User manual - Check

User manual
Check-Direct CPE for BD MAX
MAX™
Real time PCR kit for the detection
etection of carbapenemase
carbapenemase-producing
Enterobacteriaceae
Version 1.3
Date of issue: 24.01.2014
18-0081
Check-Direct CPE for BD Max™ User manual
Version 1.3, Issued 24-01-2014
48
081-04
INTENDED USE ................................................................
....................................................................................2
INTRODUCTION AND PRINCIPLE
NCIPLE OF THE METHOD ..............................................................2
KIT CONTENTS (FOR 48 REACTIONS) ...................................................................................2
................................
STORAGE, HANDLING, AND STABILITY ................................................................................2
................................
MATERIALS REQUIRED BUT
UT NOT SUPPLIED WITH THE KIT...................................................2
GOOD LABORATORY PRACTICES .........................................................................................2
................................
SPECIMEN AND CELL SUSPENSION
SPENSION PREPARATION ..............................................................4
BD MAX™ SAMPLE AND CONTROL
ONTROL PREPARATION ..............................................................4
1. SAMPLE PREPARATION ..........................................................................................................
................................
4
2. POSITIVE AND NEGATIVE CONTROL PREPARATION ...................................................................... 4
BD MAX™ SYSTEM REAL-TIME PCR .....................................................................................4
................................
1. MULTIPLEX REAL-TIME PCR (QPCR) SETUP .............................................................................. 4
2. QPCR MIX PREPARATION ......................................................................................................
................................
4
3. CREATING THE CHECK-DIRECT CPE TEST ..................................................................................
................................
4
4. BD MAX™ RACK SET-UP ......................................................................................................
................................
5
5. BD MAX™ INSTRUMENT SET-UP ............................................................................................
................................
5
BD MAX™ RESULTS ................................................................
.............................................................................6
1. HOW TO CREATE AND PRINT DATA REPORT ...............................................................................
................................
6
2. ANALYSIS ................................................................
............................................................................................ 6
3. INTERPRETATION ................................................................
.................................................................................. 6
FREQUENTLY ASKED QUESTIONS
STIONS (FAQ) & TROUBLESHOOTING
TROUB
..........................................7
LIMITATIONS ................................................................
.......................................................................................8
TECHNICAL ASSISTANCE ......................................................................................................8
................................
KEY TO SYMBOLS USED .......................................................................................................8
................................
1
Intended use
Check-Direct CPE is a qualitative in vitro diagnostic test for the rapid detection of
carbapenemase genes KPC, VIM, OXA-48 and NDM, presently the primary cause of
TM
carbapenemase production in Enterobacteriaceae.. The assay is performed on the BD MAX
system using bacterial cell suspension from clinical specimen of individuals at risk of
colonization with carbapenemase-producing Enterobacteriaceae.. Check
Check-Direct CPE is not
intended to diagnose infections with carbapenemase-producing Enterobacteriaceae nor to
guide or monitor treatment for these infections. Parallel cultures are necessary to recover
organisms for epidemiological typing, susceptibility testing and for fur
further confirmatory
identification.
Introduction and principle of the method
The worldwide emergence and dissemination of carbapenem resistance among
Enterobacteriaceae is a serious threat to public health. These organisms are associated with
high mortality rates and have the potential to spread widely. The most common cause of
carbapenem resistance in Enterobacteriaceae is the expression of carbapenemases, i.e.
Carbapenemase-Producing Enterobacteriaceae or CPE. CPE have elevated or complete
resistance to carbapenems and most other β-lactam
lactam antibiotics. Presently, the vast majority
of CPE are associated with the presence of one of the following plasmid
plasmid-encoded
carbapenemases: KPC (Klebsiella pneumoniae carbapenemase), VIM (Verona integron
integron–
encoded metallo-β-lactamase), NDM (New Delhi metallo-β-lactamase)
lactamase) or OXA
OXA-48
(Oxacillinase-48). Moreover, CPE often have other non–β-lactam
lactam resistance determinants
resulting in multidrug- and pandrug-resistant isolates.
time PCR assay for detection of the KPC, OXA
OXA-48, NDM
Check-Direct CPE is a multiplex real-time
and VIM carbapenemase genes. The assay is based on specific recognition and amplification
of target sequences by PCR, and the simultaneous
aneous detection of the accumulation of PCR
amplification products by fluorescent DNA probes. Four molecular beacon probes labelled
with four different dyes are used for the fluorescent detection and the disc
discrimination of the
carbapenemase markers.. For each of the 4 carbapenemase genes, KPC, VIM, OXA-48 and
NDM,, many gene variants exist. PCR primers and fluorescent probes of Check
Check-Direct CPE
are selected to target homologous gene segments of these carbapenemase genes, and in
this way all gene variants are reliably detected.
