SureTect Salmonella species PCR Assay PDF

Thermo Scientific™ SureTect™ Salmonella species PCR Assay PT0100A PT0100A Revision Date: 27th June 2017  SureTect Salmonella species PCR Assay PT0100A………………..96 Tests...

Thermo Scientific™ SureTect™ Salmonella species PCR Assay PT0100A PT0100A Revision Date: 27th June 2017  SureTect Salmonella species PCR Assay PT0100A………………..96 Tests EN 1. INTENDED USE The Thermo Scientific™ SureTect™ Salmonella species PCR Assay is a real-time PCR test intended to be used in conjunction with either: The Thermo Scientific™ PikoReal™ Real-Time PCR Instrument and Thermo Scientific™ SureTect™ Software Or Applied Biosystems™ 7500 Fast Real-Time PCR System and Applied Biosystems™ RapidFinder Express Software version 2.0 for the detection and identification of Salmonella species from food or food manufacturing environmental samples in laboratories undertaking microbiological analysis. 2. SUMMARY Real-time Polymerase Chain Reaction (PCR) technology is used for amplifying DNA in a reaction tube which enables detection and analysis of the DNA. SureTect PCR assays are designed for the identification of micro-organisms from foods and food manufacturing environmental samples 3. PRINCIPLE OF THE TEST The PCR pellets used in the SureTect assays contain lyophilized (freeze-dried) target-specific primers, dye labelled probes and PCR master mix components. Probes are short oligonucleotides with a quencher molecule at one end that, when not bound to target DNA, greatly reduces fluorescence from the dye at the opposite end. The oligonucleotides target unique DNA sequences found only in the target micro-organism. If present, the target DNA will be amplified and the increasing fluorescent signal generated will be detected by the Real-Time PCR Instrument and interpreted by the software The SureTect assays are based on Solaris™ qPCR technology. The probes have a molecule called Minor Groove Binder (MGB) attached to one end, which enhances the probe-template DNA bond and yields a better signal-to-noise ratio by lowering background fluorescence. Results are achieved in around one hour and twenty minutes of loading the prepared sample in the real-time PCR instrument and are displayed on the PC screen as simple positive or negative symbols with amplification plots also easily accessible for review. The SureTect Salmonella species PCR Assay targets unique DNA sequences specific to Salmonella species. The SureTect Salmonella species PCR Assay includes all of the necessary reagents for bacterial DNA release and PCR. Enriched samples are pipetted into pre-filled Lysis Tubes, along with Proteinase K and lysis reagent 2, before incubation to lyse any bacterial cells present in the sample and release their DNA into solution. The lysate is then loaded into the SureTect Salmonella species PCR Tube to re-hydrate the PCR pellet which contains all of the necessary components and reagents for PCR, including a probe, primers and DNA template for the internal amplification control (IAC). The PCR Tubes are then sealed, loaded into either the PikoReal or 7500 Fast PCR Instrument and the run started using the software relevant to the instrument. On complete of the run the interpreted results will be clearly displayed by the software and can be reported, stored, printed off and downloaded as required. 2 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay 4. SYMBOL DEFINITIONS Catalogue number Contains sufficient product for tests Consult instructions for use (IFU) Temperature limitation (Storage temperature) Batch code (Lot number) Use by (Expiration date) Manufacturer 5. KIT CONTENTS, STORAGE AND PREPARATION FOR USE The SureTect Salmonella species PCR Assay contains all the necessary reagents for DNA release and real-time PCR for 96 tests. Contents Lysis Reagent 1 Tubes (PT0010A) 96 pre-filled, sealed tubes (in 12x8 format). Each tube contains Lysis Reagent 1 (clear, pale blue liquid containing fine white particles). One tube is required for each SureTect PCR Assay. Lysis Tube Caps (PT0020A) 12 strips of 8 caps. The cap strips may be cut to enable the required number of caps to be selected for each run. Proteinase K (PT0050B) 1 capped tube containing Proteinase K (clear colorless liquid). SureTect Salmonella PCR Tubes (PT0151A) 12x8 pre-filled, sealed strips. Each tube contains one SureTect Salmonella PCR pellet (pale yellow). Strips can be cut to enable the required number of tubes to be selected for each run. PCR Caps (PT0040A) 12 strips of 8 caps. The cap strips may be cut to enable the required number of caps to be selected for each run. Storage The reagents will remain stable until the expiry date stated on the packaging when stored and handled as directed. The complete box and contents should be stored in the dark at 2-8°C when not in use. Do not use the reagents after the expiration date indicated on the label. SureTect PCR Strips may be cut, enabling unused materials to be returned to the refrigerator after a short time. The PCR Tubes should be brought to room temperature before opening. This can be facilitated by removing the PCR Tubes required from the packaging and placing on the bench for around 10 minutes before use. 3 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay 6. MATERIALS REQUIRED BUT NOT PROVIDED All of the required items listed below are also available from Thermo Fisher Scientific. Please contact your kit supplier for further information. Other culture media formats such as prepared media and Dry-Bags™ are available; please contact your local supplier for details. All items required for sample lysis and PCR set-up can be provided as part of the SureTect PCR System Start-Up Package. Please contact your local supplier for further information. Enrichment Suitable enrichment medium for growth of Salmonella species from food samples. The use of Buffered Peptone Water (ISO) has been validated by both AOAC-RI and NF VALIDATION™. The use of Buffered Peptone Water supplemented with 12mg/l novobiocin or alternatively Oxoid ONE Broth™ Salmonella supplemented with 12mg/l novobiocin have been validated by NF VALIDATION when testing dairy products (including raw milk) and pet foods. The use of Oxoid Cocoa Samples