(85 days)
The cobas® MRSA/SA Test on the cobas® 4800 system, is a qualitative in vitro diagnostic real-time PCR assay, for the direct detection of methicillin-resistant Staphylococus aureus (MRSA) and S.aureus (SA) DNA from nasal swabs to aid in the prevention and control of MRSA and SA infections in healthcare settings. The cobas® MRSA/SA Test is not intended to diagnose, guide or monitor treatment for MRSA or SA infections, or provide results of susceptibility to methicillin. A negative result does not preclude MRSA/SA nasal colonization. Concomitant cultures are necessary to recover organisms for epidemiology typing or for further susceptibility testing.
The Roche Molecular Systems (RMS) cobas® MRSA/SA Test utilizes real-time polymerase chain reaction (PCR) for the detection of Methicillin resistant Staphylococcus aureus (MRSA) and Staphylococcus aureus (SA) DNA from nasal swab specimens collected in MSwab medium to aid in the prevention and control of MRSA and SA infections in healthcare settings.
The cobas® MRSA/SA Test contains two major processes: (1) automated sample preparation to extract nucleic acids from the nasal swab specimens; (2) PCR amplification of target DNA sequences using MRSA and SA specific primers, and real-time detection of cleaved fluorescentlabeled MRSA and SA specific oligonucleotide detection probes. An Internal Control (IC), containing unrelated randomized DNA sequence, is added to all samples prior to automated sample preparation and is amplified and detected simultaneously with each sample to monitor the entire process.
The MSwab Collection, Transport and Preservation System (Copan Flock Technologies S.r.1.) is used for specimen collection, transportation and storage of specimen for the cobas MRSA/SA Test.
The cobas® MRSA/SA Test utilizes six reagent kits:
- cobas® 4800 MRSA/SA Amplification/Detection Kit
- cobas® 4800 MRSA/SA Controls and Cofactor Kit
- cobas® 4800 System Wash Buffer Kit
- cobas® 4800 System Lysis Kit 1
- cobas 4800 System Internal Control Kit 1
- cobas® 4800 System Sample Preparation Kit
The cobas® 4800 System uses the cobas x 480 Instrument for sample preparation, and the cobas z 480 Analyzer for amplification and detection. Both the cobas x 480 Instrument and the cobas z 480 Analyzer are controlled by a computer workstation running the cobas® 4800 System Software.
Here's an analysis of the acceptance criteria and study proving the device meets them, based on the provided text:
Device Name: cobas® MRSA/SA Test
1. Table of Acceptance Criteria and Reported Device Performance
The document does not explicitly present a table of acceptance criteria in the sense of predefined thresholds for performance metrics. Instead, it reports the achieved performance from various studies. However, based on the studies conducted, we can infer the performance metrics that were evaluated and for which the device demonstrated acceptable results.
Here's a table summarizing the reported device performance, categorized by the relevant studies:
| Performance Metric | Acceptance Criteria (Inferred) | Reported Device Performance | Study Section |
|---|---|---|---|
| Analytical Sensitivity (LOD) | ≥ 95% positive rate at lowest concentration | MRSA: 700 CFU/swab (highest among 2 strains), 175-750 CFU/swab (35 isolates) | 4.1, 4.2 |
| SA: 700 CFU/swab (highest among 1 strain), 175 CFU/swab (5 isolates) | 4.1, 4.2 | ||
| Genotype Inclusivity (MRSA) | Detection of diverse SCCmec types, spa types, PFGE types | 277 out of 281 MRSA isolates detected (diverse SCCmec, spa, PFGE types) | 4.3 |
| Genotype Inclusivity (SA) | Detection of diverse spa types | All 85 SA isolates detected (75 spa types) | 4.3 |
| Precision (MRSA) | Overall CV% of Ct values ≤ 1.3% | ≤ 1.3% (all concentrations) | 4.4, Table 8 |
| Precision (SA) | Overall CV% of Ct values ≤ 1.2% | ≤ 1.2% (all concentrations) | 4.4, Table 8 |
| Analytical Specificity (Non-MRSA/SA) | No cross-reactivity with common nasal flora and human cells, no interference | All 135 organisms and human cells produced negative results for targets and did not interfere with spiked targets | 4.5, Tables 9, 10 |
| Analytical Specificity (SA, BORSA, mecA dropouts) | No false negatives/positives for MRSA/SA in presence of these organisms | No false negatives/positives for MRSA with 2 SA, 10 BORSA, and 13/16 mecA dropouts (3 mecA dropouts caused false MRSA POS) | 4.5, Table 11 |
| Competitive Inhibition | No significant effect on Ct value from increasing concentrations of competing organisms | Relatively stable Ct values observed | 4.6, Table 12 |
| Interference (Common OTCs/Antibiotics) | No interference up to reasonable concentrations | No interference for most substances. Rhinaris® Nasal gel (15%), Releev™ (25%) showed interference above specified levels. Tolerated 75% whole blood, 10% mucin. | 4.7, Table 13 |
| Cross-Contamination | 0% cross-contamination rate | 0% (0/423 negative samples in checkerboard runs) | 4.8, Table 14 |
| Carry-over Contamination | 0% carry-over contamination rate | 0% (0/282 negative samples in last runs) | 4.8, Table 14 |
| Clinical Reproducibility (MRSA) PPA | High positive percent agreement for positive samples | 85.6% (Below LOD MRSA-384), 87.2% (Below LOD MRSA-43300), 100.0% (1x & 3x LOD) | 5.1.1, Table 15 |
| Clinical Reproducibility (MRSA) Ct Total CV | Low coefficient of variation for Ct values | ≤ 1.4% | 5.1.1, Table 16 |
| Clinical Reproducibility (SA) PPA | High positive percent agreement for positive samples | 50.0% (Below LOD SA), 99.4% (1x LOD SA), 100.0% (3x LOD SA) | 5.1.2, Table 17 |
| Clinical Reproducibility (SA) Ct Total CV | Low coefficient of variation for Ct values | ≤ 1.3% | 5.1.2, Table 18 |
| Clinical Performance (MRSA) Sensitivity | High sensitivity compared to reference method | 93.1% (149/160) | 5.2.1.1, Table 19 |
| Clinical Performance (MRSA) Specificity | High specificity compared to reference method | 97.5% (2281/2340) | 5.2.1.1, Table 19 |
| Clinical Performance (SA) Sensitivity | High sensitivity compared to reference method | 93.9% (620/660) | 5.2.1.1, Table 19 |
| Clinical Performance (SA) Specificity | High specificity compared to reference method | 94.2% (1734/1841) | 5.2.1.1, Table 19 |
2. Sample Size Used for the Test Set and Data Provenance
The primary clinical performance evaluation used the following test set:
- Sample Size: 2528 subjects, yielding 2504 evaluable results.
- Data Provenance:
- Country of Origin: United States. Specimens were collected at six geographically diverse sites across the US.
- Retrospective or Prospective: Prospective. Specimens were collected prospectively from eligible male and female subjects.
3. Number of Experts Used to Establish the Ground Truth for the Test Set and the Qualifications of Those Experts
The document states that the ground truth for the clinical test set was established by a reference laboratory that specialized in culture and molecular detection of methicillin-resistant MRSA and SA. However, it does not specify the number of individual experts or their specific qualifications (e.g., "radiologist with 10 years of experience"). It implies that the laboratory's established practices for culture and molecular confirmation (including non-selective direct and enrichment culture, Gram-stain, latex agglutination, Kirby-Bauer cefoxitin disc diffusion for MRSA, and laboratory developed PCR assay for femA and mecA genes) served as the "expert" ground truth.
4. Adjudication Method for the Test Set
The ground truth was established by comparing the cobas® MRSA/SA Test results against a combined direct and enrichment culture (reference method).
- Discrepant Analysis: For samples with discordant results between the cobas® MRSA/SA Test and the combined direct and enrichment culture, a second, FDA-cleared nucleic acid amplification test (NAAT) and a non-selective direct and enrichment culture were used for further analysis.
- Control Samples: A randomly selected subset of samples with concordant results were also included in this discrepant analysis as controls.
This method resembles a 2+1 adjudication model in spirit for discordant cases, where the initial test (cobas® MRSA/SA) results are compared against a reference standard (combined culture), and any discrepancies are resolved by a third, independent method (second NAAT and non-selective culture).
5. If a Multi Reader Multi Case (MRMC) Comparative Effectiveness Study was Done
No, a MRMC comparative effectiveness study was not done. The device being evaluated is an in vitro diagnostic real-time PCR assay for direct detection of bacterial DNA, not an imaging device that requires human interpretation. Therefore, the concept of "human readers" or "AI assistance" in the context of improving human reader performance is not applicable to this device.
6. If a Standalone (i.e. algorithm only without human-in-the loop performance) was Done
Yes, the primary clinical performance study (Section 5.2) and all analytical studies (Section 4) represent standalone algorithm-only performance. The cobas® MRSA/SA Test is an automated diagnostic assay that reports qualitative results (Positive/Negative for MRSA/SA) based on real-time PCR amplification and detection. The interpretation of these results is done by the cobas 4800 System Software, which then reports out the final results (Section 6.1.2). Human involvement is in specimen collection, loading, and result interpretation, but the core detection and qualitative output is automated by the device itself.
7. The Type of Ground Truth Used
The ground truth used for the clinical performance evaluation was a combined microbiological culture method:
- Combined Direct and Enrichment Culture: This involved both direct plating onto selective and differential chromogenic media, and enrichment culture in tryptic soy broth.