Check-Direct CPE for BD Max™ User manual
Version 1.3, Issued 24-01-2014
Kit contents (for 48 reactions)
Components (Mat. No.)
CPE solution (9-0072)*
Negative control (9-0070)
KPC positive control (9-0073)
VIM positive control (9-0074)
OXA-48 positive control (9-0076)
NDM positive control (9-0075)
User Manual (9-0079)
Description
Storage conditions
1 brown tube (blue inlay ) 550 μl
1 tube (white inlay ) 100 µl
1 tube (green inlay ) 100 μl
- 20°C, store in the dark
1 tube (yellow inlay ) 100 μl
1 tube (orange inlay ) 100 μl
1 tube (gold inlay ) 100 μl
Leaflet – download from website
Not critical
Storage, handling, and stability
The Check-Direct CPE kit is shipped cooled and should be stored immediately at -20°C upon
receipt. Store all opened reagents at -20°C
20°C until expiration date. Store in the dark. Please
visually inspect the box upon initial opening to ensure that its contents
content are intact.
The CPE solution should not be exposed to more than 12 freeze-thaw cycles.
Please contact the Check-Points office at support@check-points.com
support@check
if you have any further
questions.
Materials required but not supplied with the kit
Supplies
•
•
•
•
•
•
•
•
BD MAX™ ExK™ DNA-1
1 Extraction Kit (Ref:442818)
BD MAX™ DNA MMK (SPC) Master Mix (Ref: 442829)
BD MAX™ PCR Cartridges (Ref: 437519)
Disposable laboratory (powder-free)
free) gloves
Lab coat
Pipettes & disposable (filter-)) tips for volumes of 1 to 1000
µl
DNAase free 1.5 ml tubes (1.5 and/or 2ml)
PCR-grade water (e.g. Milli-Q)
Equipment
•
•
•
Real-time PCR instrument:
BD MAX™ System, software
version 2.92
Vortex mixer
Mini centrifuge
2
Good laboratory practices
Recommendations for best results
The quality of the results depends on strict compliance with the following good laboratory
practices, especially concerning PCR practices.
•
•
•
•
•
•
Users are strongly advise
vised to read the full protocol
before starting the test
The test must be performed by adequately trained personnel.
Do not use reagents after their expiration date
Before use, thaw frozen reagents completely at room temperature and vvortex briefly to
obtain a homogeneous solution. After vortexing briefly, spin down the solution to avoid
contamination when opening the lid. Avoid unnecessary freeze
freeze-thawing of the kit
content.
Follow recommendations for storage, handling and freeze-thaw
thaw cycles to preserve the
quality of the kit’s reagents.
Protect reagents from light to avoid photo-bleaching
bleaching of the dyes.
Periodically, verify the accuracy and precision of pipettes, as well as correct functioning
and calibration of the instruments.
Prevention of contaminations
Use separate rooms: a pre-PCR room and a post-PCR room.
•
•
•
Preparation of the amplification reactions are carried out in the pre
pre-PCR room.
DNA extraction and real-time PCR assays are carried out in the post
post-PCR room.
Never transfer items from the post-PCR room to the pre-PCR
PCR room.
To keep laboratory free of PCR product contamination:
Use pipettes with hydrophobic filter tips.
Make sure to always use a new pipette tip when adding solutions, test samples, and
controls to a reaction tube to avoid contamination.
• Follow proper pipette-dispensing
dispensing techniques to prevent aerosols.
• Wear clean disposable gloves and clean lab coats for the different steps of the test.
• Change gloves whenever you suspect that they are contaminated.
• Keep the tubes of all kit components and samples closed as much as possible.
• Clean the lab benches and all equipment regularly with a 0,5% sodium hypochlorite
solution.
