INNO-LiPA MYCOBACTERIA v2

KEY-CODE: FRI92473 80346 INNO-LiPA MYCOBACTERIA v2

28723 v2 2017-02-02

p 1/16

English

© Fujirebio Europe N.V.

INNO-LiPA MYCOBACTERIA v2

Manufactured by: Note changes highlighted

Fujirebio Europe N.V. Technologiepark 6 9052 Gent Belgium Tel. +32 9 329 13 29 BTW BE 0427.550.660 RPR Gent

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Fujirebio Europe N.V. Tel. +32 9 329 13 29 Fax +32 9 329 19 11 [email protected]

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80346 INNO-LiPA MYCOBACTERIA v2 / 28723 v2 / KEY CODE: FRI92473 p 2/16

TABLE OF CONTENTS

Symbols used ............................................................................................................................................ 2

Intended use .............................................................................................................................................. 3 Test Principle ............................................................................................................................................. 3 Reagents ................................................................................................................................................... 3

Description, preparation for use and recommended storage conditions ............................................. 3

Materials required but not provided ........................................................................................................... 4 Safety and environment ............................................................................................................................ 5 Specimens ................................................................................................................................................. 6 Remarks and precautions ......................................................................................................................... 6 Test procedure .......................................................................................................................................... 7

Procedural notes .................................................................................................................................. 7 Samples ................................................................................................................................................ 8 Hybridization ......................................................................................................................................... 8 Stringent wash ...................................................................................................................................... 8

Color development ............................................................................................................................... 9

Automated test procedures ....................................................................................................................... 9 Results ....................................................................................................................................................... 9

Reading ................................................................................................................................................ 9

Quality control ..................................................................................................................................... 10

Interpretation of the results ................................................................................................................. 10

Limitations of the procedure .................................................................................................................... 11

Test performance .................................................................................................................................... 11 Licenses .................................................................................................................................................. 12

Trademarks ............................................................................................................................................. 12 Interpretation chart .................................................................................................................................. 16

Symbols used

Manufacturer

In vitro diagnostic medical device

Batch code

Catalogue number

Use by

Consult instructions for use

Temperature limitation

Contains sufficient for <n> tests

Conjugate 100x

Conjugate diluent

Denaturation solution

Hybridization solution

Rinse solution 5x


Stringent wash solution

Strips

Substrate BCIP/NBT 100x

Substrate buffer

Danger

Warning

Line Probe Assay

Intended use

The INNO-LiPA MYCOBACTERIA v2 assay is a DNA probe test, for in vitro use, designed for the detection and identification of the genus Mycobacterium and 16 different mycobacterial species from liquid and solid culture, based on nucleotide differences in the 16S-23S ribosomal RNA (rRNA) spacer region.

Test Principle

INNO-LiPA MYCOBACTERIA v2 is based on the reverse hybridization principle. Biotinylated DNA material is hybridized with specific oligonucleotide probes immobilized as parallel lines on membrane-based strips. After hybridization, streptavidin labelled with alkaline phosphatase is added and bound to any biotinylated hybrid previously formed. Incubation with 5-bromo-4-chloro-3-indolyl phosphate and nitroblue tetrazolium (BCIP/NBT) chromogen results in a purple/brown precipitate.

To perform the INNO-LiPA MYCOBACTERIA v2 assay, amplification of the 16S-23S ribosomal rRNA spacer region should be carried out (see INNO-LiPA MYCOBACTERIA v2 Amp instructions for use). Amplification products are subsequently hybridized using 1 typing strip onto which 22 parallel DNA probes lines and 2 control lines are fixed (Figure 1).

INNO-LiPA MYCOBACTERIA v2: Steps involved Step 1 Amplification of 16S-23S rRNA spacer region of Mycobacterium species

(INNO-LiPA MYCOBACTERIA v2 Amp). Step 2 Hybridization and stringent wash of the amplified 16S-23S rRNA spacer

region with specific probes immobilized on a strip. Step 3 Color development. Step 4 Interpretation of the signal pattern.

Reagents

Description, preparation for use and recommended storage conditions

- When stored at 2 - 8°C, all test reagents, including the coated test strips, are stable until the expiry date of the kit. Do not freeze reagents. Do not use reagents beyond expiry date of the kit.

