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K Number
K193519
Device Name
BioFire Blood Culture Identification 2 (BCID2) Panel
Manufacturer
BioFire Diagnostics, LLC
Date Cleared
2020-03-18

(90 days)

Product Code
PEN,PAM,PEO
Regulation Number
866.3365
Type
Traditional
Panel
MI
Reference & Predicate Devices
K181493
AI/MLSaMDIVD (In Vitro Diagnostic)TherapeuticDiagnosticis PCCP AuthorizedThirdpartyExpeditedreview
Intended Use

The BioFire® Blood Culture Identification 2 (BCID2) Panel is a multiplexed nucleic acid test intended for use with FilmArray® 2.0 or FilmArray® Torch systems for the simultaneous qualitative detection and identification of multiple bacterial and yeast nucleic acids and select genetic determinants associated with antimicrobial resistance. The BioFire BCID2 Panel test is performed directly on blood culture samples identified as positive by a continuous monitoring blood culture system. Results are intended to be interpreted in conjunction with Gram stain results. The following organism types and subtypes are identified using the BioFire BCID2 Panel:

Gram Positive Bacteria

  • Enterococcus faecalis
  • · Staphylococcus spp.
  • · Streptococcus spp.
  • Enterococcus faecium
  • Staphylococcus aureus
  • · Streptococcus agalactiae (Group B)
  • Listeria monocytogenes
  • Staphylococcus epidermidis
  • Streptococcus pneumoniae
  • Staphylococcus lugdunensis
  • · Streptococcus pyogenes (Group A)

Gram Negative Bacteria

  • Acinetobacter calcoaceticus-baumannii complex
  • · Enterobacterales
  • · Bacteroides fragilis
  • Enterobacter cloacae complex
  • Haemophilus influenza
  • · Escherichia coli
  • · Neisseria meningitidis (encapsulated)
  • · Klebsiella aerogenes
  • · Pseudomonas aeruginosa
  • · Klebsiella oxytoca
  • · Stenotrophomonas maltophilia
  • · Klebsiella pneumoniae group
  • · Proteus spp.
  • · Salmonella spp.
  • · Serratia marcescens

Yeast

  • · Candida albicans
  • Candida krusei
  • · Cryptococcus neoformans/gattii
  • Candida auris
  • · Candida parapsilosis
  • · Candida tropicalis
  • Candida glabrata

The BioFire BCID2 Panel contains assays for the detection of genetic determinants associated with resistance to methicillin (mecA/C and mecA/C in conjunction with MREJ, vancomycin (vanA and vanB), 0-lactams including penicillins, cephalosporins, monobactams, and carbapenems (blaCTX-M, blaKPC, blaNDM, blaOXA48-like, bla VIM) to aid in the identification of potentially antimicrobial-resistant organisms in positive blood culture samples. In addition, the panel includes an assay for the mobilized genetic determinant mcr-1, an emerging marker of public health importance. The animicrobial resistance gene or may not be associated with the agent responsible for disease. Negative results for these select antimicrobial resistance gene and marker assays do not indicate susceptibility, as multiple mechanisms of resistance to methicillin, vancomycin, B-lactams, and colistin exist.

Antimicrobial Resistance Genes

  • CTX-M
  • КРС
  • · mecA/C
  • NDM
  • vanA/B
  • · IMP
  • mcr-1
  • · mecA/C and MREJ (MRSA)
  • OXA-48-like
  • VIM

The BioFire BCID2 Panel is indicated as an aid in the diagnosis of bloodstream infection and results should be used in conjunction with other clinical and laboratory findings. Positive results do not rule out co-infection with organisms not included in the BioFire BCID2 Panel is not intended to monitor treatment for bloodstream infection.

Subculturing of positive blood cultures is necessary to recover organisms for susceptibility testing and epidemiological typing, to identify organisms in the blood culture that are not detected by the BioFire BCID2 Panel, and for determination of species detected but not identified within complexes, groups, or genera by the BioFire BCID2 Panel assays.

Device Description

The BioFire Blood Culture Identification 2 (BCID2) Panel is designed to simultaneously identify 43 bacteria and yeast responsible for bloodstream infections, as well as select genetic determinants of antimicrobial resistance (see Table 1), in a timeframe(about an hour) that allows the test results to be used in determining appropriate patient treatment and management. The BioFire BCID2 Panel is performed directly on positive blood culture samples.