•
•
Check-Direct CPE for BD Max™ User manual
Version 1.3, Issued 24-01-2014
3
Specimen and cell suspension preparation
BD MAX™ system real-time
time PCR
• Inoculate nutrient agar plates with the clinical samples or the bacterial strains to be
tested and incubate overnight at 37°C. Typical growth media include blood agar,
MacConkey agar and Tryptic Soy agar.
8
• Prepare a bacterial cell suspension of McFarland 0.5 (≈1 x 10 CFU/ml) in cell suspension
buffer (e.g. PBS or 10mM Tris HCl pH8.0) or PCR-grade water from bacterial cells grown
6
on the agar plate. Dilute the suspension 100 times
mes to obtain a suspension of ≈1 x 10
CFU/ml.
1. Multiplex real-time
time PCR (qPCR) setup
BD MAX™ sample and control preparation
Table 1 presents the multiplex qPCR setup with the targets detected in each detector
channel of the BD MAX™ System.
Table 1: Multiplex qPCR setup
Detector
475/520
530/565
585/630
630/665
680/715
Channel
1
2
3
4
5
KPC
VIM
OXA-48 like
NDM
SPC*
Target
TM
Important points before starting: Refer to the BD MAX™ ExK
BD MAX™ System User’s Manual for detailed instructions.
DNA
DNA-1 kit user manual and
1. Sample preparation
• After specimen collection, transfer the bacterial cell suspensions to be analyzed in the
sample preparation area.
6
• Pipette 500 µL of the bacterial cell suspension (≈1 x 10 CFU/ml) into one DNA Sample
Buffer Tube SB-1 (supplied by BD with the DNA extraction kit, refer to Material required
but not supplied with the kit).
• Close the Sample Buffer Tube with a septum cap and vortex 10 second at low speed.
*SPC: Sample Preparation Control
2. qPCR Mix preparation
2.1 Calculate
culate the number of reactions for the specimen and controls (maximum 24 samples
in total in one run).
). Thaw reagents, mix well, spin down and keep on ice.
2.2 Prepare the qPCR reaction mix as described
describe in Table 2 using the CPE solution provided in
the Check-Direct
Direct CPE kit and the BD diluent provided in the BD MAX™ DNA MMK (SPC)
reaction kit. Multiply the CPE solution and the BD diluents solutions by the total number of
reactions calculated, plus 10% surplus to ensure
e
that you have enough qPCR reaction mix
for all reactions.
Table 2: qPCR reaction mix
2. Positive and negative control preparation
To validate the run, perform positive and negative control reactions for each Check
Check-Direct
CPE PCR run. The positivee and negative controls are supplied with the kit.
• Positive control(s)
Test the relevant positive control(s) provided in the kit. Pipette
ette 10 µL of positive control
(KPC (), VIM (), OXA () or NDM ()) and 500 µL of PCR-grade
grade water into one Sample
Buffer Tube. Vortex for 10 seconds. Positive controls may also be combined: add 10 µL
of each positive control to be tested and 500 µL of PCR-grade
grade water into one Sample
Buffer Tube. Vortex for 10 seconds.
• Negative control(s)
500 µL of PCRPipette 10 µL of the negative control (solution ) provided in the kit and 50
grade water into one Sample Preparation Reagents tube. Vortex for 10 second
seconds.
Check-Direct CPE for BD Max™ User manual
Version 1.3, Issued 24-01-2014
Component
BD Primer and Probe Diluent (12.5X)
CPE solution ()
Total volume for 1 strip
Volume per reaction strip
2 µl
10,5 µl
12,5 µl
3. Creating the Check-Direct
Direct CPE test
Important points before starting: Refer to BD MAX™ System User’s Manual for detailed
instructions on how to operate the BD MAX™ System and software v2.92. Skip step 3. if a
PCR test program has already been created for the Check-Direct
Check
CPE test.
parameters
3.1 Create a new Test, select Create test,, and enter the following parameters:
• Test Name: type Check-Direct CPE
• Extraction Type: select Exk DNA-1
4
•
•
•
•
•
Master Mix Format: choose Type 2 MMK (SPC),, Probes/Primers Add M
Manually
Channel detector Settings: set Gain and Threshold with parameters presented in
Table 3
GardRail: select Default
Test details: enter the PCR profile, see Table 4
Spectral Cross Talk tab: enter parameters presented in Table 5
Table 3: Gain parameters.
