Protocols for Laboratory
Verification of Performance of the
BioFire® FilmArray® Pneumonia
Panel
Laboratory Protocols for Use with a
ZeptoMetrix NATtrol™ Verification Panel
Purpose
The Clinical Laboratory Improvement Amendments (CLIA), passed in 1988,
establishes quality standards for all laboratory testing to ensure the accuracy and
reliability of patient test results, regardless of where the test is performed. The
CLIA regulations include a requirement for verifying the performance specifications
of unmodified, moderate complexity tests cleared or approved by the FDA.
This document provides examples of verification procedures to assist your
laboratory in developing a protocol for the verification of the BioFire Pneumonia
Panel performance on BioFire® FilmArray® Systems as required by CLIA. Two
possible verification schemes, compatible with the BioFire Pneumonia Panel, have
been designed using non-clinical specimens. Each verification scheme provides
positive and negative tests for each organism detected by the BioFire Pneumonia
Panel, as well as semi-quantitative bin results for bacterial interpretations to
demonstrate the ability to distinguish between relative abundance levels in a single
test. This scheme may be easily modified or expanded to meet specific criteria.
Day-to-day variation is evaluated by testing each sample on two separate days.
To evaluate user-to-user variation, multiple laboratory technicians may test the
same sample. In addition, testing patient samples representative of the different
types expected to be tested by the laboratory (ex. Sputum, ETA, BAL) for
verification of the performance of the BioFire Pneumonia Panel should be done
under the guidance of the Laboratory Director, but is not described here.
As per the CLIA regulation, the Laboratory Director is ultimately responsible for
ensuring that verification procedures meet the appropriate standards for CLIA and
applicable laboratory accrediting agencies.
BioFire Intended Use
The BioFire Pneumonia Panel is a multiplexed nucleic acid test intended for use
with BioFire® FilmArray® 1.5, BioFire® FilmArray® 2.0, or BioFire® FilmArray®
Torch systems for the simultaneous detection and identification of multiple
respiratory viral and bacterial nucleic acids, as well as select antimicrobial
resistance genes, in sputum-like specimens (induced or expectorated sputum, or
endotracheal aspirates) or bronchoalveolar lavage (BAL)-like specimens (BAL or
mini-BAL) obtained from individuals suspected of lower respiratory tract
infections.
The following bacteria are reported semi-quantitatively with bins representing
approximately 10^4, 10^5, 10^6, or ≥10^7 genomic copies of bacterial nucleic acid
per milliliter (copies/mL) of specimen, to aid in estimating relative abundance of
nucleic acids from these common bacteria within a specimen:
The following atypical bacteria, viruses, and antimicrobial resistance genes are
reported qualitatively:
The complete intended use statement and additional information about the use of
the BioFire
Pneumonia Panel Instructions for Use.
®
FilmArray® System can be found in the BioFire® FilmArray®
Performance Verification: Overview
Two different examples of performance verification procedures are described.
Both procedures evaluate the performance of each assay on the BioFire®
FilmArray® Pneumonia Panel using samples in the presence of synthetic or
clinical matrix background. A Synthetic Matrix Protocol describes the verification
of the BioFire Pneumonia Panel performance in either a synthetic background
(Negative) provided with the ZeptoMetrix NATtrol control organisms or in Artificial
Brochoalveolar Lavage Matrix (aBAL). Preparation of aBAL is described in the
Performance Verification: Protocols section below. A Clinical Matrix Protocol
evaluates the performance of each assay on the BioFire Pneumonia Panel in a
clinical specimen matrix (induced or expectorated sputum, endotracheal
aspirates or bronchoalveolar lavage (BAL)-like specimens (BAL or mini-BAL).
These protocols are examples of procedures to assist your laboratory in
developing a protocol for the verification of BioFire Pneumonia Panel
performance on BioFire Systems.
Note: It is important to characterize aBAL or clinical matrix specimens for
Pneumonia Panel targets by screening the specimen on the BioFire Pneumonia Panel
prior to starting the verification procedure. The optimal clinical matrix specimen will be
negative for all analytes tested on the BioFire Pneumonia Panel.
Targeted Low Bin Results represents bacterial detections in the semi-quantitative bins of 10^4-10^5 copies/mL.
b
Targeted High Bin results represent bacterial detections in the semi-quantitative bins of 10^6-≥10^7 copies/mL.
c
The approximate number of days for testing assumes a BioFire® FilmArray® System configured with one
instrument/module.