Recovery (CSR) Broth has been validated during the AOAC-RI PTM validation for chocolate matrices: The use of BPW (ISO) supplemented with 20mg/l novobiocin has been validated during the AOAC-RI PTM validation when testing sprouted seeds: Sample Preparation Homogenizer Bags for 25g samples (Fisher Scientific product code: BAJ–820-010N, 500 bags), or Filtered Homogenizer Bags for 25g samples (Fisher Scientific product code: BAJ-830-010G, 200 bags) Sample pipette (1-10ml) and extra long filtered pipette tips (1-10ml) Microfuge tubes (1.5ml) Sample Tube Rack CapEase™ tool Lysis Tube Rack Adjustable single channel pipette and pipette tips Two Boekel Scientific™ thermal block heaters (supplied as part of the SureTect starter pack) Optional Lysis Components Repeater pipettor (and filtered tips (for faster, easier addition of Proteinase K to multiple Lysis tubes) Multi-channel pipette (and filtered tips (to be used in place of the adjustable single channel pipette for processing multiple samples in parallel) PCR set-up Rack for PCR Tubes Multi-channel pipette and filtered tips Empty PCR Tube strips and caps (required to balance lid pressure if only 1-8 samples are processed) 4 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay The SureTect assay can be analysed using either the SureTect PikoReal Real-Time PCR Instrument combined with SureTect Software or the Applied Biosystems 7500 Fast Real-Time PCR System combined with RapidFinder Express Software version 2.0. NOTE: When using the PikoReal Real-Time PCR Instrument, the instrument must be connected to a PC loaded with the SureTect Software version 1.2 and assay specific kit file version 1.2.7.34 or higher. NOTE: When using the Applied Biosystems 7500 Fast Real-Time PCR System, the instrument must be connected to a PC loaded with Windows 7 and RapidFinder Express Software version 2.0 and assay specific kit file version 1. The 7500 Fast Instrument must have been calibrated according to the instructions in the Applied Biosystems 7300/7500/7500 Fast Real Time PCR System Installation and Maintenance Guide8. Please review the appropriate software manual or contact our technical support team for details of kit components or PC specifications (Europe/ROW: email: [email protected] telephone: +44 (0)1256 694238/ USA: email: [email protected] telephone 1-800-255-6730) for PC specifications. Equipment required but not provided as part of the SureTect System The following items are not supplied as part of the SureTect System but can be purchased from Thermo Fisher Scientific Microbiology. Homogenizer Laboratory Blender (available from Thermo Fisher Scientific, DB5000A, or similar) Homogenizer bag rack (DB5002A, or equivalent) Incubators (37°C ±1°C, 41.5°C ±1°C) Sterile water, for use when running the SureTect assay on the Applied Biosystems 7500 Fast (available from Thermo Fisher Scientific, BO0209B, or similar). Confirmation of positive Results Suitable culture medium for isolation and identification of Salmonella colonies. The use of Oxoid Brilliance™ Salmonella Agar is recommended and has been validated by both AOAC-RI and NF VALIDATION. 7. TEST PROCEDURE The SureTect Salmonella species PCR assay has been validated for a wide range of sample types using the enrichment protocols details below. For preparation of initial suspensions, follow the instructions detailed in ISO 6887 parts 1-53 and/or ISO 65794 standards. Comply with Good Laboratory Practices (refer to ISO 7218 5). Additionally, it is advised that users follow the general requirements described in ISO 22174:20056 when using PCR methods. For samples where no specific protocol has been validated during the AOAC-RI or AFNOR Certification validation studies, it is strongly recommended that a full evaluation of a suitable enrichment procedure is undertaken before implementing the test for that sample type. Depending on the sample type it may be necessary to modify the enrichment procedure, e.g. culture medium, selective agents, incubation time/conditions etc., to obtain satisfactory results. It is recommended that any non-validated sample preparation and enrichment procedure is compared to a suitable reference method to help determine the appropriate pre-treatment and enrichment procedures appropriate for specific sample type, e.g. refer to ISO 6887 Parts 1-53 or ISO 65794. If you would like more information, including the recommended minimum enrichment time for your specific sample type, please contact our technical support team (Europe/ROW: email: [email protected] telephone: +44 (0)1256 694238/ USA: email: [email protected] telephone 1-800-255-6730). 5 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay 7.1 Sampling and enrichment When preparing culture media for enrichment and confirmation steps in-house, carefully follow the instructions provided by the supplier. In the context of NF VALIDATION: Enrichment protocols for use with the PikoReal Real-Time PCR Instrument and SureTect Software Raw beef meat (short enrichment protocol): Weigh 25g of the sample to be tested into a homogenizer bag and add 1:10 ratio of pre-warmed (41.5°C) Buffered Peptone Water (ISO). Homogenize thoroughly for 30 seconds to one minute using a homogenizer or by hand for samples containing hard particles, such as bone, etc. Incubate according to table below. NOTE: The short protocols of detection are sensitive to incubation conditions. It is required to scrupulously respect the conditions of temperature indicated in the technical specification. Notably, you must verify that the temperature of pre-warming of the enrichment broth reaches the required temperature. The time of preparation of samples, delay between the end of the pre- warming step of the enrichment broth and the beginning of the incubation step with the food sample does not exceed 45 minutes. Using a ventilated incubator during the incubation is recommended. Remove the enriched sample from the incubator and remove around 1.5ml and dispense into a new microfuge tube and close until ready to process the sample to the next stage. Store at 2-8°C for up to 72 hours if not processing immediately. NOTE: In the context of NF VALIDATION, test portions weighing more than 25g have not been tested. Remove