- Confirmatory Tests: Suspect isolates from these cultures were further identified by Gram-stain, latex agglutination, and for MRSA, Kirby-Bauer cefoxitin disc diffusion.
- Discrepant Analysis: For discordant results, a second FDA-cleared NAAT and non-selective direct and enrichment culture were used, with identification of isolates confirmed using a laboratory developed PCR assay for femA and mecA genes.
This represents a robust, multi-faceted ground truth derived from established microbiological techniques and molecular confirmation.
8. The Sample Size for the Training Set
The document does not explicitly state the sample size for a "training set."
Medical device submissions for in vitro diagnostics like this PCR assay typically focus on analytical validation (LOD, specificity, precision) and clinical validation with an independent test set. The algorithms for interpreting PCR cycle thresholds are generally fixed and based on scientific principles rather than being "trained" on a large dataset in the same way machine learning models are. However, the analytical studies used various isolates to define parameters and confirm performance:
- Analytical Sensitivity (LOD): 2 MRSA culture isolates and 1 SA culture isolate for initial LOD, and 35 additional MRSA and 5 additional SA culture isolates for genotype LOD verification.
- Geographical Inclusivity: 281 MRSA and 85 SA isolates from diverse geographical locations.
- Precision: 2 MRSA culture isolates and 1 SA culture isolate.
- Analytical Specificity: 43 CoNS/MR-CoNS organisms, 93 non-MRSA/SA microorganisms and human cells, 2 SA isolates, 10 BORSA isolates, and 16 mecA dropouts.
These isolates were used to characterize the device's analytical performance across various conditions and strains, which could be considered akin to "training" or extensive characterization data, but not in the machine learning sense of model optimization.
9. How the Ground Truth for the Training Set Was Established
As noted above, there isn't a "training set" in the machine learning context described. The ground truth for the various analytical studies (e.g., sensitivity, specificity, inclusivity) was established through:
- Quantified Culture Isolates: For LOD and precision studies, specific MRSA and SA culture isolates with known concentrations (CFU/swab) were used.
- Characterized Clinical Isolates: For genotype LOD and inclusivity studies, isolates were selected based on known characteristics such as SCCmec type, spa type, PFGE type, MIC values, and geographical origin.
- Established Microbiological Methods: For analytical specificity, cultures of known microorganisms (both targets and non-targets) were used, often from ATCC or other reference collections, and their identity was presumably confirmed by standard microbiological identification techniques.
Essentially, for these analytical studies, the "ground truth" was defined by standard reference strains and well-characterized clinical isolates, obtained and verified through established microbiology laboratory practices.
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Food and Drug Administration 10903 New Hampshire Avenue Document Control Center - WO66-G609 Silver Spring, MD 20993-0002
ROCHE MOLECULAR SYSTEMS, INC. WILK VON GUSTEDT, PH.D. SR. REGULATORY SPECIALIST II 4300 HACIENDA DRIVE PLEASANTON CA 94588-2722
December 17, 2014
Re: K142721
Trade/Device Name: cobas MRSA/SA Test Regulation Number: 21 CFR 866.1640 Regulation Name: Antimicrobial susceptibility test powder Regulatory Class: II Product Code: NOX, OOI Dated: September 22, 2014 Received: September 23, 2014
Dear Dr. von Gustedt:
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.
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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.
Uwe Scherf -S for
Sally A. Hojvat. M.Sc., Ph.D. Director Division of Microbiology Devices Office of In Vitro Diagnostics and Radiological Health Center for Devices and Radiological Health
Enclosure
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Indications for Use
510(k) Number (if known) K142721
Device Name cobas® MRSA/SA Test
Indications for Use (Describe)
The cobas® MRSA/SA Test on the cobas® 4800 system, is a qualitative in vitro diagnostic real-time PCR assay, for the direct detection of methicillin-resistant Staphylococus aureus (MRSA) and S.aureus (SA) DNA from nasal swabs to aid in the prevention and control of MRSA and SA infections in healthcare settings. The cobas® MRSA/SA Test is not intended to diagnose, guide or monitor treatment for MRSA or SA infections, or provide results of susceptibility to methicillin. A negative result does not preclude MRSA/SA nasal colonization. Concomitant cultures are necessary to recover organisms for epidemiology typing or for further susceptibility testing.
Type of Use (Select one or both, as applicable)
X Prescription Use (Part 21 CFR 801 Subpart D)
_ Over-The-Counter Use (21 CFR 801 Subpart C)
PLEASE DO NOT WRITE BELOW THIS LINE - CONTINUE ON A SEPARATE PAGE IF NEEDED.
FOR FDA USE ONLY
Concurrence of Center for Devices and Radiological Health (CDRH) (Signature)
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510(k) Summary
| Submitter Name | Roche Molecular Systems, Inc. |
|---|---|
| Address | 4300 Hacienda DrivePleasanton, CA 94588-2722 |
| Contact | Wilk von GustedtPhone: (925) 730-8046FAX: (925) 225-0207 |
| Date Prepared | September 18, 2014 |
| Proprietary Name | cobas® MRSA/SA Test |
| Common Name | MRSA/SA Test |
| Classification Name | Antimicrobial susceptibility test powder. (21 CFR 866.1640)Real Time Nucleic Acid Amplification System (21 CFR 862.2570) |
| Product Codes | NQX: System, Nucleic Acid amplification Test, DNA, Methicillin ResistantStaphylococcus aureus, Direct SpecimenOOI: Real Time Nucleic Acid Amplification System |
| Predicate Devices | Roche Lightcycler MRSA, K091409 |
| Establishment Registration | Branchburg: 2243471Pleasanton: 3004141078Indianapolis: 1823260 |
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1. DEVICE DESCRIPTION
The Roche Molecular Systems (RMS) cobas® MRSA/SA Test utilizes real-time polymerase chain reaction (PCR) for the detection of Methicillin resistant Staphylococcus aureus (MRSA) and Staphylococcus aureus (SA) DNA from nasal swab specimens collected in MSwab medium to aid in the prevention and control of MRSA and SA infections in healthcare settings.
The cobas® MRSA/SA Test contains two major processes: (1) automated sample preparation to extract nucleic acids from the nasal swab specimens; (2) PCR amplification of target DNA sequences using MRSA and SA specific primers, and real-time detection of cleaved fluorescentlabeled MRSA and SA specific oligonucleotide detection probes. An Internal Control (IC), containing unrelated randomized DNA sequence, is added to all samples prior to automated sample preparation and is amplified and detected simultaneously with each sample to monitor the entire process.
The MSwab Collection, Transport and Preservation System (Copan Flock Technologies S.r.1.) is used for specimen collection, transportation and storage of specimen for the cobas MRSA/SA Test.
The cobas® MRSA/SA Test utilizes six reagent kits:
-
- cobas® 4800 MRSA/SA Amplification/Detection Kit
-
- cobas® 4800 MRSA/SA Controls and Cofactor Kit
-
- cobas® 4800 System Wash Buffer Kit
-
- cobas® 4800 System Lysis Kit 1
-
- cobas 4800 System Internal Control Kit 1
-
- cobas® 4800 System Sample Preparation Kit
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1.1. Target Selection
The well-characterized Right Extremity (RE) junction between the Staphylococcus aureus orfX gene and SCCmec cassette carrying the mecA drug-resistant gene was chosen to be the target to specifically detect MRSA. The capsular polysaccharide enzyme CAP5N (CPE) gene was chosen as the target for Staphylococcus aureus identification. This gene is conserved in Staphylococcus aureus and present in both methicillin resistant and methicillin sensitive organisms. Internal Control (IC) DNA sequence is unique and unrelated to either MRSA or SA target sequences.
Test Principle 1.2.
Sample Preparation 1.1.1.
Sample preparation for the cobas® MRSA/SA Test is automated with the use of the cobas x 480 instrument. Organisms in nasal swab specimens collected in MSwab medium are lysed with chaotropic agent, proteinase K, and SDS reagents. Released nucleic acids, along with added Internal Control DNA, are bound by magnetic glass particles. They are washed and then eluted into a small volume of buffer. The instrument then takes an aliquot of the eluted material and sets up the PCR reaction with an activated Master Mix.
1.1.2. PCR Amplification and TaqMan® Detection
The PCR cycling steps and detection of target signal occurs in the cobas z 480 Analyzer. The Master Mix reagent contains primer pairs and probes for orfX (MRSA), CPE (SA) and IC targets. If the target nucleic acid sequences are present, amplification with the corresponding primers will occur by a thermostable DNA polymerase, generating PCR products (amplicons). These products are detected by specific TaqMan probes containing a fluorescent dye and a quencher. Normally, the quencher suppresses the fluorescence of the dye. However, if the PCR product is present, the probe hybridizes to the product and gets cleaved by the 5' to 3' nuclease activity of the polymerase. This reaction allows the fluorescence to be emitted from the dye, and the signal is recorded in real time during each PCR cycle by the cobas z 480 analyzer. The signal is interpreted by the cobas 4800 System Software and reported as final results.
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cobas® 4800 System Description 1.3.
The cobas® 4800 System uses the cobas x 480 Instrument for sample preparation, and the cobas z 480 Analyzer for amplification and detection. Both the cobas x 480 Instrument and the cobas z 480 Analyzer are controlled by a computer workstation running the cobas® 4800 System Software.
The system hardware is unchanged from that originally approved for IVD use in PMA P100020 (cobas® HPV Test, April 19, 2011). The software version has been updated to software release 2.1 in order to support the expanded test menu. The updated software was cleared for other currently available tests on the cobas® 4800 System per Special 510(K) 140887.
INDICATIONS FOR USE 2.