Material
Part Number
BioFire® FilmArray® Pneumonia Panel Kit
(30 tests per kit)
BioFire Diagnostics,LLC (RFIT-ASY-0144)
BioFire® FilmArray® Pneumonia Instruction
for Use
BioFire Diagnostics,LLC (RFIT-PRT-0575)
BioFire® FilmArray® Pneumonia Panel
Quick Guide
BioFire Diagnostics,LLC (RFIT-PRT-0368)
Control Organisma
ZeptoMetrix NATPPA-BIO and NATPPQBIO
5 mL sample tubes
Various manufacturers
Transfer pipettes
VWR Part # 13-711-43 (or similar)
Human genomic DNA (1mL of 0.2mg/mL)
or equivalentb
Roche 11691112001
A BioFire® FilmArray® System is defined as all BioFire® FilmArray® Instruments or
modules that are connected to and controlled by a single computer system. If the
laboratory director chooses not to perform the entire verification protocol on each
individual instrument, it is advised that test replicates are evenly distributed among
the instruments or modules.
The procedures have been designed to take advantage of the multiplex nature of
the BioFire® FilmArray® Pneumonia Panel. Verification testing efficiency is
maximized by evaluating multiple target organisms in a single test run. Each
procedure described below will generate multiple positive and negative
detections for each of the BioFire Pneumonia Panel assays. In addition, semiquantitative bacteria are reported with relative bin values of 10^4, 10^5, 10^6, or
≥10^7 copies/mL. The protocols described will generate detections in high bins
(10^6-≥10^7) and low bins (10^4-10^5) to demonstrate the ability to differentiate
organism levels in a single test run. The procedures were developed using a
Pneumonia Verification Panel available from ZeptoMetrix™ Corporation, Buffalo,
NY (NATPPA-BIO + NATPPQ-BIO).
Clinical/patient samples may be used in place of or in addition to the verification
schemes described here in order to assess clinical sensitivity/specificity and
sample matrix effects as part of the performance verification of the BioFire
Pneumonia Panel.
Table 1. Overview of Verification Protocols
Performance Verification: Materials
The following materials may be used to perform verification procedures:
Table 2. Recommended materials for verification protocol
Sterile normal saline (0.85 - 0.9% sodium
chloride)b
Medline PCS1650 or equivalent
10 mL sample tubesb
Various manufacturers
a
Any appropriate source of organism may be used for verification of any or all of the
assays in the BioFire® FilmArray® Pneumonia Panel. However, when alternate organism
sources are used (i.e. not the ZeptoMetrix material), the sample volumes or pooling
schemes suggested in the examples below may need to be adjusted.
b
Optional; needed for preparation aBAL matrix
Performance Verification: Protocols
Synthetic Matrix Protocol
The Synthetic Matrix Protocol evaluates BioFire Pneumonia Panel performance
in a synthetic matrix. Sample material (ZeptoMetrix NATPPA-BIO and NATPPQBIO) is pooled and added to an equal volume of synthetic matrix. The proposed
organism pooling scheme (Table 3) should be followed to obtain the expected
results for each assay in a time and resource-efficient manner.
Note: Dilution of ZeptoMetrix Pneumonia Verification Panel organisms beyond
levels proposed in these guidelines may lead to inconsistent results and is not
recommended.
The Synthetic Matrix Protocol can be followed to test 20 pooled samples,
providing 4 positive results and 16 negative results per assay, as well as 32 low
bin and 36 high bin detections. Sample distribution in the targeted low and high
bins are approximate and bin variation may occur due to sampling differences
and run variability. The pooling scheme provides sufficient volume for testing
more samples if desired. The number of samples tested per day should be
determined by the individual laboratory. The testing scheme can be modified to
run more samples per day based on the number of instruments configured on the
BioFire® FilmArray® System.
Note: Target bin levels are relative and may vary between test runs.
Pooled samples may be stored overnight (or up to 3 days) at refrigeration
temperature (2–8°C) for subsequent testing to evaluate day-to-day variation. To
evaluate user-to-user variation, multiple laboratory technicians may perform
testing.
The estimated total time for completion for this verification example is 4 days for
a BioFire® FilmArray® System configured with 1 instrument/module. A proposed
organism pooling scheme is presented above in Table 3. Refer to Figure 1 for the
suggested workflow.
Note: It is important to prepare only the number of sample pools that will be tested
within 3 days of preparation. The suggestion to prepare 3 sample pools is based on
testing up to 6 pouches per day. The number of samples prepared may be increased or
decreased based on the laboratory’s work schedule and number of instruments
connected within a BioFire System.
Day 1
1. Organize materials needed (Table 2). If using Artificial Brochoalveolar
Lavage Matrix (aBAL) - follow the optional protocol below to prepare the
synthetic matrix before starting Step 2.