Detector
475/520
530/565
585/630
630/665
680/715
Gain
40
80
30
80
40
4.2. Prepare Unitized Reagents Strips:
4.2.a Snap the appropriate DNA extracti
raction Reagent tube (white cap) into positions 1 into
the DNA Strip, see Figure 1.
4.2.b Snap in a DNA MMK (SPC) Master
aster Mix tube (green/yellow cap) into position 2 of
the DNA strip, see Figure 1.
4.2.c Snap a Conical Tube into position
on 3 (Figure 1). Pipette 12.5 µl of qPCR mix (Table 2)
into the Conical
nical Tube in position 3. Avoid bubbles and make sure the liquid is at the
bottom of the tube.
Threshold
100
150
200
300
300
Table 4: Real-time protocol parameters.
Step Name
Denaturation
Step Name
Amplification &Detection
Profile Type
Hold
Profile Type
2 - temperature
Cycles
1
Cycles
45
Time (s) Temp(°C)
600
98
Time (s) Temp(°C)
15
98
62
60
Detect
NO
Detect
NO
YES
Figure 1: DNA Unitized Reagent Strip setup.
Table 5: Spectral cross-talk parameters.
475/520
530/565
Excitation
585/630
Channel
630/665
680/715
False Receiving Channel
475/520 530/565 585/630 630/665 680/715
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
7.4
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
4.4
3.2 Select Save Test.
4. BD MAX™ Rack set-up
4.1. Load the BD MAX™
™ system racks with the number of DNA Unitized Reagents Strips
necessary for the number of samples to test. Gently tap each strip to make sure all liquids
are at the bottom of their container.
Check-Direct CPE for BD Max™ User manual
Version 1.3, Issued 24-01-2014
5. BD MAX™ instrument set-up
5.1 Open the Run screen of the BD MAX™ System software v2.92.
5.2 In the Assay menu select Check-Direct
Direct CPE.
CPE
5.3 Enter the Sample Preparation reagent
nt tube
tu barcode using the barcode scanner (you can
also enter the barcode manually). Start with position 1 of rack A.
5.4 Place each of the Sample Buffer Tubes
ubes in their corresponding position in the BD MAX™
racks (with septum cap).
5.5
.5 Enter the specimen or patient identification information into the work list. Check that
each specimen or patient information correspond to its specific Sample Buffer Tubes in the
Rack.
5.6
.6 Load the Rack(s) into the BD MAX™ System. (Rack A is positioned on the left side of the
instrument and Rack B on the right side).
5.7 Load the BD MAX™ PCR cartridge(s).
5.8 Close the instrument door and select Start Run.
Run
5
BD MAX™ Results
Important points before starting: For a detailed description on how to analyze data, refer
to BD MAX™ System User’s manual.
Always visually inspect the amplification plot for each sample tested versus CT values
obtained with the software.
1. How to create and print data report
1.1 In the main menu, select Results and double click on the run to be analyzed.
1.2 Select the Run to analyze.
1.3 In the Print tab select the box for Results Protocol Details and PCR.
1.4 Select create report. The report can be saved as pdf file format. To print it select Print
Report.
Valid run reports:
• No BD MAX™ System failures during the run
• Positive controls with a CT value for the carbapenemase targets and sample processing
control (SPC) as depicted in Table 6.
• Negative control with a CT value of -1
1 in channel 1 (475/520), 2 (530/565), 3 (585/630)
and 4 (630/665) and a CT value of 29
2 ±3 for the sample processing control (SPC) in
channel 5 (680/715).
Table 6: Criteria for a valid run with Check-Direct
Direct CPE test.
CT 475/520
KPC
CT 530/565
VIM
CT 585/630
OXA-48 like
CT 630/665
NDM
CT 680/715
SPC
Positive controls
32 ±3
30 ±3
29 ±3
31 ±3
29 ±3
Negative sample
-1
-1
-1
-1
29 ±3
Sample Type*
* If observed CT values vary significantly from expected CT
C values , see FAQ and Troubleshooting section
2. Analysis
The BD MAX™ software reports CT values and amplification curves for each detector
channel of each specimen tested in the following way:
• CT value of 0 indicates that there was no CT value calculated by the software.
