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The BioCode Gastrointestinal Pathogen Panel (GPP) is a qualitative multiplexed in vitro diagnostic test intended for use with the BioCode MDx 3000 Instrument. The BioCode GPP is capable of the simultaneous detection of nucleic acids from multiple bacteria, viruses, and parasites extracted directly from unpreserved in Cary-Blair transport medium obtained from individuals with simptoms 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)
• 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. For In Vitro Diagnostic Use Only. For Prescription Use Only.

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 gastroenteriis 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 Adenovinus 40/41, Campylobacter, E. coli 0157, Shigella(EIEC, Yersinia enterocolitica, and Giardia lamblia were established additionally with retrospective clinical specimens. Performance characteristica, Giardia lamblia, Yersinia enterocolitica and Vibrio (V. parahaemolyticus, 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 easyMAG, MagNA Pure 96, KingFisher Flex and KingFisher Apex Dx. 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.

The provided text describes the BioCode Gastrointestinal Pathogen Panel (GPP), a diagnostic test for gastrointestinal pathogens, and a study to demonstrate its substantial equivalence to a predicate device.

Here's an analysis of the acceptance criteria and study data:

1. Acceptance Criteria and Reported Device Performance

The acceptance criteria for each pathogen are implied by the reported Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) compared to the easyMAG extraction method (used with the predicate device) for each extraction system (KingFisher Flex and KingFisher Apex Dx). While explicit pre-defined acceptance criteria values are not stated, the tables present the achieved performance with 95% Confidence Intervals. Generally, a high PPA and NPA (typically >90-95%) with narrow confidence intervals are expected for substantial equivalence for diagnostic tests.

Here's a summary of the reported performance for the BioCode GPP using KingFisher Flex and KingFisher Apex Dx, focusing on the "All Archived" data as it covers a larger sample size for each target. Targets with PPA

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The BioCode Respiratory Pathogen Panel (RPP) is a qualitative multiplexed nucleic acid-based in vitro diagnostic test intended for use with BioCode MDx 3000 Instrument. The BioCode of the simultaneous detection and identification of nucleic acids from multiple viruses and bacteria extracted from nasopharyngeal swab (NPS) samples obtained from individuals with signs and/or symptoms of respiratory tract infection. The following pathogens and subtypes are identified using the BioCode RPP:

• Adenovirus
• · Coronavirus (229E, OC43, HKU1, and NL63)
• Human Metapneumovirus A/B
• · Influenza A, including subtypes H1, H1 2009 Pandemic, and H3
• Influenza B
• Parainfluenza Virus 1
• Parainfluenza Virus 2
• · Parainfluenza Virus 3
• · Parainfluenza Virus 4
• · Respiratory Syncytial Virus A/B
• Rhinovirus/Enterovirus
• · Bordetella pertussis
• Chlamydia pneumoniae
• Mycoplasma pneumoniae

The detection and identification of specific viral and bacterial nucleic acids from individuals exhibiting signs and/or symptoms of a respiratory infection aids in the diagnosis of respiratory infection if used in conjunction with other clinical and epidemiological information. The results of this test should not be used as the sole basis for diagnosis, treatment, or other patient management decisions.

Negative results in the setting of a respiratory illness may be due to infection with pathogens that are not detected by this test, or lower respiratory tract infection that may not be detected by a nasopharyngeal swab specimen. Positive results do not rule out co-infection with other organisms: the agent(s) detected by the BioCode RPP may not be the definite cause of disease. Additional laboratory testing (e.g. bacterial and viral culture, immunofluorescence, and radiography) may be necessary when evaluating a patient with possible respiratory tract infection.

Due to the genetic similarity between Human Rhinovirus, the BioCode RPP cannot differentiate them. A positive BioCode RPP Rhinovirus/Enterovirus result should be followed up using an alternate method (e.g., cell culture or sequence analysis) if differentiation is required. The BioCode RPP detects Human Rhinovirus with reduced sensitivity. If a more accurate Rhinovirus result is required, it is recommended that specimens found to be negative for Human Rhinovirus/Enterovirus after examination using BioCode RPP be confirmed by an alternate method (e.g. FDA cleared molecular tests).

