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The Joint Biological Agent Identification and Diagnostic System (JBAIDS) Plague Detection Kit is a real-time polymerase chain reaction (PCR) test kit intended for the qualitative in vitro diagnostic (IVD) detection of target DNA sequences of Yersinia pestis. The kit can be used to test human whole blood collected in sodium citrate or sputum collected aseptically from individuals greater than 18 years of age suspected of having septic or pneumonic plague. In addition, positive blood cultures and colonies may be tested. The JBAIDS Plague Target 2 assay is used as a supplementary test only after a positive result with the Target 1 Assay.
The JBAIDS Plague Target 1 and Target 2 assays are run on the JBAIDS instrument using the Diagnostic Wizard. Results are for the presumptive identification of Y. pestis in conjunction with culture and other laboratory tests. The definitive identification of Y. pestis from colony growth, liquid blood culture growth, or from blood or sputum specimens requires additional testing and confirmation procedures in consultation with public health or other authorities for whom reports are required.

The diagnosis of plague must be made based on history, signs, symptoms, exposure likelihood, and other laboratory evidence in addition to the identification of Y. pestis from cultures or directly from whole blood or sputum specimens.

The JBAIDS Plague Detection Kit is intended for use by trained clinical laboratory personnel who have received specific training on the use of the JBAIDS Plague Detection Kit. The level of Y. pestis that would be present in blood or sputum from individuals with early systemic infection is unknown. Due to the difficulty in obtaining clinical specimens, these assays were not evaluated with blood or sputum from individuals with septic or pneumonic plague.

The Joint Biological Agent Identification and Diagnostic System (JBAIDS) Plague Detection Kit is a real-time polymerase chain reaction (PCR) reagent kit, which, when used with the JBAIDS instrument and software, allows the qualitative in vitro diagnostic (IVD) detection of target DNA sequences within the pathogenic bacterium, Yersinia pestis, the causative agent of plague. The kit contains two assays, Plague Target 1 and Target 2, each of which consists of oligonucleotide primers and a fluorescent-labeled target assay probe that specifically detect Y. pestis DNA. The Target 2 assay is reserved for samples that test positive with the Target 1 assay. The kit is designed for use with the JBAIDS instrument, a portable thermocycler and real-time fluorimeter that performs PCR in glass capillaries.

Before testing, samples are purified using Idaho Technology's 1-2-3TM Sample Purification Kits (or validated equivalent). The resulting purified sample is added to an Unknown reagent vial and an Inhibition Control reagent vial, along with reconstitution buffer. When the organism is present, a fragment of Y. pestis DNA is amplified. The amplicon is detected by fluorescence using a specific hydrolysis probe. The hydrolysis probe contains a short oligonucleotide that hybridizes to an internal sequence of the amplified fragment during the annealing phase of the PCR cycle. This probe has the 5' and 3' ends labeled with a reporter dye and a quenching dye, respectively. When the probe hybridizes to the specific DNA target, the Taq polymerase enzyme replicating the target-specific DNA hydrolyzes the probe, separating the two fluorophores and allowing the reporter dye to fluoresce.

The JBAIDS instrument measures the level of fluorescence from each unknown sample and control. JBAIDS Software analyzes the fluorescence amplification curves and reports results as positive, negative, inhibited, or uncertain. A failure of the Positive or Negative Control will result in the entire run being called invalid. Failure of the Inhibition Control yields an inhibited result when the associated sample has a negative result for the target assay and requires retesting of that sample.

Due to the nature of the provided document (a 510(k) summary for a diagnostic test kit), the study performed is a diagnostic accuracy study rather than a study evaluating the performance of an AI/ML device. Therefore, many of the requested fields (MRMC study, effect size of human readers improving with AI, number of experts for ground truth establishment, etc.) are not applicable and will be marked as "N/A".

