(91 days)
The BioCode Gastrointestinal Pathogen Panel (GPP) is a qualitative multiplexed nucleic acid-based in vitro diagnostic test intended for use with the BioCode MDx 3000 Instrument. The BioCode GPP is capable of the simultaneous detection and identification of nucleic acids from multiple bacteria, viruses, and parasites extracted directly from unpreserved stool samples or stool preserved in Cary-Blair transport medium obtained from individuals with signs and/or symptoms of gastrointestinal infection. The following bacteria, parasites, and viruses are identified using the BioCode Gastrointestinal Pathogen Panel:
- · Campylobacter (C. jejuni/C. coli)
- · Clostridium difficile (C. difficile) toxin A/B (Fresh samples only)
- · Salmonella spp
- · Vibrio (V. parahaemolyticus/V. vulnificus/ V. cholerae), including specific identification of Vibrio parahaemolyticus
- · Yersinia enterocolitica
- · Enteroaggregative Escherichia coli (EAEC)
- · Enterotoxigenic Escherichia coli (ETEC) lt/st
- · E. coli 0157 serogroup
- Shiga-like toxin-producing Escherichia coli (STEC) stx1/stx2
- Shigella/ Enteroinvasive Escherichia coli (EIEC)
- · Cryptosporidium spp (C. parvum/C. hominis)
- Entamoeba histolytica
- · Giardia lamblia (also known as G. intestinalis and G. duodenalis)
- Adenovirus F 40/41
- Norovirus GI/GII
- Rotavirus A
The BioCode GPP is indicated as an aid in the diagnosis of gastrointestinal illness and results are meant to be used in conjunction with other clinical, laboratory, and epidemiological data.
Positive results do not rule out co-infection with organisms not included in the BioCode GPP. The agent detected may not be the definite cause of the disease. Negative results in the setting of clinical illness compatible with gastroenteritis may be due to infection by pathogens that are not detected by this test or non-infectious causes such as ulcerative colitis, irritable bowel syndrome, or Crohn's disease.
Concomitant culture is necessary for organism recovery and further typing of bacterial agents.
This device is not intended to monitor or guide treatment for C. difficile infection.
Due to the small number of positive specimens collected for certain organisms during the prospective clinical study, performance characteristics for Adenovirus 40/41, Campylobacter, E. coli 0157, Shigella/EIEC, Yersinia enterocolitica, and Giardia lamblia were established additionally with retrospective clinical specimens. Performance characteristics for Entamoeba histolytica, Giardia lamblia, Yersinia enterocolitica and Vibrio (V. parahaemolyticus, V. vulnificus, and V. cholerae) were established primarily using contrived clinical specimens.
The BioCode Gastrointestinal Pathogen Panel (GPP) is a multiplexed nucleic acid-based test designed to be used with the BioCode MDx 3000 system. The BioCode MDx 3000 is an automated system that integrates PCR amplification, target capture, signal generation and optical detection for multiple gastrointestinal pathogens from a single stool specimen, either unpreserved or in Cary Blair. Stool specimens are processed and nucleic acids extracted with the easyMAG and MagNa Pure. Once the PCR plate is set up and sealed, all other operations are automated on MDx 3000. The BioCode MDx 3000 Gastrointestinal Infection Panel simultaneously tests for 17 pathogens (see table below) from unpreserved stool specimens or stool collected in Cary-Blair transport medium. Results from the BioCode Gastrointestinal Pathogen Panel (GPP) test are available within less than 4 hours.
Here's a breakdown of the acceptance criteria and study information for the BioCode Gastrointestinal Pathogen Panel (GPP) as described in the provided document:
Acceptance Criteria and Device Performance for BioCode GPP (with MagNA Pure 96 extraction)
The document focuses on demonstrating the substantial equivalence of the BioCode GPP when used with the MagNA Pure 96 extraction system, compared to its previously cleared version with the easyMAG extraction system (K180041, the predicate device). Therefore, the acceptance criteria and performance are largely derived from the comparison to the existing predicate and the analytical studies.
General Acceptance Criteria (Implied from Clinical Performance Tables):
The acceptance criteria are generally implied to be high positive agreement (PPA) and negative agreement (NPA) with reference methods, typically in the range of 80-100% for PPA and 90-100% for NPA, within a 95% Confidence Interval. For analytical studies, reproducibility is expected to be high (>95%), and the limit of detection (LoD) should be comparable between extraction methods.
Table of Acceptance Criteria and Reported Device Performance (Summary):
| Target Pathogen/Toxin | Specimen Type | Acceptance Criteria (Implied) - PPA (95% CI) | Acceptance Criteria (Implied) - NPA (95% CI) | Reported Device Performance (MP96) - PPA (95% CI) | Reported Device Performance (MP96) - NPA (95% CI) |
|---|---|---|---|---|---|
| Clinical Performance (Archived Specimens - N=464) | |||||
| Campylobacter spp. | Inoculated/Cary-Blair | High (>90%) | High (>90%) | 95.65% (79.0–99.2) | 98.20% (94.9–99.4) |
| Unpreserved (Frozen) | High (>90%) | High (>90%) | 100% (87.5-100) | 98.80% (96.5-99.6) | |
| All Archived | High (>90%) | High (>90%) | 98.0% (89.5-99.6) | 98.60% (96.9–99.3) | |
| Clostridium difficile | Inoculated/Cary-Blair | High (>90%) | High (>90%) | 90.91% (62.3–98.4) | 99.44% (96.9–99.9) |
| Unpreserved (Frozen) | High (>90%) | High (>90%) | 95.45% (78.2–99.2) | 99.20% (97.2–99.8) | |
| All Archived | High (>90%) | High (>90%) | 93.94% (80.4-98.3) | 99.30% (98.0-99.8) | |
| E. coli O157 | Inoculated/Cary-Blair | High (100%) | High (100%) | 100% (43.9-100) | 100% (98.0-100) |
| Unpreserved (Frozen) | High (100%) | High (100%) | 100% (78.5-100) | 100% (98.5-100) | |
| All Archived | High (100%) | High (100%) | 100% (81.6-100) | 100% (99.1-100) | |
| Enteroaggregative E. coli (EAEC) | Inoculated/Cary-Blair | High (>85%) | High (>95%) | 88.24% (65.7-96.7) | 98.8% (95.9-99.7) |
| Unpreserved (Frozen) | High (>95%) | High (>95%) | 100% (88.3-100) | 99.59% (97.7-99.9) | |
| All Archived | High (>90%) | High (>95%) | 95.65% (85.5-98.8) | 99.50% (98.3-99.9) | |
| Enterotoxigenic E. coli (ETEC) | Inoculated/Cary-Blair | Moderate (>60%) | High (100%) | 60.00% (23.1-88.2) | 100% (98.0-100) |
| Unpreserved (Frozen) | High (100%) | High (100%) | 100% (77.2-100) | 100% (98.5-100) | |
| All Archived | High (>85%) | High (100%) | 88.89% (67.2-96.9) | 100% (99.1-100) | |
| Shiga toxin-producing E. coli (STEC) | Inoculated/Cary-Blair | High (>90%) | High (100%) | 92.31% (66.7-98.6) | 100% (97.9-100) |
| Unpreserved (Frozen) | High (>95%) | High (>95%) | 96.67% (83.3-99.4) | 99.60% (97.7-99.9) | |
| All Archived | High (>90%) | High (>95%) | 95.35% (84.5-98.7) | 99.80% (98.7-100) | |
| Salmonella spp. | Inoculated/Cary-Blair | High (100%) | High (>95%) | 100% (81.6-100) | 97.70% (94.2-99.1) |
| Unpreserved (Fresh) | High (>90%) | High (>95%) | 92.59% (76.6-97.9) | 99.60% (97.7-99.9) | |
| All Archived | High (>90%) | High (>95%) | 95.45% (84.9-98.7) | 98.80% (97.2-99.5) | |
| Shigella/EIEC | Inoculated/Cary-Blair | High (100%) | High (100%) | 100% (70.1-100) | 100% (97.9-100) |
| Unpreserved (Frozen) | High (>90%) | High (100%) | 90.91% (72.2-97.5) | 100% (98.5-100) | |
| All Archived | High (>90%) | High (100%) | 93.55% (79.3-98.2) | 100% (99.1-100) | |
| Vibrio parahaemolyticus | Inoculated/Cary-Blair | High (100%) | High (100%) | 100% (20.7-100) | 100% (98.0-100) |
| Unpreserved (Frozen) | High (100%) | High (>99%) | 100% (20.7-100) | 99.6% (98.0-99.9) | |
| All Archived | High (100%) | High (>99%) | 100% (34.2-100) | 99.8% (99.8-100) | |
| Vibrio spp. (not parahaemolyticus) | Inoculated/Cary-Blair | N/A | High (100%) | N/A | 100% (98.0-100) |
| Unpreserved (Frozen) | Low (0%) | High (>99%) | 0% (N/A) | 99.6% (N/A) | |
| All Archived | Low (0%) | High (>99%) | 0% (N/A) | 99.8% (98.8-100) | |
| Yersinia enterocolitica | Inoculated/Cary-Blair | High (100%) | High (100%) | 100% (43.9-100) | 100% (98.0-100) |
| Unpreserved (Frozen) | High (100%) | High (>99%) | 100% (43.9-100) | 99.26% (97.3-99.8) | |
| All Archived | High (100%) | High (>99%) | 100% (61.0-100) | 99.6% (98.4-99.9) | |
| Cryptosporidium spp. | Inoculated/Cary-Blair | High (>90%) | High (100%) | 91.67% (64.6-98.5) | 100% (97.9-100) |
| Unpreserved (Frozen) | High (>90%) | High (>99%) | 91.67% (74.2-97.7) | 99.20% (97.1-99.8) | |
| All Archived | High (>90%) | High (>99%) | 91.67% (78.2-97.1) | 99.5% (98.3-99.9) | |
| Entamoeba histolytica | Inoculated/Cary-Blair | N/A | High (100%) | N/A | 100% (98.0-100) |
| Unpreserved (Frozen) | N/A | High (100%) | N/A | 100% (98.6-100) | |
| All Archived | N/A | High (100%) | N/A | 100% (99.2-100) | |
| Giardia lamblia | Inoculated/Cary-Blair | High (100%) | High (100%) | 100% (43.90-100) | 100% (98.0-100) |
| Unpreserved (Frozen) | High (100%) | High (>98%) | 100% (78.5-100) | 98.1% (95.6-99.2) | |
| All Archived | High (100%) | High (>98%) | 100% (81.6-100) | 98.9% (97.4-99.5) | |
| Adenovirus 40/41 | Inoculated/Cary-Blair | Moderate (>70%) | High (>98%) | 70.00% (39.7-89.2) | 98.32% (95.2-99.4) |
| Unpreserved (Frozen) | Moderate (>75%) | High (>96%) | 78.60% (52.4-92.4) | 96.90% (94.0-98.4) | |
| All Archived | Moderate (>85%) | High (>97%) | 87.50% (69.0-95.7) | 97.5% (95.6-98.6) | |
| Norovirus (GI/GII) | Inoculated/Cary-Blair | High (100%) | High (>98%) | 100% (83.2-100) | 98.20% (95.0-99.4) |
| Unpreserved (Frozen) | High (>95%) | High (>98%) | 95.45% (78.2-99.2) | 98.40% (96.0-99.4) | |
| All Archived | High (>90%) | High (>98%) | 90.24% (77.5-96.1) | 98.3% (96.6-99.2) | |
| Rotavirus A | Inoculated/Cary-Blair | High (>90%) | High (>99%) | 92.31% (66.7-98.6) | 99.44% (96.9-99.9) |
| Unpreserved (Frozen) | High (100%) | High (>98%) | 100% (79.6-100) | 98.5% (96.1-99.4) | |
| All Archived | High (>95%) | High (>98%) | 96.43% (82.3-99.4) | 98.9% (97.3-99.5) | |
| Clinical Performance (Fresh Specimens - N=53) | |||||
| Clostridium difficile | Unpreserved (Fresh) | High (100%) | High (100%) | 100% (88.6-100) | 100% (85.1-100) |
| Salmonella spp. | Unpreserved (Fresh) | High (100%) | High (100%) | 100% (20.7-100) | 100% (92.3-100) |
| Shigella/EIEC | Unpreserved (Fresh) | High (100%) | High (100%) | 100% (20.7-100) | 100% (92.3-100) |
| Norovirus (GI/GII) | Unpreserved (Fresh) | High (100%) | High (100%) | 100% (20.7-100) | 100% (92.3-100) |
| Analytical Performance (Reproducibility) | |||||
| All targets (various concentrations) | In Vitro | >95% agreement with expected | N/A | >99% (most 100%) | N/A |
2. Sample Size for the Test Set and Data Provenance:
-
Clinical Test Set:
- Archived Samples: 466 leftover, de-identified samples (275 frozen unpreserved and 191 inoculated Cary-Blair).
