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The Great Basin Shiga Toxin Direct Test performed on the Portrait™ Analyzer is an automated, in vitro diagnostic assay for the qualitative detection of Shiga toxin 1 (stxl) / Shiga toxin 2 (stx2) genes and specific identification of a conserved genetic region of the E. coli O157 serogroup. Shiga toxin genes are found in Shiga toxin-producing strains of E. coli (STEC) and Shigella dysenteriae. The E. coli 0157 test result is reported only if a Shiga toxin gene is also detected.

The test is performed directly from Cary-Blair or C&S Medium preserved stool specimens from symptomatic patients with suspected acute gastroenteritis, or colitis in hospital laboratories. The assay is intended for use in conjunction with clinical presentation as an aid in the diagnosis of STEC infections. Positive results do not rule out oninfection with other organisms, and may not be the definitive cause of patient illness.

The results of this test should not be used as the sole basis for diagnosis, treatment, or other patient management decisions. Shiga Toxin Direct Test 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.

The Portrait System is a fully automated system that includes the Portrait Analyzer, single-use Great Basin Shiga Toxin Direct Test cartridges, and the Portrait System data analysis software. The Portrait System is designed to perform automated sample preparation, PCR, and optical chip-based detection with integrated data analysis in approximately 2 hours.

The single-use Test Cartridge contains blister packs, fluidic channels, processing chambers, a waste chamber, and an assay chip coated with an array of sequence-specific detection probes. All reagents are contained within the integrated blister packs with the exception of the amplification reagents and SPC, which are dried into the Amplification Chamber and SPC Chambers of the Cartridge, respectively.

The appropriate specimen for use in the Test Cartridge is an aliquot of stool from symptomatic patients preserved in Cary-Blair or C&S transport media. A preserved stool specimen is placed into the sample port of the Test Cartridge for processing. Multiple fluidic channels move reagents from integrated blister packs to chambers where reagent mixing and sample processing occur. A waste chamber, self-contained and segregated within the Test Cartridge, collects and stores reagent waste.

Here's a breakdown of the acceptance criteria and study details for the Great Basin Shiga Toxin Direct Test, as extracted from the provided text:

1. Table of Acceptance Criteria and Reported Device Performance:

The document doesn't explicitly state "acceptance criteria" as a separate, pre-defined set of values that the device must meet to be approved. Instead, it presents the clinical performance (sensitivity, specificity, PPA, NPA) as results from the studies, which are then compared to a predicate device (though specific performance metrics for the predicate are noted as "Not Reported").

However, based on the performance data presented, here's a summary of the device's reported performance which implicitly serve as the achieved acceptance level, especially when compared against itself in different study types. The comparison chart with the predicate device also indicates a qualitative "same" for intended use and target sequences which are fundamental acceptance points.

2. Sample Size Used for the Test Set and Data Provenance:

• Prospective Clinical Study:

  • Sample Size: 1,082 clinical specimens.
  • Data Provenance:
    • Origin: Collected prospectively (fresh) at five sites.
    • Retrospective/Prospective: Prospective.
    • Timeframe: June to September 2015 (three-month period).

• Frozen Retrospective Clinical Study:

  • Sample Size: 88 unique frozen clinical specimens (from an initial panel of 92).
  • Data Provenance:
    • Origin: Previously characterized clinical specimens.
    • Retrospective/Prospective: Retrospective.

3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications of Those Experts:

The document does not specify the number of experts used or their qualifications to establish the ground truth for the clinical test sets. It mentions "reference clinical microbiology protocols" for the prospective study and "Clinical Characterization - Molecular and/or Shiga Toxin EIA" for the retrospective study as the basis for ground truth.

4. Adjudication Method for the Test Set:

The document does not detail any specific adjudication method (e.g., 2+1, 3+1). It states that the device's performance was compared to "reference clinical microbiology protocols" and "Molecular and/or Shiga Toxin EIA" results. For discrepant results in the prospective study, it notes:

• "Shiga toxin was detected in 8/8 false positive specimens by both bi-directional sequencing and alternate, FDA-cleared comparator NAAT."
• "O157 serogroup was detected in 2/2 false positive specimens by alternate, FDA-cleared comparator NAAT."
  This describes a characterization process for disagreements rather than a multi-expert adjudication method for the initial ground truth.

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done, If So, What Was the Effect Size of How Much Human Readers Improve with AI vs Without AI Assistance:

This device is an in-vitro diagnostic assay for direct detection of nucleic acids, not an imaging device or an AI-assisted diagnostic tool that involves human readers. Therefore, an MRMC comparative effectiveness study involving human readers and AI assistance is not applicable and was not performed.

6. If a Standalone (i.e., algorithm only without human-in-the-loop performance) Was Done:

Yes, the studies evaluate the Great Basin Shiga Toxin Direct Test (a molecular diagnostic assay run on an automated system) as a standalone device. The device's output (qualitative detection of Shiga toxin genes and E. coli O157) is the primary subject of the performance evaluation. It is an automated, in-vitro diagnostic assay.

7. The Type of Ground Truth Used:

• Prospective Clinical Study: "Reference clinical microbiology protocols for the detection of both Shiga Toxin and the E. coli O157 Serotype." This typically involves culture, immunoassay (EIA), and potentially molecular methods. For discrepant results, bi-directional sequencing and FDA-cleared comparator NAAT were used for confirmation.
• Frozen Retrospective Clinical Study: "Clinical Characterization - Molecular and/or Shiga Toxin EIA."

8. The Sample Size for the Training Set:

The document does not explicitly mention a "training set" in the context of machine learning or AI algorithm development because this is a molecular diagnostic test. However, the document details various analytical studies which are foundational to the device's design and calibration. These studies use panels of known strains and concentrations:

• Analytical Sensitivity (LoD): Involved testing specific E. coli strains (ATCC BAA-2191, ATCC 51434, ATCC BAA-2192, ATCC 43895) at varying concentrations (e.g., 25/25, 21/22, 26/26, 20/20 correct results for LoD determination, indicating numerous replicates).
• Analytical Reactivity (Inclusivity): Tested 33 known positive strains (30 STEC, 3 Shigella dysenteriae) with 3 replicates each, totaling 99 tests.
• Analytical Specificity (Exclusivity): Tested 118 microorganisms (bacteria, fungi, yeasts, parasites, viruses) and human genomic DNA, each typically with 3 replicates (e.g., 3/3 results mentioned frequently).
• Microbial Interference: Tested 42 microorganisms, each typically with 3 or more replicates, against two STEC strains (ATCC 43895 and ATCC 43894) at 2X LoD.
• Interfering Substances: Tested 26 different substances, each with 3 replicates, in both positive and negative stool matrices.

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

For these analytical studies, the ground truth was established by using well-characterized reference strains (e.g., ATCC strains) with known genetic profiles (presence of stx1, stx2, O157 genes) and established concentrations. This allows for precise control and verification of the device's ability to detect specific targets and its limits of detection, and to ensure it does not cross-react with non-targets. For other studies like specimen stability, known positive samples were contrived by spiking these characterized strains into negative stool matrix.

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