- The kit should be stored isolated from any source of contaminating DNA, especially amplified DNA products.

- All reagents and the plastic tubes containing the test strips should be brought to room temperature (20 - 25°C) approximately 30 minutes before use and should be returned to the refrigerator immediately after use.


- To minimise the possibility that strips curl before use, it is recommended to store the tube horizontally.

Reagents supplied:

Component Quantity Ref. Description

Strips 1x 20 57218 Containing 20 strips for INNO-LiPA MYCOBACTERIA v2.

Conjugate 100x 0.8 mL 60685 Streptavidin labeled with alkaline phosphatase in a buffer containing protein stabilizers and preservatives, to be diluted 1/100 in conjugate diluent before use. Prepare 2 mL conjugate working solution for each test trough + 2 mL in excess. After preparation, the conjugate working solution is stable for 24 hours at room temperature (20 - 25°C) when stored in the dark.

Conjugate diluent 80 mL 56951 Phosphate buffer containing NaCl, Triton, protein stabilizers and 0.01% MIT/<0.1% CAA as preservative.

Denaturation solution

1 mL 56718 Alkaline solution containing EDTA. Caution!!! The vial containing the denaturation solution should be closed immediately after use; prolonged exposure of this solution to air leads to rapid deterioration.

Hybridization solution

80 mL 57219 Containing SSC buffer with detergent and preservatives.

Stringent wash solution

200 mL 57220 Containing SSC buffer with detergent and preservatives.

Rinse solution 5x 80 mL 56721 Phosphate buffer containing NaCl, Triton, and 0.05% MIT/ 0.48% CAA as preservative, to be diluted 1/5 (1 part + 4 parts) in distilled or deionized water before use. Prepare 8 mL rinse working solution for each test trough + 10 mL in excess. The rinse working solution is stable for 2 weeks at 2 - 8°C.

Substrate BCIP/NBT 100x

0.8 mL 56954 5-Bromo-4-chloro-3-indolyl phosphate p-Toluidine salt and 4-Nitro-blue tetrazolium in dimethylformamide, to be diluted 1/100 in substrate buffer before use. Prepare 2 mL substrate working solution for each test trough + 2 mL in excess (substrate working solution can be prepared during conjugate incubation). The substrate working solution is stable for 24 hours at room temperature (20 - 25°C) if stored in the dark.

Substrate buffer 180 mL 56953 Tris buffer containing NaCl, MgCl2 and 0.01% MIT/ <0.1% CAA as preservative.

Incubation trays 3 - Containing 8 troughs each.

Reading Card Data reporting sheet

1 2

- -

For identification of positive probes. For storage of developed strips.

Materials required but not provided

- Water bath with shaking platform (80 rpm; with inclined lid; temperature adjustable to 62°C ± 0.5°C).

- Aspiration apparatus. - Calibrated thermometer. - Distilled or deionized water. - Disposable gloves. - Disposable sterile pipette tips (preferably cotton-plugged).


- Forceps for strip handling. - Graduated cylinders (10, 25, 50, and 100 mL). - Orbital, reciprocal or rocking platform shaker.

Recommendations: For an orbital shaker: The diameter of the circular motion should be equal or superior to 13 mm. Recommended speed for a 13-mm circular motion is 160 rpm For a reciprocal shaker: Recommended speed for the to-and-fro motion is 80 movements per minute. For a rocking platform shaker: The shaking angle should not exceed 13° to avoid spilling of liquid. Recommended speed is 50 rpm.

- Adjustable pipettes to deliver 1 - 20 µL, 20 - 200 µL, and 200 - 1000 µL. - Dispensing Multipette (Eppendorf, optional). - Timer, 2 hours (± 1 minute). - Vortex mixer or equivalent.

Safety and environment

Please refer to the Safety Data Sheet (SDS) and product labelling for information on potentially hazardous components. The most recent SDS version is available on the website www.fujirebio-europe.com.