- Provenance: Prospectively collected for the clinical study that resulted in the K180041 BioCode GPP clearance. This suggests the samples were originally collected for diagnostic purposes in a real-world setting, then archived and de-identified for the current study. The country of origin is not explicitly stated but is implied to be within the scope of previous FDA clearance.
- Fresh Samples: 53 freshly collected leftover samples (specifically for C. difficile testing initially, but used for other targets as well).
- Provenance: Freshly collected, though the specific clinical sites or countries are not mentioned.
- Contrived Samples: 120 samples
- Provenance: Primarily used to establish performance characteristics for Entamoeba histolytica, Giardia lamblia, Yersinia enterocolitica and Vibrio (V. parahaemolyticus, V. vulnificus, and V. cholerae) due to small numbers of naturally positive clinical specimens. These are laboratory-prepared samples.
- Archived Samples: 466 leftover, de-identified samples (275 frozen unpreserved and 191 inoculated Cary-Blair).
-
Analytical Test Set (Reproducibility Study): Consisted of 7 contrived samples, with combinations of 12 representative targets at 1.5x LoD (Low) and 3x LoD (Medium). Each sample was extracted in triplicate and assayed in singlet. This involved testing across 3 instruments by 3 operators, 2 runs per day for 5 days (total of 30 runs).
-
Analytical Test Set (LoD Study):
- Initial screening: 4 replicates of each concentration (near LoD) in negative stool and Cary-Blair, extracted on both easyMAG and MagNA Pure 96, and tested in singlet.
- Confirmation: 20 replicates of each sample type/extraction method, tested in singlet, at or near presumptive LoD.
- Norovirus GI and GII LoD used positive clinical specimens with serial dilutions.
3. Number of Experts Used to Establish Ground Truth for the Test Set and Qualifications:
The document mentions "Reference methods" which include culture, FDA cleared NAT, PCR/sequencing, and enrichment culture/cleared antigen test. While reference methods are used, the document does not explicitly state the number of experts used to establish the ground truth or their qualifications. It refers to "historical Reference results (K180041)" and "Reference assay". This implies that the ground truth was established by laboratory testing using established diagnostic methods, rather than clinical experts' consensus.
4. Adjudication Method for the Test Set:
The document describes discordant analysis for clinical samples. Specifically, "Sixty-four (64) archived samples with discordant results were retested twice with both easyMag and/or MagNA Pure 96 systems." The retesting appears to be the primary adjudication method. There is no mention of a particular adjudication method like 2+1 or 3+1 involving human experts. The "Comment" section for discordant results often indicates further molecular testing (PCR/Seq) to resolve discrepancies.
5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done, and Effect Size:
No, an MRMC comparative effectiveness study was not done. This device is an in vitro diagnostic test that provides qualitative detection of pathogens. Its performance is evaluated based on its agreement (sensitivity and specificity) with established reference methods, not on how it assists human readers in interpreting images or making diagnoses. Therefore, there is no discussion of human reader improvement with or without AI assistance.
6. If a Standalone (Algorithm Only Without Human-in-the Loop Performance) Was Done:
Yes, the studies are standalone performance evaluations of the BioCode GPP diagnostic test. The device itself is an automated system that performs nucleic acid extraction, amplification, detection, and decoding to provide qualitative results. The "Clinical Performance" and "Analytical Performance" sections directly assess the accuracy of the device's output against reference methods. There is no human-in-the-loop component in the direct operation or interpretation of the assay results in the way it would apply to, for example, an AI-powered image analysis tool. The results are interpreted by the MDx 3000 system.
7. The Type of Ground Truth Used:
The ground truth for the clinical studies was established using reference laboratory methods, including:
- Culture: For Campylobacter (C. jejuni, C. coli), Escherichia coli (E. coli) 0157, Salmonella, Shigella, Vibrio spp., Yersinia enterocolitica.
- FDA cleared NAT (Nucleic Acid Test): For Clostridium difficile toxin A/B.
- PCR/sequencing: For Adenovirus 40/41, Cryptosporidium (C. parvum, C. hominis), Entamoeba histolytica, Enteropathogenic E. coli (EPEC), Enterotoxigenic E. coli (ETEC) LT/ST, Enteroaggregative E. coli (EAEC), Giardia lamblia /intestinalis, Norovirus GI/GII, Rotavirus A.
- Enrichment culture/cleared antigen test: For Shiga-like Toxin producing E. coli (STEC) stx1/stx2.
Some ground truth for less common organisms (Entamoeba histolytica, Giardia lamblia, Yersinia enterocolitica and Vibrio) was established with contrived clinical specimens, where the pathogen presence and concentration are precisely known.
8. The Sample Size for the Training Set:
The document does not explicitly mention a "training set" in the context of machine learning for an AI device. This is a molecular diagnostic assay, not an AI/ML algorithm that requires training data in the typical sense. The studies presented are primarily for validation and verification of the device's performance. The "K180041 BioCode GPP clearance" mentioned as the source of archived samples suggests previous validation, but that wouldn't necessarily be considered a "training set" for the current device.
9. How the Ground Truth for the Training Set Was Established:
Since there is no explicit "training set" for an AI/ML algorithm mentioned, this question is not directly applicable. The performance is validated against clinical and analytical studies using reference methods as described in point 7.
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June 5, 2019
Applied Biocode. Inc. Robert Tullio Regulatory Consultant 10020 Pioneer Blvd. Suite 102 Santa Fe Springs, California 90067-0
Re: K190585
Trade/Device Name: Biocode Gastrointestinal Pathogen Panel (GPP) Regulation Number: 21 CFR 866.3990 Regulation Name: Gastrointestinal microorganism multiplex nucleic acid-based assay Regulatory Class: Class II Product Code: PCH, OOI Dated: March 4, 2019 Received: March 6, 2019
Dear Robert Tullio:
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. Although this letter refers to your product as a device, please be aware that some cleared products may instead be combination products. The 510(k) Premarket Notification Database located at https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfpmn/pmn.cfm identifies combination product submissions. 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
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requirements, including, but not limited to: registration and listing (21 CFR Part 807); labeling (21 CFR Part 801 and Part 809); medical device reporting of medical device-related adverse events) (21 CFR 803) for devices or postmarketing safety reporting (21 CFR 4, Subpart B) for combination products (see https://www.fda.gov/combination-products/guidance-regulatory-information/postmarketing-safety-reportingcombination-products); good manufacturing practice requirements as set forth in the quality systems (OS) regulation (21 CFR Part 820) for devices or current good manufacturing practices (21 CFR 4, Subpart A) for combination products; and, if applicable, the electronic product radiation control provisions (Sections 531-542 of the Act); 21 CFR 1000-1050.
Also, please note the regulation entitled, "Misbranding by reference to premarket notification" (21 CFR Part 807.97). For questions regarding the reporting of adverse events under the MDR regulation (21 CFR Part 803), please go to https://www.fda.gov/medical-device-safety/medical-device-reportingmdr-how-report-medical-device-problems.
For comprehensive regulatory information about mediation-emitting products, including information about labeling regulations, please see Device Advice (https://www.fda.gov/medicaldevices/device-advice-comprehensive-regulatory-assistance) and CDRH Learn (https://www.fda.gov/training-and-continuing-education/cdrh-learn). Additionally, you may contact the Division of Industry and Consumer Education (DICE) to ask a question about a specific regulatory topic. See the DICE website (https://www.fda.gov/medical-device-advice-comprehensive-regulatoryassistance/contact-us-division-industry-and-consumer-education-dice) for more information or contact DICE by email (DICE@fda.hhs.gov) or phone (1-800-638-2041 or 301-796-7100).
Sincerely,
Uwe Scherf, M.Sc., Ph.D. Director Division of Microbiology Devices OHT7: Office of In Vitro Diagnostics and Radiological Health Office of Product Evaluation and Quality Center for Devices and Radiological Health
Enclosure
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Indications for Use
510(k) Number (if known) K190585
Device Name
BioCode Gastrointestinal Pathogen Panel (GPP)
Indications for Use (Describe)
The BioCode Gastrointestinal Pathogen Panel (GPP) is a qualitative multiplexed nucleic acid-based in vitro diagnostic test intended for use with the BioCode MDx 3000 Instrument. The BioCode GPP is capable of the simultaneous detection and identification of nucleic acids from multiple bacteria, viruses, and parasites extracted directly from unpreserved stool samples or stool preserved in Cary-Blair transport medium obtained from individuals with signs and/or symptoms of gastrointestinal infection. The following bacteria, parasites, and viruses are identified using the BioCode Gastrointestinal Pathogen Panel:
- · Campylobacter (C. jejuni/C. coli)
- · Clostridium difficile (C. difficile) toxin A/B (Fresh samples only)
- · Salmonella spp
- · Vibrio (V. parahaemolyticus/V. vulnificus/ V. cholerae), including specific identification of Vibrio parahaemolyticus
- · Yersinia enterocolitica
- · Enteroaggregative Escherichia coli (EAEC)
- · Enterotoxigenic Escherichia coli (ETEC) lt/st
- · E. coli 0157 serogroup
- Shiga-like toxin-producing Escherichia coli (STEC) stx1/stx2
- Shigella/ Enteroinvasive Escherichia coli (EIEC)
- · Cryptosporidium spp (C. parvum/C. hominis)
- Entamoeba histolytica
- · Giardia lamblia (also known as G. intestinalis and G. duodenalis)
- Adenovirus F 40/41
- Norovirus GI/GII
- Rotavirus A
The BioCode GPP is indicated as an aid in the diagnosis of gastrointestinal illness and results are meant to be used in conjunction with other clinical, laboratory, and epidemiological data.
Positive results do not rule out co-infection with organisms not included in the BioCode GPP. The agent detected may not be the definite cause of the disease. Negative results in the setting of clinical illness compatible with gastroenteritis may be due to infection by pathogens that are not detected by this test or non-infectious causes such as ulcerative colitis, irritable bowel syndrome, or Crohn's disease.
Concomitant culture is necessary for organism recovery and further typing of bacterial agents.
This device is not intended to monitor or guide treatment for C. difficile infection.
Due to the small number of positive specimens collected for certain organisms during the prospective clinical study, performance characteristics for Adenovirus 40/41, Campylobacter, E. coli 0157, Shigella/EIEC, Yersinia enterocolitica, and Giardia lamblia were established additionally with retrospective clinical specimens. Performance characteristics for Entamoeba histolytica, Giardia lamblia, Yersinia enterocolitica and Vibrio (V. parahaemolyticus, V. vulnificus, and V. cholerae) were established primarily using contrived clinical specimens.
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510(k) SUMMARY
Introduction: According to the requirements of 21 CFR 807.92, the following provides sufficient information to understand the basis for a determination of substantial equivalence.
Submitted by:
Applied BioCode, Inc. 10020 Pioneer Blvd. Suite 102 Santa Fe Springs, CA 90670
Contact:
Robert Di Tullio Regulatory Consultant rditullio@apbiocode.com Telephone: 310 801 1235 Fax: 323 372 3816
Date Submitted:
March 5, 2019
Trade Name:
BioCode Gastrointestinal Pathogen Panel (GPP)
Classification Name and Regulation Number:
Gastrointestinal microorganism multiplex nucleic acid-based assay (21 CFR 866.3990)
Predicate Device:
K180041 – BioCode Gastrointestinal Pathogen Panel (GPP)
Intended Use:
The BioCode Gastrointestinal Pathogen Panel (GPP) is a qualitative multiplexed nucleic acid-based in vitro diagnostic test intended for use with the BioCode MDx 3000 Instrument. The BioCode GPP is capable of the simultaneous detection and identification of nucleic acids from multiple bacteria, viruses, and parasites extracted directly from unpreserved stool samples or stool preserved in Cary-Blair transport medium obtained from individuals with signs and/or symptoms of gastrointestinal infection. The following bacteria, parasites, and viruses are identified using the BioCode Gastrointestinal Pathogen Panel:
- " Campylobacter (C. jejuni/C. coli)
- Clostridium difficile (C. difficile) toxin A/B (Fresh samples only)
- l Salmonella spp
- " Vibrio (V. parahaemolyticus/V. vulnificus/ V. cholerae), including specific identification of Vibrio parahaemolyticus
- Yersinia enterocolitica
- " Enteroaggregative Escherichia coli (EAEC)
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- " Enterotoxigenic Escherichia coli (ETEC) It/st
- י E. coli 0157 serogroup
- . Shiga-like toxin-producing Escherichia coli (STEC) stx1/stx2
- . Shigella/ Enteroinvasive Escherichia coli (EIEC)
- " Cryptosporidium spp (C. parvum/C. hominis)
- . Entamoeba histolytica
- " Giardia lamblia (also known as G. intestinalis and G. duodenalis)
- " Adenovirus F 40/41
- " Norovirus GI/GII
- . Rotavirus A
The BioCode GPP is indicated as an aid in the diagnosis of gastrointestinal illness and results are meant to be used in conjunction with other clinical, laboratory, and epidemiological data.