Performance characteristics for Influenza A were established when Influenza A H1 2009 Pandemic and A H3 were the predominant Influenza A viruses in circulation. Performance of detecting Influenza A may vary if other Influenza A strains are circulating or a novel Influenza A virus emerges.

The BioCode® Respiratory Pathogen Panel is a respiratory pathogen multiplex nucleic acid test designed for use 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 viral and bacterial pathogens from a single nasopharyngeal swab specimen collected in transport media. Specimens are processed and nucleic acids extracted with the NucliSens easyMAG or Roche MagNA Pure 96 automated systems. Once the PCR plate is set up and sealed, all other operations are automated on MDx-3000. The BioCode® RPP simultaneously tests for 17 pathogens and/or subtypes (see table below) from nasopharyngeal swab specimens collected in UTM or VTM. Results from the BioCode RPP test are available within about 5 hours, including off-board nucleic acids extraction.

Here's a breakdown of the acceptance criteria and the study that proves the device meets them, based on the provided text.

Based on the provided text, the device is an in vitro diagnostic test (BioCode Respiratory Pathogen Panel - RPP). The primary evidence for meeting acceptance criteria comes from clinical performance studies and analytical performance studies. The document does not explicitly state pre-defined acceptance criteria values (e.g., "Positive Agreement must be > X%"), but rather presents the results achieved and implicitly confirms they meet regulatory expectations for substantial equivalence.

Acceptance Criteria and Reported Device Performance

Since explicit numerical acceptance criteria were not stated, I'll present the reported performance, which implicitly met the necessary thresholds for FDA clearance. The document focuses on Positive Percent Agreement (PA) and Negative Percent Agreement (NA) compared to an FDA-cleared molecular multiplexed respiratory pathogen panel (the "comparator test").

Table of Acceptance Criteria (Implicit) and Reported Device Performance (Clinical Study - Total Specimens)

Study Details:

1. Sample Size and Data Provenance:

   • Clinical Test Set (Prospective Study):
     • Sample Size: 2649 residual nasopharyngeal swab (NPS) specimens in VTM or UTM.
     • Data Provenance: Prospectively collected from patients suspected of respiratory tract infections at five geographically diverse clinical sites in the U.S. (August 2017 to May 2019). Specimens were either tested freshly (stored 2-8°C for no more than 7 days) or stored frozen and thawed later.
   • Clinical Test Set (Archived Specimens - Retrospective Study):
     • Sample Size: 165 clinical specimens (archived NPS in VTM or UTM).
     • Data Provenance: Retrospective, preselected archives from source laboratories, chosen because they had previously tested positive for low-prevalence pathogens or were negative. These specimens were then randomized and blinded.
   • Contrived Specimens (Analytical Performance):
     • Chlamydia pneumoniae & Influenza A H1: 50 unique negative natural NPS in VTM or UTM specimens were spiked to create 100 positive samples (2X LOD or greater) and interspersed with negative samples. A total of 110 samples were tested.
     • Reproducibility Study: 6 contrived positive samples and 1 negative sample, each extracted in triplicate, each assayed in singlet. This translates to 90 samples per concentration level per extraction type (easyMAG, MagNA Pure 96) across multiple sites/runs, total 90 (3x LoD) + 90 (1.5x LoD) + 450 (no analyte) = 630 for each virus/bacteria category listed (e.g., Adenovirus, Coronavirus, Human Metapneumovirus).
     • Limit of Detection (LoD): 20 replicates for each target at or near the presumptive LoD.
     • Analytical Reactivity/Inclusivity: Triplicate extractions for each strain/serotype.
     • Analytical Specificity/Cross Reactivity: Triplicate extractions for each off-panel and on-panel organism.
     • Interfering Substances/Microbes: Triplicate extractions for each sample/substance combination.
     • Competitive Inhibition: Triplicate extractions for each pooled sample.
     • Specimen Stability: Triplicate extractions for each time point and storage condition.
     • Matrix Equivalency: Quadruplicate extractions for each pool/matrix combination.