The BioFire BCID2 Panel is compatible with BioFire's PCR-based in vitro diagnostic FilmArray Torch systems for infectious disease testing, A specific software module (i.e., BioFire BCID2 Panel pouch module) is used to perform BioFire BCID2 Panel testing on these systems.

A test is initiated by loading Hydration Solution into one port of the FilmArray pouch and positive blood culture specimen mixed with the provided Sample Buffer into the other port of the BioFire BCID2 Panel pouch and placing it in a FilmArray instrument. The pouch contains all of the reagents required for specimen testing and analysis in a freeze-dried format: the addition of Hydration and Sample/Buffer Mix rehydrates the reagents. After the pouch is prepared, the FilmArray Software quides the user through the pouch into the instrument, scanning the pouch barcode, entering the sample identification, and initiating the run.

The FilmArray instruments contain coordinated systems of inflatable bladders and seal points, which act on the pouch to control the movement of liquid between the pouch blisters. When a bladder is inflated over a reagent blister, it forces liquid from the blister into connecting channels. Alternatively, when a seal is placed over a connecting channel it acts as a valve to open or close a channel. In addition, electronically-controlled pneumatic pistons are positioned over multiple plungers in order to deliver the rehydrated reagents into the blisters at the appropriate times. Two Peltier devices control heating and cooling of the PCR reactions and the melt curve analysis.

Nucleic acid extraction occurs within the FilmArray pouch using mechanical lysis followed by purification using standard magnetic bead technology. After extracting and purifying nucleic acids from the unprocessed sample, the FilmArray performs a nested multiplex PCR that is executed in two stages. During the first stage, the FilmArray performs a single, large volume, highly multiplexed reverse transcription PCR (rt-PCR) reaction. The products from first stage PCR are then diluted and combined with a fresh, primer-free master mix and a fluorescent double-stranded DNA binding dye (LC Green® Plus, BioFire Diagnostics). The solution is then distributed to each well of the array. Array wells contain sets of primers designed specifically to amplify sequences internal to the PCR products generated during the first stage PCR reaction. The 2nd stage PCR, is is performed in singleplex fashion in each well of the conclusion of the 2nd stage PCR, the array is interrogated by melt curve analysis for the detection of signature amplicons denoting the presence of specific targets. A digital camera placed in front of the 2nd stage PCR captures fluorescent images of the PCR reactions and software interprets the data.

The FilmArray Software automatically interprets the results of each DNA melt curve analysis and combines the data with the results of the internal pouch controls to provide a test result for each organism on the panel.

AI/ML Overview

Here is a summary of the acceptance criteria and the study that proves the device meets them, based on the provided text:

1. Table of Acceptance Criteria and Reported Device Performance

The acceptance criteria are generally implied to be high sensitivity and specificity for each analyte. Rather than explicit criteria, the document presents the achieved performance.