Danger Contains sodium hydroxide H314 P260 P280 P303+P361+P353 P305+P351+P338 P310 P363

Warning Contains 2-chloroacetamide H317 P280 P261 P362+P364 P333+P313 P302+P352

Danger Contains N,N-Dimethylformamide, 5,5'-diphenyl-3,3'-bis (4-nitrophenyl)-2,2'-(3,3'-dimethoxybiphenyl-4,4'-ylene)ditetrazolium dichloride and methanol H312 H332 H319 H360D P261 P280 P201 P303+P361+P353 P305+P351+P338 P308+P313

Hazard statements H312 Harmful in contact with skin. H314 Causes severe skin burns and eye damage. H317 May cause an allergic skin reaction. H319 Causes serious eye irritation. H332 Harmful if inhaled. H360D May damage the unborn child.

Precautionary statements P201 Obtain special instructions before use. P260 Do not breathe mist/vapours/spray. P261 Avoid breathing mist/vapours/spray. P280 Wear protective gloves/protective clothing/eye protection/face

protection.

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P302+P352 IF ON SKIN: Wash with plenty of water/… P303+P361+P353 IF ON SKIN (or hair): Take off immediately all contaminated

clothing. Rinse skin with water/shower. P305+P351+P338 IF IN EYES: Rinse cautiously with water for several minutes.

Remove contact lenses, if present and easy to do. Continue rinsing.

P308+P313 If exposed or concerned: Get medical advice/attention. P310 Immediately call a POISON CENTER/doctor/... P333+P313 If skin irritation or rash occurs: Get medical advice/attention. P362+P364 Take off contaminated clothing and wash it before reuse. P363 Wash contaminated clothing before reuse.

- Only adequately trained personnel should be permitted to perform the test procedure.

- Specimens should always be handled as potentially infectious. Therefore, all blood components and biological materials should be considered as being potentially infectious and should be handled as such.

- All blood components and biological materials should be disposed of in accordance with established safety procedures. Autoclave for at least 15 minutes at 121°C. Incinerate disposable material. Mix liquid waste with sodium hypochlorite so that the final concentration is ± 1%

sodium hypochlorite. Allow to stand overnight before disposal. CAUTION: Neutralize liquid waste that contains acid before adding sodium

hypochlorite. - Use of personal protective equipment is necessary: gloves and safety spectacles

when manipulating dangerous or infectious agents. - Waste should be handled according to the institution's waste disposal guidelines.

All federal, state, and local environmental regulations should also be observed.

Specimens

This test utilizes biotinylated amplified DNA material. An amplification kit, utilizing biotinylated oligonucleotide primers, is available as an accompanying tool for amplification of 16S-23S rRNA spacer region of Mycobacterium species (INNO-LiPA MYCOBACTERIA v2 Amp) from the specimen: fully grown cultured samples (liquid or solid culture) from e.g. sputum. This amplified material is used on INNO-LiPA MYCOBACTERIA v2 to detect the Mycobacterium genus and the following Mycobacterium species: M. tuberculosis complex, M. kansasii, M. xenopi, M. gordonae, M. genavense, M. simiae, M. marinum and M. ulcerans, M. celatum, MAIS, M. avium, M. intracellulare, M. scrofulaceum, M. haemophilum, M. chelonae complex, M. fortuitum complex and M. smegmatis.

Remarks and precautions

- Do not mix reagents with different lot numbers. - Avoid microbial contamination of reagents. - Use tweezers to handle strips. Do not touch strips with your hands as the oils from

your hands could interfere with hybridization and color development. - Use only pencil to write on the strips. The assay reagents may remove ink from the

strips.


- Make sure that the test strips are placed in the troughs with the side bearing the coated membrane facing upwards (this side is marked).

- The strips are designed to be used only once! - All vessels used to prepare conjugate and substrate working solutions should be

cleaned thoroughly and rinsed with distilled water. - Use a new sterile pipette tip (cotton-plugged) for each specimen. - To prevent PCR contamination, maximize the physical separation of the pre- and

post-amplification steps. Do not return samples, equipment, or reagents to the area where you performed the previous step. If you need to return to a previous work area, first perform the appropriate anti-contamination safeguards.

- Do not reuse the troughs.