2. Number of Experts and Qualifications for Ground Truth:

   • The document states that the BioCode RPP test results were compared against those from an "FDA-cleared molecular multiplexed respiratory pathogen panel" (Standard of Care/Comparator Test). This FDA-cleared comparator test serves as the primary "ground truth" for the clinical studies.
   • For discrepant results in the clinical studies, further investigation was conducted by "performing independent molecular tests, including analytically validated PCR followed by bi-directional sequencing assays and alternate NAATs." This implies the use of specialized laboratory personnel with expertise in molecular diagnostics, but the exact number or specific qualifications (e.g., "radiologist with 10 years of experience") are not specified as this is a molecular diagnostic device, not an imaging device typically read by radiologists. The ground truth for presence/absence of pathogens is established by these comparator and confirmatory molecular tests.

3. Adjudication Method for the Test Set:

   • For the clinical studies (prospective and archived), the method for addressing discrepancies between the BioCode RPP and the comparator test was to perform "independent molecular tests, including analytically validated PCR followed by bi-directional sequencing assays and alternate NAATs." This serves as an adjudication method, where an orthogonal, high-accuracy method is used to determine the true positivity or negativity of discrepant samples. The specific "2+1" or "3+1" concensus type is not explicitly mentioned, but the retesting with confirmatory methods acts as a form of adjudication.

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

   • No, an MRMC study was not done. This type of study (comparative effectiveness with human readers) is typical for AI-powered imaging devices where human interpretation is a key component. The BioCode RPP is an in vitro diagnostic (IVD) molecular test where the output is directly from the instrument analysis, not reliant on human interpretation of complex images. The study focuses on comparing the device's accuracy against a legally marketed predicate device/standard of care, not on improving human reader performance.

5. Standalone Performance (Algorithm Only):

   • Yes, the primary performance evaluation is standalone. The device ("BioCode RPP") is a qualitative multiplexed nucleic acid-based in vitro diagnostic test for use with the "BioCode MDx-3000 Instrument." The instrument integrates PCR, target capture, signal generation, and optical detection. The results are generated by the system (the "algorithm" in this context refers to the instrument's processing logic and interpretation algorithm), and the performance metrics (PA, NA) are reported for this system. There is no human interpretation component in the direct testing process that could be "assisted" by the algorithm.

6. Type of Ground Truth Used:

   • The ground truth for the clinical test sets (prospective and archived) was established by an FDA-cleared molecular multiplexed respiratory pathogen panel (Standard of Care).
   • For discrepant results, expert molecular laboratory retesting using analytically validated PCR followed by bi-directional sequencing assays and alternate NAATs served as the confirmatory ground truth. This is a form of expert consensus/confirmatory testing using highly accurate molecular methods.
   • For the analytical studies (e.g., LoD, inclusivity, specificity, inhibition), the ground truth was based on known concentrations of purified organisms/nucleic acids or genetically characterized strains (e.g., ATCC strains, Zeptometrix controls). This is a form of analytical ground truth where the content is precisely controlled and known.

7. Sample Size for the Training Set:

   • The document does not specify a separate "training set" sample size. For IVD devices, especially those based on molecular assays, a distinct "training set" as understood in machine learning (where an algorithm learns from labeled data) is not typically described in the same way. The device's underlying "algorithm" is the biochemical and optical detection system itself, and its performance characteristics are established through extensive analytical and clinical validation, not by training on a large dataset of patient samples in the AI sense. The design and validation are based on principles of molecular biology and traditional assay development.

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

   • As there isn't a "training set" in the machine learning sense, this question isn't directly applicable for this type of IVD device. The development of the assay (e.g., primer and probe design) would rely on known genetic sequences of the target pathogens. The validation data (clinical and analytical studies) demonstrate that the final, developed assay meets its intended performance, rather than being used to train a model in an iterative machine learning manner.