The cobas® MRSA/SA Test on the cobas® 4800 system, is a qualitative in vitro diagnostic realtime PCR assay, for the direct detection of methicillin-resistant Staphylococcus aureus (MRSA) and S.aureus (SA) DNA from nasal swabs to aid in the prevention and control of MRSA and SA infections in healthcare settings. The cobas® MRSA/SA Test is not intended to diagnose, guide or monitor treatment for MRSA or SA infections, or provide results of susceptibility to methicillin. A negative result does not preclude MRSA/SA nasal colonization. Concomitant cultures are necessary to recover organisms for epidemiology typing or for further susceptibility testing.
TECHNOLOGICAL CHARACTERISTICS 3.
As indicated in Table 1, the RMS cobas® MRSA/SA Test has the same general intended use as the predicate device. The subject device is substantially equivalent from its technological characteristics to the currently legally marketed predicate device.
Differences reside in sample collection and preparation. The candidate test utilizes an automated extraction process while the predicate uses a manual process. However both devices are similar in the method used for extraction of nucleic acids from specimens, using glass beads together with Lysis buffer. The additional (SA) target detected by the cobas® MRSA/SA test uses the same technological methodology as used for detection of the MRSA target.
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| Submitted Device:RMS cobas® MRSA/SA Test | Predicate Device:Lightcycler® MRSA Advanced TestK091409 | |
|---|---|---|
| Intended Use | The cobas® MRSA/SA Test on thecobas® 4800 system, is a qualitative invitro diagnostic real-time PCR assay, forthe direct detection of methicillin-resistantStaphylococcus aureus (MRSA) andS.aureus (SA) DNA from nasal swabs toaid in the prevention and control of MRSAand SA infections in healthcare settings.The cobas® MRSA/SA Test is notintended to diagnose, guide or monitortreatment for MRSA or SA infections, orprovide results of susceptibility tomethicillin. A negative result does notpreclude MRSA/SA nasal colonization.Concomitant cultures are necessary torecover organisms for epidemiology typingor for further susceptibility testing. | The LightCycler® MRSA Advanced Test isa qualitative in vitro diagnostic test for thedirect detection of nasal colonization withmethicillin-resistant (MRSA) to aid in theprevention and control of MRSA infectionsin healthcare settings. The test isperformed on the LightCycler® 2.0Instrument with nasal swab specimensfrom patients suspected of colonization,uses swab extraction and mechanical lysisfor specimen preparation followed bypolymerase chain reaction (PCR) for theamplification of MRSA DNA, andfluorogenic target specific hybridizationprobes for the detection of the amplifiedDNA.The LightCycler® MRSA Advanced Test isnot intended to diagnose, guide or monitortreatment for MRSA infections.Concomitant cultures are necessary torecover organisms for epidemiology typingor for further susceptibility testing. |
| Conditions for use | For prescription use | Same |
| Sample Types | Nasal swab | Same |
| Amplification Technology | Real-time PCR | Same |
| Detection Chemistry | paired target-specific hybridization probesusing Förster resonance energy transfer(FRET) | Same |
| Controls used | Sample processing control (IC)Positive and negative control | Same |
| Analyte Target | SCCmec cassette Right Extremity (RE)junction of methicillin-resistantStaphylococcus aureus (MRSA) | Same target region for MRSA detection |
Similarities and Differences between the cobas® MRSA/SA Test Table 1: and the Predicate Device
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| Submitted Device:RMS cobas® MRSA/SA Test | Predicate Device:Lightcycler® MRSA Advanced TestK091409 | ||||
|---|---|---|---|---|---|
| Differences | |||||
| Sample Collection Devices | Copan MSwab Collection, Transportand Preservation System | Liquid Stuart Swabs, Amies Gel withCharcoal Swabs, Amies Gel withoutCharcoal Swabs | |||
| Analyte Target | wt Staphylococcus aureus (SA) | methicillin-resistant Staphylococcusaureus (MRSA) only | |||
| Sample PreparationProcedure | Automated by cobas® x480 | Lysis of the nasal swab specimens isperformed by using the LightCycler®Advanced Lysis Kit and the MagNA LyserInstrument. | |||
| Result Analysis | Based on PCR cycle threshold analysis | Melting peak analysis |
In summary, the intended use and technological characteristics of the cobas® MRSA/SA Test as compared to the predicate device do not raise any new types of safety or effectiveness questions and are substantially equivalent.
4. NON-CLINICAL PERFORMANCE EVALUATION
Analytical Sensitivity 4.1.
The analytical sensitivity (Limit of Detection or LOD) for the cobas® MRSA/SA Test was determined by analyzing 2 MRSA culture isolates and 1 SA culture isolate. Quantified cultures were diluted to 8-9 concentration levels into a simulated nasal swab background matrix to determine the LOD. All levels were analyzed using cobas® MRSA/SA Test with 3 unique lots of MRSA/SA specific reagents. The LOD of the test was determined as the lowest concentration exhibiting at least 95% positive rate for which all higher concentrations were greater than or equal to 95% positive rate.
The highest LOD among 3 reagent lots are shown in Table 2. The highest claimed LOD between the 2 MRSA strains tested was 700 CFU/swab and for SA it was 700 CFU/swab based on 95% positive rate.
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| Isolate Name | Source ID | RE type | SCCmectype | spa type | PFGEtype | MICvalue | LOD(CFU/swab) |
|---|---|---|---|---|---|---|---|
| MRSA 10364 | NARSA 384 | 2 | IVa | t008 | USA300-0114 | 32 | 650 |
| MRSA 8065 | ATCC 43300 | 2 | II | t007 | Sac-15 | n/a | 700 |
| SA 10851 | NARSA 164 | n/a | n/a | t084 | n/a | n/a | 700 |
cobas® MRSA/SA Test Limit of Detection Table 2:
Genotype LOD verification 4.2.
The sensitivity of the cobas MRSA/SA Test was determined for 35 additional MRSA culture isolates and 5 additional SA culture isolates. The genotype LOD panel consisted of at least three concentrations per isolate in simulated nasal swab background matrix. The LOD was calculated as the lowest concentration level with ≥ 95 % positive rate for which all higher concentration levels show ≥ 95 % positive rate. A minimum of one lot of reagents was used for this study.
The genotype LOD study results are listed in Table 4. As shown in Table 3, the LOD is ranging from 175 to 750 CFU/swab for the 35 MRSA isolates tested. The cobas MRSA/SA Test detected the RE types 1, 2, 3, 4, 6, 9, 11, 14, 24 and 25. The cobas MRSA/SA Test detected MRSA SCCmec types I, II, III, IV, V, VI and VIII, as well as MRSA PFGE types USA 100 to 1000. Five SA isolates tested represent 5 different spa types, and the LOD is 175 CFU/swab for all isolates (Table 4).
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| Isolate # | RE Type | SCCmec Type | spa Type | Cefoxitin MIC Value*(μg/mL) | PFGE Type | LOD (CFU/Swab) |
|---|---|---|---|---|---|---|
| 1 | 11 | new | t002 | ≥8 | Unknown | 485 |
| 2 | 6 | II | t242 | ≥8 | Unknown | 720 |
| 3 | 9/11 | new | t024 | ≥8 | Unknown | 175 |
| 4 | 14 | Unknown | Unknown | Unknown | Unknown | 700 |
| 5 | 25 | Unknown | t003 | ≥8 | Unknown | 175 |
| 6 | 6 | II | t216 | ≥8 | USA100 | 720 |
| 7 | 2 | IV | t008 | ≥8 | USA300 | 350 |
| 8 | 2 | II | t037 | ≥8 | USA200 | 700 |
| 9 | 2 | IV | t1578 | ≥8 | USA300 | 700 |
| 10 | 2 | II | t002 | ≥8 | USA100 | 720 |
| 11 | 2 | IV | t008 | ≥8 | USA800 | 750 |
| 12 | 2 | IV | t008 | ≥8 | USA300 | 266 |
| 13 | 2 | IV | t064 | ≥8 | USA500 | 260 |
| 14 | 2 | IV | t148 | ≥8 | USA700 | 700 |
| 15 | 2 | IV | t688 | ≥8 | USA800 | 271 |
| 16 | 2 | IV | t688 | ≥8 | USA300 | 700 |
| 17 | 2 | II | t042 | ≥8 | USA100 | 463 |
| 18 | 2 | II | t018 | ≥8 | USA200 | 350 |
| 19 | 2 | IV | t008 | ≥8 | USA300 | 410 |
| 20 | 2 | IV | t008 | ≥8 | USA300 | 175 |
| 21 | 2 | IV | t5576 | ≥8 | USA800 | 202 |
| 22 | 2 | II | t004 | ≥8 | USA600 | 350 |
| 23 | 2 | IV | t216 | ≥8 | USA1000 | 350 |
| 24 | 2 | IV | t064 | ≥8 | Iberian | 175 |
| 25 | 2 | II | t266 | ≥8 | USA600 | 700 |
| 26 | 2 | IV | t008 | ≥8 | USA300 | 700 |
| 27 | 2 | IV | t008 | ≥8 | USA300 | 350 |
| 28 | 2 | IV | t002 | ≥8 | USA800 | 350 |
| 29 | 3 | V | t242 | ≥8 | USA1000 | 350 |
| 30 | 24 | new | t476 | ≥8 | Unknown | 350 |
| 31 | 1 | I | t149 | ≥8 | Unknown | 175 |
| 32 | 3 | VIII | Unknown | ≥8 | Unknown | 700 |
| 33 | 4 | IV | Unknown | ≥8 | Unknown | 350 |
| 34 | 2 | III | t030 | ≥8 | Unknown | 700 |
| 35 | 25 | VI | Unknown | Unknown | Unknown | 175 |
Table 3: MRSA isolate LOD Results
*Isolates 1,2,5-10, 12-29, 31 and 34 have Cefoxitin MC values 3,11 and 32 have Cefoxitin
MC values of ≥16 µg/mL; isolate 33 has an Cefoxitin MC value of 12 µg/mL; isolate value of 8 µg/mL.