the enriched sample from the incubator and mix the liquid in the homogenizer bag by hand for a few seconds. Allow any food particles to settle. Open the homogenizer bag and using a pipette with an extra long filtered pipette tip remove around 1.5ml and dispense into a new microfuge tube and close until ready to process the sample to the next stage. Store at 2-8°C for up to 72 hours if not processing immediately. NOTE: The 1.5ml portions of enriched samples can be stored at 2-8oC and retained for confirmation of PCR positive results and in case the PCR analysis needs to be repeated (for up to 72 hours post enrichment). Meat products, poultry, seafood, vegetable products, egg products Weigh 25g of the sample to be tested into a homogenizer bag and add 1:10 ratio of Buffered Peptone Water (ISO). Incubate according to table below. Dairy products Weigh 25g of the sample to be tested into a homogenizer bag and add 1:10 ratio of either: (1) Buffered Peptone Water (ISO) supplemented with 12mg/l novobiocin or (2) ONE Broth Salmonella supplemented with 12mg/l novobiocin. Incubate according to table below. 6 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay Pet foods: Weigh 25g of the sample to be tested into a homogenizer bag and add 1:10 ratio of ONE Broth Salmonella supplemented with 1 vial of ONE Broth Salmonella supplement for 225 ml of ONE Broth Salmonella. Homogenize samples thoroughly for 30 seconds to one minute using a homogenizer or by hand for samples containing hard particles, such as bone, etc. Incubate according to the table below. NF VALIDATION validated enrichment conditions for use when analysing samples with the SureTect PikoReal and SureTect Software Category Incubation temperature Incubation time Raw beef meat (short 41.5°C ±1°C 8-24 h protocol) Meat, Poultry, Seafood, 37°C ±1°C 20-24 h vegetables, egg products Dairy 37°C ±1°C 20-24 h Pet Food 37°C ±1°C 20-24 h Remove the enriched sample from the incubator and remove around 1ml and dispense into a new microfuge tube and close until ready to process the sample to the next stage. Store at 2-8°C for up to 72 hours if not processing immediately. NOTE: In the context of NF VALIDATION, test portions weighing more than 25g have not been tested. Enrichment protocols for use with the Applied Biosystems 7500 Fast Real-Time PCR System and RapidFinder Express Software version 2.0 In the context of NF VALIDATION: Raw beef meat (short enrichment protocol): NOTE: In the context of NF VALIDATION, test portions weighing more than 25g have not been tested. NOTE: Filtered homogenizer bags should be used to help with fat and particle separation Weigh 25g of the sample to be tested into a homogenizer bag and add 1:10 ratio of pre-warmed (41.5°C) Buffered Peptone Water (ISO). Homogenize thoroughly for 30 seconds to one minute using a homogenizer or by hand for samples containing hard particles, such as bone, etc. Incubate according to table below. NOTE: The short protocols of detection are sensitive to incubation conditions. It is required to scrupulously respect the conditions of temperature indicated in the technical specification. Notably, you must verify that the temperature of pre-warming of the enrichment broth reaches the required temperature. The time of preparation of samples, delay between the end of the pre- warming step of the enrichment broth and the beginning of the incubation step with the food sample does not exceed 45 minutes. Using a ventilated incubator during the incubation is recommended. 7 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay Remove the enriched sample from the incubator and remove around 1.5ml and dispense into a new microfuge tube and close until ready to process the sample to the next stage. Store at 2-8°C for up to 72 hours if not processing immediately. NOTE: The 1.5ml portions of enriched samples can be stored at 2-8oC and retained for confirmation of PCR positive results and in case the PCR analysis needs to be repeated (for up to 72 hours post enrichment). Meat products: NOTE: In the context of NF VALIDATION, test portions weighing more than 25g have not been tested. Weigh 25g of the sample to be tested into a homogenizer bag and add 1:10 ratio of Buffered Peptone Water (ISO) supplemented with 12mg/l novobiocin. Incubate according to table below. Dairy products Weigh 25g of the sample to be tested into a homogenizer bag and add 1:10 ratio of either: (1) Buffered Peptone Water (ISO) supplemented with 12mg/l novobiocin or (2) ONE Broth Salmonella supplemented with 12mg/l novobiocin. Incubate according to table below. Powdered infant formula (probiotic and non-probiotic): NOTE: In the context of NF VALIDATION, test portions weighing more than 25g have not been tested. Incubate according to table below. Weigh 25g of the sample to be tested into a homogenizer bag and add 1:10 ratio of Buffered Peptone Water. Seafood and Vegetable products NOTE: In the context of NF VALIDATION, test portions weighing more than 25g have not been tested. Weigh 25g of sample to be tested into a homogenizer bag and add 1:10 ratio of Buffered Peptone Water (ISO) supplemented with 12mg/l novobiocin. Incubate according to table below. Production environment samples: Pre-moisten a sterile sampling swab, cloth or sponge in a suitable diluent (e.g. sterile Peptone water). For sampling of areas that have been cleaned or treated with disinfectants and other cleaning agents, pre-moisten the swab, cloth or sponge with a neutralizing broth, such as Dey- Engley Broth, prior to sampling. Sample the entire area by rubbing the swab, cloth or sponge in both a horizontal and vertical direction across the entire sampling area. Next, place the swab, cloth or sponge into the original packaging (suitable for transport). Samples may be held for up to 2 hours at room temperature or 8 hours in the refrigerator prior to proceeding with the next step. Add swabs to 10ml, sponges to 100ml, or wipes and 25g of dust or solid production environment samples and 25ml of liquid samples to 225ml of Buffered Peptone Water at room temperature. Homogenize samples, then incubate according to table below. 