Analyte (Type/Species)Study TypeSensitivity (PPA)Specificity (NPA)
Gram Positive Bacteria
Enterococcus faecalisOverall95.3% (41/43)99.9% (1582/1583)
Enterococcus faeciumOverall100% (37/37)99.8% (1586/1589)
Listeria monocytogenesOverall100% (44/44)100% (1818/1818)
Staphylococcus spp.Overall99.8% (511/512)98.8% (1101/1114)
Staphylococcus aureusOverall100% (159/159)99.9% (1465/1467)
Staphylococcus epidermidisOverall96.5% (221/229)96.6% (816/845)
Staphylococcus lugdunensisOverall100% (50/50)99.8% (1714/1717)
Streptococcus spp.Overall98.4% (121/123)99.8% (949/951)
Streptococcus agalactiae (Group B)Overall100% (25/25)100% (1285/1285)
Streptococcus pneumoniaeOverall100% (26/26)100% (1048/1048)
Streptococcus pyogenes (Group A)Overall96.7% (29/30)100% (1280/1280)
Gram Negative Bacteria
Acinetobacter calcoaceticus-baumannii complexOverall97.0% (65/67)99.9% (1695/1697)
Bacteroides fragilisOverall100% (52/52)99.8% (1712/1715)
EnterobacteralesOverall99.8% (497/498)95.2% (1074/1128)
Enterobacter cloacae complexOverall100% (40/40)100% (1821/1821)
Escherichia coliOverall99.5% (202/203)99.9% (1421/1423)
Klebsiella aerogenesOverall100% (60/60)100% (1707/1707)
Klebsiella oxytocaOverall100% (30/30)100% (1831/1831)
Klebsiella pneumoniae groupOverall99.3% (147/148)100% (1478/1478)
Proteus spp.Overall100% (39/39)99.9% (1810/1811)
Salmonella spp.Overall100% (58/58)100% (1709/1709)
Serratia marcescensOverall100% (27/27)100% (1283/1283)
Haemophilus influenzaeOverall97.0% (32/33)100% (1277/1277)
Neisseria meningitidisOverall100% (38/38)100% (1824/1824)
Pseudomonas aeruginosaOverall96.4% (53/55)99.9% (1569/1571)
Stenotrophomonas maltophiliaOverall88.5% (54/61)100% (1704/1704)
Yeast
Candida albicansOverall100% (38/38)99.9% (1821/1822)
Candida aurisOverall100% (31/31)100% (1609/1609)
Candida glabrataOverall100% (26/26)99.8% (1280/1282)
Candida kruseiOverall100% (44/44)100% (1818/1818)
Candida parapsilosisOverall96.8% (30/31)99.9% (1276/1277)
Candida tropicalisOverall100% (55/55)99.9% (1805/1806)
Cryptococcus neoformans/gattiiOverall100% (36/36)100% (1731/1731)
Antimicrobial Resistance Genes
CTX-MOverall99.1% (109/110)100% (510/510)
IMPOverall100% (29/29)100% (591/591)
KPCOverall100% (63/63)100% (549/549)
mcr-1Overall100% (30/30)100% (429/429)
mecA/CProspective100% (195/195)100% (60/60)
mecA/C and MREJ (MRSA)Overall91.9% (57/62)98.0% (97/99)
NDMOverall100% (36/36)100% (594/594)
OXA-48-likeOverall100% (30/30)100% (521/521)
vanA/BOverall97.5% (39/40)100% (38/38)
VIMOverall100% (34/34)100% (592/592)

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

The "test set" for clinical performance was comprised of:

  • Prospective Multi-center Study: 1093 residual PBC specimens, with 1074 evaluable for final analysis.
    • Data Provenance: Nine geographically distinct study sites (seven in the EU) participated. Data collected from October 2018 to May 2019. Specimens were a mix of fresh (1005) and frozen (69) for later testing.
  • Archived Specimens: 427 frozen archived PBC specimens, with 395 evaluable. 370 contained confirmed analytes of interest.
    • Data Provenance: Collected from 12 external laboratories (countries not specified, but likely a mix given the mention of EU sites for prospective study). Retrospective.
  • Seeded Blood Culture Specimens: 552 seeded specimens.
    • Data Provenance: Laboratory-generated.

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

The document does not explicitly state the "number of experts" or their specific qualifications for establishing ground truth. However, it indicates the following methods were used for reference:

  • Bacteria and Cryptococcus: Standard manual and automated microbiological/biochemical identification methods (performed by SOC labs and abstracted from medical charts).
  • Candida species: SOC identification for genus level, followed by PCR & sequencing of isolates for species identification.
  • AMR Genes:
    • Method 1: One PCR assay performed direct from PBC followed by sequencing of PCR amplicon.
    • Method 2: Commercially available FDA-cleared and CE-marked molecular IVD assays performed on PBC.
    • Method 3: PCR & sequencing for specific resistance gene from applicable cultured isolates.
    • Method 4: Phenotypic antimicrobial susceptibility testing (AST) methods on cultured isolates.

It can be inferred that trained laboratory personnel and potentially infectious disease or microbiology experts interpreted these results, consistent with standard clinical laboratory practices.

4. Adjudication Method for the Test Set

The document details investigations for discrepant results. For example:

  • For Enterococcus faecalis FN specimens, additional molecular methods were used for re-testing.
  • For Staphylococcus epidermidis FN specimens, additional molecular testing and sequencing were performed.
  • For mecA/C and MREJ (MRSA) discrepancies, isolates were tested by PCR/sequencing and had phenotypic AST. Original Cepheid Xpert® MRSA/SA BC tests were also re-tested.