Test procedure

Please read Remarks and precautions before performing the test. NOTE: - Throughout the different incubation steps, the test strips should always remain in the

same trough. - Before incubation, check the temperature of the water bath using a calibrated

thermometer, and adjust the temperature if necessary before placing the tray in the water bath. Always close the lid.

Procedural notes

- The hybridization and stringent wash incubation at exactly 62°C ± 0.5°C are the most critical steps to avoid false-positive (temperature too low) or false-negative/very weak signals (temperature too high). A shaking water bath (80 rpm) with a closed lid allows good control of temperature variations. Strict temperature control with a calibrated thermometer is necessary.

- The shaking of the solutions over the strips is critical in achieving maximum sensitivity and homogeneous staining. During shaking, the strip surface should be completely submerged. Do not use a hot air shaker.

- The amplitude of the motion generated by both the shaking water bath (hybridization procedure) and the orbital, reciprocal shaker or rocking platform (color development procedure) is critical in achieving maximum sensitivity and homogeneous staining. The amplitude should be as high as possible. However, spilling of liquid over the edges of the troughs must be avoided!

- For hybridization and stringent wash, the troughs should be placed on the shaking platform of the water bath. Adjust the water level to between 1/3 and 1/2 of the height of the trough. Make sure that the troughs do not float on the water. The water should be in direct contact with the troughs.

- Shaking during incubation of the strips should be performed in such a way that both the liquid and the test strips move back and forth in the trough, without liquid being spilled over the edge of the troughs.

- Always close the lid of the water bath during incubation. - Do not cover the tray. - The liquid is aspirated from the trough with a pipette, preferably attached to a

vacuum aspirator. The tray is held at an angle to allow all liquid to flow to one end of the trough. Add 2 mL of the appropriate solution to each trough and follow the


protocol. Repeat this step as many times as are indicated in the test procedure (a dispensing Multipette (Eppendorf) is useful for this purpose). NOTE: Do not allow the strips to dry between the washing steps. Make sure the surfaces of the strips are not damaged when aspirating. Preferably

aspirate the liquid at the top of the strip above the marker line. Make sure the whole strip is thoroughly washed by complete submersion in the

solution. Alter the speed of the shaker when necessary.

Samples

1. Mycobacterial 16S-23S rRNA spacer amplified product (use 10 µL). 2. Blank amplified control sample (negative control) (use 10 µL).

Hybridization

1. Heat a shaking water bath to 62°C ± 0.5°C. Check the temperature using a calibrated thermometer, and adjust the temperature if necessary. Prewarm the hybridization solution and stringent wash solution to at least 37°C and do not exceed 62°C. Mix before use. All crystals should be dissolved.

2. Using forceps, remove the required number of INNO-LiPA MYCOBACTERIA v2 strips from the tube (1 strip per sample) and pencil an identification number above the blue marker line on the strip. Always include a strip for the negative control sample (no DNA added).

3. Take the required number of test troughs (1 trough per strip) and place them in the tray.

4. Pipette 10 µL denaturation solution into the upper corner of each trough. NOTE: Close the vial immediately after use.

5. Add either 10 µL amplified biotinylated product or 10 µL negative control sample to the denaturation solution and carefully mix by pipetting up and down. Always use cotton-plugged sterile pipette tips. Allow denaturation to proceed for 5 minutes at room temperature (20 - 25°C).

6. Shake the prewarmed hybridization solution and gently add 2 mL to the denatured amplified product in each trough. Take care not to contaminate neighboring troughs during pipetting.

7. Immediately place the strip into the trough with the marked side (blue Marker Line) of the membrane facing upwards. The strips should be completely submerged in the solution. NOTE: Wear disposable gloves and use forceps.

8. Place the tray in the 62°C ± 0.5°C shaking water bath (approximately 80 rpm; see “Procedural notes”), close the lid, and incubate for 30 ± 3 minutes.

Stringent wash

1. After hybridization, remove the tray from the water bath. 2. Hold the tray at a low angle and aspirate the liquid from the trough with a pipette,

preferably attached to a vacuum aspirator. Add 2 mL pre-warmed stringent wash solution into each trough and rinse by rocking the tray for 60 ± 30 seconds at room temperature. Aspirate the solution from each trough.