Positive results do not rule out co-infection with organisms not included in the BioCode GPP. The agent detected may not be the definite cause of the disease. Negative results in the setting of clinical illness compatible with gastroenteritis may be due to infection by pathogens that are not detected by this test or non-infectious causes such as ulcerative colitis, irritable bowel syndrome, or Crohn's disease. Concomitant culture is necessary for organism recovery and further typing of bacterial agents. This device is not intended to monitor or guide treatment for C. difficile infection.
Due to the small number of positive specimens collected for certain organisms during the prospective clinical study, performance characteristics for Adenovirus 40/41, Campylobacter, E. coli 0157, Shigella/EIEC, Yersinia enterocolitica, and Giardia lamblia were established additionally with retrospective clinical specimens. Performance characteristics for Entamoeba histolytica, Giardia lamblia, Yersinia enterocolitica and Vibrio (V. parahaemolyticus, V. vulnificus, and V. cholerae) were established primarily using contrived clinical specimens.
Device Description:
The BioCode Gastrointestinal Pathogen Panel (GPP) is a multiplexed nucleic acid-based test designed to be used with the BioCode MDx 3000 system. The BioCode MDx 3000 is an automated system that integrates PCR amplification, target capture, signal generation and optical detection for multiple gastrointestinal pathogens from a single stool specimen, either unpreserved or in Cary Blair. Stool specimens are processed and nucleic acids extracted with the easyMAG and MagNa Pure. Once the PCR plate is set up and sealed, all other operations are automated on MDx 3000. The BioCode MDx 3000 Gastrointestinal Infection Panel simultaneously tests for 17 pathogens (see table below) from unpreserved stool specimens or stool collected in Cary-Blair transport medium. Results from the BioCode Gastrointestinal Pathogen Panel (GPP) test are available within less than 4 hours.
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Bacteria, Viruses, Diarrheagenic E. coli/Shigella, and Parasites Detected by the BioCode MDx Gastrointestinal Pathogen Panel (GPP)
| Bacteria | Parasites |
|---|---|
| ■ Campylobacter spp. (C. jejuni, C. coli) | ■ Cryptosporidium spp. |
| ■ Clostridium difficile toxin A/B (Fresh samples only) | ■ Entamoeba histolytica |
| ■ Enteroaggregative E. coli (EAEC) | ■ Giardia lamblia |
| ■ Enterotoxigenic E. coli (ETEC): LT/ST | Viruses |
| ■ Shiga-toxin producing E. coli (STEC): stx1/stx2 | ■ Adenovirus 40/41 |
| ■ E.coli O157 | ■ Norovirus GI/GII |
| ■ Shigella spp. /Enteroinvasive E.coli (EIEC) | ■ Rotavirus A |
| ■ Salmonella spp. | RNA Internal Control |
| ■ Vibrio parahaemolyticus | |
| ■ Vibrio spp (not parahaemolyticus) | |
| ■ Yersinia enterocolitica |
Device Comparison:
Comparison of the Applied BioCode GPP with the Predicate Device
| Characteristic | Proposed Device | Predicate |
|---|---|---|
| Name | BioCode Gastrointestinal Pathogen Panel (GPP) | BioCodeGastrointestinalPathogen Panel(GPP) |
| CommonName | Gastrointestinal Microorganism Multiplex Nucleic acid-basedassay | GastrointestinalMicroorganismMultiplex Nucleicacid-based assay |
| 510(k) No. | N/A | K180041 |
| Regulation | 21CFR 866.3990 | 21CFR 866.3990 |
| Product Code | PCH, OOI | PCH, OOI |
| Device Class | II | II |
| Similarities | ||
| Intended Use | The BioCode Gastrointestinal Pathogen Panel (GPP) is aqualitative, multiplexed nucleic acid-based in vitro diagnostic testintended for use with the BioCode MDx 3000 Instrument. TheBioCode GPP is capable of the simultaneous detection andidentification of nucleic acids from multiple bacteria, viruses, andparasites extracted directly from unpreserved stool samples orstool preserved in Cary-Blair transport medium obtained fromindividuals with signs and/or symptoms of gastrointestinalinfection. The following bacteria, parasites, and viruses areidentified using the BioCode Gastrointestinal Pathogen Panel:Campylobacter ( C. jejuni/C. coli ) Clostridium difficile ( C. difficile ) toxin A/B (Fresh samples only) Salmonella spp Vibrio ( V. parahaemolyticus/V. vulnificus/ V. cholerae ),including specific identification of Vibrio parahaemolyticus Yersinia enterocolitica Enteroaggregative Escherichia coli (EAEC) Enterotoxigenic Escherichia coli (ETEC) lt/st E. coli O157 serogroup Shiga-like toxin-producing Escherichia coli (STEC) stx1/stx2 Shigella/ Enteroinvasive Escherichia coli (EIEC) Cryptosporidium spp ( C. parvum/C. hominis ) Entamoeba histolytica Giardia lamblia (also known as G. intestinalis and G. duodenalis ) Adenovirus F 40/41 Norovirus GI/GII Rotavirus A The BioCode GPP is indicated as an aid in the diagnosis ofspecific agents of gastrointestinal illness and results are meant tobe used in conjunction with other clinical, laboratory, andepidemiological data. For In Vitro Diagnostic Use Only. ForPrescription Use Only.Positive results do not rule out co-infection with organismsnot included in the BioCode GPP. The agent detected may not bethe definite cause of the disease. Negative results in the settingof clinical illness compatible with gastroenteritis may be due toinfection by pathogens that are not detected by this test or non-infectious causes such as ulcerative colitis, irritable bowelsyndrome, or Crohn's disease. Concomitant culture is necessaryfor organism recovery and further typing of bacterial agents. Thisdevice is not intended to monitor or guide treatment for C. difficile infection. | Same |
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Premarket Notification 510(k)
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| Premarket Notification 510(k) | ||
|---|---|---|
| -- | ------------------------------- | -- |
| Characteristic | Proposed Device | Predicate |
|---|---|---|
| Instrument | Nucleic Acid Purification SystemBioCode MDx 3000 | Same |
| Sample Type | Unpreserved stool and stool in Cary Blair Medium | Same |
| Controls | Externally Sourced - Zeptometrix | Same |
| Methodology | Multiplex RT-PCR and probe hybridization to biotinylated PCRproduct(s) followed by fluorescence detection and decoding ofbarcoded magnetic beads (BMB) that are coupled to target-specific probes | Same |
| Calibrators | Internal Calibration | Same |
| Difference | ||
| SampleExtraction | Roche MagNA Pure 96 | easyMAG |
Summary of Performance Characteristics of the Biocode GPP.
Clinical Performance
A clinical investigational study was performed in which a total of 466 leftover, de-identified samples (275 frozen unpreserved and 191 inoculated Cary-Blair) that were prospectively collected for the clinical study that resulted in the K180041 BioCode GPP clearance were extracted using the MagNA Pure 96 and the easyMAG, and tested on the MDx 3000 system. Fifty-three (53) freshly collected leftover samples were used for the C. difficile testing. In addition, a total of 120 samples were contrived and tested to determine the performance characteristics for Entamoeba histolytica, Yersinia enterocolitica and Vibrio (V. parahaemolyticus, V. vulnificus, and V. cholerae). The results of the clinical investigational study follow.
| Archived Samples | |
|---|---|
| Total Specimen Count | 466 |
| Gender | |
| Male | 248/466 (53.22%) |
| Female | 211/466 (45.28%) |
| Unknown | 7/466 (1.50%) |
| Age Category | |
| ≤ 5 yrs | 85/466 (18.24%) |
| 6-21 yrs | 91/466 (19.53%) |
| 22-59 yrs | 194/466 (41.63%) |
| 60+yrs | 89/466 (19.10%) |
| Unknown | 7/466 (1.50%) |
Table. Demographic data for archived specimens (frozen unpreserved and inoculated Cary-Blair)
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| Fresh Samples | |
|---|---|
| Total Specimen Count | 53 |
| Gender | |
| Male | 9/53 (16.98%) |
| Female | 44/53 (83.02%) |
| Age Category | |
| ≤ 5 yrs | 1/53 (1.89%) |
| 6-21 yrs | 5/53 (9.43%) |
| 22-59 yrs | 23/53 (43.40%) |
| 60+yrs | 24/53 (45.28%) |
Table. Demographic data for fresh specimens (unpreserved)
Clinical sensitivity (positive agreement) was calculated as TP/(TP + FN). TP = true positive by both the EasyMag and the MagNA Pure 96; FN = false negative by the MagNA Pure 96 only. Clinical specificity (negative agreement) was calculated as TN/(TN + FP). TN = true negative or negative by the EasyMag and the MagNA Pure 96; FP = false positive by the MagNA Pure 96 only. The exact binomial two-sided 95% confidence interval was calculated. The results stratified by sample type and storage method are presented in the table below.
Table. Performance compared to historical Reference results. Stratified by sample type and extraction method. N=290 samples. 1 Invalid for EasyMAG (Cary-Blair sample); 3 Invalid for MP96 (1 Cary-Blair, 2 Unpreserved).