{12}------------------------------------------------
| SA Isolate # | spa Type | LOD (CFU/Swab) |
|---|---|---|
| 1 | t238 | 175 |
| 2 | t018 | 175 |
| 3 | t008 | 175 |
| 4 | t002 | 175 |
| 5 | t088 | 175 |
Table 4: SA Isolates LOD Results
4.3. Geographical Inclusivity
In addition to 37 MRSA isolates and 6 SA isolates tested in analytical LOD and genotype LOD studies shown above, the inclusivity was also examined by testing a broad collection of MRSA and SA isolates from diverse geographical locations. Two hundred and eighty-one (281) MRSA from 16 European countries or regions, US, Japan and Australia and 85 SA isolates from diverse locations within US were tested. The MRSA collection contained MRSA isolates of different SCCmec types (I, II, III, IV, IVa, V, VI, VII, and new), and 71 spa types and cefoxitin MIC value from 6 to greater than 256. All 85 SA isolates sourced from the US contains 75 spa types were detected by the cobas® MRSA/SA Test. The geographical inclusivity study results for MRSA isolates are listed in Table 5. Of the two hundred eighty-one MRSA isolates, two hundred seventy-seven of the MRSA isolates were detected. The four MRSA isolates not detected by the cobas® MRSA/SA Test were sequenced, and the results suggested that the target regions contained sequences not recognized by the primers and probes in the cobas MRSA/SA Test. One of the four isolates was a mec ALGA251 (also known as mec C) strain.
{13}------------------------------------------------
| Geographical Origin | Total Number of MRSA Isolates | Detected by cobas® MRSA/SA Test |
|---|---|---|
| England | 58 | 58 |
| Germany | 51 | 51 |
| Denmark | 37 | 36 |
| France | 33 | 31 |
| US | 20 | 20 |
| Spain | 20 | 20 |
| Switzerland | 18 | 18 |
| Japan | 15 | 15 |
| Sweden | 7 | 7 |
| Australia | 6 | 5 |
| Netherlands | 5 | 5 |
| Italy | 4 | 4 |
| Belgium | 3 | 3 |
| Scotland | 2 | 2 |
| Ireland | 1 | 1 |
| Norway | 1 | 1 |
| Total | 281 | 277 |
Geographical Coverage of the cobas® MRSA/SA Test for MRSA Isolates Table 5:
4.4. Precision
In-house precision study was conducted with 2 MRSA culture isolates and 1 SA culture isolate a concentrations below, near and above Limit of Detection (LOD) of the cobas® MRSA/SA Test. The study used three unique lots of cobas® MRSA/SA Test reagents and three instruments for a total of 36 runs over 12 days (3 runs per day). A description of the precision panels, the study results, and variance components are shown in Table 6. An analysis of the variance of the Ct values from valid tests was performed on positive panel members above LOD concentrations. Overall, most of the variation in the cobas® MRSA/SA Test was attributed to random factors (41.2% - 44.9%) with contribution from reagent lot, kit size and run/day of testing (Table 7). The overall CV% of Ct values for cobas® MRSA/SA Test was less than or equal to 1.3% indicating good reproducibility (Table 8).
{14}------------------------------------------------
| Target | TargetConcentration | Result interpretation | TotalSampleTested | %Detected | 2-sided95% LowerCL | 2-sided95% UpperCL | ||
|---|---|---|---|---|---|---|---|---|
| Negative | No analyte | 72 | 0 | 0 | 72 | 0.0% | 0.0% | 5.0% |
| MRSACultureIsolate 10364(NARSA 384) | < 1.0 x LOD | 0 | 15 | 57 | 72 | 79.2% | 68.0% | 87.8% |
| MRSACultureIsolate 10364(NARSA 384) | ~ 1.0 x LOD | 0 | 0 | 72 | 72 | 100.0% | 95.0% | 100.0% |
| MRSACultureIsolate 10364(NARSA 384) | ~ 3.0 x LOD | 0 | 0 | 72 | 72 | 100.0% | 95.0% | 100.0% |
| MRSACultureIsolate 8065(ATCC43300) | < 1.0 x LOD | 0 | 9 | 63 | 72 | 87.5% | 77.6% | 94.1% |
| MRSACultureIsolate 8065(ATCC43300) | ~ 1.0 x LOD | 0 | 0 | 72 | 72 | 100.0% | 95.0% | 100.0% |
| MRSACultureIsolate 8065(ATCC43300) | ~ 3.0 x LOD | 0 | 0 | 72 | 72 | 100.0% | 95.0% | 100.0% |
| SA CultureIsolate 10851(NARSA 164) | < 1.0 x LOD | 4 | 67 | 0 | 71* | 94.4% | 86.2% | 98.4% |
| SA CultureIsolate 10851(NARSA 164) | ~ 1.0 x LOD | 0 | 72 | 0 | 72 | 100.0% | 95.0% | 100.0% |
| SA CultureIsolate 10851(NARSA 164) | ~ 3.0 x LOD | 0 | 72 | 0 | 72 | 100.0% | 95.0% | 100.0% |
Table 6: In-House Precision Study Positive Rate Analysis
*One of 72 samples tested could not be processed due to sample pipetting error on the instrument.
| Table 7: Variance Components Analysis of MRSA and SA Ct for cobas MRSA/SA Test |
|---|
| Variance Components/Percent Contribution to Total | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Target | N | MeanCt | Lot | Kit Size | Instrument | Run/Day | Random | Total | |
| MRSA CultureIsolate 10364(NARSA 384) | 72 | 36.9 | 0.057 | 0.003 | 0.027 | 0.057 | 0.101 | 0.244 | |
| 23.2% | 1.2% | 11.1% | 23.3% | 41.2% | 100.0% | ||||
| MRSA CultureIsolate 8065(ATCC 43300) | 72 | 38.0 | 0.003 | 0.024 | 0.007 | 0.010 | 0.037 | 0.082 | |
| 4.1% | 29.6% | 8.9% | 12.5% | 44.9% | 100.0% | ||||
| SA CultureIsolate 10851(NARSA 164) | 72 | 35.6 | 0.050 | 0.023 | 0.007 | 0.032 | 0.082 | 0.193 | |
| 25.9% | 11.7% | 3.6% | 16.5% | 42.3% | 100.0% |
{15}------------------------------------------------
| Target | N | Mean Ct | Standard Deviation Components/CV Percent | |||||
|---|---|---|---|---|---|---|---|---|
| Lot | Kit Size | Instrument | Run/Day | Random | Total | |||
| MRSA CultureIsolate 10364(NARSA 384) | 72 | 36.9 | 0.238 | 0.054 | 0.165 | 0.239 | 0.317 | 0.494 |
| 0.6% | 0.1% | 0.4% | 0.6% | 0.9% | 1.3% | |||
| MRSA CultureIsolate 8065(ATCC 43300) | 72 | 38.0 | 0.058 | 0.156 | 0.086 | 0.102 | 0.192 | 0.287 |
| 0.2% | 0.4% | 0.2% | 0.3% | 0.5% | 0.8% | |||
| SA CultureIsolate 10851(NARSA 164) | 72 | 35.6 | 0.224 | 0.150 | 0.084 | 0.178 | 0.286 | 0.440 |
| 0.6% | 0.4% | 0.2% | 0.5% | 0.8% | 1.2% |
Standard Deviation Components/CV Percent for cobas® MRSA/SA Test Table 8:
Analytical Specificity 4.5.
Analytical specificity of the cobas® MRSA/SA Test was examined by testing non-MRSA/SA microorganisms commonly present in nasal flora, including coagulase negative and positive Staphylococcus species, as well as human cells in the presence or absence of MRSA and SA targets. For the MRSA target, SA organisms including BORSA strains and "empty cassette variants" (also known as "mec A drop outs") were also tested at high concentration to examine any cross-reactivity and/or interference with MRSA detection.
Table 9 shows the result for Coagulase-Negative Staphylococcus (CoNS) and Methicillin-Resistant Coagulase-Negative Staphylococcus (MR-CoNS) Organisms. Table 10 summarizes results of microorganisms commonly found in nasal flora including human cell line HCT-15.
All target negative samples generated negative MRSA and SA results, demonstrating that the cobas® MRSA/SA Test does not cross-react with these microorganisms and human DNA. None of the 135 organisms and the human cells interfered with the detection of both MRSA and SA targets by the cobas® MRSA/SA Test.
Table 11 presents the analytical specificity results in presence of 2 SA isolates, 10 BORSA isolates and 16 mecA dropouts.
The cobas® MRSA/SA Test did not generate false negative and false positive results for MRSA in the presence of 2 SA isolates, 10 BORSA, and 13 of 16 mecA dropouts.