8 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay NF VALIDATION validated enrichment conditions for use when analysing samples with the Applied Biosystems 7500 Fast and RapidFinder Express Software 2.0 Category Temperature Time Meat short enrichment 41.5°C ±1°C 9-24 h Meat 37°C ±1°C 20-24 h Dairy 37°C ±1°C 20-24 h Powdered Infant Formula 37°C ±1°C 16-20 h Seafood and Vegetables 37°C ±1°C 20-24 h Production environmental 37°C ±1°C 20-24 h samples In the context of AOAC-RI Performance Tested MethodsSM certification Enrichment protocols for use with the SureTect PikoReal Real-Time PCR Instrument and SureTect Software or Applied Biosystems 7500 Fast Real-Time PCR System and RapidFinder Express Software version 2.0 Food samples: Weigh the sample to be tested into a homogenizer bag and the appropriately validated enrichment broth (see table below and section 11, “Performance Validation” for specific AOAC-RI and NF VALIDATION validated matrices and enrichment conditions). Homogenize samples thoroughly for 30 seconds to one minute using a homogenizer or by hand for samples containing hard particles, such as bone, peppercorns, etc, then incubate according to the enrichment conditions details below. AOAC-RI PTM validated enrichment conditions Matrix Validated Enrichment Conditions Incubate 9-24 hours in pre-warmed 375g: Raw ground beef (short enrichment protocol) mTSB at 41.5°C ±1°C Incubate 8-24 hours in pre-warmed 25g: Raw ground beef (short enrichment protocol) BPW (ISO) at 41.5°C ±1°C 25g: Non-fat dried milk powder, raw ground beef Incubate 18-24 hours in room (using the standard protocol) and liquid whole egg temperature BPW (ISO) at 37°C ±1°C 25g: Cooked shrimp, pork Frankfurters, lettuce, chilled ready to eat meal (containing beef), raw ground pork, raw chicken breast, wet cat food, dry Incubate 20-24 hours in room dog food, pasteurized milk, cantaloupe melon, temperature BPW (ISO) at 37°C ±1°C chilled pizza dough, black peppercorns, ice cream and peanut butter Incubate 20-24 hours in room 25g Sprouted seeds temperature BPW (ISO) supplemented with 20mg/l novobiocin at 41.5°C ±1°C 9 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay Incubate 20-24 hours in room temperature CSR Broth at 37°C ±1°C. 25g: Chocolate Dilute the enrichment 1:5 before proceeding to lysis. NOTE: When analysing samples of raw beef meat with the short (8-24 hour) enrichment protocol it is essential to use thoroughly pre-warmed (41.5°C) enrichment broth. For testing of 375g samples of raw beef, add the sample to be tested to a homogenizer bag and add 1.5 litres of pre-warmed (41.5°C) mTSB For chocolate samples, it is necessary to dilute the enriched CSR Broth sample 1:5 using sterile CSR Broth or Peptone Salt solution/Maximum Recovery Diluent before proceeding with the lysis protocol. Remove enriched samples from the incubator and mix the liquid in the homogenizer bag by hand for a few seconds. Allow any food particles to settle. Open the homogenizer bag and using a pipette with an extra long filtered pipette tip remove around 1.5ml and dispense into a new microfuge tube and close until ready to process the sample to the next stage. NOTE: Filtered homogenizer bags should be used to help with fat and particle separation. NOTE: When following the short enrichment protocol, it is essential to ensure that the enrichment broth is thoroughly pre-warmed. This can be achieved by placing the prepared broth in an incubator for 18-24 hours before adding to the prepared food samples. Production environment samples: Pre-moisten a sterile sampling swab, cloth or sponge in a suitable diluent (e.g. sterile Peptone water). For sampling of areas that have been cleaned or treated with disinfectants and other cleaning agents, pre-moisten the swab, cloth or sponge with a neutralizing broth, such as Dey- Engley Broth, prior to sampling. Sample the entire area by rubbing the swab, cloth or sponge in both a horizontal and vertical direction across the entire sampling area. Next, place the swab, cloth or sponge into the original packaging (suitable for transport). Samples may be held for up to 2 hours at room temperature or 8 hours in the refrigerator prior to proceeding with the next step. Add the swab, cloth or sponge to 225ml of Buffered Peptone Water at room temperature. Homogenize thoroughly and incubate at 37°C ±1°C for 20-24 hours (see section 11, “Performance Validation” for specific AOAC-RI validated matrices and enrichment conditions). AOAC-RI PTM validated enrichment conditions Matrix Validated Enrichment Conditions Incubate 18-24 hours in room stainless steel and plastic environmental surfaces temperature BPW (ISO) at 37°C ±1°C 10 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay Remove the enriched sample from the incubator and remove around 1.5ml and dispense into a new microfuge tube and close until ready to process the sample to the next stage. Store at 2-8°C for up to 72 hours if not processing immediately. NOTE: The 1.5ml portions of samples should be stored at 2-8oC and retained for confirmation of PCR positive results and in case the PCR analysis needs to be repeated (up to 3 days post enrichment). 7.2 Sample lysis NOTE: When analysing samples with the Applied Biosystems 7500 Fast, a negative control sample must be set up for each PCR run. The control must be set up by replacing 10µl of the enriched sample with 10µl of sterile water in the steps detailed below. Ensure that the two heating blocks are at the correct temperatures: 37°C ±2°C and 95°C ±2°C. Take the required number of Lysis Reagent 1 Tubes and place into a suitable rack. Tap the rack of tubes onto the bench or flick your wrist whilst holding the tubes to remove any liquid from the cap area and to collect the reagents at the bottom of each tube. Bring to room temperature before opening by leaving on the bench for around ten minutes. Using a suitable single or repeat pipettor, add 10µl of Proteinase K to each Lysis Tube. To avoid contamination, it is important to use a fresh filtered tip every time Proteinase K is withdrawn from the stock tube. Using a suitable pipette and filtered tip, take 10µl of the aliquoted enriched sample/control (or diluted sample in the case of chocolate samples) and add it to one of the opened Lysis Tubes. Ensure when adding the sample