| EasyMAG | MP96 | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Target | Specimen Type | PositiveAgreementPPA (%) | NegativeAgreementNPA (%) | PositiveAgreementPPA (%) | NegativeAgreementNPA (%) | |||||
| Campylobacter spp. | InoculatedCary-Blair | 3/3 (100%) | 135/140 (96%) | 3/3 (100%) | 134/140 (96%) | |||||
| Unpreserved | 1/1 (100%) | 139/145 (96%) | 1/1 (100%) | 135/143 (94%) | ||||||
| All Archived | 4/4 (100%) | 274/285 (96%) | 4/4 (100%) | 269/283 (95%) | ||||||
| Clostridium difficile | InoculatedCary-Blair | 9/12 (75%) | 131/131 (100%) | 9/12 (75%) | 131/131 (100%) | |||||
| Unpreserved | 12/13(92%) | 131/133 (98%) | 12/13 (92%) | 127/131 (97%) | ||||||
| All Archived | 21/25(84%) | 262/264 (99%) | 21/25 (84%) | 258/262 (98%) | ||||||
| E. coli 0157 | InoculatedCary-Blair | 1/1 (100%) | 141/142 (99%) | 0/1 (N/A) | 141/142 (99%) | |||||
| Unpreserved | 0/0 (N/A) | 144/146 (99%) | 0/0 (N/A) | 142/144 (99%) | ||||||
| All Archived | 1/1 (100%) | 285/288 (99%) | 0/1 (N/A) | 283/286 (99%) | ||||||
| Enteroaggregative E.coli (EAEC) | InoculatedCary-Blair | 14/14(100%) | 128/129 (99%) | 13/14 (93%) | 127/129 (98%) | Unpreserved | 13/14(93%) | 131/132 (99%) | 13/14 (93%) | 130/131 (99%) |
| Enteroaggregative E.coli (EAEC) | InoculatedCary-Blair | 14/14(100%) | 128/129 (99%) | 13/14 (93%) | 127/129 (98%) | |||||
| Unpreserved | 13/14(93%) | 131/132 (99%) | 13/14 (93%) | 130/131 (99%) |
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| EasyMAG | MP96 | ||||
|---|---|---|---|---|---|
| Target | Specimen Type | PositiveAgreementPPA (%) | NegativeAgreementNPA (%) | PositiveAgreementPPA (%) | NegativeAgreementNPA (%) |
| All Archived | 27/28(96%) | 259/261 (99%) | 26/28 (93%) | 257/260 (99%) | |
| Enterotoxigenic E. coli(ETEC) | InoculatedCary-Blair | 3/6 (50%) | 137/137 (100%) | 3/6 (50%) | 137/137 (100%) |
| Unpreserved | 6/7 (86%) | 139/139 (100%) | 6/7 (86%) | 138/138 (100%) | |
| All Archived | 9/13 (69%) | 276/276 (100%) | 9/13 (69%) | 275/275 (100%) | |
| Shiga toxin-producingE. coli (STEC) | InoculatedCary-Blair | 1/3 (33%) | 139/140 (99%) | 1/3 (33%) | 139/140 (99%) |
| Unpreserved | 0/0 (N/A) | 144/146 (99%) | 0/0 (N/A) | 142/144 (99%) | |
| All Archived | 1/3 (33%) | 283/286 (99%) | 1/3 (33%) | 281/284 (99%) | |
| Salmonella spp. | InoculatedCary-Blair | 8/10 (80%) | 129/133 (97%) | 9/10 (90%) | 126/133 (95%) |
| Unpreserved | 10/10(100%) | 132/136 (97%) | 10/10 (100%) | 131/134 (98%) | |
| All Archived | 18/20(90%) | 261/269 (97%) | 19/20 (95%) | 257/267 (96%) | |
| Shigella/ EIEC | InoculatedCary-Blair | 3/3 (100%) | 134/140 (96%) | 3/3 (100%) | 134/140 (96%) |
| Unpreserved | 2/2 (100%) | 136/144 (94%) | 2/2 (100%) | 135/142 (95%) | |
| All Archived | 5/5 (100%) | 270/284 (95%) | 5/5 (100%) | 269/282 (95%) | |
| Vibrioparahaemolyticus | InoculatedCary-Blair | 0/0 (N/A) | 142/143 (99%) | 0/0 (N/A) | 142/143 (99%) |
| Unpreserved | 0/0 (N/A) | 145/146 (99%) | 0/0 (N/A) | 143/144 (99%) | |
| All Archived | 0/0 (N/A) | 287/289 (99%) | 0/0 (N/A) | 285/287 (99%) | |
| Vibrio spp. (notparahaemolyticus) | InoculatedCary-Blair | 0/0 (N/A) | 143/143 (100%) | 0/0 (N/A) | 143/143 (100%) |
| Unpreserved | 0/0 (N/A) | 146/146 (100%) | 0/0 (N/A) | 144/144 (100%) | |
| All Archived | 0/0 (N/A) | 289/289 (100%) | 0/0 (N/A) | 287/287 (100%) | |
| Yersinia enterocolitica | InoculatedCary-Blair | 0/0 (N/A) | 141/143 (99%) | 0/0 (N/A) | 141/143 (99%) |
| Unpreserved | 0/0 (N/A) | 146/146 (100%) | 0/0 (N/A) | 144/144 (100%) | |
| All Archived | 0/0 (N/A) | 287/289 (99%) | 0/0 (N/A) | 285/287 (99%) | |
| Cryptosporidium spp. | InoculatedCary-Blair | 3/4 (75%) | 139/139 (100%) | 2/4 (50%) | 139/139 (100%) |
| Unpreserved | 3/4 (75%) | 142/142 (100%) | 3/4 (75%) | 140/140 (100%) | |
| All Archived | 6/8 (75%) | 281/281 (100%) | 5/8 (63%) | 279/279 (100%) | |
| Entamoeba histolytica | InoculatedCary-Blair | 0/0 (N/A) | 143/143 (100%) | 0/0 (N/A) | 143/143 (100%) |
| Target | Specimen Type | EasyMAGPositiveAgreementPPA (%) | EasyMAGNegativeAgreementNPA (%) | MP96PositiveAgreementPPA (%) | MP96NegativeAgreementNPA (%) |
| Giardia lamblia | Unpreserved | 0/0 (N/A) | 146/146 (100%) | 0/0 (N/A) | 144/144 (100%) |
| All Archived | 0/0 (N/A) | 289/289 (100%) | 0/0 (N/A) | 287/287 (100%) | |
| InoculatedCary-Blair | 1/1 (100%) | 141/142 (99%) | 1/1 (100%) | 141/142 (99%) | |
| Giardia lamblia | Unpreserved | 1/1 (100%) | 142/145 (98%) | 1/1 (100%) | 140/143 (98%) |
| Giardia lamblia | All Archived | 2/2 (100%) | 283/287 (99%) | 2/2 (100%) | 281/285 (99%) |
| Adenovirus 40/41 | InoculatedCary-Blair | 1/2 (50%) | 142/142 (100%) | 1/2 (50%) | 138/141 (98%) |
| Unpreserved | 5/6 (83%) | 137/140 (98%) | 5/6 (83%) | 134/138 (97%) | |
| All Archived | 6/8 (75%) | 279/282 (99%) | 6/8 (75%) | 272/279 (97%) | |
| Norovirus (GI/GII) | InoculatedCary-Blair | 19/19(100%) | 124/124 (100%) | 19/19 (100%) | 122/124 (98%) |
| Unpreserved | 19/19(100%) | 125/127 (98%) | 19/19 (100%) | 124/125 (99%) | |
| All Archived | 38/38(100%) | 249/251 (99%) | 38/38 (100%) | 246/249 (99%) | |
| Rotavirus A | InoculatedCary-Blair | 11/11(100%) | 130/132 (98%) | 11/11 (100%) | 132/133 (99%) |
| Unpreserved | 9/9 (100%) | 135/137 (99%) | 9/9 (100%) | 130/135 (96%) | |
| All Archived | 20/20(100%) | 264/269 (99%) | 20/20 (100%) | 262/268 (98%) |
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Footnotes (D = Detected, N = Not Detected)
| HistoricalResults(K180041) | MP96Extraction(K190585) | |||||
|---|---|---|---|---|---|---|
| Target | SpecimenID | Reference | BioCodeGPP | easyMAG | MP96 | Comment |
| 01-0027 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq C. jejuni, but contig too short;concordant with historical GPP result | |
| Campylobacterspp | 01-0048 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/Seq C. jejuni; concordant withhistorical GPP result |
| 01-0137 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/Seq C. jejuni; concordant withhistorical GPP result | |
| 01-0237 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/Seq C. jejuni; concordant withhistorical GPP result | |
| 01-0352 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/Seq C. jejuni; concordant withhistorical GPP result | |
| 02-0159 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/Seq C. jejuni; concordant withhistorical GPP result | |
| 02-0183 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/Seq C. jejuni; concordant withhistorical GPP result | |
| 02-0367 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/Seq not detected, concordant withhistorical GPP result | |
| 03-0153 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/Seq not detected, concordant withhistorical GPP result | |
| HistoricalResults(K180041) | MP96Extraction(K190585) | |||||
| Target | SpecimenID | Reference | BioCodeGPP | easyMAG | MP96 | Comment |
| Clostridiumdifficile | 03-0308 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/Seq C. jejuni; concordant withhistorical GPP result |
| 03-0334 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/Seq C. jejuni; concordant withhistorical GPP result | |
| 02-0069 | N | D | N | D | Reference assay (culture) not as sensitive, PCR/Seq C. jejuni; MP96 concordantwith historical GPP result | |
| 02-0193 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 03-0364 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 01-0031 | N | D | D | D | Reference Ct beyond cut-off (38.7); concordant with historical GPP Result | |
| 01-0063 | N | D | D | D | Reference Ct beyond cut-off with ref (38.3); concordant with historical GPP Result | |
| 02-0201 | D | N | D | N | Late Ct with ref (36.6) tested fresh, low positive; see repeat results for additionalinformations | |
| 02-0350 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 03-0053 | D | D | N | D | Late Ct with ref (36.2) tested fresh; low positive; see repeat results for additionalinformations | |
| 03-0351 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 01-0002 | D | N | N | N | Late Ct with ref (36.6) tested fresh; concordant with historical GPP Result (frozen) | |
| 02-0378 | D | N | N | N | Late Ct with ref (36.6) tested fresh; concordant with historical GPP Result (fresh) | |
| 03-0353 | D | D | N | N | Late Ct with ref (35.5) tested frozen; possible sample degradation | |
| E. coli 0157 | 02-0080 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq O157; concordant withhistorical GPP result |
| 02-0082 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq O157; concordant withhistorical GPP result | |
| 02-0206 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq 0157; concordant withhistorical GPP result | |
| 02-0279 | D | D | N | N | Possible sample degradation; current testing concordant | |
| 03-0140 | N | D | D | D | Late Ct with ref (37.1) on repeat testing; concordant with historical GPP Result | |
| 02-0183 | N | N | D | N | Possible low positive; see repeat results for additional information | |
| Enteroaggregative E. coli (EAEC) | 03-0004 | D | D | D | N | Possible low positive; see repeat results for additional information |
| 02-0367 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 03-0046 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| EnterotoxigenicE. coli (ETEC) | 02-0203 | D | N | N | N | Reference result could not be confirmed by 2 additional rounds of PCR/Seq;concordant with historical GPP Result |
| 02-0203 | D | N | N | N | Reference result could not be confirmed by 2 additional rounds of PCR/Seq;concordant with historical GPP Result | |
| 02-0207 | D | N | N | N | Late Ct (35.2) Reference result could not be confirmed by 2 additional rounds ofPCR/Seq; concordant with historical GPP Result | |
| 03-0004 | D | N | N | N | Reference result could not be confirmed by 2 additional rounds of PCR/Seq;concordant with historical GPP Result | |
| 02-0391 | D | D | N | N | Late Ct (37.8) with ref tested fresh; possible sample degradation | |
| Salmonella spp. | 01-0091 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq S.enterica; concordant withhistorical GPP result |
| HistoricalResults(K180041) | MP96Extraction(K190585) | |||||
| Target | SpecimenID | Reference | BioCodeGPP | easyMAG | MP96 | Comment |
| 01-0137 | N | N | D | N | Possible Contamination; see repeat results | |
| 01-0278 | D | D | N | D | See repeat results for additional information | |
| 01-0346 | D | D | N | N | Possible sample degradation; current testing concordant | |
| 02-0195 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 02-0213 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq S.enterica; concordant withhistorical GPP result | |
| 02-0260 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 02-0378 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 03-0116 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq S.enterica; concordant withhistorical GPP result | |
| 03-0147 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq S.enterica; concordant withhistorical GPP result | |
| 03-0173 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq S.typhi; concordant withhistorical GPP result | |
| 03-0189 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq S.enterica; concordant withhistorical GPP result | |
| 03-0206 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq S.typhi; concordant withhistorical GPP result | |
| Shiga toxin-producing E. coli(STEC) | 01-0098 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq STEC; concordant with historicalGPP result |
| 02-0367 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq STEC; concordant with historicalGPP result | |
| 02-0393 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq STEC; concordant with historicalGPP result | |
| 02-0279 | D | D | D | N | See repeat results for additional information | |
| 02-0081 | D | D | N | N | Possible sample degradation; current testing concordant | |
| 01-0019 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| 01-0020 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| 01-0027 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| 01-0099 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| 01-0199 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| Shigella/EIEC | 01-0201 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result |
