% CI (93.5%-98.3%) | |||
| Site 2 | |||
| Lyra | Composite Culture | ||
| GCS/GGS | Negative | Total | |
| GCS/GGS | 22 | 12 | 34 |
| Negative | 2 | 593 | 595 |
| Total | 24 | 605 | 629 |
| Sensitivity: 91.7% (22/24) 95% CI (74.2%-97.7%) | |||
| Specificity: 98.0% (593/605) 95% CI (96.6%-98.9%) | |||
| Site 3 | |||
| Lyra | Composite Culture | ||
| GCS/GGS | Negative | Total | |
| GCS/GGS | 16 | 1 | 17 |
| Negative | 1 | 381 | 382 |
| Total | 17 | 382 | 399 |
| Sensitivity: 94.1% (16/17) 95% CI (73.0%-99.0%) |
Г
These study results are acceptable.
13
The external quality control isolates used in these studies were from the Lyra A+G Control Set #M111 consisting of Streptococcus pyogenes Z018 (for the GAS primer set) and Streptococcus dysgalactiae Z068 (for the GCS/GGS primer set), which serve as processing and extraction controls. The control isolates were tested with acceptable results.
-
b. Clinical specificity:
See table above. -
c. Other clinical supportive data (when a. and b. are not applicable):
Not applicable. -
- Clinical cut-off:
Not Applicable.
- Clinical cut-off:
-
- Expected values/Reference range:
The overall incidence of Group A B-hemolytic Streptococcus in patients tested during this study was 8.4% (108/1293). The combined overall incidence of pyogenic Group C and G ß-hemolytic Streptococcus was 5.2% (67/1293). All clinical specimens collected during this study were collected between August, 2013 and October 2013.
- Expected values/Reference range:
M. Instrument Name:
ABI 7500 Fast DX Thermocycler
N. System Descriptions:
-
- Modes of Operation:
Please see the Decision Summary for the Applied Biosystems 7500 Fast Dx - K082562.
- Modes of Operation:
-
- Software:
FDA has reviewed applicant's Hazard Analysis and software development processes for this line of product types:
- Software:
Yes
The results of the validation and verification testing results were provided for v1.4 of the Applied Biosystems 7500 Fast Dx software. These results are acceptable.
-
- Specimen Identification:
Not applicable - specimen identification is manually entered.
- Specimen Identification:
14
4. Specimen Sampling and Handling:
Specimens are manually transferred to processing tubes prior to amplification.
-
- Calibration:
Please see the manual for the Applied Biosystems 7500 Fast Dx.
- Calibration:
6. Quality Control:
The Lyra Direct Strep Assay incorporates internal controls to monitor assay performance. The Process Control is used during sample processing and amplification in the assay. External positive and negative controls streptococcal controls can be purchased commercially or a previously characterized specimen may be used. These controls must be treated as a patient specimen and should be performed in accordance with lab standards.
O. Other Supportive Instrument Performance Characteristics Data Not Covered In The "Performance Characteristics" Section above:
Not applicable.
P. Proposed Labeling:
The labeling is sufficient and it satisfies the requirements of 21 CFR Part 809.10, 21 CFR 801.109, and the special controls.
O. Identified Potential Risks and Required Mitigation Measures:
| Identified Potential Risks | Mitigation Measures |
|---|---|
| Incorrect identification of a pathogenic | |
| microorganism by the device can lead to | |
| improper patient management. | Special controls (1), (2), (3), (4), (5) and (6) |
| Failure to correctly interpret test results | Special control (7) |
| Failure to correctly operate the | |
| instrument | Special controls (8) |
15
R. Benefit/Risk Analysis:
| Summary | |
|---|---|
| Summary of | |
| the Benefit(s) | When used for the proposed intended use, the benefits to the clinician and the patient |
| include: 1) the first assay submitted to FDA to detect pyogenic group C and group G | |
| streptococcus as part of a multiplexed assay that also detects group A streptococcus |
- establishment of the device performance in a manner that demonstrates consistent
accurate test results; and 3) ability to use a well validated device to diagnose group A
streptococcus and pyogenic G/C streptococcus from nucleic acids isolated from throat
swab specimens obtained from patients with signs and symptoms of pharyngitis,
which will allow prompt patient management including that ability to initiate disease
specific treatment. |
| Summary of
the Risk(s) | The Lyra™ Direct Strep Assay can yield false positive and false negative results
through 1) incorrect identification of a pathogenic microorganism by the device,
leading to improper patient management, 2) failure to correctly interpret test results,
and 3) failure to correctly operate the instrument.
Risks associated with the device are false negative and false positive results; false
negative results are well mitigated by culture confirmation of negative results, which is
clearly indicated in device labeling. The risk from a false positive result is unnecessary
treatment. The risks of unnecessary treatment from penicillin (and alternative
antibiotics) are well recognized and include rash, allergic/hypersensitivity reactions,
gastrointestinal reactions, candidiasis, and many less common possible adverse effects.
Serious adverse reactions are uncommon. |
| Conclusions
Do the
probable
benefits
outweigh the
probable risks? | The probable benefits of this device outweigh the probable risks associated with its
use. There are no substantial clinical concerns with the classification of this device in
Class II given the combination of general and special controls. |
S. Conclusion:
The information provided in this de novo submission is sufficient to classify this device into class II under regulation 21 CFR 866.2680 with special controls. FDA believes that special controls, along with the applicable general controls, provide reasonable assurance of the safety and effectiveness of the device type. The device is classified under the following:
Streptococcus spp. nucleic acid-based assay Device Type:
Class: II (special controls)
Regulation: 21 CFR 866.2680
16
- (a) Identification. A Streptoccus spp. nucleic acid-based assay is a qualitative in vitro diagnostic device intended to simultaneously detect and identify various Streptococcus 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 genus Streptococcus 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:
-
- 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.
-
- 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.
-
- 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.
-
- Premarket notification submissions must include detailed documentation for device software, including, but not limited to, software applications and hardwarebased devices that incorporate software.
-
- Premarket notification submissions must include database implementation methodology, construction parameters and quality assurance protocols, as appropriate.
-
- The device labeling must include limitations regarding the need for culture confirmation of negative specimens, as appropriate.
-
- 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.
-
- Premarket notification submissions must include details on an end user device training program that will be offered while marketing the device, as appropriate.
-