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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):

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.

• 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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The BioCode Gastrointestinal Pathogen Panel (GPP) is a qualitative, gastrointestinal microorganism multiplexed nucleic acid-based assay capable of detecting of nucleic acids from the following organisms in unpreserved stool and Cary-Blair media:

• Adenovirus 40/41 ●
• Campylobacter (C. jejuni, C. coli) ●
• Clostridium difficile (C. difficile) toxin A/B (from fresh specimens only) ●
• Cryptosporidium (C. parvum, C. hominis) 0
• Entamoeba histolytica ●
• Escherichia coli (E. coli) 0157 ●
• Enterotoxigenic E. coli (ETEC) LT/ST ●
• Enteroaggregative E. coli (EAEC) 0
• Giardia lamblia (also known as G. intestinalis and G. duodenalis) ●
• Norovirus GI/GII ●
• Rotavirus A ●
• Salmonella spp. .
• Shiga-like Toxin producing E. coli (STEC) stx1/stx2 ●
• Shigella (S. boydii, S. sonnei, S. flexneri, S. dysenteriae)/EIEC ●
• Vibrio spp. (V. cholerae, V. parahaemolyticus, V. vulnificus), specific identification of V. ● parahaemolyticus
• Yersinia enterocolitica

The BioCode Gastrointestinal Pathogen Panel (GPP) is indicated as an aid in the diagnosis of specific agents 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 Gastrointestinal Pathogen Panel (GPP). The agent detected may not be the cause of patient illness. 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 Campylobacter spp., E. coli 0157, Shigella/EIEC, Yersinia enterocolitica, and Adenovirus 40/41 were established primarily with retrospective clinical specimens.

Performance characteristics for Entamoeba histolytica, and Vibrio spp. (V. parahaemolyticus, V. vulnificus, and Vibrio cholerae) were established primarily using contrived clinical specimens.

The BioCode Gastrointestinal Pathogen Panel (GPP) is a multiplex nucleic acid test designed to be used with the BioCode MDx 300 system. The BioCode MDx 3000 is an automated system that integrates PCR amplification, target capture, signal generation and optical detection for nultiple gastrointestinal pathogens from a single stool speciment or in Cary Blair. Stool specimens are processed and nucleic acids extracted with easyMAG, an automated system. Once the PCR plate is set up and sealed, all other operations are automated on MDx 3000. The BioCode Gastrointestinal Pathogen 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 test are available within less than 5 hours.

Here's a breakdown of the acceptance criteria and study details for the BioCode Gastrointestinal Pathogen Panel (GPP) based on the provided document:

1. Table of Acceptance Criteria and Reported Device Performance

The document does not explicitly state pre-defined acceptance criteria for the clinical performance metrics (PPA and NPA). Instead, it presents the calculated agreement rates and their 95% confidence intervals from the clinical study. The reproducibility study, however, does have clear acceptance criteria defined (>= 95% detection for positive targets, and >= 95% non-detection for negative targets).

Here's a table summarizing the reported clinical performance. Note that "Acceptance Criteria" for clinical performance are inferred based on general expectations for diagnostic assays submitted to the FDA; explicit numerical targets were not provided in the text for these. The Reproducibility section does state explicit criteria.

2. Sample Sizes and Data Provenance

• Clinical Study (Prospective):

  • Sample Size: 1558 leftover, de-identified samples.
  • Data Provenance: Prospectively collected from patients in the United States (Baltimore, MD; Tampa, FL; Memphis, TN; Los Angeles, CA). Samples collected between January 2015 and August 2017.
  • Specimen Breakdown:
    • Unpreserved (Fresh): 237 samples
    • Unpreserved (Frozen): 960 samples
    • Cary-Blair (Fresh): 361 samples
  • Inoculated Cary-Blair Samples: 400 unpreserved stool samples from Sites 1 and 2 were thawed and inoculated into Cary-Blair to supplement numbers for specific analytes (pg 21).