| 01-0202 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| 01-0259 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| 02-0176 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| 03-0056 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| 03-0090 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| 03-0238 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| HistoricalResults(K180041) | MP96Extraction(K190585) | |||||
| Target | SpecimenID | Reference | BiocodeGPP | easyMAG | MP96 | Comment |
| 03-0380 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq Shigella spp; concordant withhistorical GPP result | |
| 01-0319 | N | N | D | N | Possible low positive; see repeat results for additional information | |
| Vibrioparahaemolyticus | 03-0194 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq V.parahaemolyticus; concordantwith historical GPP result |
| 03-0351 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq V.parahaemolyticus; concordantwith historical GPP result | |
| Yersiniaenterocolitica | 01-0024 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq V.parahaemolyticus; concordantwith historical GPP result |
| 03-0307 | N | D | D | D | Reference assay (culture) not as sensitive, PCR/seq not detected; concordant withhistorical GPP result | |
| 01-0212 | D | D | D | N | See repeat results for additional information | |
| Cryptosporidiumparvum | 01-0265 | D | D | N | N | Possible sample degradation; current testing concordant |
| 01-0285 | D | D | N | N | Possible sample degradation; current testing concordant | |
| 01-0002 | N | D | D | D | Reference assay (PCR/Seq) not as sensitive; concordant with historical GPP result | |
| Giardiaintestinalis | 01-0300 | N | D | D | D | Reference assay (PCR/Seq) not as sensitive; concordant with historical GPP result |
| 02-0258 | N | D | D | D | Reference assay (PCR/Seq) not as sensitive; concordant with historical GPP result | |
| 03-0140 | N | D | D | D | Reference assay (PCR/Seq) not as sensitive; concordant with historical GPP result | |
| Humanadenovirus40/41 | 01-0128 | N | N | D | D | concordant with historical GPP result |
| 01-0021 | N | N | D | N | Possible Contamination; see repeat results for additional information | |
| 02-0288 | N | N | D | N | Possible Contamination; see repeat results for additional information | |
| 01-0137 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 02-0161 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 02-0183 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 02-0379 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 02-0391 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 03-0400 | N | N | N | D | Possible Contamination; see repeat results for additional information | |
| 02-0137 | D | N | N | N | Reference result could not be confirmed by 2 additional rounds of PCR/Seq;concordant with historical GPP Result | |
| 02-0147 | D | D | N | N | Possible sample degradation; current testing concordant | |
| Norovirus GI/GII | 01-0004 | N | D | D | D | concordant with historical GPP result |
| 01-0036 | N | N | D | N | Low positive based on MFI (3150) | |
| 02-0376 | N | N | N | D | Low positive based on MFI (1265) | |
| 02-0394 | N | N | N | D | Low positive based on MFI (2249) | |
| Human rotavirusA | 01-0128 | N | N | D | D | Current testing concordant |
| Target | Specimen ID | Reference | Historical Results(K180041)BioCode GPP | MP96 Extraction(K190585)easy MAG | MP96MP 96 | Comment |
| 01-0337 | N | D | D | D | concordant with historical GPP result | |
| 02-0175 | N | D | D | D | concordant with historical GPP result | |
| 02-0246 | N | D | D | N | Possible low positive; see repeat results for additional information | |
| 01-0098 | N | D | N | D | Possible low positive; see repeat results for additional information | |
| 01-0202 | N | N | N | D | Possible Contamination/low positive; see repeat results for additional information | |
| 03-0400 | N | N | N | D | Possible Contamination; see repeat results for additional information |
{12}------------------------------------------------
{13}------------------------------------------------
{14}------------------------------------------------
{15}------------------------------------------------
Comparator (Reference) methods from BioCode GPP original submission
Target Pathogen/Toxin
| Target Pathogen/Toxin | Reference Method |
|---|---|
| Adenovirus 40/41 | Composite result of PCR/sequencing |
| Campylobacter (C. jejuni, C. coli) | Culture |
| Clostridium difficile (C. difficile) toxin A/B | FDA cleared NAT |
| Cryptosporidium (C. parvum, C. hominis) | PCR/sequencing |
| Entamoeba histolytica | PCR/sequencing |
| Escherichia coli (E. coli) 0157 | Enrichment culture |
| Enteropathogenic E. coli (EPEC) | Composite result of PCR/sequencing |
| Enterotoxigenic E. coli (ETEC) LT/ST | Composite result of PCR/sequencing |
| Enteroaggregative E. coli (EAEC) | Composite result of PCR/sequencing |
| Giardia lamblia /intestinalis | Composite result of PCR/sequencing |
| Norovirus GI/GII | Composite result of PCR/sequencing |
| Rotavirus A | Composite result of PCR/sequencing |
| Salmonella | Enrichment culture |
| Shiga-like Toxin producing E. coli (STEC) stx1/stx2 | Enrichment culture/cleared antigen test |
| Shigella (S. boydii, S. sonnei, S. flexneri, S. dysenteriae)/EIEC | Enrichment culture |
| Vibrio spp. (V. cholerae, V. parahaemolyticus, V. vulnificus) | Culture |
| Yersinia enterocolitica | Culture |
| Target | SpecimenType | (n) | Positive Agreement | Negative Agreement | ||
|---|---|---|---|---|---|---|
| PPA (%) | 95% CI | NPA (%) | 95% CI | |||
| Campylobacterspp.a | InoculatedCary-Blair | 190 | 22/23 (95.65) | 79.0 – 99.2 | 164/167 (98.20) | 94.9 – 99.4 |
| Unpreserved(Frozen) | 274 | 27/27 (100) | 87.5 - 100 | 244/247 (98.80) | 96.5 - 99.6 | |
| All Archived | 464 | 49/50 (98.0) | 89.5 - 99.6 | 408/414 (98.60) | 96.9 – 99.3 | |
| Clostridiumdifficile b | InoculatedCary-Blair | 190 | 10/11 (90.91) | 62.3 – 98.4 | 178/179 (99.44) | 96.9 – 99.9 |
| Unpreserved(Frozen) | 274 | 21/22 (95.45) | 78.2 – 99.2 | 250/252 (99.20) | 97.2 – 99.8 | |
| Target | Specimen Type | (n) | Positive Agreement | Negative Agreement | ||
| All Archived | 464 | 31/33 (93.94) | 80.4 - 98.3 | 428/431 (99.30) | 98.0 - 99.8 | |
| InoculatedCary-Blair | 190 | 3/3 (100) | 43.9 - 100 | 187/187 (100) | 98.0 - 100 | |
| E. coli O157 | Unpreserved(Frozen) | 274 | 14/14 (100) | 78.5 - 100 | 260/260 (100) | 98.5 - 100 |
| All Archived | 464 | 17/17 (100) | 81.6 - 100 | 447/447 (100) | 99.1 - 100 | |
| InoculatedCary-Blair | 190 | 15/17 (88.24) | 65.7 - 96.7 | 171/173 (98.8) | 95.9 - 99.7 | |
| EnteroaggregativeE. coli (EAEC) c | Unpreserved(Frozen) | 274 | 29/29 (100) | 88.3 - 100 | 244/245 (99.59) | 97.7 - 99.9 |
| All Archived | 464 | 44/46 (95.65) | 85.5 - 98.8 | 416/418 (99.50) | 98.3 - 99.9 | |
| InoculatedCary-Blair | 190 | 3/5 (60.00) | 23.1 - 88.2 | 185/185 (100) | 98.0 - 100 | |
| EnterotoxigenicE. coli (ETEC) d | Unpreserved(Frozen) | 274 | 13/13 (100) | 77.2 - 100 | 261/261 (100) | 98.5 - 100 |
| All Archived | 464 | 16/18 (88.89) | 67.2 - 96.9 | 446/446 (100) | 99.1 - 100 | |
| Shiga toxin-producing E. coli(STEC) e | InoculatedCary-Blair | 190 | 12/13 (92.31) | 66.7 - 98.6 | 177/177 (100) | 97.9 - 100 |
| Unpreserved(Frozen) | 274 | 29/30 (96.67) | 83.3 - 99.4 | 243/244 (99.60) | 97.7 - 99.9 | |
| All Archived | 464 | 41/43 (95.35) | 84.5 - 98.7 | 420/421 (99.80) | 98.7 - 100 | |
| InoculatedCary-Blair | 190 | 17/17 (100) | 81.6 - 100 | 169/173 (97.70) | 94.2 - 99.1 | |
| Salmonella spp.f | Unpreserved(Fresh) | 274 | 25/27 (92.59) | 76.6 - 97.9 | 246/247 (99.60) | 97.7 - 99.9 |
| All Archived | 464 | 42/44 (95.45) | 84.9 - 98.7 | 415/420 (98.80) | 97.2 - 99.5 | |
| Shigella/ EIEC g | InoculatedCary-Blair | 190 | 9/9 (100) | 70.1 - 100 | 181/181 (100) | 97.9 - 100 |
| Unpreserved(Frozen) | 274 | 20/22 (90.91) | 72.2 - 97.5 | 252/252 (100) | 98.5 - 100 | |
| All Archived | 464 | 29/31 (93.55) | 79.3 - 98.2 | 433/433 (100) | 99.1 - 100 | |
| Vibrioparahaemolyticus h | InoculatedCary-Blair | 190 | 1/1 (100) | 20.7 - 100 | 189/189 (100) | 98.0 - 100 |
| Unpreserved(Frozen) | 274 | 1/1 (100) | 20.7 - 100 | 272/273 (99.6) | 98.0 - 99.9 | |
| All Archived | 464 | 2/2 (100) | 34.2 - 100 | 461/462 (99.8) | 99.8 - 100 | |
| Vibrio spp. (notparahaemolyticus)i | InoculatedCary-Blair | 190 | N/A | N/A | 190/190 (100) | 98.0 - 100 |
| Unpreserved(Frozen) | 274 | 0/1 (0%) | N/A | N/A | 273/274 (99.6) | |
| All Archived | 464 | 0/1 (0%) | N/A | 463/464 (99.8) | 98.8 - 100 | |
| Yersiniaenterocolitica j | InoculatedCary-Blair | 190 | 3/3 (100) | 43.9 - 100 | 187/187 (100) | 98.0 - 100 |
| Unpreserved(Frozen) | 274 | 3/3 (100) | 43.9 - 100 | 269/271 (99.26) | 97.3 - 99.8 | |
| All Archived | 464 | 6/6 (100) | 61.0 - 100 | 456/458 (99.6) | 98.4 - 99.9 | |
| SpecimenType | (n) | Positive Agreement | Negative Agreement | |||
| Target | PPA (%) | 95% CI | NPA (%) | 95% CI | ||
| Cryptosporidiumspp.k | InoculatedCary-Blair | 190 | 11/12 (91.67) | 64.6 – 98.5 | 178/178 (100) | 97.9 - 100 |
| Unpreserved(Frozen) | 274 | 22/24 (91.67) | 74.2 - 97.7 | 248/250 (99.20) | 97.1 - 99.8 | |
| All Archived | 464 | 33/36 (91.67) | 78.2 – 97.1 | 426/428 (99.5) | 98.3 - 99.9 | |
| Entamoebahistolytica | InoculatedCary-Blair | 190 | N/A | N/A | 190/190 (100) | 98.0 - 100 |
| Unpreserved(Frozen) | 274 | N/A | N/A | 274/274 (100) | 98.6 - 100 | |
| All Archived | 464 | N/A | N/A | 464/464 (100) | 99.2 - 100 | |
| Giardia lamblial | InoculatedCary-Blair | 190 | 3/3 (100) | 43.90 - 100 | 187/187 (100) | 98.0 - 100 |
| Unpreserved(Frozen) | 274 | 14/14 (100) | 78.5 - 100 | 255/260 (98.1) | 95.6 - 99.2 | |
| All Archived | 464 | 17/17 (100) | 81.6 - 100 | 442/447 (98.9) | 97.4 - 99.5 | |
| Adenovirus 40/41m | InoculatedCary-Blair | 190 | 7/10 (70.00) | 39.7 – 89.2 | 177/180 (98.32) | 95.2 - 99.4 |
| Unpreserved(Frozen) | 274 | 11/14 (78.60) | 52.4 - 92.4 | 252/260 (96.90) | 94.0 - 98.4 | |
| All Archived | 464 | 21/24 (87.50) | 69.0 - 95.7 | 429/440 (97.5) | 95.6 - 98.6 | |
| Norovirus(GI/GII)n | InoculatedCary-Blair | 190 | 19/19 (100) | 83.2 - 100 | 168/171 (98.20) | 95.0 - 99.4 |
| Unpreserved(Frozen) | 274 | 21/22 (95.45) | 78.2 – 99.2 | 248/252 (98.40) | 96.0 - 99.4 | |
| All Archived | 464 | 37/41 (90.24) | 77.5 - 96.1 | 416/423 (98.3) | 96.6 - 99.2 | |
| Rotavirus Ao | InoculatedCary-Blair | 190 | 12/13 (92.31) | 66.7 – 98.6 | 176/177 (99.44) | 96.9 - 99.9 |
| Unpreserved(Frozen) | 274 | 15/15 (100) | 79.6 - 100 | 255/259 (98.5) | 96.1 - 99.4 | |
| All Archived | 464 | 27/28 (96.43) | 82.3 - 99.4 | 431/436 (98.9) | 97.3 - 99.5 |
Table. Summary of Clinical Investigational Study Results (Archived Specimens) stratified by sample type and storage
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Sixty-four (64) archived samples with discordant results were retested twice with both easyMag and/or MagNA Pure 96 systems.
a - Campylobacter spp. One (1) false negative retested became true positives retested, 2 were true negative, one became true positive, two remained false positive not retested due to insufficient volume to retest.
b - Clostridium difficile: Of the 2 false negatives retested, 1 became true positive, the other one was true negative. Of the 3 false positives retested, 2 were true negative and 1 was true positive.
c - EAEC: Of the 2 false negatives retested, 1 was false positive. Of the 3 false positive. Of the 3 false positives retested, 2 were true negative and 1 was true positive.
d - ETEC: Two (2) false negatives tested were true negative.
e - STEC: Of 3 false positives retested, 2 were true positive and 1 was true negative.
f - Salmonella spp. Of the 2 false negatives retested, one was false positive and the other one was true negative. Of the 5 false positives retested, 4 were true negative and 1 was true positive.
g - Shigella/EIEC: Of the 2 false negatives retested, 1 was true positive and the other remained false negative.
h - Vibrio parahaemolyticus: The 1 false positive retested was true negative.
i - Vibrio spp. The 1 false negative retested remained false negative. Detected as Vibrio parahaemolyticus by MP96.
j - Yersinia enterocolitica: Two (2) false positives retested were true negative.
k - Cryptosporidium spp: Of the 3 false negative and 2 were false negative and 2 were false negative. The 2 false positives retested remained false positive.