Amplification curve of the sample showing a “0” CT value must be checked manually.
• CT value of -1 indicates that no amplification process has occurred. Check that there is
no amplification curve for the sample with a CT value of -1 on the graphical results
results.
• Any other CT value should be interpreted in correlation
lation with the amplification curve (PCR
Analysis tab) and according to the interpretation method, see Table 66-7
3. Interpretation
3.1 Run validation
Verify that the real-time
time PCR run is valid before data interpretation of the results. Check
that there is no report of BD MAX™ System failure. Check the positive and negative control
amplification curves. Table 6 shows criteria for a valid real-time
time Check
Check-Direct CPE run on the
BD MAX™ System.
Expected CT values for the positive and the negative controls are given as an indication not a
definitive result. These values will depend on the threshold set by the software
software. If the
controls CT values are not as expected
ected refer to FAQ and Troubleshooting “3”.
Check-Direct CPE for BD Max™ User manual
Version 1.3, Issued 24-01-2014
3.2 Results interpretation
If the run has been validated, interpret
nterpret results as positive, negative or invalid with the CT
values obtained for the samples following
ing the
t guidelines outlined below and summarized in
Table 7.
• Positive carbapenemase samples will show a CT value in channel 1 (475/520), 2
(530/565), 3 (585/630) and/or 4 (630/665).
(630/665) Positive carbapenemase samples will also
show a CT value for the SPC in channel 5 (680/715).
• Negative carbapenemase samples will show no CT value in channel 1 (475/520), 2
(530/565), 3 (585/630) and 4 (630/665). In channel 5 (680/715) a CT value for the SPC is
expected of 29 ±3.
• Samples with carbapenemase target CT of -1, and with a SPC showing no CT value or a CT
≥ 32 means that the assay is not
ot valid and should be repeated,
repeated see FAQ and
Troubleshooting 3 to 6.
Table 7: Data interpretation guidelines.
KPC, VIM, OXA, NDM
CT values
SPC CT values
alues
Interpretation
YES
YES
Positive sample
-1
29 ±3
Negative sample
-1
-1 or >32
Invalid
6
Frequently asked questions (FAQ) & Troubleshooting
Refer to “the troubleshooting” section of the BD MAX™ System User’s Manual for additional
information
1.
2.
3.
Real-time results show no CT values or interpretation indicating that the sample is
invalid. Possible causes and troubleshooting:
• The PCR reaction has been inhibited by exogenous or endogenous substances.
Please repeat sample testing.
• The sample tested with Check-Direct
Direct CPE is negative and the internal control was
not amplified.
• The DNA extraction failed since the SPC was not detected.
• CPE Solution or The BD MAX™ DNA MMK (SPC) PCR mix was not added to the
assay. Please repeat the test.
• The BD MAX™ DNA MMK (SPC) PCR mix may have expired.
• A error in liquid handling has occurred: check unitized reagent strips and
microfluidic cartridge to determine where liquid handling problem has occurred
(example: air bubble in the cartridge) and re-run
run the sample. If the problem
persists, contact your local BD representative.
Troubleshooting for invalid results.
For Invalid results: Repeat test with the original specimen by preparing a new Sample
Buffer Tube. Alternatively, test newly collected specimen.
Real-time results show no CT values for the positive control or interpretation
indicating that sample is invalid?
Possible causes and troubleshooting:
• The positive control solution was not added.
• qPCR reaction mix (CPE Solution with Primer/Probe Diluent) was not added to the
assay. Please repeat the test.
• The BD MAX™ DNA MMK (SPC) PCR mix was not added or may have expired.
Check-Direct CPE for BD Max™ User manual
Version 1.3, Issued 24-01-2014
4.
flu
signals in all samples and detector
Real-time results show very low fluorescent
channels, including the internal control signal.
Possible causes and troubleshooting:
• The CPE solution containing the fluorescent probes and primers is degraded.
Please check expiration date,, the number of thaw/freezing cycle that the CPE
solution tube has undergo, and if the kit has been stored correctly.