2. Prepare one sample pool (i.e. pool #1) from ZeptoMetrix NATPPQ-BIO and
NATPPA-BIO control material. Organism vials should be well mixed prior to
preparing each pool. Refer to Table 3 for example organism pooling schemes
and specific volumes for each pool.
a. Transfer 1.2 mL (or 1.0 mL for pool 2) of Synthetic Matrix (either
ZeptoMetrix Negative or aBAL) into a tube large enough to hold the entire
organism pool volume (at least 3 mL).
b. Use a transfer pipette to remove the entire contents of the ZeptoMetrix
organism vial (approximately 0.2 mL) and transfer to the larger tube
containing Synthetic Matrix.
c. Repeat with the second (and subsequent) organisms to combine the
appropriate organisms for each pool into a single tube (approximately 2.0
mL total volume for five organisms or 2.4 mL for six organisms).
d. Ensure the pooled sample is well mixed prior to removing a sample for
testing.
e. Refrigerate samples (2–8°C) for up to 3 days for the evaluation of day-to-
day variation.
3. Prepare and test 2 samples from a single pool (i.e. pool 1). The duplicate
samples should be tested in a single day by different users.
Note: For each sample, follow instructions in the BioFire® FilmArray® Pneumonia
Panel Instructions for Use and the BioFire® FilmArray® Pneumonia Panel Quick Guide for
pouch preparation, pouch hydration, sample loading, and sample testing.
4. Repeat Steps 2 and 3 for remaining sample pools to be tested that day.
Note: The proposed organism pooling scheme (Table 3) provides sufficient material
for running samples as described in Figure. 1. The volume is sufficient for testing more
To evaluate day-to-day variation, test the remaining volume of the sample pools
prepared on Day 1 by repeating Step 3 above.
Day 3
Prepare 2 new sample pools (i.e. pools #4 and #5) as described in Step 2. Test
samples according to Step 3 above.
Day 4
To evaluate day-to-day variation, test the samples prepared on Day 3 by repeating
Step 2 and 3 above.
Optional Protocol: Preparation of Artificial Brochoalveolar Lavage
Matrix (aBAL)
1. Thoroughly decontaminate the work area with 10% bleach followed by water
wipes.
2. Prepare a 20 ng/uL solution of Human genomic DNA (hgDNA) by adding 1.0
mL hgDNA stock solution (0.2mg/mL) to 9 mL sterile saline in a 10 mL tube.
3. Mix by vortexing or inversion.
4. Characterize aBAL matrix by running a BioFire® FilmArray® Pneumonia Panel
test prior to performing verification schemes. The BioFire Pneumonia Panel
should test negative for all analytes on the panel.
5. Aliquots of aBAL matrix may be stored refrigerated at 4°C for up to 3 days or
stored frozen at ≤ -70°C.
Note: It is important to characterize aBAL or clinical matrix specimens for
Pneumonia Panel targets by screening the specimen on the BioFire Pneumonia Panel
prior to starting the verification procedure. The optimal clinical matrix specimen will be
negative for all analytes tested on the BioFire Pneumonia Panel.
The Clinical Matrix Protocol evaluates BioFire® FilmArray® Pneumonia Panel
performance in a clinical specimen matrix. The laboratory will require a clinical
specimen (induced or expectorated sputum, endotracheal aspirates or
bronchoalveolar lavage (BAL)-like specimens (BAL or mini-BAL) appropriate for
the laboratory’s verification needs and in a volume sufficient for testing as
described in Table 3. The number of different sample types to be tested is up to
the discretion of the laboratory director; multiple specimens may be used, if
necessary. Clinical specimens should be screened in the BioFire Pneumonia
Panel in order to characterize the sample.
Note: It is important to characterize aBAL or clinical matrix specimens for
Pneumonia Panel targets by screening the specimen on the BioFire Pneumonia Panel
prior to starting the verification procedure. The optimal clinical matrix specimen will be
negative for all analytes tested on the BioFire Pneumonia Panel.
Sample material (ZeptoMetrix NATPPA-BIO and NATPPQ-BIO) is pooled and
added to an equal volume of clinical matrix. The proposed organism pooling
scheme (Table 3) should be followed to obtain the expected results for each
assay in a time and resource-efficient manner. Specimen consistency may make
accurate measurement difficult, but care should be taken to try to add the volume
indicated.
Note: Dilution of ZeptoMetrix Pneumonia Verification Panel organisms beyond
levels proposed in these guidelines may lead to inconsistent results and is not
recommended.