Here's an analysis of the provided text based on your request:

JBAIDS Plague Detection Kit Performance Study Analysis

1. Table of Acceptance Criteria and Reported Device Performance

The document does not explicitly state "acceptance criteria" for the clinical trial in terms of specific performance metrics that needed to be met for FDA clearance. However, it details the design of the clinical specificity study and the resulting performance. For analytical studies, it provides "LOD" (Limit of Detection) and inclusivity/exclusivity data which serve as performance measures.

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

• Analytical Test Set:
  • Inclusivity: 18 isolates of virulent Y. pestis (subtypes and strains)
  • Exclusivity: A "panel" of 24 isolates (phylogenetically related and unrelated organisms)
  • Data Provenance: Not explicitly stated, but typically research laboratory settings for analytical studies. Retrospective in nature.
• Clinical Test Set:
  • Whole Blood: 132 samples
  • Sputum: 36 samples
  • Data Provenance: The study was a "multisite clinical trial". The samples were obtained from "subjects with clinical signs and symptoms consistent with systemic plague and for whom a blood and/or sputum culture had been ordered." Since clinical plague is rare, and the document explicitly states "Due to the difficulty in obtaining clinical specimens, these assays were not evaluated with blood or sputum from individuals with septic or pneumonic plague," these samples were likely from individuals suspected of plague but ultimately found to be negative. Thus, these are clinical samples, but representative of a "negative" population in the context of plague in humans. Retrospective in nature.

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

• N/A. For this in vitro diagnostic (IVD) device, the ground truth for analytical studies is established by known bacterial stocks and for clinical studies, by established laboratory culture methods.
• The ground truth for the clinical study was "laboratory culture results" which were considered the "gold standard." These methods are typically performed by trained microbiologists or clinical laboratory scientists, not "experts" in the sense of physicians adjudicating medical imaging or complex interpretations.

4. Adjudication Method for the Test Set

• N/A. For analytical studies, the ground truth (presence/absence of specific bacteria, concentration) is determined by established microbiological methods and known samples, without adjudication.
• For the clinical specificity study, the ground truth was "laboratory culture results." These are typically definitive for bacterial presence/absence. No adjudication among experts is mentioned or typically needed for this type of ground truth.

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done

• No. This is an in vitro diagnostic (IVD) device, not an AI/ML device requiring human-in-the-loop performance evaluation. The device provides an automated "positive, negative, inhibited, or uncertain" result.
• Effect size of how much human readers improve with AI vs. without AI assistance: N/A.

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

• Yes, in essence. The JBAIDS system operates as a standalone diagnostic test. The "JBAIDS Software analyzes the fluorescence amplification curves and reports results as positive, negative, inhibited, or uncertain." This is the standalone performance of the analytical system.
• While the kit is "intended for use by trained clinical laboratory personnel," their role is to operate the instrument and interpret the automated results within a clinical context, not to perform a subjective interpretation of a raw signal that the algorithm then enhances.

7. The Type of Ground Truth Used

• Analytical Studies: Known strains/isolates of Y. pestis and other bacteria, with confirmed identification and concentrations (e.g., CFU/mL).
• Clinical Studies: "Laboratory culture results," which are considered the "gold standard" for bacterial identification in clinical samples.

8. The Sample Size for the Training Set

• Not explicitly stated in terms of a "training set." For IVDs, assay development and optimization (which can be considered analogous to training) involve numerous preliminary experiments with various dilutions, strains, and conditions, but these aren't typically documented as a formal "training set" with a defined size in the same way an AI/ML model would. The document describes the assay's design and then its validation/testing.

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

• N/A (as no formal "training set" is described). However, for the development of PCR assays (like this kit), the ground truth for optimizing primers and probes would be established by:
  • Using purified genomic DNA of Yersinia pestis and other closely related and common organisms.
  • Sequencing to confirm target regions.
  • Utilizing known bacterial cultures and dilutions with confirmed concentrations.
  • These foundational truths are based on established molecular biology and microbiology techniques.

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