• The BD MAX™ System
ystem can be responsible
respons
for these results. Please refer to BD
MAX™ User’s manual
ual or contact your BD local representative.
5.
ystem states an error or failure.
The BD MAX™ System
Refer to the BD MAX™ instrument user manual or contact your BD local representative.
6.
All amplification curves show a spike at the same point in time.
A problem with the power supply may have occurred. Verify that the system is
correctly connected to its un-interruptible
interruptible power supply and repeat experiment.
7.
I have left Solutions (CPE or Positive
ive control) out of the -20°C (-4˚F) storage.
These reagents must be stored at -20°C
20°C (-4°F)
(
for proper performance of the test. The
performance of the product cannott be fully guaranteed if these solutions were left out
of -20°C (-4˚F) for more than 24 hours.
s.
8.
Duplicate samples tested with Check-Direct CPE test do not yield identical results.
CT values of identical samples may vary
var between individual reactions. Large variations,
> 2 CT values, suggest pipetting errors
erro or other differences between the duplicate
samples.
7
Limitations
Check-Direct
Direct CPE uses a range of specific DNA markers to detect the presence of the
carbapenemase genes KPC, NDM, OXA-48,
48, and VIM, which currently represent the clinically
most prevalent carbapenemases.. The test detects all presently known variants of KPC,
NDM, OXA-48 and VIM, except VIM-7,
7, a rare variant only found in Pseudomonas
aeruginosa.. It should be noted that other rare carbapenemase gene families are not
detected.
Check-Direct CPE was developed for bacterial cell suspension.. The quality of the input DNA
is an important factor for obtaining reliable results with Check-Direct
Direct CPE. DNA must be
extracted from bacterial cell suspension validated with Check-Direct
Direct CPE and d
described in
this manual. The assay has been tested extensively with purified DNA from gram
gram-negative
bacteria, such as Escherichia, Salmonella, Klebsiella, Enterobacter
Enterobacter, Citrobacter and
Pseudomonas,, with excellent results. However, it may never be excluded that other Gram
Gramnegative bacteria
eria or certain strains of the above species will yield poor results. Check
Check-Direct
CPE cannot and does not make any representation or warranty that it is capable of correctly
detecting the carbapenemase genes in all gram-negative
negative species, subspecies or typ
types or in
all clinical sample source. Results may need to be confirmed by additional methodologies in
specific cases (e.g. for regulatory samples). Due to the high variability of bacterial genomes
it is possible that certain subtypes might not be detected. Thee test reflects the state of
knowledge of Check-Points Health B.V.
The presence of multiple bacterial species in a sample may hamper the interpretation of the
test. As with other diagnostic assays, the results of this test may only be interpreted in
combination
nation with additional laboratory and clinical data available to the responsible person.
Use of this assay is limited to appropriately qualified personnel, well
well-trained in performing
DNA-based molecular detection methods.
Key to symbols used
For In Vitro Diagnostic Use
Negative control
Catalog number
KPC positive control
Batch code
VIM positive control
IFU number
NDM positive control
OXA-48 positive control
CPE solution
Consult instructions for use
Temperature limitation
Use before YYYY-MM
Manufacturer
Contains sufficient for < n > tests
Despite the utmost care in the development and preparation of the protocol Check-Points
Check
cannot take any
responsibility for errors, omissions and/or future changes herein.
Literature Citation:: When describing a procedure for publication using this product, please refer to it as the CheckDirect CPE.
Notice to Purchaser:
This product is sold under license from PHRI Propertie
erties and may be used under PHRI Properties patent rights only
for human in vitro diagnostics, food testing, veterinary testing, or research.
research
Dye & quencher compounds in this product are sold
ld under
u
license from Biosearch Technologies, Inc. and protected
by U.S. and world-wide
wide patents either issued or in application. The license grant
g
covers human in vitro diagnostic
(IVD) applications
Trademarks
BD, BD MAX™ are trademarks Becton Dickinson GmbH
Technical assistance
support@check-points.com
+31 317 453 908
Check-Points Health BV
Binnenhaven 5
6709 PD Wageningen
The Netherlands
Check-Direct CPE for BD Max™ User manual
Version 1.3, Issued 24-01-2013
Tel: +31 317 453 908
Fax: +31 317 210 147
info@check-points.com
www.check-points.com
8
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