{16}------------------------------------------------
| Organisms | Strain/ATCC ID | No target | MRSA 10364(NARSA 384) | MRSA 8065(ATCC 43300) | SA 10851(NARSA 164) | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| MRSA | SA | MRSA | SA | MRSA | SA | MRSA | SA | |||
| 1 | Staphylococcus arlettae | ATCC43957 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 2 | Staphylococcus auricularis(Methicillin-resistant) | ATCC33753 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 3 | Staphylococcus caprae(Methicillin-resistant) | ATCC35538 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 4 | Staphylococcus captis | ATCC35661 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 5 | Staphylococcus carnosus | ATCC51365 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 6 | Staphylococcus chromogenes | ATCC43764 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 7 | Staphylococcus cohnii | ATCC35662 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 8 | Staphylococcus delphini | MayoClinicH18859** | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 9 | Staphylococcus epidermidis(Methicillin-resistant) | ATCC14990 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 10 | Staphylococcus epidermidis(Methicillin-resistant) | ATCC35547 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 11 | Staphylococcus epidermidis(Methicillin-resistant) | ATCC35983 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 12 | Staphylococcus epidermidis(Methicillin-resistant) | ATCC35984 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 13 | Staphylococcus epidermidis(Methicillin-resistant) | ATCC51624 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| Organisms | Strain/ATCC ID | No target | MRSA 10364(NARSA 384) | MRSA 8065(ATCC 43300) | SA 10851(NARSA 164) | |||||
| MRSA | SA | MRSA | SA | MRSA | SA | MRSA | SA | |||
| 14 | Staphylococcus epidermidis(Methicillin-resistant) | ATCC51625 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 15 | Staphylococcus epidermidis | ATCC700583 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 16 | Staphylococcus epidermidis(Methicillin-resistant) | ATCC27676 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 17 | Staphylococcus equorum | ATCC43958 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 18 | Staphylococcus felis | ATCC49168 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 19 | Staphylococcus gallinarum | ATCC35539 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 20 | Staphylococcus haemolyticus(Methicillin-resistant) | ATCC29968 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 21 | Staphylococcus haemolyticus | ATCC29970 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 22 | Staphylococcus haemolyticus | ATCC43252 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 23 | Staphylococcus hominis | ATCC25615 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 24 | Staphylococcus hominis | ATCC35982 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 25 | Staphylococcus hominis subsp. Hominis | ATCC27844 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 26 | Staphylococcus hominis subsp. Hominis | ATCC27845 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 27 | Staphylococcus intermedius | ATCC29663 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 28 | Staphylococcus kloosii | ATCC43959 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 29 | Staphylococcus lentus | ATCC29070 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 30 | Staphylococcus lugdunensis | ATCC49576 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 31 | Staphylococcus pasteuri | ATCC51129 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 32 | Staphylococcus pseudointermedius | DSMZ21284** | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 33 | Staphylococcus pulvereri | ATCC51698 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| Organisms | Strain/ATCC ID | No target | MRSA 10364(NARSA 384) | MRSA 8065(ATCC 43300) | SA 10851(NARSA 164) | |||||
| MRSA | SA | MRSA | SA | MRSA | SA | MRSA | SA | |||
| 34 | Staphylococcus saprophyticus | ATCC15305 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 35 | Staphylococcus schleiferi(subspecies coagulans) | ATCC43808 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 36 | Staphylococcus sciuri | ATCC49575 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 37 | Staphylococcus simulans(Methicillin-resistant) | ATCC27848 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 38 | Staphylococcus simulans | ATCC11631 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 39 | Staphylococcus warneri | ATCC27836 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 40 | Staphylococcus warneri(Methicillin-resistant) | ATCC27839 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 41 | Staphylococcus warneri | RMSCC 1224** | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 42 | Staphylococcus xylosus | ATCC35663 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 43 | Staphylococcus xylosus | ATCC29971 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| Organisms | Strain/ATCC ID | No target | MRSA 10364(NARSA 384) | MRSA 8065(ATCC 43300) | SA 10851(NARSA 164) | |||||
| MRSA | SA | MRSA | SA | MRSA | SA | MRSA | SA | |||
| 1 | Acinetobacter baumannii | ATCC19606 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 2 | Acinetobacter haemolyticus | ATCC17906 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 3 | Bacillus cereus | ATCC13472 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 4 | Bordetella bronchioseptica | ATCC19395 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 5 | Bordetella parapertussis | ATCC15311 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 6 | Bordetella pertussis | ATCC9797 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 7 | Burkholderia cepacia | ATCC25416 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 8 | Candida albicans | ATCC10231 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 9 | Candida glabrata | ATCC2001 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 10 | Candida parapsilosis | ATCC22019 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 11 | Candida tropicalis | ATCC750 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 12 | Chlamydia pneumoniae | CDC-CWL-011 strain | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 13 | Citrobacter freundii | ATCC8090 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 14 | Citrobacter koseri | ATCC27028 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 15 | Corynebacterium amycolatum | ATCC49368 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 16 | Corynebacterium bovis | ATCC7715 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 17 | Corynebacterium flavescens | ATCC10340 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 18 | Corynebacterium genitalium | ATCC33030 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 19 | Corynebacterium glutamicum | ATCC13032 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 20 | Corynebacterium jeikeium | ATCC43734 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 21 | Cryptococcus neoformans | ATCC32719 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| Organisms | Strain/ATCC ID | No target | MRSA 10364(NARSA 384) | MRSA 8065(ATCC 43300) | SA 10851(NARSA 164) | |||||
| MRSA | SA | MRSA | SA | MRSA | SA | MRSA | SA | |||
| 22 | Eikenella corrodens | ATCC23834 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 23 | Enterobacter aerogenes | ATCC13048 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 24 | Enterobacter cloacae | ATCC13047 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 25 | Enterococcus flavescens | ATCC49996 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 26 | Enterococcus gallinarum | ATCC49573 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 27 | Enterococcus hirae | ATCC8043 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 28 | Escherichia coli | ATCC11775 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 29 | Finegoldia magna | RMSCC 974** | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 30 | Haemophilus aphrophilus | ATCC19415 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 31 | Haemophilus influenzae | ATCC33391 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 32 | Haemophilus parainfluenzae | ATCC33392 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 33 | Issatchenkia orientalis | ATCC6258 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 34 | Klebsiella oxytoca | ATCC33496 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 35 | Klebsiella pneumoniae (KPCproducing) | ATCC700603 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 36 | Klebsiella pneumoniae (KPCproducing) | ATCC BAA1900 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 37 | Lactobacillus crispatus | ATCC33820 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 38 | Lactobacillus delbrueckii | ATCC12315 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 39 | Legionella pneumophila | ATCC33152 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 40 | Leifsonia aquatica (formerly known asCorynebacterium aquaticum) | ATCC14665 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 41 | Listeria monocytogenes | ATCC15313 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 42 | Microbacterium testaceum | ATCC15829 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| Organisms | Strain/ATCC ID | No target | MRSA 10364(NARSA 384) | MRSA 8065(ATCC 43300) | SA 10851(NARSA 164) | |||||
| MRSA | SA | MRSA | SA | MRSA | SA | MRSA | SA | |||
| 43 | Micrococcus luteus | ATCC4698 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 44 | Moraxella catarrhalis | ATCC8176 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 45 | Mycobacterium tuberculosis avirulent | ATCC25177 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 46 | Mycoplasma pneumoniae | ATCC15531 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 47 | Mycoplasma salivarium | ATCC23064 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 48 | Neisseria meningitidis | ATCC13077 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 49 | Parvimonas micra | ATCC33270 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 50 | Pasteurella aerogenes | ATCC27883 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 51 | Planococcus maritimus | RMSCC11454** | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 52 | Proteus mirabilis | ATCC29906 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 53 | Proteus vulgaris | RMSCC204** | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 54 | Providencia stuartii | ATCC22914 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 55 | Pseudomonas aeruginosa | ATCC33584 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 56 | Pseudomonas fluorescens | ATCC11250 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 57 | Rhodococcus equi | ATCC6939 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 58 | Rothia mucilaginosa | ATCC25296 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 59 | Salmonella enterica subsp. Enterica(formerly known as Salmonellatyphimurium) | RMSCC374* | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 60 | Serratia marcescens | ATCC8100 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 61 | Shigella sonnei | ATCC29930 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 62 | Streptococcus agalactiae | RMSCC983** | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 63 | Streptococcus anginosus | ATCC12395 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| Organisms | Strain/ATCC ID | No target | MRSA 10364(NARSA 384) | MRSA 8065(ATCC 43300) | SA 10851(NARSA 164) | |||||