{18}------------------------------------------------
l - Giardia lamblia: Of the 5 false positives retested, 1 became true negative. The remaining 2 were not retested due insufficient volume to retest.
m- Adenovirus 40/41: All 6 false negatives. Of the 11 false positives, 9 were retested and became true negative, and the remaining 2 were not retested due insufficient volume to retest.
n - Norovirus G1/G2: The 1 false negative retested was true negatives retested, 6 were true negative and one became true positive.
o - Rotavirus: The 1 false negative retested was true negatives retested, 1 was true positive, 3 were true negative, and 1 remained false positive.
| Target | Sample Name | SampleType | Extraction | Original Run | Reflex TestingResult | Final Result |
|---|---|---|---|---|---|---|
| 01-0079 | InoculatedCary-Blair | EasyMag | IC Invalid | IC Valid | Valid | |
| Internal Control(MS2) | 01-0073 | InoculatedCary-Blair | MagNAPure | IC Invalid | IC Invalid | Invalid |
| 02-0211 | Unpreserved | MagNaPure | IC Invalid | IC Invalid | Invalid | |
| 02-0228 | Unpreserved | EasyMag | IC Invalid | IC Valid | Valid | |
| Mayo-G1_124 | Unpreserved | MagNAPure | IC Invalid | IC Valid | Valid |
Table. Results of Reflex Testing of Invalid Samples (Archived Samples)
Note. Five (5) archived samples were invalid. After relflex testing, two samples (1 inoculated Cary-Blair and 1 unpreserved) were still invalid.
| Target | Specimen | (n) | Positive Agreement | Negative Agreement | ||
|---|---|---|---|---|---|---|
| Type | PPA (%) | 95% CI | NPA (%) | 95% CI | ||
| Campylobacter spp. | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4-100 |
| Clostridium difficile | Unpreserved(Fresh) | 52 | 30/30 (100) | 88.6-100 | 22/22 (100) | 85.1-100 |
| E. coli 0157 | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4-100 |
| Enteroaggregative E.coli (EAEC) | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4-100 |
| EnterotoxigenicE. coli (ETEC) | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4-100 |
| Shiga toxin-producingE. coli (STEC) | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4-100 |
| Salmonella spp. | Unpreserved(Fresh) | 47 | 1/1 (100) | 20.7-100 | 46/46 (100) | 92.3-100 |
| Shigella/ EIEC | Unpreserved(Fresh) | 47 | 1/1 (100) | 20.7-100 | 46/46 (100) | 92.3-100 |
| Vibrioparahaemolyticus | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4-100 |
| Vibrio spp. (notparahaemolyticus) | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4-100 |
| Yersinia enterocolitica | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4-100 |
Table. Summary of Clinical Investigational Study Results of Fresh Specimens
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| Target | Specimen | (n) | Positive Agreement | Negative Agreement | ||
|---|---|---|---|---|---|---|
| Type | PPA (%) | 95% CI | NPA (%) | 95% CI | ||
| Cryptosporidium spp. | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4- 100 |
| Entamoeba histolytica | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4- 100 |
| Giardia lamblia¹ | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4- 100 |
| Adenovirus 40/41 | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4- 100 |
| Norovirus(GI/GII) | Unpreserved(Fresh) | 47 | 1/1 (100) | 20.7 -100 | 46/46 (100) | 92.3- 100 |
| Rotavirus A | Unpreserved(Fresh) | 47 | N/A | N/A | 47/47(100) | 92.4- 100 |
Note. Fifty-three (53) fresh unpreserved samples were tested. The Internal Control (MS2) result of the 5 C. difficile positives and 1 C. difficile negative were invalid. Therefore, one sample for C. difficile target was invalid. For the remaining targets, 6 samples were invalid.
Table. Summary of Contrived Specimen Results
| Target | Specimen Type | (n) | Positive Agreement | Negative Agreement | ||
|---|---|---|---|---|---|---|
| PPA (%) | 95% CI | NPA (%) | 95% CI | |||
| Vibrio parahaemolyticus a | Unpreserved (Frozen) | 119 | 28/30 (93.3) | 78.7 – 98.2 | 89/89 (100) | 95.9 – 100 |
| Vibrio spp. (not parahaemolyticus) b | Unpreserved (Frozen) | 118 | 29/29 (100) | 88.3 - 100 | 89/89 (100) | 95.9 - 100 |
| Yersinia enterocolitica | Unpreserved (Frozen) | 118 | 30/30 (100) | 88.6 – 100 | 88/88 (100) | 95.8 – 100 |
| Entamoeba histolytica | Unpreserved (Frozen) | 118 | 30/30 (100) | 88.6 – 100 | 88/88 (100) | 96.8 – 100 |
| All other targets | Unpreserved (Frozen) | 118 | N/A | N/A | 118/118 (100) | 96.8 – 100 |
Note. One hundred twenty (120) contrived samples were tested. ª The Internal control (MS2) result of one of the Vibrio parahaemolyticus positives was invalid. * One (1) of the Vibrio spp. positives was negative and invalid (IC negative) with both the easyMag and the MagNA Pure 96.
Table. Clinical Co-infection Summary
| Co-infection summary | |
|---|---|
| +1 Target | 246/466 (52.8%) |
| +2 Targets | 78/466 (16.7%) |
| +3 Targets | 13/466 (2.8%) |
Analytical Performance
{20}------------------------------------------------
The results of the analytical studies summarized in the following paragraphs met the acceptance criteria and successfully demonstrated the analytical performance characteristics of the proposed BioCode GPP using the MagNA Pure 96 extraction system.
REPRODUCIBILITY STUDY
A study was performed to assess the Reproducibility of the BioCode GPP using samples extracted with the MagNA Pure 96. This study was designed to assess intra-assay (within run), Inter-assay (run-to-run), day-to-day and instrument-to-instrument (operator) reproducibility. One lot of reagents was assayed at Applied BioCode on 3 instruments by 3 operators, 2 runs per day per operator for 5 days (total of 30 runs). The reproducibility panel consisted of 7 contrived samples (sample 7 a negative control) extracted in triplicate and each assayed in singlet. The samples consisted of combinations of 12 representative targets at 1.5x LoD (Low) and 3x LoD (Medium). Reproducibility was > 99%.
All results are as expected with the exception of two false negative results for Cryptosporidium parvum (one low positive and one medium positive).
| % Agreement with Expected Result | |||||||
|---|---|---|---|---|---|---|---|
| Organism Tested | TargetProbe | Concentration Tested | ExpectedResults | Instrument1- Operator 1 | Instrument2- Operator 2 | Instrument3- Operator 3 | AllInstruments/Operators |
| Campylobacterjejuni spp. jejuniATCC 33292 | Campy | Medium Positive 3xLoD1.05 x 103 CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) |
| Low Positive 1.5xLoD5.25 x 102 CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| None | NotDetected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) | ||
| Clostridiumdifficile(toxinotype III;Nap1)Zeptometrix0801619cf | tcdB | Medium Positive 3xLoD1.25 x 103 CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) |
| Low Positive 1.5xLoD6.23 x 102 CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| None | NotDetected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) | ||
| EnteroaggregativeE. coli 092:H33(EAEC)STEC TW04440 | EAEC | Medium Positive 3xLoD2.10 x 103 CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) |
| Low Positive 1.5xLoD1.05 x 103 CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| Organism Tested | TargetProbe | Concentration Tested | ExpectedResults | Instrument1- Operator 1 | Instrument2- Operator 2 | Instrument3- Operator 3 | AllInstruments/Operators |
| Enterotoxigenic E.coli 078:H11H10407 (ETEC)ATCC 35401 | ST-1a | None | NotDetected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) |
| Medium Positive 3xLoD8.40 x 10² CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| Low Positive 1.5xLoD4.20 x 10² CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| Salmonellaenterica ssp.entericaATCC 14028 | Salm | None | NotDetected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) |
| Medium Positive 3xLoD3.30 x 10³ CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| Low Positive 1.5xLoD1.65 x 10³ CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| Shiga-like toxinproducing E. coli(STEC)ATCC BAA-2217 | stx2 | None | NotDetected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) |
| Medium Positive 3xLoD3.75 x 10³ CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| Low Positive 1.5xLoD1.88 x10³ CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| Shigella sonneiATCC 29930 | Shig | None | NotDetected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) |
| Medium Positive 3xLoD6.60 x 10² CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| Low Positive 1.5xLoD3.30 x 10² CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| VibrioparahaemolyticusATCC 17802 | V.para | None | NotDetected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) |
| Medium Positive 3xLoD1.95 x10¹ CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | ||
| % Agreement with Expected Result | |||||||
| Organism Tested | TargetProbe | Concentration Tested | ExpectedResults | Instrument1- Operator 1 | Instrument2- Operator 2 | Instrument3- Operator 3 | AllInstruments/Operators |
| YersiniaenterocoliticaATCC 23715 | Low Positive 1.5xLoD9.75x10° CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | |
| YersiniaenterocoliticaATCC 23715 | None | NotDetected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) | |
| YersiniaenterocoliticaATCC 23715 | Medium Positive 3xLoD2.25 x103 CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | |
| YersiniaenterocoliticaATCC 23715 | Y.ent | Low Positive 1.5xLoD1.13 x103 CFU/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) |
| YersiniaenterocoliticaATCC 23715 | None | NotDetected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) | |
| Cryptosporidiumparvumwaterborne P102 | Medium Positive 3xLoD9.30 x 103 oocysts/mL | Detected | 30/30(100%) | 30/30(100%) | 29/30(97%) | 89/90 (99%) | |
| Crypto | Low Positive 1.5xLoD4.65 x 103 oocysts/mL | Detected | 30/30(100%) | 30/30(100%) | 29/30(97%) | 89/90 (99%) | |
| None | NotDetected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) | ||
| Giardia intestinalis(aka G. lamblia)waterborne P101 | Medium Positive 3xLoD2.70 x 103 cysts/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | |
| G.lam | Low Positive 1.5xLoD1.35 x 103 cysts/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | |
| Giardia intestinalis(aka G. lamblia)waterborne P101 | None | NotDetected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) | |
| RotavirusATCC VR-2018 | Medium Positive 3xLoD3.75 x 103 TCID50/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | |
| Rota | Low Positive 1.5xLoD1.88 x 102 TCID50/mL | Detected | 30/30(100%) | 30/30(100%) | 30/30(100%) | 90/90 (100%) | |
| Organism Tested | Target Probe | Concentration Tested | Expected Results | % Agreement with Expected Result | |||
| Instrument1 - Operator 1 | Instrument2 - Operator 2 | Instrument3 - Operator 3 | All Instruments/ Operators | ||||
| None | Not Detected | 150/150(100%) | 150/150(100%) | 150/150(100%) | 450/450(100%) |
Table. Reproducibility of BioCode GPP with MP96 extractions- Qualitative results.