The Clinical Matrix Protocol can be followed to test 20 pooled samples, providing
4 positive results and 16 negative results per assay, as well as 32 low bin and 36
high bin detections. Sample distribution in the targeted low and high bins are
approximate and bin variation may occur due to sampling differences and run
variability. The pooling scheme provides sufficient volume for testing more
samples if desired. The number of samples tested per day should be determined
by the individual laboratory. The testing scheme can be modified to run more
samples per day based on the number of instruments configured on the BioFire®
FilmArray® System.
Note: Target bin levels are relative and may vary between test runs.
Pooled samples may be stored overnight at refrigeration temperature (2–8°C) for
subsequent testing to evaluate day-to-day variation; but all tests should be
completed within a day. To evaluate user-to-user variation, multiple laboratory
technicians may perform testing.
Note: Clinical specimens may contain inhibitors and enzymes which may degrade
the organism mixture and lead to unpredictable results. It is important to prepare the
organism pools and test samples within a day to achieve expected results.
The estimated total time for completion for this verification example is 4 days for
a BioFire System configured with 1 instrument/module. A proposed organism
pooling scheme is presented above in Table 3. Refer to Figure 2 for the
suggested workflow.
Note: It is important to prepare only the number of sample pools that will be tested
within a day of preparation. The suggestion to prepare 3 sample pools is based on
testing up to 6 pouches per day. The number of samples prepared may be increased or
decreased based on the laboratory’s work schedule and number of instruments
connected within a BioFire System.
Day 1
1. Organize materials needed (Table 2.) Clinical specimens should be
screened in the BioFire® FilmArray® Pneumonia Panel in order to
characterize the sample prior to preparing pools.
2. Prepare one sample pool (i.e. pool #1) from ZeptoMetrix NATPPQ-BIO and
NATPPA-BIO control material. Organism vials should be well mixed prior to
preparing each pool. Refer to Table 3 for example organism pooling schemes
and specific volumes for each pool.
a. Transfer 1.2 mL (or 1.0 mL for pool 2) of clinical specimen matrix into a
tube large enough to hold the entire organism pool volume (at least 3 mL).
Care should be taken to transfer the correct volume. Organism to matrix
ratios that differ from recommendations in Table 3 may affect detection
results.
b. Use a transfer pipette to remove the entire contents of the ZeptoMetrix
organism vial (approximately 0.2 mL) and transfer to the larger tube
containing clinical specimen matrix.
c. Repeat with the second (and subsequent) organisms to combine the
appropriate organisms for each pool into a single tube (approximately 2.0
mL total volume for five organisms or 2.4 mL for six organisms).
d. Ensure the pooled sample is well mixed prior to removing a sample for
testing.
e. Refrigerate samples (2–8°C) for up to a day for the evaluation of day-to-
day variation.
3. Prepare and test 2 samples from a single pool (i.e. pool 1). The duplicate
samples should be tested in a single day by different users.
Note: For each sample, follow instructions in the BioFire® FilmArray® Pneumonia
Panel Instructions for Use and the BioFire® FilmArray® Pneumonia Panel Quick Guide for
pouch preparation, pouch hydration, sample loading, and sample testing.
4. Repeat Steps 2 and 3 for remaining sample pools to be tested that day.
Note: The proposed organism pooling scheme (Table 3) provides sufficient material
for running samples as described in Figure. 2. The volume is sufficient for testing more
To evaluate day-to-day variation, test the remaining volume of the sample pools
prepared on Day 1 by repeating Step 3 above.
Day 3
Prepare 2 new sample pools (i.e. pools #4 and #5) as described in Step 2. Test
samples according to Step 3 above.
Day 4
To evaluate day-to-day variation, test the samples prepared on Day 3 by repeating
Step 2 and 3 above.
Figure 2. Workflow for Clinical Matrix Protocol
Expanding the protocols
The protocols described above can be expanded by increasing the number of tests
from each of the organism pools. Each organism pool contains approximately 2
mL, which is enough material to complete many tests for each pool.
Verification of Loaner, Repaired, and Permanent Replacement
Instruments
If it becomes necessary to verify the performance of a loaner, repaired, or
permanent replacement instrument, the following protocol may serve as a
guideline but should be verified by the Laboratory Director.
1. Select a few specimens and/or proficiency samples (any combination of
positives and negatives) previously tested on the BioFire® FilmArray®
Pneumonia Panel. The Laboratory Director should determine the appropriate
number of samples to test. Proficiency samples should not be pooled or
diluted.
2. Select a set of controls that verify detection of all targets on the BioFire
Pneumonia Panel.
3. Test the selected specimens/samples/controls on the loaner, repaired, or
permanent replacement instrument and document the results.
Technical Support Contact Information
BioFire is dedicated to providing the best customer support available. If
you have any questions or concerns about this process, please contact
the FilmArrayTechnical Support team for assistance.