| MRSA | SA | MRSA | SA | MRSA | SA | MRSA | SA | |||
| 64 | Streptococcus mitis | ATCC33399 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 65 | Streptococcus mutans | ATCC25175 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 66 | Streptococcus pneumoniae | ATCC33400 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 67 | Streptococcus pyogenes | ATCC12344 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 68 | Streptococcus salivarius | ATCC7073 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 69 | Streptococcus sanguinis | ATCC10556 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 70 | Streptococcus suis | ATCC43765 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 71 | Yersinia enterocolitica | ATCC9610 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 72 | Adenovirus Type 7 | VR-7 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 73 | Adenovirus Type 40 | Dugan (VR-40) | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 74 | Coronavirus 229E | VR-740 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 75 | Coronavirus OC43 | VR-1558 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 76 | Cytomegalovirus | AD-169 (VR-538) | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 77 | Epstein Barr Virus | B95-8 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 78 | HSV 1 | MacIntyre (VR-539) | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 79 | Human Adenovirus type 1 | VR-1 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 80 | Human enterovirus 71 | VR-1775 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 81 | Human metapneumovirus | Peru6-2003 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 82 | Influenza A/H1N1 | A/PR/8/34 (VR-95) | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 83 | Influenza A/H3N2 A/HongKong/8/68 | H3N2 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 84 | Influenza B | N/A | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 85 | Measles virus | N/A | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 86 | Mumps virus | Enders (VR-106) | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| Organisms | Strain/ATCC ID | No target | MRSA 10364(NARSA 384) | MRSA 8065(ATCC 43300) | SA 10851(NARSA 164) | |||||
| MRSA | SA | MRSA | SA | MRSA | SA | MRSA | SA | |||
| 87 | Parainfluenza 1 | C-35 (VR-94) | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 88 | Parainfluenza 2 | Greer (VR-92) | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 89 | Parainfluenza 3 | C-243 (VR-93) | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 90 | Rhinovirus type 1A | VR-1559 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 91 | RSV A | VR-1540 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 92 | RSV B | VR-1400 | NEG | NEG | POS | POS | POS | POS | NEG | POS |
| 93 | HCT-15 cells (human genomic DNA) | RMSCC3515** | NEG | NEG | POS | POS | POS | POS | NEG | POS |
- Analytical Specificity for Coagulase-Negative Staphylococcus (CoNS) and Methicillin-Resistant Coagulase-Negative Table 9: Staphylococcus (MR-CoNS) Organisms
{17}------------------------------------------------
{18}------------------------------------------------
- RMSCC indicates Roche Culture Collection ID, MayoClinic collection ID, DSMZ indicates DSMZ Penzburg collection ID
{19}------------------------------------------------
Table 10: Analytical Specificity for Non MRSA/SA Microorganisms and Human Cells
{20}------------------------------------------------
{21}------------------------------------------------
{22}------------------------------------------------
{23}------------------------------------------------
**RMSCC indicates Roche Culture Collection ID, MayoClinic collection ID, DSMZ indicates DSMZ Penzburg collection ID
{24}------------------------------------------------
| RMSCultureCollectionID | MRSA 10364(NARSA 384) | MRSA 8065(ATCC 43300) | MRSA 10364(NARSA 384) | |||||
|---|---|---|---|---|---|---|---|---|
| MRSA | SA | MRSA | SA | MRSA | SA | |||
| 1 | Staphylococcus aureus | 10851 | NEG | POS | POS | POS | POS | POS |
| 2 | Staphylococcus aureus | 10852 | NEG | POS | POS | POS | POS | POS |
| 3 | Staphylococcus aureus (BORSA) | 10319 | NEG | POS | POS | POS | POS | POS |
| 4 | Staphylococcus aureus (BORSA) | 10320 | NEG | POS | POS | POS | POS | POS |
| 5 | Staphylococcus aureus (BORSA) | 10321 | NEG | POS | POS | POS | POS | POS |
| 6 | Staphylococcus aureus (BORSA) | 10322 | NEG | POS | POS | POS | POS | POS |
| 7 | Staphylococcus aureus (BORSA) | 10323 | NEG | POS | POS | POS | POS | POS |
| 8 | Staphylococcus aureus (BORSA) | 10324 | NEG | POS | POS | POS | POS | POS |
| 9 | Staphylococcus aureus (BORSA) | 10325 | NEG | POS | POS | POS | POS | POS |
| 10 | Staphylococcus aureus (BORSA) | 10326 | NEG | POS | POS | POS | POS | POS |
| 11 | Staphylococcus aureus (BORSA) | 10327 | NEG | POS | POS | POS | POS | POS |
| 12 | Staphylococcus aureus (BORSA) | 10328 | NEG | POS | POS | POS | POS | POS |
| 13 | Staphylococcus aureus (mec A drop out) | 10332 | NEG | POS | POS | POS | POS | POS |
| 14 | Staphylococcus aureus (mec A drop out) | 10335 | POS | POS | POS | POS | POS | POS |
| 15 | Staphylococcus aureus (mec A drop out) | 10336 | NEG | POS | POS | POS | POS | POS |
| 16 | Staphylococcus aureus (mec A drop out) | 10339 | NEG | POS | POS | POS | POS | POS |
| 17 | Staphylococcus aureus (mec A drop out) | 10340 | NEG | POS | POS | POS | POS | POS |
| 18 | Staphylococcus aureus (mec A drop out) | 10341 | NEG | POS | POS | POS | POS | POS |
| 19 | Staphylococcus aureus (mec A drop out) | 10342 | NEG | POS | POS | POS | POS | POS |
| 20 | Staphylococcus aureus (mec A drop out) | 10343 | NEG | POS | POS | POS | POS | POS |
| 21 | Staphylococcus aureus (mec A drop out) | 10344 | NEG | POS | POS | POS | POS | POS |
| 22 | Staphylococcus aureus (mec A drop out) | 10348 | NEG | POS | POS | POS | POS | POS |
| 23 | Staphylococcus aureus (mec A drop out) | 10349 | NEG | POS | POS | POS | POS | POS |
| 24 | Staphylococcus aureus (mec A drop out) | 10354 | NEG | POS | POS | POS | POS | POS |
| 25 | Staphylococcus aureus (mec A drop out) | 10355 | NEG | POS | POS | POS | POS | POS |
| 26 | Staphylococcus aureus (mec A drop out) | 10356 | POS | POS | POS | POS | POS | POS |
| 27 | Staphylococcus aureus (mec A drop out) | 10359 | POS | POS | POS | POS | POS | POS |
| 28 | Staphylococcus aureus (mec A drop out) | 10360 | NEG | POS | POS | POS | POS | POS |
Table 11: Analytical Specificity Results on MSSA, BORSA and Empty Cassette Variants
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Competitive Inhibition 4.6.
Panels were constructed with two MRSA isolates and one SA isolate as targets at 3 x Limit of Detection (LOD) of the cobas® MRSA/SA Test, and competing Staphylococcus aureus and Methicillin-Resistant Staphylococcus epidermidis (MRSE) isolates at increasing concentrations. The increasing concentration of SA or MRSE did not affect the detection of MRSA/SA targets, as shown by their relatively stable Ct value (Table 12).
| Competing Organism | Target | |||
|---|---|---|---|---|
| Name | Concentration | MRSA 10364(NARSA 384) | MRSA 8065(ATCC 43300) | SA 10851(NARSA 164) |
| Staphylococcus aureus10851 | 1 x target | 38.2 | 38.8 | N/A |
| 100 x target | 38.1 | 39.1 | N/A | |
| 10000 x target | 38.4 | 38.8 | N/A | |
| Staphylococcus aureus10852 | 1 x target | 38.1 | 39.0 | N/A |
| 100 x target | 38.5 | 39.3 | N/A | |
| 10000 x target | 37.4 | 39.0 | N/A | |
| Staphylococcus epidermidis5649 | 1 x target | 37.9 | 39.5 | 36.5 |
| 100 x target | 38.6 | 38.6 | 36.5 | |
| 10000 x target | 38.1 | 39.7 | 37.0 | |
| Staphylococcus epidermidis5657 | 1 x target | 39.0 | 40.1 | 36.9 |
| 100 x target | 38.4 | 39.1 | 36.5 | |
| 10000 x target | 38.3 | 39.7 | 36.7 |
Competitive Inhibition Study Results with Methicillin Sensitive SA and MRSE Table 12:
N/A: Not applicable
4.7. Interference
Twenty five commonly used OTC products and antibiotic medicines, as well as whole blood and mucin were tested for potential interference effects with the cobas® MRSA/SA Test. All products were tested at or above the levels reasonably expected to be in a nasal swab specimen. Two MRSA isolates and 1 SA isolate were spiked to ~ 3 x LOD of the cobas® MRSA/SA Test and used as targets.
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No interference was observed for most OTC products. Only Rhinaris® Nasal gel and Releev™ interfered with the performance of the cobas® MRSA/SA Test when present above 15% (Rhinaris® Nasal gel) and above 25% (ReleevTM) of the swab capacity. The cobas® MRSA/SA Test was able to tolerate up to 75% whole blood and 10% mucin (Table 13).
| Substance | Results |
|---|---|
| Whole blood | No interference up to 75% of swab capacity |
| Mucin | No interference up to 10% of swab capacity |
| Afrin Nasal Spray | No interference |
| Beconase Nasal Spray | No interference |
| Bepanthen® nasal ointment | No interference |
| Chloraseptic Max Sore Throat Lozenges | No interference |
| Fluticasone Propionate (50 mcg) Nasal Spray | No interference |
| FluMist® (Afluria, Influenza virus vaccine) | No interference |
| Flunisolide Nasal Solution USP, 0.025% | No interference |
| Mupirocin Ointment | No interference |
| Dristan"™ Nasal Mist | No interference |
| Luffeel ''M | No interference |
| Triamcinolone Acetonide Nasal spray | No interference |
| NasalCrom Nasal Spray | No interference |
| Nasonex Nasal Spray | No interference |
| Neo-Synephrine | No interference |
| Otrivine Nasal Spray | No interference |
| Relenza® | No interference up to 6.25% of swab capacity* |
| Budesonide Inhalation Suspension 0.25 mg/2 mL | No interference |
| Azelastin HCL Nasal Solution | No interference |
| Equate Saline Nasal Moisturizing Spray | No interference |
| Rhinaris® Nasal gel | No interference up to 15% of swab capacity |
| Tobramycin and Dexamethasone Ophthalmic Solution | No interference |
| Releev (for cold sores) | No interference up to 25% of swab capacity |
| Zicam Nasal Gel | No interference |
| QVAR (40 mcg) Inhalation Aerosol | No interference |
| Nostrilla | No interference |
Table 13: Results from Interference Substances Testing
*This concentration represents the whole amount of Relenza that would be applied in a single use according to prescription information.
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Cross Contamination 4.8.
The cross contamination rate for the cobas " MRSA/SA Test was assessed by testing high titer MRSA and negative samples that were processed in a checkerboard configuration on the cobas® 4800 system. High titer samples were prepared by spiking MRSA culture to simulated nasal swab matrix to generate a Ct that exceeded 95% of signal from specimens of infected patients of the clinical specimen population.