3. Repeat this washing step once see also Procedural notes.


4. Finally, aspirate the solution and incubate each strip in 2 mL pre-warmed stringent wash solution in the shaking water bath at 62°C ± 0.5°C for 10 ± 2 minutes. Close the lid of the water bath. Before incubation, check the temperature of the water bath using a calibrated thermometer, and adjust the temperature if necessary. Always close the lid. NOTE: Prepare rinse working solution and conjugate working solution during

stringent wash incubation.

Color development

All subsequent incubations are carried out at 20 - 25°C on a shaker. During the incubations, the liquid and test strips should move back and forth in the trough for homogeneous staining.

1. Wash each strip twice for 60 - 90 seconds using 2 mL rinse working solution (see “Procedural notes”). Aspirate.

2. Add 2 mL of conjugate working solution to each trough and incubate for 30 ± 3 minutes while shaking. Aspirate. NOTE: Prepare substrate working solution about 10 minutes prior to the end of the

conjugate incubation. 3. Wash each strip twice for 60 - 90 seconds using 2 mL rinse working solution and

wash once more using 2 mL substrate buffer. Aspirate. 4. Add 2 mL of substrate working solution to each trough and incubate for

30 ± 3 minutes while shaking. Aspirate. 5. Stop the color development by washing the strips twice in 2 mL distilled water while

shaking for at least 3 minutes. 6. Using forceps, remove the strips from the troughs and place them on absorbent

paper. Let the strips dry completely before reading the results. Store the developed and dried strips in the dark.

Automated test procedures

Instruments and associated protocols are available from Fujirebio Europe N.V. (see www.fujirebio-europe.com/automation).

Results

Reading

Figure 1 illustrates the position of the different oligonucleotide probes on the INNO-LiPA MYCOBACTERIA v2 strip. A line is considered positive when a clear purple/brown band appears at the end of the test procedure

Figure 1: Location of the different probes on the INNO-LiPA MYCOBACTERIA v2 strip. A blue marker line is drawn on the top of the strips for orientation

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Quality control

- The uppermost blue line is the marker line. This line controls for the positioning of the plastic reading card.

- The first positive line is the conjugate control line. This line controls for the addition of reactive conjugate and substrate working solution during the detection procedure. It should always be positive and should have approximately the same intensity on each strip in the same test run.

- The second line is the Mycobacterium genus probe line (MYC genus on the reading card and data reporting sheet) which detects the presence of Mycobacterium in the test sample, and indicates whether or not an appropriate amount of amplified material was added for hybridization as the intensity of other positive lines must be compared with the intensity of this line.

- The negative control should be blank except for the conjugate control line. This demonstrates that no contamination has occurred.

Interpretation of the results

The presence of a clearly visible line is considered a positive reaction. Identify all line numbers which are positive on the INNO-LiPA MYCOBACTERIA v2 strip and determine the Mycobacterium species by using the INNO-LiPA MYCOBACTERIA v2 interpretation chart.

Line Probe Taxa reacting with the probe

2 MYC genus Presence of Mycobacterium in the test sample

3 *MTB M tuberculosis complex: M. tuberculosis, M. bovis, M. microti, M. africanum

4 *MKA-1 M. kansasii (group I)

5 *MKA-2 M. kansasii (group II)

6 *MKA-3 M. kansasii (group III, V) M. kansasii (group IV), M. gastri

7 MXE M. xenopi

8 *MGO M. gordonae

9 MGV M. genavense

10 MSI M. simiae

11 *MMU M. marinum + M. ulcerans

12 MCE M. celatum

13 *MAIS M. avium, M. intracellulare, M. scrofulaceum, MAC, M. malmoense

14 MAV M. avium, M. paratuberculosis, M. silvaticum

15 *MIN-1 M. intracellulare (sequevars Min-A, -B, -C and -D)

16 *MIN-2 M. intracellulare (sequevar Mac-A)

17 MSC M. scrofulaceum

18 MML M. malmoense

19 MHP M. haemophilum

20 *MCH-1 M. chelonae complex (group I, II, III, IV, M. abscessus)

21 *MCH-2 M. chelonae complex (group III, M. abscessus)

22 *MCH-3 M. chelonae (group I)

23 *MFO M. fortuitum - M. peregrinum complex

24 MSM M. smegmatis

* Remarks: - Line 3: Probe line 3 (MTB) displays a positive reaction with M. tuberculosis, M.

bovis, M. microti, M. africanum. - Line 4 to 6: Discrimination of M. kansasii into 5 groups is based on data derived from

16S-23S rRNA spacer nucleoticle sequences.