that the pipette tip reaches the bottom of the Lysis Tube to facilitate complete mixing of the sample with the Lysis reagent. Seal the Lysis Tubes with Lysis Caps using the CapEase tool and incubate in the heating block at 37°C ±2°C for 10 minutes. Immediately transfer the tubes to the heating block at 95°C ±2°C and incubate for a further 5 minutes. Immediately remove the tubes from the block and allow to cool at ambient temperature for 2 minutes before starting the PCR set-up. The prepared lysates can be stored at 2-8°C for a maximum of 24 hours once the lysis procedure has been completed. This will allow repeat analysis, if required. It is not recommended that lysates are stored for longer than 24 hours. If required, store an aliquot of the enrichment at 2- 8°C for up to 72 hours and repeat the lysis procedure on the stored enrichment. NOTE: Care should be taken to ensure that incubation temperatures and times are closely adhered to during the sample lysis steps. NOTE: Care should be taken when cutting strips of caps or tubes to ensure that they are not cut too close to the wall of the tube or cap lid, otherwise the lid will not seal adequately when carrying out the lysis protocol. 7.3 PCR set-up IMPORTANT: The SureTect Salmonella species PCR Assay must only be run with version 1.2 of the SureTect Software and Salmonella species kit file version 1.1.6.54 or higher. 11 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay NOTE: Ensure that the correct assay is selected from the assay options. In RapidFinder Express Software version 2.0 ensure that “SalmonellaSpp. SureTect” is selected. Create the template setup on either the SureTect or RapidFinder Express 2.0 Software. Refer to the appropriate software manual1,2 for directions on how to set a template up. Remove the required number of SureTect Salmonella species PCR Tubes from the packaging and place into a suitable tube rack. Tap the rack of PCR Tubes onto the bench to ensure the SureTect PCR pellets inside the tubes are located at the bottom. Allow the PCR Tubes to come to room temperature by leaving on the bench for 5 minutes before opening. It is important to return any remaining PCR pellets to the bag, seal and store at 2-8°C as soon as possible. NOTE: PCR pellets should appear as pale yellow pellets. If the pellet is collapsed or not pale yellow in colour, do not use the pellet. Open the Lysis Tubes using the CapEase tool and using a suitable pipette with filtered tips take 20µl of the lysate. Ensure the lysate is removed from the top half of the liquid, taking care not to disrupt the particles at the bottom of the Lysis Tube. If the particles become disturbed leave the tube for 1-2 minutes to allow the particles to re-settle. CAUTION: Particular care should be taken to ensure that no particles are transferred from the lysate tube into the PCR Tube. The presence of these particles during the PCR process may inhibit PCR from occurring (the internal amplification control and any target DNA will both fail to amplify). Transfer the 20µl of lysate into the opened PCR Tube to rehydrate the SureTect PCR pellet. Take care not to touch the pellet when adding the lysate. Touching the pipette tip end to the inside of the PCR Tube will help to ensure that all of the liquid is expelled while keeping the tip away from the pelletEnsure the lysate reaches the bottom of the tube for full rehydration of the pellet NOTE: For ease of use a multi-channel pipette can be used to transfer multiple lysates to the PCR Tubes. If on opening the PCR Tube the pellet is not positioned at the bottom of the tube, take a sterile empty pipette tip and gently move the pellet to the bottom of the well. Seal the PCR Tubes with the flat optical caps provided (pre-cut to the number required). Ensure the tubes are properly sealed by pressing down firmly over each opening. Please note, the CapEase tool should not be used for sealing the PCR tubes. 7.4 Starting a run Open the drawer of the Real-Time PCR Instrument. Load the PCR Tubes according to the plate setup created. Ensure the plate is balanced properly, if running samples with the SureTect PikoReal you must fill at least 2 full rows with tubes. Use blank tubes if necessary. When running samples with the Applied Biosystems 7500 Fast follow the prescribed template. Close the drawer and start the run. Refer to the SureTect or RapidFinder Express 2.0 Software Manuals for detailed directions. CAUTION: Once the lysate has been added to the PCR pellets the PCR run should be started within 30 minutes. 7.5 Reviewing results 12 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay When the run is completed, remove the processed samples and review the results on the computer screen. Refer to the SureTect or RapidFinder Express 2.0 Software manual for help with result interpretation. 7.6 Confirming positive results & reporting Positive results can be confirmed by pipetting 10µl of the enriched sample onto Brilliance Salmonella Agar. Inoculate the plate using a diminishing sweep technique and incubate at 37°C ±1°C for 24 hours. Observe the plate for presumptive Salmonella colonies (purple colonies), then confirm as positive using the Oxoid Salmonella Latex Test and/or Microbact GNB 24E kit or the confirmatory tests in the ISO horizontal method for the detection of Salmonella4. Where high levels of background contamination are present selective enrichment will be required to culturally confirm the PCR result. This can be conducted by adding 0.1ml of the BPW (ISO) enrichment to 10ml of Rappaport-Vassiliadis Soya (RVS) (ISO) Broth (CM0866). Incubate at 41.5°C ±1°C for 24 hours. 