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Table. Reproducibility of BioCode GPP with MP96 extractions- Quantitative results
| Organism | TargetProbe | Test Level | Instrument/Operator | MFI Reproducibility | ||||
|---|---|---|---|---|---|---|---|---|
| Mean | StDev | %CV | Min | Max | ||||
| Campylobacter jejuni spp. jejuniATCC 33292 | Campy | ModeratePositive3xLoD$1.05 x 10^3$CFU/mL | C2- Operator 1 | 26128 | 4013 | 15 | 8265 | 29801 |
| C3- Operator 2 | 28562 | 2652 | 9 | 22187 | 33021 | |||
| C4- Operator 3 | 24154 | 2714 | 11 | 18890 | 28822 | |||
| All Instruments/Operators | 26281 | 3637 | 14 | 8265 | 33021 | |||
| Low Positive1.5xLoD$5.25 x 10^2$CFU/mL | C2- Operator 1 | 24831 | 3563 | 14 | 14326 | 30367 | ||
| C3- Operator 2 | 25831 | 4285 | 17 | 14406 | 31649 | |||
| C4- Operator 3 | 21655 | 4326 | 20 | 10566 | 30156 | |||
| All Instruments/Operators | 24106 | 4407 | 14 | 10566 | 31649 | |||
| Clostridium difficile(toxinotype III;Nap1)Zeptometrix0801619cf | tcdB | ModeratePositive3xLoD$1.25 x 10^3$CFU/mL | C2- Operator 1 | 27589 | 2276 | 8 | 22487 | 31505 |
| C3- Operator 2 | 22672 | 3726 | 16 | 17112 | 32047 | |||
| C4- Operator 3 | 22780 | 2838 | 11 | 16926 | 27598 | |||
| All Instruments/Operators | 24347 | 3762 | 15 | 16926 | 32047 | |||
| Low Positive1.5xLoD$6.23 x 10^2$CFU/mL | C2- Operator 1 | 25007 | 1761 | 7 | 20436 | 27552 | ||
| C3- Operator 2 | 20116 | 3513 | 17 | 13752 | 27461 | |||
| C4- Operator 3 | 20902 | 2561 | 11 | 15608 | 27662 | |||
| All Instruments/Operators | 22008 | 3438 | 16 | 13752 | 27662 | |||
| Enteroaggregati ve E. coli092:H33 (EAEC)STEC TW04440 | EAEC | ModeratePositive3xLoD$2.10 x 10^3$CFU/mL | C2- Operator 1 | 30474 | 1672 | 5 | 25616 | 33694 |
| C3- Operator 2 | 28424 | 3220 | 14 | 20108 | 34967 | |||
| C4- Operator 3 | 25129 | 2198 | 9 | 18787 | 28489 | |||
| All Instruments/Operators | 28009 | 3281 | 12 | 18787 | 34967 | |||
| Low Positive1.5xLoD$1.05 x 10^3$CFU/mL | C2- Operator 1 | 29161 | 1492 | 5 | 26343 | 31716 | ||
| C3- Operator 2 | 25402 | 3630 | 14 | 18723 | 32890 | |||
| C4- Operator 3 | 22836 | 2538 | 11 | 15300 | 27002 | |||
| All Instruments/Operators | 25800 | 3734 | 15 | 15300 | 32890 | |||
| Enterotoxigenic E. coli 078:H11H10407 (ETEC)ATCC 35401 | ST-1a | ModeratePositive3xLoD$8.40 x 10^2$CFU/mL | C2- Operator 1 | 35769 | 1009 | 3 | 33677 | 38306 |
| C3- Operator 2 | 34358 | 4831 | 14 | 25398 | 42656 | |||
| C4- Operator 3 | 28730 | 3638 | 13 | 22254 | 35493 | |||
| All Instruments/Operators | 32952 | 4648 | 14 | 22254 | 42656 | |||
| Low Positive1.5xLoD$4.20 x 10^2$CFU/mL | C2- Operator 1 | 32795 | 2240 | 7 | 28536 | 36716 | ||
| C3- Operator 2 | 30726 | 3040 | 10 | 24219 | 35644 | |||
| C4- Operator 3 | 24907 | 2765 | 11 | 20236 | 30170 | |||
| All Instruments/Operators | 29476 | 4291 | 15 | 20236 | 36716 | |||
| Salm | C2- Operator 1 | 15291 | 1496 | 10 | 12588 | 18918 | ||
| Organism | TargetProbe | Test Level | Instrument/Operator | Mean | StDev | %CV | Min | Max |
| Salmonellaenterica ssp.entericaATCC 14028 | ModeratePositive3xLoD3.30 x 103CFU/mL | C3- Operator 2 | 13931 | 2645 | 19 | 6284 | 18489 | |
| C4- Operator 3 | 15701 | 1456 | 9 | 13306 | 19184 | |||
| All Instruments/Operators | 14974 | 2068 | 14 | 6284 | 19184 | |||
| Low Positive1.5xLoD1.65 x 103CFU/mL | C2- Operator 1 | 17247 | 1108 | 6 | 15153 | 19682 | ||
| C3- Operator 2 | 14880 | 1682 | 11 | 10847 | 19127 | |||
| C4- Operator 3 | 16234 | 1455 | 7 | 13301 | 19674 | |||
| All Instruments/Operators | 16120 | 1721 | 10 | 10847 | 19682 | |||
| Shiga-like toxinproducing E. coli(STEC)ATCC BAA-2217 | stx2 | ModeratePositive3xLoD3.75 x 103CFU/mL | C2- Operator 1 | 27217 | 1112 | 4 | 23606 | 30023 |
| C3- Operator 2 | 31888 | 1316 | 4 | 29183 | 34448 | |||
| C4- Operator 3 | 26310 | 1515 | 6 | 22970 | 30028 | |||
| All Instruments/Operators | 28472 | 2785 | 10 | 22970 | 34448 | |||
| Low Positive1.5xLoD1.88 x103CFU/mL | C2- Operator 1 | 27467 | 1547 | 6 | 23914 | 30339 | ||
| C3- Operator 2 | 31460 | 1501 | 5 | 28002 | 34121 | |||
| C4- Operator 3 | 25293 | 2097 | 8 | 20340 | 29403 | |||
| All Instruments/Operators | 28073 | 3089 | 11 | 20340 | 34121 | |||
| Shigella sonneiATCC 29930 | Shig | ModeratePositive3xLoD6.60 x 102CFU/mL | C2- Operator 1 | 17531 | 1173 | 7 | 15327 | 19469 |
| C3- Operator 2 | 15369 | 3781 | 25 | 7573 | 21561 | |||
| C4- Operator 3 | 16454 | 2056 | 13 | 11910 | 21114 | |||
| All Instruments/Operators | 16451 | 2697 | 16 | 7573 | 21561 | |||
| Low Positive1.5xLoD3.30 x 102CFU/mL | C2- Operator 1 | 13919 | 1862 | 13 | 9233 | 17022 | ||
| C3- Operator 2 | 12242 | 2503 | 20 | 6435 | 16434 | |||
| C4- Operator 3 | 12832 | 2184 | 17 | 8352 | 17489 | |||
| All Instruments/Operators | 12998 | 2283 | 18 | 6435 | 17489 | |||
| Vibrioparahaemolyticus ATCC 17802 | V.para | ModeratePositive3xLoD1.95 x101CFU/mL | C2- Operator 1 | 23605 | 2305 | 10 | 17750 | 29798 |
| C3- Operator 2 | 21458 | 3112 | 15 | 13138 | 27526 | |||
| C4- Operator 3 | 17486 | 2821 | 16 | 8543 | 22789 | |||
| All Instruments/Operators | 20850 | 3739 | 18 | 8543 | 29798 | |||
| Low Positive1.5xLoD9.75x100CFU/mL | C2- Operator 1 | 22628 | 2402 | 11 | 17145 | 26762 | ||
| C3- Operator 2 | 18000 | 6067 | 34 | 6043 | 27526 | |||
| C4- Operator 3 | 16263 | 3060 | 19 | 6989 | 23597 | |||
| All Instruments/Operators | 18964 | 4922 | 26 | 6043 | 27526 | |||
| YersiniaenterocoliticaATCC 23715 | Y.ent | ModeratePositive3xLoD2.25 x103CFU/mL | C2- Operator 1 | 14365 | 1847 | 13 | 10209 | 17892 |
| C3- Operator 2 | 15303 | 1786 | 12 | 10813 | 17893 | |||
| C4- Operator 3 | 14256 | 2325 | 16 | 9523 | 19982 | |||
| All Instruments/Operators | 14641 | 2033 | 14 | 9523 | 19982 | |||
| Low Positive1.5xLoD1.13 x103CFU/mL | C2- Operator 1 | 14741 | 1694 | 11 | 11853 | 19628 | ||
| C3- Operator 2 | 15592 | 2014 | 13 | 12978 | 20765 | |||
| C4- Operator 3 | 14732 | 2253 | 16 | 10750 | 19994 | |||
| All Instruments/Operators | 15022 | 2019 | 13 | 10750 | 20765 | |||
| Organism | TargetProbe | Test Level | Instrument/Operator | Mean | StDev | %CV | Min | Max |
| Cryptosporidium parvumwaterborneP102 | Crypto | ModeratePositive3xLoD$9.30 x 10^3$oocysts/mL | C2- Operator 1 | 18731 | 4323 | 23 | 9904 | 28443 |
| C3- Operator 2 | 20843 | 3978 | 19 | 11526 | 28678 | |||
| C4- Operator 3* | 14867 | 4457 | 31 | 5669 | 26611 | |||
| All Instruments/Operators | 18222 | 4873 | 26 | 5669 | 28678 | |||
| Low Positive1.5xLoD$4.65 x 10^3$oocysts/mL | C2- Operator 1 | 13816 | 5170 | 37 | 2572 | 24148 | ||
| C3- Operator 2 | 15402 | 3996 | 26 | 8166 | 22933 | |||
| C4- Operator 3* | 10785 | 3409 | 33 | 4413 | 18053 | |||
| All Instruments/Operators | 13363 | 4631 | 35 | 2572 | 24148 | |||
| Giardiaintestinalis (akaG. lamblia)waterborneP101 | G.lam | ModeratePositive3xLoD$2.70 x 10^3$cysts/mL | C2- Operator 1 | 14327 | 4487 | 31 | 7696 | 30050 |
| C3- Operator 2 | 21743 | 5006 | 23 | 8932 | 31538 | |||
| C4- Operator 3 | 16963 | 3780 | 22 | 11527 | 25036 | |||
| All Instrument/Operators | 17677 | 5377 | 30 | 7696 | 31538 | |||
| Low Positive1.5xLoD$1.35 x 10^3$cysts/mL | C2- Operator 1 | 17340 | 3668 | 21 | 11338 | 25626 | ||
| C3- Operator 2 | 24751 | 4701 | 19 | 12478 | 31282 | |||
| C4- Operator 3 | 19821 | 3772 | 20 | 12677 | 25949 | |||
| All Instruments/Operators | 20637 | 5081 | 25 | 11338 | 31282 | |||
| RotavirusATCC VR-2018 | Rota | ModeratePositive3xLoD$3.75 x 10^3$TCID50/mL | C2- Operator 1 | 39523 | 2086 | 5 | 35835 | 44023 |
| C3- Operator 2 | 39162 | 3400 | 9 | 28863 | 44274 | |||
| C4- Operator 3 | 32899 | 2956 | 8 | 25107 | 38361 | |||
| All Instruments/Operators | 37195 | 4170 | 13 | 25107 | 44274 | |||
| Low Positive1.5xLoD$1.88 x 10^2$TCID50/mL | C2- Operator 1 | 36515 | 5114 | 14 | 16127 | 40941 | ||
| C3- Operator 2 | 36312 | 3863 | 11 | 26491 | 41547 | |||
| C4- Operator 3 | 31925 | 3280 | 10 | 21114 | 36158 | |||
| All Instruments/Operators | 34917 | 4628 | 11 | 16127 | 41547 |
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*The one replicate with 'Not detected' result was not included in the calculations.
SINGLE VS. MULTI-SPIKE
To demonstrate that the LoD is equivalent when spiking with single versus multiple organisms, LoD for representative organisms (S. enterica, C. difficile, G. lamblia, and Rotavirus) were performed as single targets and with all representative organisms combined, using both extraction systems. The results of spiking single versus multiple organisms showed equivalent LoD (see Table below). LoD for the remaining organisms were performed in pairs, except for norovirus which was tested from positive clinical specimens.
Single and multi-spiked samples both achieved ≥95% detection of 20 replicates (≥19 out of 20) at same concentrations for the challenge organisms (concentrations indicated in the tables below).
Table. Comparison of results for limit of detection testing with single or multiple spiked samples for easyMAG extractions assayed with BioCode GPP.
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| Strain | SingleSpike/MultipleSpike | Source | TargetProbe | UnpreservedStool LoD | Unpreserved StoolDetection | Cary-Blair StoolLoD | Cary-BlairStoolDetection |
|---|---|---|---|---|---|---|---|
| Clostridiumdifficile(toxinotype 0) | SingleSpike | ATCC 9689 | tcdB | $9.50 x 10^1$CFU/mL | 20/20 | $9.50 x 10^1$CFU/mL | 20/20 |
| MultiSpike | 20/20 | 19/20 | |||||
| Salmonellaenterica ssp.enterica | SingleSpike | ATCC 14028 | Salm | $1.10 x 10^3$CFU/mL | 20/20 | $1.10 x 10^3$CFU/mL | 20/20 |
| MultiSpike | 20/20 | 20/20 | |||||
| Giardiaintestinalis(aka G. lamblia) | SingleSpike | waterborneP101 | G.lam | $9.00 x 10^2$cysts/mL | 20/20 | $9.00 x 10^2$cysts/mL | 20/20 |
| MultiSpike | 20/20 | 20/20 | |||||
| Rotavirus A | SingleSpike | ATCC VR-2018 | Rota | $2.50 x 10^3$TCID50/mL | 20/20 | $1.25 x 10^3$TCID50/mL | 20/20 |
| MultiSpike | 20/20 | 20/20 |
Table. Comparison of results for limit of detection testing with single or multiple spiked samples for MP96 extractions assayed with BioCode GPP.
| Strain | SingleSpike/MultipleSpike | Source | TargetProbe | UnpreservedStool LoD | Unpreserved StoolDetection | Cary-Blair StoolLoD | Cary-BlairStoolDetection |
|---|---|---|---|---|---|---|---|
| Clostridiumdifficile(toxinotype 0 ) | SingleSpikeMultiSpike | ATCC 9689 | tcdB | $9.50 x 10^1$CFU/mL | 20/2020/20 | $9.50 x 10^1$CFU/mL | 20/2020/20 |
| Salmonellaenterica ssp.enterica | SingleSpikeMultiSpike | ATCC 14028 | Salm | $1.10 x 10^3$CFU/mL | 20/2020/20 | $1.10 x 10^3$CFU/mL | 20/2020/20 |
| Giardiaintestinalis(aka G. lamblia) | SingleSpikeMultiSpike | waterborneP101 | G.lam | $9.00 x 10^2$cysts/mL | 20/2020/20 | $9.00 x 10^2$cysts/mL | 20/2020/20 |
| Rotavirus A | SingleSpikeMultiSpike | ATCC VR-2018 | Rota | $1.25 x 10^3$TCID50/mL | 20/2020/20 | $1.25 x 10^3$TCID50/mL | 20/2020/20 |
LIMIT OF DETECTION (LoD)
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A study was performed to assess the performance of the BioCode GPP on the BioCode MDx 3000 at the Limit of Detection (LoD) for both unpreserved Stool and Cary-Blair specimens. In this study the Gl Panel was tested with quantified bacteria, virus or parasite stocks (except norovirus which used clinical samples). For initial screening, four replicates of each concentration (near LoD for the predicate) in negative stool and Cary-Blair were extracted on the easyMAG and MagNA Pure 96 Systems and tested in singlet with the BioCode GPP on the BioCode MDx 3000 system. The LoD was confirmed by extracting 20 replicates of each sample type/extraction method and testing each in singlet for a total of 20 replicates at or near presumptive LoD. LoD for each stock was defined as the lowest concentration with ≥95% detection of 20 replicates (19 out of 20), and was determined separately unpreserved stool and Cary-Blair preserved stool. The LoDs determined from the quantitated stocks or clinical samples are presented below and in the labeling. The LoDs were the same or within 2-fold for each extraction system.