• Pre-selected Archived Specimens (Category III):

  • Sample Size: 260 preselected archived specimens.
  • Data Provenance: Archived clinical specimens that were previously tested positive by different methods (retrospective). These were spiked with known positives and randomized with negative specimens. (pg 23)

• Contrived Specimens (Category IV):

  • Sample Size: 612 samples total, with 485 positive samples.
  • Data Provenance: Prepared using specimens previously tested negative for all BioCode GPP analytes, then spiked at levels of up to 3X LOD or greater. (pg 25)

• Asymptomatic Volunteers (Clinical Specificity):

  • Sample Size: 125 clinical stool samples.
  • Data Provenance: Collected from healthy asymptomatic donors from Tampa General Hospital and University of Maryland. (pg 30-31)

• Reproducibility Study:

  • Sample Size: 7 contrived samples (6 positive, 1 negative control) extracted in triplicate and each assayed in singlet over 10 runs per site. Total 90 replicates per target. (pg 32)
  • Data Provenance: Performed at 3 sites. (pg 32)

• Limit of Detection (LoD):

  • Sample Size: 20 replicates for each tested organism and sample type (unpreserved stool and Cary-Blair). (pg 35)

• Interfering Substances:

  • Each sample extracted in triplicate and tested in singlet. (pg 37)

• Cross Contamination/Sample Carryover:

  • Five complete runs in "checkerboard" pattern. (pg 50)

3. Number of Experts and Qualifications for Ground Truth

The document does not specify the number or qualifications of experts used to establish ground truth for the clinical test set. Instead, it relies on reference methods for clinical performance evaluation (pg 13).

4. Adjudication Method for the Test Set

The document does not describe an adjudication method involving human experts. For the clinical study, the reference method for each target pathogen was used as the ground truth. In some cases, discrepancies between the BioCode GPP and the initial reference method were subjected to bidirectional sequencing or additional rounds of sequencing for "confirmation" (e.g., footnotes on pages 14, 15, 17, 22), which can be considered a form of analytical adjudication to determine the true state of the specimen.

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

No MRMC study was mentioned. The device is a "multiplex nucleic acid-based assay," indicating an automated laboratory test, not an imaging AI diagnostic that assists human readers. Therefore, the concept of "human readers improve with AI vs without AI assistance" does not apply here.

6. Standalone (Algorithm Only Without Human-in-the-Loop Performance)

Yes, the studies presented are for the standalone performance of the BioCode Gastrointestinal Pathogen Panel (GPP) system, without human interpretation or assistance beyond typical laboratory operational procedures. The results, as quantitative fluorescence intensity (MFI) values, are processed by the BioCode MDx 3000 system to determine positive or negative results.

7. Type of Ground Truth Used

• Clinical Study (Prospective):

  • Reference standard methods: Culture, FDA-cleared NAAT (Nucleic Acid Amplification Test), or Composite results of two PCR/sequencing assays (pg 13).
  • For discrepancies, bidirectional sequencing or additional rounds of sequencing were used as further confirmation/adjudication (e.g., footnotes on pages 14, 15, 17, 22).

• Archived Specimens: Previously tested positive by different methods, and verified using analyte-specific PCR followed by bi-directional sequencing performed by Applied BioCode, Inc. (pg 23).

• Contrived Specimens: Known concentrations of quantified bacteria, viruses, or parasites spiked into negative clinical matrix. (pg 25)

8. Sample Size for the Training Set

The document does not explicitly mention a "training set" in the context of machine learning. This device is a molecular diagnostic assay, not a machine learning algorithm that is trained on a dataset. The studies described are performance validation studies for an established assay.

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

Since this is not a machine learning device trained on a "training set," this question is not applicable. The device's probes and primers for detecting targets are designed based on known genetic sequences, not through a data-driven training process like that used for AI/ML.

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