- Line 8: Probe line 8 (MGO) reacts positive with M. gordonae. Note that a weak false positive reaction may be observed with M. simiae isolates.

- Line 11: Probe line 11 (MMU) reacts with the species M. ulcerans and M. marinum. Both Mycobacterium species share the same spacer sequences.

- Line 13: Probe line 13 (MAIS) displays a positive reaction for all M. avium, M. intracellulare, M. scrofulaceum, and MAC isolates. Also M. malmoense reacts with this probe. A weak positive reaction with this probe may be observed for M. haemophilum isolates, which are identified by a positive MHP probe on line 19.

- Line 15 and 16: Probe line 15 (MIN-1) displays a positive reaction for M. intracellulare sequevars Min-A, -B, -C and -D. The probe MIN-2 (line 16) reacts with M. intracellulare sequevar Mac-A.

- Line 20 to 22: According to 16S-23S rRNA nucleotide sequences, M. chelonae complex isolates (= M. chelonae and M. abscessus) can be subdivided into four genotypical clusters, cluster I, II, III, and IV; M. abscessus is included in cluster III. Probe MCH-1 is a general M. chelonae-complex probe detecting all four clusters (including M. abcessus). Probe MCH-2 reacts specifically with cluster III which encompasses M. abscessus. Probe MCH-3 reacts specifically with cluster I isolates which are also predominantly isolated from human samples. Note that a weak false positive reaction may be observed with line 20 (MCH-I) with M. xenopi isolates.

- Line 23: Probe line 23 (MFO) displays a positive reaction for isolates belonging to the M. fortuitum - M. peregrinum complex. M. smegmatis also reacts positive with this probe, but is clearly distinguished from this complex by a positive MSM probe on line 24.

Limitations of the procedure

- Use of this product should be limited to personnel well trained in the techniques of amplification and hybridization.

- Good laboratory practice as well as careful performance of the procedures specified will allow specific amplification.

- Polymerase inhibition might be the reason for complete failure of the assay! - Powder from disposable gloves and sodium hypochlorite has an inhibiting effect on

amplification. - A polymorphism in the target region, although rare, may result in a false positive or

negative reaction of one of the probe lines.

Test performance

The INNO-LiPA MYCOBACTERIA v2 was evaluated at one Belgian center (Antwerp) and internally on a selected sample population, representing predominantly those species for which probes were added or improved on the INNO-LiPA MYCOBACTERIA v2.

A total of 73 mycobacterium specimens, 21 non-mycobacterium species and 25 media were tested at the center. All 73 Mycobacterium strains reacted with the Mycobacterium genus (MYC) probe. Sixty-six of these isolates gave concordant results with the reference method after initial testing, while after discrepancy testing 71 of the 73 isolates were concordant. The 2 remaining discordant samples were M. intracellulare 2 isolates that were correctly classified as members of the MAIS complex.


All 11 mycobacterial species tested in-house reacted with the Mycobacterium genus (MYC) probe and 10 of these strains gave an interpretable LiPA result concordant with the reference method.

Overall, diagnostic sensitivity was 98.8%. Accuracy after initial testing was 91.6% and after discrepancy testing, 97.6%. Amplification was obtained for 20 of the 21 non-mycobacterial species and none of the amplified material reacted with the Mycobacterium genus (MYC) probe (100% specificity). The 25 medium samples were negative on strip except for the conjugate control line.

Licenses

The purchase of this product allows the purchaser to use it for the performance of diagnostic services for human in vitro diagnostics. No general patent or other license of any kind other than this specific right of use from purchase is granted hereby.

Trademarks

INNO-LiPA, and Auto-LiPA are trademarks of Fujirebio Europe N.V., registered in US and other countries.





Interpretation chart

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INNO-LiPA MYCOBACTERIA v2