Five runs were performed on each of the three cobas® 4800 systems (total: 15 runs). The first run on each system contained only the negative samples to confirm the instrument was clean. The three subsequent runs on each system had alternating positive and negative samples in checkerboard configurations to assess the cross contamination rate. The last run on each system contained only the negative samples to assess the carry-over contamination rate.
Results from this study are summarized in Table 14. There were no cross-contamination events in any of the nine checkerboard runs across the three cobas® 4800 systems (a total of 423 MRSA negative samples) for an observed cross-contamination rate of 0%. All results in the last 3 runs containing only the negative samples were negative, suggesting that there was no carry-over runto-run contamination.
| Run category | No. of Runs | Total Negative Samples | Number of Positive Results in Negative Samples | Contamination Rate |
|---|---|---|---|---|
| Checkerboard run(Cross Contamination) | 9 | 423 | 0 | 0% |
| Last run with all NEG(Carryover Contamination) | 3 | 282 | 0 | 0% |
Table 14: Cross Contamination and Carry-over Contamination Rate
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5. CLINICAL PERFORMANCE EVALUATION
5.1. Reproducibility
The reproducibility of the cobas® MRSA/SA Test on the cobas 4800 System was established in a multi-site, investigation using contrived clinical samples evaluated across lot, site/instrument, operator, day, and run.
The MRSA/SA reproducibility test panels were prepared by seeding MRSA strains NRS384 (MRSA-384) and ATCC 43300 (MRSA-43300), or SA strain RMSCC 10851(NRS-164) into contrived sample matrix (simulated clinical MSwab nasal specimens with mucin and human epithelial cells) at 1 of 4 concentrations (Negative, Below LOD, 1 × LOD, and 3 × LOD). In all, there were 10 members per test panel with 3 replicates per panel member included in each run. Panels were tested at 3 sites by 2 operators per site with 1 run per operator per day, for 5 days per lot, over 2 lots for a total of 1,800 tests (180 tests/panel member or 90 tests/panel member/lot). Overall, 60 runs were performed and all were valid runs. There were no failed/invalid tests
MRSA Reproducibility Results 5.1.1. -
Table 15 summarizes the MRSA reproducibility results for Ct values and the percent agreement (two-sided 95% exact CI) by site and panel member. The positive percent agreement for the MRSA-positive panel members, "Below LOD MRSA-384" and "Below LOD MRSA-43300," were 85.6% (95% CI: 79.6% to 90.3%) and 87.2% (95% CI: 81.4% to 91.7%), respectively; the positive percent agreement for all other MRSA-positive panel members was 100.0% (95% CI: 98.0% to 100.0%). The total SD and total CV (%) of Ct values across all MRSA-positive panel members were ≤ 0.51% and ≤1.4%, respectively.
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| Valid | Ct | Percent Agreement by Site(n/N) | Total Agreement | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Panel Member | Tests(n) | Mean | SD | CV (%) | 1 | 2 | 3 | Percent(n/N) | (95% CI) | |
| Negative | 180 | N/A | N/A | N/A | 100.0(60/60) | 100.0(60/60) | 100.0(60/60) | 100.0%(180/180) | (98.0%,100.0%) | |
| Below LODMRSA-384 | 180 | 40.3 | 0.43 | 1.1 | 95.0(57/60) | 83.3(50/60) | 78.3(47/60) | 85.6%(154/180) | (79.6%,90.3%) | |
| 1 x LOD MRSA-384 | 180 | 38.0 | 0.49 | 1.3 | 100.0(60/60) | 100.0(60/60) | 100.0(60/60) | 100.0%(180/180) | (98.0%.100.0%) | |
| 3 x LOD MRSA-384 | 180 | 36.3 | 0.44 | 1.2 | 100.0(60/60) | 100.0(60/60) | 100.0(60/60) | 100.0%(180/180) | (98.0%.100.0%) | |
| Below LODMRSA-43300 | 180 | 40.4 | 0.40 | 1.0 | 91.7(55/60) | 81.7(49/60) | 88.3(53/60) | 87.2%(157/180) | (81.4%.91.7%) | |
| 1 x LOD MRSA-43300 | 180 | 38.9 | 0.45 | 1.1 | 100.0(60/60) | 100.0(60/60) | 100.0(60/60) | 100.0%(180/180) | (98.0%,100.0%) | |
| 3 x LOD MRSA-43300 | 180 | 37.4 | 0.51 | 1.4 | 100.0(60/60) | 100.0(60/60) | 100.0(60/60) | 100.0%(180/180) | (98.0%.100.0%) |
Table 15: Summary of MRSA Reproducibility Results- Ct Values and Percent Agreement by Site and Panel Member
Table 16 presents the SD and CV (%) of Ct values for MRSA-positive panel members overall and attributable to lot, site/instrument, operator, day and within-run.
| Standard Deviation and Percent Coefficient of Variation | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MRSA | Lot | Site/Inst. | Operator | Day | Within-Run | Total | |||||||||
| PanelMember | N | MeanCt | SD | CV(%) | SD | CV(%) | SD | CV(%) | SD | CV(%) | SD | CV(%) | SD | CV(%) | |
| Below LODMRSA-384 | 154 | 40.3 | 0.00 | 0.0 | 0.06 | 0.2 | 0.00 | 0.0 | 0.23 | 0.6 | 0.36 | 0.9 | 0.43 | 1.1 | |
| 1 x LODMRSA-384 | 180 | 38.0 | 0.07 | 0.2 | 0.18 | 0.5 | 0.00 | 0.0 | 0.17 | 0.5 | 0.41 | 1.1 | 0.49 | 1.3 | |
| 3 x LODMRSA-384 | 180 | 36.3 | 0.12 | 0.3 | 0.20 | 0.6 | 0.02 | 0.1 | 0.15 | 0.4 | 0.35 | 1.0 | 0.44 | 1.2 | |
| Below LODMRSA-43300 | 157 | 40.4 | 0.03 | 0.1 | 0.07 | 0.2 | 0.06 | 0.1 | 0.02 | 0.0 | 0.39 | 1.0 | 0.40 | 1.0 | |
| 1 x LODMRSA-43300 | 180 | 38.9 | 0.00 | 0.0 | 0.11 | 0.3 | 0.00 | 0.0 | 0.19 | 0.5 | 0.39 | 1.0 | 0.45 | 1.1 | |
| 3 x LODMRSA-43300 | 180 | 37.4 | 0.13 | 0.4 | 0.24 | 0.6 | 0.12 | 0.3 | 0.10 | 0.3 | 0.40 | 1.1 | 0.51 | 1.4 |
Table 16: Overall Mean, Standard Deviations, and Coefficients of Variation (%) for Ct Values from Valid Results for MRSA Positive Panel Members
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SA Reproducibility Results 5.1.2.
Table 17 summarizes the SA reproducibility results for Ct values and the percent agreement (two-sided 95% exact CI) by site and panel member. The positive percent agreement for the SApositive panel members "Below LOD SA," "1 × LOD SA" and "3 × LOD SA" were 50.0% (95% Cl: 42.5% to 57.5%), 99.4% (95% CI: 96.9% to 100.0%), and 100.0% (95% CI: 98.0% to 100.0%), respectively. The total SD and total CV (%) of Ct values across all SA-positive panel members were ≤ 0.49 and ≤ 1.3%, respectively. The negative percent agreement for the MRSA/SA-negative panel members was 100.0% (95% CI: 98.0% to 100.0%).
Table 17: Summary of SA Reproducibility Results- Ct Values and Percent Agreement by Site and Panel Member.
| Panel Member | Valid Tests (n) | Ct | Percent Agreement by Site (n/N)a | Total Agreement | |||||
|---|---|---|---|---|---|---|---|---|---|
| Mean | SD | CV (%) | 1 | 2 | 3 | Percent (n/N) | (95% CI)b | ||
| Negative | 180 | N/A | N/A | N/A | 100.0 (60/60) | 100.0 (60/60) | 100.0 (60/60) | 100.0% (180/180) | (98.0%, 100.0%) |
| Below LOD SA | 180 | 38.6 | 0.46 | 1.2 | 23.3 (14/60) | 60.0 (36/60) | 66.7 (40/60) | 50.0% (90/180) | (42.5%, 57.5%) |
| 1 x LOD SA | 180 | 36.8 | 0.49 | 1.3 | 100.0 (60/60) | 98.3 (59/60) | 100.0 (60/60) | 99.4% (179/180) | (96.9%, 100.0%) |
| 3 x LOD SA | 180 | 35.1 | 0.38 | 1.1 | 100.0 (60/60) | 100.0 (60/60) | 100.0 (60/60) | 100.0% (180/180) | (98.0%, 100.0%) |
Table 18 presents the SD and CV (%) of Ct values for SA-positive panel members overall and attributable to lot, site/instrument, operator, day and within-run.
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| SA | Standard Deviation and Percent Coefficient of Variation | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Lot | Site/Inst. | Operator | Day | Within-Run | Total | |||||||||
| PanelMember | N | MeanCt | SD | CV(%) | SD | CV(%) | SD | CV(%) | SD | CV(%) | SD | CV(%) | SD | CV(%) |
| BelowLOD SA | 90 | 38.6 | 0.00 | 0.0 | 0.00 | 0.0 | 0.00 | 0.0 | 0.00 | 0.0 | 0.46 | 1.2 | 0.46 | 1.2 |
| 1 x LODSA | 179 | 36.8 | 0.14 | 0.4 | 0.29 | 0.8 | 0.13 | 0.3 | 0.16 | 0.4 | 0.31 | 0.8 | 0.49 | 1.3 |
| 3 x LODSA | 180 | 35.1 | 0.11 | 0.3 | 0.14 | 0.4 | 0.12 | 0.3 | 0.02 | 0.1 | 0.31 | 0.9 | 0.38 | 1.1 |
Table 18: Overall Mean, Standard Deviations, and Coefficients of Variation (%) for Ct Values from Valid Results for SA Positive Panel Members
Clinical Performance 5.2.