10µl of the RVS (ISO) Broth should be streaked onto Brilliance Salmonella Agar using the diminishing streak technique. Incubate at 37°C ±1°C for 24 hours and confirm any presumptive Salmonella colonies as detailed above using the Oxoid Salmonella Latex kit and/or Microbact GNB 24E kit or the confirmatory tests detailed in the ISO horizontal method for the detection of Salmonella. CAUTION: In the event of a positive SureTect PCR result, which cannot be confirmed using the steps described above, all necessary measures must be taken by the laboratory to establish the true status of the sample before reporting the result. Refer to section 10 - PERFORMANCE LIMITATIONS for further guidance. Refer to the SureTect or RapidFinder Express 2.0 Software Manual for result storage, download and reporting options. Confirmation of positive results obtained using the methods certified by NF VALIDATION In the context of NF VALIDATION, all samples identified as positive by the SureTect Salmonella species assay must be confirmed. If confirmation is not started immediately after a positive SureTect test result, store the enrichments at 2-8°C. Confirmation must be started within 72 hours following the end of incubation. To confirm the SureTect assay result use one of the following methods: 1. Using the conventional tests described in the methods standardized by CEN or ISO from colonies (including the purification step). The confirmation step must start from the BPW or ONE Broth Salmonella enrichment broth. Identify 1 to 5 typical colonies using the conventional tests described within the ISO 65794 reference method. 2. a. For samples originating from egg products, sea foods, produce, or pet foods: pipette 10µl of the BPW (ISO) or ONE Broth Salmonella enriched sample onto Brilliance Salmonella Agar. Inoculate the plate using a diminishing sweep technique and incubate at 37°C ±1°C for 24 hours. Observe the plate for presumptive Salmonella colonies (purple colonies), then confirm directly, without purification, as positive using the Oxoid Salmonella Latex Test and/or Microbact GNB 24E kit. b. For samples originating from raw meats and dairy products: add 0.1ml of the BPW (ISO) or ONE Broth Salmonella enrichment to 10ml of Rappaport-Vassiliadis Soya (RVS) (ISO) Broth (CM0866) and incubate at 41.5°C ±1°C for 24 hours. Streak 10µl of the RVS (ISO) Broth onto Brilliance Salmonella Agar using the diminishing streak technique. Incubate at 37°C ±1°C for 13 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay 24 hours and confirm directly, without purification, any presumptive Salmonella colonies as detailed above using the Oxoid Salmonella Latex kit and/or Microbact GNB 24E kit. NOTE: Brilliance Salmonella Agar may fail to identify isolates of Salmonella Dublin due to the low esterase activity of this serotype with the chromogen used in this and other similar commercially available chromogenic culture media. In the event of discrepant results (positive with the alternative method, non-confirmed by one of the means described above, and in particular for the Latex test) the laboratory must follow the necessary steps to ensure the validity of the result obtained. 8. DISPOSAL Once the PCR run is completed, open the Real-Time PCR Instrument using the button on the front of the instrument and remove the processed samples. Dispose as hazardous microbiological waste according to local and/or national guidelines. WARNING: Do not, under any circumstances open PCR tubes following the completion or partial completion of a PCR run. The amplified DNA (amplicon) in the PCR tubes could easily contaminate equipment and the nearby laboratory environment leading to false results in future experiments. Refer to the Real-Time PCR Instrument Manual for guidelines on cleaning equipment and handling possible amplicon contamination. Dispose of all inoculated culture media, even if shown to be negative for the target organism, as hazardous microbiological waste according to local guidelines. For disposal of uninoculated culture media or any of the reagents and materials included in the SureTect Salmonella Species PCR Assay and associated tests, refer to the manufacturer’s material safety data sheets and appropriate local guidelines. 9. QUALITY CONTROL 9.1 Internal Amplification Control All SureTect PCR pellets contain a probe, primers and DNA template for an internal amplification control (IAC). During PCR the IAC template will be amplified alongside any target DNA present. The probe used for the IAC uses a different coloured fluorescent dye to the probes that are used within the assay to detect target DNA and so can be detected by the Real-Time PCR Instrument through a separate dye channel. The result is that after a successful PCR run the instrument will detect IAC amplification. In the absence of any target DNA being detected by the assay, the presence of IAC amplification curve is confirmation that the PCR process has occurred. NOTE: Occasionally, the presence of a high level of the target DNA present at the start of the PCR process may cause the IAC to fail to produce an amplification curve. This usually occurs when the target DNA concentration is far more abundant than the IAC control concentration and the target DNA competes more effectively for the components of the PCR reaction. The absence of an IAC amplification curve in the presence of a strong target amplification curve is confirmation that PCR has occurred and a positive call will be made by the SureTect or RapidFinder Express Software version 2.0. If verification of this is required the test may be repeated by first diluting the enriched sample 1:10 – 1:100 and proceeding as before. The failure of both the IAC and the assay target to produce an amplification curve indicates that PCR is invalid and the software will return a ”!” result. In this case the test should be repeated. 14 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay 9.2 Using control organisms It should not be necessary to incorporate a positive control organism with routine testing of samples, since it can be shown that the test is functioning through the presence of an amplification curve for the Internal Amplification Control (IAC) or presence of a strong amplification curve for the target DNA (in the absence of an amplification curve for the IAC). However, if for any reason it is required to run control organisms suitable positive and negative control organisms should be selected. These may then be taken through the complete test procedure (including sample enrichment, lysis and PCR) and processed in parallel to the test samples. Quality control organisms are available from Thermo Fisher Scientific, Microbiology Division. Contact your local supplier for further information. 