This suggests an internal adjudication process involving further molecular testing and phenotypic analysis to confirm the true status of discrepant samples, rather than a formal blinded 2+1 or 3+1 expert adjudication. Discrepant results were not simply resolved by majority vote but by further in-depth laboratory investigation.

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

No multi-reader multi-case (MRMC) comparative effectiveness study comparing human readers with AI assistance versus without AI assistance was mentioned or conducted. The BioFire BCID2 Panel is a standalone diagnostic device that provides qualitative detection and identification of microbial nucleic acids and resistance genes, not an assistive AI tool for human interpretation.

6. Standalone Performance

Yes, extensive standalone performance studies were conducted. The clinical performance tables (Tables 12-24) and the analytical performance sections (Limit of Detection, Analytical Reactivity (Inclusivity), Analytical Specificity (Cross-Reactivity and Exclusivity), Reproducibility, Interference) directly demonstrate the algorithm's performance without human intervention in result interpretation. The system automatically interprets results and generates reports.

7. Type of Ground Truth Used

The ground truth for the clinical studies was established using a combination of:

  • Culture-based microbiology: Standard manual and automated microbiological/biochemical identification methods, followed by species identification where necessary (e.g., Candida species by PCR & sequencing).
  • Molecular methods: PCR and sequencing of isolates or direct from positive blood cultures, and commercially available FDA-cleared/CE-marked molecular IVD assays for AMR genes.
  • Phenotypic Antimicrobial Susceptibility Testing (AST): Used for AMR gene concordance, particularly for cases like mecA/C and MREJ (MRSA).

For seeded specimens, the "known analyte composition" served as ground truth.

8. Sample Size for the Training Set

The document does not explicitly state the sample size for a "training set" in the context of machine learning. The BioFire BCID2 Panel is a nucleic acid amplification test (PCR-based), where the "training" analogous to model development for AI would involve the design and optimization of primers and probes, and the setting of fluorescence thresholds for detection. This process is primarily based on analytical studies and known genetic sequences, not a labeled dataset like in typical AI development.

However, a large number of isolates were used in the Analytical Reactivity (Inclusivity) study (over 450 isolates) and Analytical Specificity (Cross-Reactivity and Exclusivity) study (many on-panel and off-panel organisms tested, some at high concentrations). These studies would contribute to the robust development and validation of the oligonucleotide sequences and parameters used in the panel tests.

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

As explained above, for a nucleic acid amplification test like the BioFire BCID2 Panel, the "training set" doesn't strictly align with AI/ML terminology. The development of the assays (e.g., primer and probe design) relied on:

  • In silico analysis of sequences: Public databases of genetic sequences were used to design assays that are inclusive of target strains and exclusive of non-target organisms.
  • Testing of characterized isolates: Over 450 isolates (representing genetic, geographic, and temporal diversity) were tested at varying concentrations to ensure reliable detection. The "ground truth" for these isolates would have been their known identity (species/subspecies) and genetic markers (e.g., AMR genes) determined by established microbial identification techniques and sequencing (e.g., ATCC strains, clinical isolates with known characteristics).

This rigorous analytical evaluation forms the basis of the device's "knowledge" or "training" on targets and non-targets.

§ 866.3365 Multiplex nucleic acid assay for identification of microorganisms and resistance markers from positive blood cultures.

(a)
Identification. A multiplex nucleic acid assay for identification of microorganisms and resistance markers from positive blood cultures is a qualitative in vitro device intended to simultaneously detect and identify microorganism nucleic acids from blood cultures that test positive by Gram stain or other microbiological stains. The device detects specific nucleic acid sequences for microorganism identification as well as for antimicrobial resistance. This device aids in the diagnosis of bloodstream infections when used in conjunction with other clinical and laboratory findings. However, the device does not replace traditional methods for culture and susceptibility testing.(b)
Classification. Class II (special controls). The special control for this device is FDA's guideline document entitled “Class II Special Controls Guideline: Multiplex Nucleic Acid Assay for Identification of Microorganisms and Resistance Markers from Positive Blood Cultures.” For availability of the guideline document, see § 866.1(e).