The clinical performance of the cobas® MRSA/SA Test was established in an IRB-approved, prospective, multi-site, investigation comparing the results with direct chromogenic culture, and direct chromogenic culture combined with enrichment culture (reference method), using nasal swabs from eligible male and female subjects.
Specimens were collected at six geographically diverse sites across the US. One or two swab specimens were collected from each subject; one swab was collected for Standard-of-Care testing (if applicable) and one swab, an MSwab (Copan Flock Technologies S.r.1., Brescia, Italy), was collected for the cobas® MRSA/SA Test and for direct and enrichment culture.
The cobas® MRSA/SA Test was performed at three sites and the direct and enrichment culture was performed at a reference laboratory that specialized in culture and molecular detection of methicillin-resistant MRSA and SA. Briefly, aliquots of MSwab sample from each subject was transferred directly to one plate each of selective and differential chromogenic media for MRSA and SA (direct culture), and to a tube containing tryptic soy broth (TSB) with 6.5% NaCl (enrichment culture). Suspect isolates and positive enrichment broth cultured to 5% sheep blood agar and isolates identified as SA by Gram-stain and latex agglutination testing. Putative MRSA isolates were confirmed using a Kirby-Bauer cefoxitin disc diffusion test for methicillin resistance.
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A MRSA/SA culture positive specimen was defined as a specimen positive for MRSA/SA by either direct or enrichment culture technique. A MRSA/SA culture negative specimen was defined as a specimen negative for MRSA/SA for both direct and enrichment culture.
Discrepant analysis was performed on all samples with discordant results between the cobas® MRSA/SA Test and combined direct and enrichment culture (reference culture), using a second, FDA-cleared nucleic acid amplification test and a non-selective direct and enrichment culture; a randomly selected subset of samples with concordant results were included as controls. Briefly, an aliquot of remnant (leftover) MSwab sample was transferred to a chocolate agar plate (non-selective direct culture) and to TSB without NaCl (non-selective enrichment culture). Isolates recovered from non-selective direct and enrichment culture were characterized as described. In addition, the identification of suspicious, atypical isolates were confirmed using a laboratory developed PCR assay for femA and mecA genes according to the reference laboratory's established practice.
5.2.1. Results
Specimens were collected from 2528 subjects with 2504 (99.1%) evaluable results from 1372 males (54.8%) and 1132 (45.2%) female subjects. The majority of subjects were > 50 years of age (67.2%) and ranged in age from 18 to 101 (median age = 57). There were a total of 160 MRSA-positive and 660 SA-positive specimens.
Performance of the cobas® MRSA/SA Test Compared to Combined Direct 5.2.1.1. and Enrichment Culture (Reference Method)
The performance of the cobas® MRSA/SA test compared to combined direct and enrichment culture from 2500 evaluable results for MRSA, and from 2501 evaluable results for SA, is shown in Table 19.
The sensitivity and specificity for MRSA compared to combined direct and enrichment culture was 93.1% (149/160) and 97.5% (2281/2340), respectively; and the prevalence, PPV and NPV was 6.4%, 71.6% and 99.5%, respectively.
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The sensitivity and specificity for SA compared to combined direct and enrichment culture was 93.9% (620/660) and 94.2% (1734/1841), respectively, and the prevalence, PPV and NPV was 26.4%, 85.3% and 97.7%, respectively.
| Direct and Enrichment Culture (Reference Method) | ||||||||
|---|---|---|---|---|---|---|---|---|
| MRSA | SA | |||||||
| Positive | Negative | Total | Positive | Negative | Total | |||
| cobas® | MRSA/SATest | Positive | 149 | 59 | 208 | 620 | 107 | 727 |
| Negative | 11 | 2281 | 2292 | 40 | 1734 | 1774 | ||
| Total | 160 | 2340 | 2500 | 660 | 1841 | 2501 | ||
| MRSA | ||||||||
| Sensitivity: 93.1% (149/160) (95% CI: 88.1-96.1%) | ||||||||
| Specificity: 97.5% (2281/2340) (95% CI: 96.8-98.0%) | ||||||||
| Prevalence: 6.4% | ||||||||
| PPV: 71.6% | ||||||||
| NPV: 99.5% | ||||||||
| SA | ||||||||
| Sensitivity: 93.9% (620/660) (95% CI: 91.9-95.5%) | ||||||||
| Specificity: 94.2% (1734/1841) (95% CI: 93.0-95.2%) | ||||||||
| Prevalence: 26.4% | ||||||||
| PPV: 85.3% | ||||||||
| NPV: 97.7% |
Table 19: Comparison of Results from the cobas® MRSA/SA Test with Direct and Enrichment Culture (Reference Method)
Comparison of Results of the cobas® MRSA/SA Test with Direct Culture 5.2.1.2. Results of the cobas® MRSA/SA test were compared to direct culture from 2504 evaluable results is shown in Table 20.
The overall, positive and negative percent agreement of the cobas® MRSA/SA Test for MRSA compared to direct culture was 96.9% (2427/2504), 97.1% (135/139) and 96.9% (2292/2365); and the prevalence was 5.6%.
The overall, positive and negative percent agreement of the cobas® MRSA/SA Test for SA compared to direct culture was 93.3% (2336/2504), 97.0% (577/595) and 92.1% (1759/1909), respectively; and the prevalence was 23.8%.
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| Direct Culture | |||||||
|---|---|---|---|---|---|---|---|
| MRSA | SA | ||||||
| Positive | Negative | Total | Positive | Negative | Total | ||
| cobas® | Positive | 135 | 73 | 208 | 577 | 150 | 727 |
| MRSA/SA | Negative | 4 | 2292 | 2296 | 18 | 1759 | 1777 |
| Test | Total | 139 | 2365 | 2504 | 595 | 1909 | 2504 |
Table 20: Comparison of Results from the cobas® MRSA/SA Test with Direct Culture
MRSA
Positive Percent Agreement: 97.1% (135/139) (95% CI: 92.8-98.9%) Negative Percent Agreement: 96.9% (2292/2365) (95% Cl: 96.1-97.5%) Overall Percent Agreement: 96.9% (2427/2504) (95% Cl: 96.2-97.5%) Prevalence: 5.6%
SA Positive Percent Agreement: 97.0% (577/595) (95% CI: 95.3-98.1%) Negative Percent Agreement: 92.1% (1759/1909) (95% Cl: 90.8-93.3%) Overall Percent Agreement: 93.3% (2336/2504) (95% Cl: 92.2-94.2%) Prevalence: 23.8%
Discrepant Analysis of Discordant and Concordant Samples 5.2.1.3.
Discrepant analysis was performed on all discordant samples, and a random subset of concordant samples included as controls, between the cobas® MRSA/SA Test and combined direct and enrichment culture, using a second, FDA-cleared nucleic acid amplification test (NAAT) and a non-selective direct and enrichment culture.
There were a total of 70 specimens with MRSA discordant results (11 MRSA False-negative results and 59 MRSA False-positive results). Of the 11 MRSA False-negative specimens, five tested MRSA-negative by a second NAAT method and non-selective direct and enrichment culture. Of the 59 MRSA False-positive specimens, 20 tested MRSA-positive by a second NAAT method or non-selective direct and/or enrichment culture.
There were a total of 147 specimens with SA discordant results (40 SA False-negative results and 107 SA False-positive results). Of the 40 SA False-negative specimens, 31 tested SAnegative by a second NAAT method and non-selective direct and enrichment culture. Of the 107 SA False-positive specimens, 24 tested SA-positive by a second NAAT method or non-selective direct and/or enrichment culture.
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There were 74 randomly selected concordant samples included as controls in the discrepant analysis (25 MRSA-positive, 25 SA-negative and 24 SA-positive/MRSA-negative concordant samples). Of the 74 controls, all 25 MRSA-positive specimens tested MRSA-positive by a second NAAT method or non-selective direct and/or enrichment culture; all 25 SA-negative specimens tested SA-negative by a second NAAT method and non-selective direct and enrichment culture; and, of the 24 SA-positive specimens, 21 tested SA-positive by a second NAAT method or non-selective direct and/or enrichment culture, 1 tested MRSA-positive by nonselective enrichment culture, and two tested SA-negative by a second NAAT method and non-selective direct and enrichment culture.
5.3. Summary
Based on the clinical performance evaluation as documented in the reproducibility and clinical study, the cobas® MRSA/SA test was found to have a safety and effectiveness profile that is similar to the predicate device.
CONCLUSIONS 6.
A comparison of the intended use, technological characteristics, and the results of non-clinical and clinical performance studies support that the cobas® MRSA/SA Test is substantially equivalent to the predicate device.
§ 866.1640 Antimicrobial susceptibility test powder.
(a)
Identification. An antimicrobial susceptibility test powder is a device that consists of an antimicrobial drug powder packaged in vials in specified amounts and intended for use in clinical laboratories for determining in vitro susceptibility of bacterial pathogens to these therapeutic agents. Test results are used to determine the antimicrobial agent of choice in the treatment of bacterial diseases.(b)
Classification. Class II (performance standards).