10 PERFORMANCE LIMITATIONS 10.1 False negative results The concentration of the target organism must reach around 104 CFU/ml during the enrichment stage for detection to be possible. Failure of the target organism to reach this level of growth may lead to a false negative result for PCR. Thermo Fisher Scientific can provide detailed information on assay protocols, including enrichment procedures, for the sample matrices that have been externally validated, please contact our technical support team (Europe/ROW: email: [email protected] telephone: +44 (0)1256 694238/ USA: email: [email protected] telephone 1-800-255-6730). For other matrices a suitable enrichment protocol must be determined prior to the method being adopted for routine use. Certain sample types may contain components that are inhibitory to the growth of the target organism. Therefore, it may be necessary to pre-treat or dilute the sample. Refer to the appropriate local, national or international guidelines, e.g. ISO 68873. NOTE: Some foods may contain compounds that inhibit PCR. Where PCR inhibition is suspected or present during an assay run, the enriched sample should be diluted 1:5 or 1:10 with sterile water before repeating the lysis protocol and analysis. When testing a sample type or culture media that has not been validated, it is recommended that a selection of known negative and spiked or known positive samples are tested to ensure that expected results are achieved. 10.2 False positive results PCR is recognized to be a very sensitive technique for the detection of micro-organisms. It is possible that the SureTect Salmonella species Assay may produce a positive result that cannot be confirmed by the recommended culture confirmation steps (see section 7.6). If this is the case it will be necessary to conduct further steps to confirm the PCR result obtained. The following steps are recommended: Subculture 0.1ml of the retained enrichment broth into 10ml of Rappaport-Vassiliadis Soya (RVS) (ISO) Broth (CM0866) and incubate at 41.5°C ±1°C for 24 hours. Plate out 10µl of the incubated RVS Broth onto Brilliance Salmonella Agar and incubate at 37°C ±1°C for 24 hours (see section 7.6). 11.PERFORMANCE VALIDATION AOAC-RI Performance Tested MethodsSM Program (Licence Number: 051303) The SureTect Salmonella species PCR assay has been validated by AOAC-RI using: 1. SureTect Software v1.2 and kit file version 1.1.6.54 and the SureTect PikoReal PCR Instrument. 15 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay 2. Applied Biosystems RapidFinder Express Software version 2.0 e, assay specific kit file version 1 and the 7500 Fast PCR Instrument. according to the Performance Tested MethodsSM validation scheme for the following food matrices and surface samples: AOAC-RI Performance Tested MethodsSM Validated Matrices and Enrichment conditions Matrix Validated Enrichment Conditions Incubate 9-24 hours in pre-warmed 375g: Raw ground beef (short enrichment protocol)* mTSB at 41.5°C ±1°C Incubate 8-24 hours in pre-warmed 25g: Raw ground beef (short enrichment protocol) BPW (ISO) at 41.5°C ±1°C 25g: Non-fat dried milk powder, stainless steel and Incubate 18-24 hours in room plastic environmental surfaces, raw ground beef temperature BPW (ISO) at 37°C (using the standard protocol) and liquid whole egg ±1°C 25g: Cooked shrimp, pork Frankfurters, lettuce, chilled ready to eat meal (containing beef), raw ground pork, Incubate 20-24 hours in room raw chicken breast, wet cat food, dry dog food, temperature BPW (ISO) at 37°C pasteurized milk, cantaloupe melon, chilled pizza ±1°C dough, black peppercorns, ice cream and peanut butter Incubate 20-24 hours in room temperature BPW (ISO) 25g Sprouted seeds supplemented with 20mg/l novobiocin at 41.5°C ±1°C Incubate 20-24 hours in room temperature CSR Broth at 37°C 25g: Chocolate ±1°C. Dilute the enrichment 1:5 before proceeding to lysis. *The sample preparation and enrichment protocol for 375g raw ground beef is exactly the same and allows analysis of the sample/lysate with the Thermo Scientific™ SureTect™ Escherichia coli O157:H7 PCR Kit (PT0400A). NF VALIDATION™ by AFNOR Certification (Certificate number: UNI 03/07-11/13) In the context of NF VALIDATION, the SureTect Salmonella species Assay has been certified as an alternative method for the analysis of the following categories and enrichment protocols: NF VALIDATION certified categories and enrichment conditions Category PCR Validated Enrichment Conditions Instrument/Software 25g: Raw beef (short PikoReal/SureTect Incubate 8-24 hours in pre-warmed enrichment protocol) Software BPW at 41.5°C ±1°C 25g: Raw beef (short 7500 Fast/RapidFinder Incubate 9-24 hours in pre-warmed enrichment protocol) Express 2.0 Software BPW (ISO) at 41.5°C ±1°C 16 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay 25g: Meat products, PikoReal/SureTect Incubate 20-24 hours in room seafood and fish Software temperature BPW (ISO) at 37°C ±1°C products, egg products Incubate 20-24 hours in room PikoReal/SureTect temperature ONE Broth Salmonella 25g: Pet food Software supplemented with ONE Broth Salmonella supplement at 37°C ±1°C Incubate 20-24 hours in room 7500 Fast/RapidFinder 25g Meat products temperature BPW (ISO) supplemented Express 2.0 Software with 20mg/l novobiocin at 37°C ±1°C Incubate 20-24 hours in either room PikoReal/SureTect temperature BPW (ISO) supplemented Software or 7500 with 12mg/l novobiocin or room 25g: Dairy products Fast/RapidFinder temperature ONE Broth Salmonella Express 2.0 Software supplemented with 12mg/l novobiocin at 37°C ±1°C. 7500 Fast/RapidFinder Incubate 16-20 hours in room 25g Infant formula Express 2.0 Software temperature BPW (ISO) at 37°C ±1°C Incubate 20-24 hours at room 25g Seafood and fish 7500 Fast/RapidFinder temperature BPW (ISO) supplemented products and vegetables Express 2.0 Software with 12mg/l novobiocin at 37°C ±1°C Add swabs to 10ml, sponges to 100ml Wipes, sponges, swabs 7500 Fast/RapidFinder and wipes, 25g and 25ml samples to or 25g production Express 2.0 Software 225ml room temperature BPW (ISO). environment samples Incubate 20-24 hours at 37°C ±1°C The validations have been obtained in comparison with the reference method described in the international standard ISO 65794 according to ISO 