| EasyMag | MagNA Pure 96 | ||||
|---|---|---|---|---|---|
| Strain | Source | Unpreserved StoolLoD | Detection | Unpreserved StoolLoD | Detection |
| Campylobacter coli | ATCC 33559 | 2.81 x 101 CFU/mL | 19/20 | 2.81 x 101 CFU/mL | 20/20 |
| Campylobacter jejunispp. jejuni | ATCC 33292 | 3.50 x 102 CFU/mL | 19/20 | 3.50 x 102 CFU/mL | 19/20 |
| Clostridium difficile(toxinotype 0 ) | ATCC 9689 | 9.50 x 101 CFU/mL | 20/20 | 9.50 x 101 CFU/mL | 20/20 |
| Clostridium difficile(toxinotype III; Nap1) | Zeptometrix0801619cf | 4.15 x 102 CFU/mL | 20/20 | 4.15 x 102 CFU/mL | 20/20 |
| Enteroaggregative E.coli 092:H33 (EAEC) | STEC TW04440 | 7.00 x 102 CFU/mL | 20/20 | 7.00 x 102 CFU/mL | 20/20 |
| Enteroinvasive E. coli029:NM (EIEC) | ATCC 43892 | 3.60 x 102 CFU/mL | 20/20 | 1.80 x 102 CFU/mL | 20/20 |
| Enterotoxigenic E. coli078:H11 H10407(ETEC) | ATCC 35401 | 2.80 x 102 CFU/mL | 20/20 | 2.80 x 102 CFU/mL | 20/20 |
| Salmonella bongori | SGSC 4900 | 1.40 x 103 CFU/mL | 20/20 | 1.40 x 103 CFU/mL | 20/20 |
| Salmonella entericassp. enterica | ATCC 14028 | 1.10 x 103 CFU/mL | 20/20 | 1.10 x 103 CFU/mL | 20/20 |
| Shiga-like toxinproducing E. coli (STEC) | ATCC BAA-2217 | 1.25 x 103 CFU/mL | 20/20 | 1.25 x 103 CFU/mL | 20/20 |
| E. coli 0157 | ATCC 700376 | 1.65 x 103 CFU/mL | 20/20 | 1.65 x 103 CFU/mL | 20/20 |
| Shigella sonnei | ATCC 29930 | 2.20 x 102 CFU/mL | 20/20 | 2.20 x 102 CFU/mL | 20/20 |
| Vibrio cholerae | ATCC 25870 | 2.45 x 102 CFU/mL | 20/20 | 2.45 x 102 CFU/mL | 20/20 |
| Vibrioparahaemolyticus | ATCC 17802 | 6.50 x 100 CFU/mL | 20/20 | 6.50 x 100 CFU/mL | 20/20 |
Table. Comparison of results for limit of detection testing for Unpreserved Stool extracted with the easyMAG or MP96 and assayed with BioCode GPP.
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| EasyMag | MagNA Pure 96 | ||||
|---|---|---|---|---|---|
| Strain | Source | Unpreserved StoolLoD | Detection | Unpreserved StoolLoD | Detection |
| Yersinia enterocolitica | ATCC 23715 | $7.50 x 10^2$ CFU/mL | 20/20 | $7.50 x10^2$ CFU/mL | 20/20 |
| Cryptosporidiumparvum | waterborneP102C | $3.10 x 10^3$ oocysts/mL | 20/20 | $3.10 x10^3$ oocysts/mL | 20/20 |
| Entamoeba histolyticaHB-301:NIH | BEI NR-178 | $1.55 x 10^{-1}$ cysts/mL | 20/20 | $1.55 x10^{-1}$ cysts/mL | 20/20 |
| Giardia intestinalis (akaG. lamblia) | waterborneP101 | $9.00 x 10^2$ cysts/mL | 20/20 | $9.00 x10^2$ cysts/mL | 20/20 |
| Adenovirus 40 (dugan) | Zeptometrix0810084 | $2.00 x 10^{-1}$ TCID50/mL | 20/20 | $1.00 x10^{-1}$ TCID50/mL | 20/20 |
| Adenovirus 41 (TAK) | Zeptometrix0810085 | $9.4 x 10^{-2}$ TCID50/mL | 20/20 | $4.70 x10^{-2}$ TCID50/mL | 20/20 |
| Rotavirus A | ATCC VR-2018 | $2.5 x 10^3$ TCID50/mL | 20/20 | $1.25 x10^3$ TCID50/mL | 20/20 |
Table. Comparison of results for limit of detection testing for Cary-Blair Stool extracted with the easyMAG or MP96 and assayed with BioCode GPP.
| Strain | Source | Cary-Blair Stool LoD | Detection | Cary-Blair Stool LoD | Detection |
|---|---|---|---|---|---|
| Campylobacter coli | ATCC 33559 | $5.61 x 10^1$ CFU/mL | 20/20 | $2.81 x 10^1$ CFU/mL | 20/20 |
| Campylobacter jejunispp. jejuni | ATCC 33292 | $3.50 x10^2$ CFU/mL | 20/20 | $7.00 x10^2$ CFU/mL | 20/20 |
| Clostridium difficile(toxinotype 0 ) | ATCC 9689 | $9.50 x 10^1$ CFU/mL | 20/20 | $9.50 x 10^1$ CFU/mL | 20/20 |
| Clostridium difficile(toxinotype III; Nap1) | Zeptometrix0801619cf | $4.15 x10^2$ CFU/mL | 20/20 | $4.15 x10^2$ CFU/mL | 20/20 |
| Enteroaggregative E.coli 092:H33 (EAEC) | STEC TW04440 | $7.00 x10^2$ CFU/mL | 20/20 | $7.00 x10^2$ CFU/mL | 20/20 |
| Enteroinvasive E. coli029:NM (EIEC) | ATCC 43892 | $3.60 x10^2$ CFU/mL | 20/20 | $1.80 x10^2$ CFU/mL | 20/20 |
| Enterotoxigenic E. coli078:H11 H10407(ETEC) | ATCC 35401 | $2.80 x10^2$ CFU/mL | 20/20 | $2.80 x10^2$ CFU/mL | 19/20 |
| Salmonella bongori | SGSC 4900 | $1.40 x10^3$ CFU/mL | 19/20 | $1.40 x10^3$ CFU/mL | 20/20 |
| Salmonella entericassp. enterica | ATCC 14028 | $1.10 x10^3$ CFU/mL | 20/20 | $1.10 x10^3$ CFU/mL | 20/20 |
| Shiga-like toxinproducing E. coli (STEC) | ATCC BAA-2217 | $1.25 x10^3$ CFU/mL | 20/20 | $1.25 x10^3$ CFU/mL | 20/20 |
| E. coli 0157 | ATCC 700376 | $3.30 x10^3$ CFU/mL | 20/20 | $1.65 x10^3$ CFU/mL | 20/20 |
{29}------------------------------------------------
| Premarket Notification 510(k) | ||
|---|---|---|
| -- | ------------------------------- | -- |
| EasyMag | MagNA Pure 96 | ||||
|---|---|---|---|---|---|
| Strain | Source | Cary-Blair Stool LoD | Detection | Cary-Blair Stool LoD | Detection |
| Shigella sonnei | ATCC 29930 | 2.20 x102 CFU/mL | 20/20 | 2.20 x102 CFU/mL | 20/20 |
| Vibrio cholerae | ATCC 25870 | 2.45 x102 CFU/mL | 20/20 | 2.45 x102 CFU/mL | 20/20 |
| Vibrioparahaemolyticus | ATCC 17802 | 6.50 x100 CFU/mL | 20/20 | 6.50 x100 CFU/mL | 20/20 |
| Yersinia enterocolitica | ATCC 23715 | 7.50 x102 CFU/mL | 20/20 | 7.50 x102 CFU/mL | 20/20 |
| Cryptosporidiumparvum | waterborneP102C | 3.10 x103 oocysts/mL | 20/20 | 3.10 x103 oocysts/mL | 20/20 |
| Entamoeba histolyticaHB-301:NIH | BEI NR-178 | 1.55 x10-1 cysts/mL | 20/20 | 1.55 x10-1 cysts/mL | 20/20 |
| Giardia intestinalis (akaG. lamblia) | waterborneP101 | 9.00 x102 cysts/mL | 20/20 | 9.00 x102 cysts/mL | 20/20 |
| Adenovirus 40 (dugan) | Zeptometrix0810084 | 2.00 x10-1 TCID50/mL | 20/20 | 1.00 x10-1 TCID50/mL | 20/20 |
| Adenovirus 41 (TAK) | Zeptometrix0810085 | 4.70 x10-2 TCID50/mL | 20/20 | 4.70 x10-2 TCID50/mL | 20/20 |
| Rotavirus A | ATCC VR-2018 | 1.25 x103 TCID50/mL | 20/20 | 1.25 x103 TCID50/mL | 20/20 |
For Norovirus GI and GII targets, positive clinical specimens were used, and serial dilutions (initial 10-fold dilution series followed by finer dilutions) were performed. Four replicates of each dilution in negative unpreserved stool and Cary-Blair stool were extracted with the easyMAG and MagNA Pure 96 Systems and tested with the BioCode GPP on the BioCode MDx 3000 system. The LoD was confirmed by extracting 20 replicates of each sample type with each extraction method and testing at or near presumptive LoD. For unpreserved stool, LoD with the easyMag extraction was 2-fold and 8.3-fold lower than the MagNA Pure 96 extraction for Norovirus GI and Norovirus GII, respectively. For Cary-Blair stool, LoD with the easyMag extraction was less than 2-fold lower than the MagNA Pure 96 extraction for both Norovirus Gl and GII.
Table. Norovirus - Comparison of results for limit of detection testing for Unpreserved Stool extracted with the easyMAG or MP96 and assayed with BioCode GPP.
| Target | Source | TargetProbe | EasyMag | MagNA Pure 96 | ||
|---|---|---|---|---|---|---|
| UnpreservedStool Dilution | Detection | UnpreservedStool Dilution | Detection | |||
| Norovirus GI | Clinical Sample ID#60 | NoVG1 | 1:10,000 | 20/20 | 1:5,000 | 19/20 |
| Norovirus GII | Clinical Sample ID#54 | NoVG2 | 1:250,000 | 20/20 | 1:30,000 | 20/20 |
Table. Norovirus - Comparison of results for limit of detection testing for Cary-Blair Stool extracted with the easyMAG or MP96 and assayed with BioCode GPP.
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| Target | Source | TargetProbe | EasyMag | MagNA Pure 96 | ||
|---|---|---|---|---|---|---|
| Cary-BlairStool Dilution | Detection | Cary-BlairStool Dilution | Detection | |||
| Norovirus GI | Clinical Sample ID#60 | NoVG1 | 1:50,000 | 20/20 | 1:80,000 | 19/20 |
| Norovirus GII | Clinical Sample ID#54 | NoVG2 | 1:100,000 | 20/20 | 1:80,000 | 20/20 |
Conclusion:
The intended use and fundamental scientific technology of the BioCode GPP using the MagNA Pure 96 is substantially equivalent to the predicate device. Clinical and non-clinical studies have established that the BioCode GPP with the MagNA Pure 96 is substantially equivalent to the predicate device.
§ 866.3990 Gastrointestinal microorganism multiplex nucleic acid-based assay.
(a)
Identification. A gastrointestinal microorganism multiplex nucleic acid-based assay is a qualitativein vitro diagnostic device intended to simultaneously detect and identify multiple gastrointestinal microbial nucleic acids extracted from human stool specimens. The device detects specific nucleic acid sequences for organism identification as well as for determining the presence of toxin genes. The detection and identification of a specific gastrointestinal microbial nucleic acid from individuals exhibiting signs and symptoms of gastrointestinal infection aids in the diagnosis of gastrointestinal infection when used in conjunction with clinical evaluation and other laboratory findings. A gastrointestinal microorganism multiplex nucleic acid-based assay also aids in the detection and identification of acute gastroenteritis in the context of outbreaks.(b)
Classification. Class II (special controls). The special controls are set forth in FDA's guideline document entitled: “Class II Special Controls Guideline: Gastrointestinal Microorganism Multiplex Nucleic Acid-Based Assays for Detection and Identification of Microorganisms and Toxin Genes from Human Stool Specimens.” For availability of the guideline document, see § 866.1(e).