161407 and ISO 16140-29. The validation included the use of either the Thermo Scientific SureTect PikoReal 24 well real-time PCR cycler with Thermo Scientific SureTect software (v1.2) and SureTect Salmonella species specific kit file version 1.1.6.54 or the Applied Biosystems 7500 Fast real-time PCR cycler with Applied Biosystems RapidFinder Express 2.0 Software and SureTect Salmonella species specific kit file version 1. The validation certificate can be obtained from our Technical Support team (Europe: email: [email protected] telephone: +44 (0)1256 694238) or from AFNOR Certification (http://nf-validation.afnor.org/en/). For more information about the end of validity of the NF VALIDATION certification, please refer to the certificate UNI 03/07-11/13 available at http://nf-validation.afnor.org/en/ or from our technical support team (see above). UNI 03/07 – 11/13 17 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay ALTERNATIVE ANALYTICAL METHODS FOR AGRIBUSINESS http://nf-validation.afnor.org/en/ 12.ENRICHMENT MEDIA AND CONFIRMATION PRODUCTS The following enrichment media and biochemical confirmation kits are available from Thermo Fisher Scientific, Microbiology. Please contact your kit supplier for further information. Oxoid Buffered Peptone Water (ISO) (CM1049B-500g or CM1049R-2.5kg, 500g makes 25 litres) ONE Broth Salmonella (CM1091B, 500g makes 20 litres) ONE Broth Salmonella Supplement (SR0242E, 10 vials each for 225ml) Oxoid CSR Broth (CM1155B, 500g makes 7.7 litres) Novobiocin 20mg/litre (SR0181E, 10 vials each for 500ml) Suitable culture medium for isolation and identification of Salmonella colonies. The use of Oxoid Brilliance™ Salmonella Agar is recommended and has been validated during the AOAC Research Institute (RI) and NF VALIDATION studies (Brilliance Salmonella Agar Base plus selective supplement): Brilliance Salmonella Agar Base (CM1092B-500g, 500g makes 9.2 litres) Brilliance Salmonella Selective Supplement (SR0194E-10 vials for 500ml) Rappaport-Vassiliadis Soya Peptone (RVS) Broth (CM0669B) Further identification reagents such as a miniaturized biochemical identification panel, e.g. Microbact GNB 24E (MB1131A-40 tests, MB1074A-80 tests –and accompanying reagents, e.g. Microbact Reagent Set D (MB1082A) and/or latex test, e.g. Oxoid Salmonella Latex Test (DR1108A). 13.BIBLIOGRAPHY 13.1 References 1. SureTect Software User Manual, Rev 1.2; 2013, Thermo Fisher Scientific. 2. Applied Biosystems RapidFinder Express Software Version 2.0. Quick Reference. Pub 4480999 Pub C. 2015. Thermo Fisher Scientific. 3. ISO 6887 Parts 1-5 (most recent edition should be used); Microbiology of food and animal feeding stuffs-Preparation of test samples, initial suspension and decimal dilutions for microbiological examination. 4. ISO 6579:2002/Cor 1:2004; Microbiology of food and animal feeding stuffs-Horizontal method for the detection of Salmonella spp. 5. ISO 7218:2007/Amd 1:2013; Microbiology of food and animal feeding stuffs-General requirements and guidance for microbiological examinations. 6. ISO 22174:2005; Microbiology of food and animal feeding stuffs-Polymerase chain reaction (PCR) for the detection of food pathogens-General requirements and definitions. 7. ISO 16140:2003; Microbiology of food and animal feeding stuffs-Protocol for the validation of alternative methods. 8. Applied Biosystems 7300/7500/7500 Fast Real-Time PCR System Installation and Maintenance Guide, Rev A; 2006 Thermo Fisher Scientific. 9. ISO 16140-2:2016; Microbiology of food and animal feed-Method validation-Part 2: Protocol for the validation of alternative (proprietary) methods against a reference method. 13.2 Trademark & licensing information 18 of 19 D11908_10 www.thermofisher.com/contactus  SureTect Salmonella species PCR Assay “Thermo Scientific”, “Oxoid”, ” SureTect”, ”PikoReal”, ”Brilliance”, ”Solaris”, ”CapEase”, ”Microbact”, ”Dry-Bags”, “RapidFinder” and “Applied Biosystems” are trademarks or registered trademarks of Thermo Fisher Scientific Inc and its subsidiaries. All other trademarks and registered trademarks are the property of their respective holders. Probes and primers manufactured for Thermo Fisher Scientific by Epoch Biosciences. This product or portions hereof are subject to proprietary rights of Epoch Biosciences, Inc. and are made and sold under license from Epoch under the patents and patent applications as may be designated by Epoch from time to time set forth, including one or more of the following: U.S. Patent Nos. 5,801,155, 6,127,121, 6,312,894, 6,426,408, 6,485,906, 6,492,346, 6,660,845, 6,683,173, 6,699,975, 6,790,945, 6,949,367, 6,972,328, 7,045,610, 7,205,105, 7,319,022, 7,368,549, 7,381,818, 7,556,923, 7,671,218, 7,715,989, 7,718,374, 7,723,038, 7,751,982, 7,794,945, RE 38,416, European Patent Nos. 0819133B1, 1144429B1, 1068358B1 and applications currently pending. Purchase of this product carries with it a limited, non-transferable, non-exclusive (without the right to resell, repackage, or sublicense) license under U.S. Patent Nos. 6,030,787; 5,723,591; and 5,876,930, and corresponding foreign patents, solely to use this product in an assay in which the detection of a nucleic acid sequence does not include the cleavage of a nucleic acid probe, and for no other purpose. 13.3 Field of use Data obtained from the Thermo Scientific SureTect System should not be used for human diagnostic or human treatment purposes. The PikoReal or 7500 Fast Instrument used in conjunction with the SureTect or RapidFinder Express 2.0 Software and other components of the SureTect PCR System are not approved by the United States Food and Drug Administration or any other US or non-US agency for use in human diagnosis or treatment. The SureTect System should not be used as the sole basis for determining the microbiological safety of products for release to consumers. The information generated is only for use in conjunction with the user’s regular quality assurance program. Use for research and development, quality assurance and quality control only, performed by, or under the supervision of a technically qualified person. Thermo Fisher Scientific, Ratastie 2, FI-01620, Vantaa, Finland. 19 of 19 D11908_10 www.thermofisher.com/contactus