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Thermo Scientific™ - Microbiology - MicroSEQ & RapidFinder STEC PCR Assays

MicroSEQ® Rapid Microbial Identification System

The MicroSEQ® ID microbial identification system, based on comparative rDNA sequencing of the 16S region (for bacteria) or the LSU D2 region (for fungi), is a proven method for rapid and accurate microbial identification. The optimized design, integrated workflow, and superior accuracy of the MicroSEQ® ID Rapid System enable top pharmaceutical companies, medical devices companies, public health laboratories, and government agencies worldwide to reliably perform a wide range of microbial identification tasks, including routine QC microbiology tests.

Lyophilized for efficiency and ease of use

For maximum ease of use, and consistency of results, the reagents used in the MicroSEQ® Listeria monocytogenes Detection Kit are lyophilized into preformatted assay beads. The beads hold the active enzyme, the target-specific primer and probe set, Internal Positive Control (IPC) and other reagents for PCR. The IPC is provided to help eliminate false negatives by detecting the presence of materials that can inhibit target amplification. 

Simple, three-step procedure

There is minimal training or prior experience needed for you to perform the assay in these three simple steps:

  1. Enrich sample 
  2. Prepare DNA 
  3. Run test 

AOAC certified

The full workflow including the MicroSEQ® Listeria monocytogenes Detection Kit, PrepSEQ™ sample preparation kits, 7500 Fast instrument and RapidFinder Express software has earned the Performance Tested Methods certification from the AOAC Research Institute.

Optimized sample preparation

The MicroSEQ Listeria monocytogenes Detection Kit is optimized for use with PrepSEQ™ Sample Preparation Kits. PrepSEQ kits reduce pre-enrichment time, enhance assay performance and enable you to enrich and prepare high quality samples from a broad range of food sample types for detection of 1-3 cfu per 25 grams of sample.

Clear results using a software-guided procedure

After sample enrichment and preparation, RapidFinder® Express software guides you through the entire workflow with on-screen instructions. Amplification, detection, data collection and analysis are fully automated. When the assay is complete, the software presents an easy-to-read screen that allows you to view the results in each reaction tube. Results are clearly displayed and can be labeled with flags, notifications and prompts that enable you to quickly interpret the data and take appropriate action. 

The RapidFinder STEC Detection Workflow provides:

  • Greater confidence in results—part of a validated workflow for detection of as little as 1-5 CFU of pathogenic STEC in your sample
  • Simplified workflow—simultaneous detection of E. coli O157:H7 and the Big 6 non-O157:H7 strains in 375 g beef samples with a closed-tube, single-step lyophilized detection format that fits within your existing testing program
  • Reduced chance of false results—through use of high-quality DNA preparation, proprietary assay design, and internal positive control
  • Same day detection of pathogenic STECs and clearance of STEC-negative beef samples in as little as 12 hours, supporting early product release
  • Minimized costs and laboratory space with the use a lower volume of a nonproprietary single-step enrichment medium, eliminating the need to purchase proprietary media
  • Compatibility with RapidFinder™ Express software v.1.2 and later—enables easy, automated presence/absence detection and interpretation of results


Studies have shown that the RapidFinder STEC assays have a high level of sensitivity and specificity for E. coli O157:H7 and the Big 6 non-O157 STEC strains. They detected all inclusion strains and showed no cross-reactivity to any of the exclusion strains tested. The stx assays detected all known variants of stx1 and stx2, including stx2f and stx2g. The optimized workflow co-developed with USDA-ARS showed equivalent detection to the MLG reference method, and the internal positive control in both assays significantly reduces the risk of false-negatives.

Applications

The RapidFinder STEC Detection Workflow is intended for use by microbiological analysts who need to test for STEC in beef samples. Combined with the Applied Biosystems 7500 Fast RT-PCR System, RapidFinder STEC screening and confirmation assays provide a comprehensive solution for rapid detection, identification, and confirmation of Big 6 STECs and E. coli 0157:H7 to meet importation and exportation requirements for the beef industry. Specific workflows are detailed in the figures below and include both automated and spin column-based DNA isolation and real-time PCR detection of E. coli O157:H7 and Big 6 non-O157 strains in beef samples.

RapidFinder express software

When integrated into the RapidFinder STEC Detection Workflow, RapidFinder Express Software automates data interpretation and generates user instructions on how to proceed with a sample. Data displays are available for novice and advanced users, showing simple presence/absence calls or raw data files using 7500 Fast System SDS Software.

RapidFinder STEC Screening and Confirmation Assays meet USDA FSIS guidance
The RapidFinder STEC Detection Workflow, a two-stage real-time PCR method, is designed to accurately detect, identify, and confirm E. coli O157:H7 and the Big 6 serogroups of non-O157 Shiga toxin-producing E. coli defined by the USDA Food Safety and Inspection Service (FSIS) as adulterants in the American beef industry.

Available models

arget Organism Class:
E. coli
Strain or Genotype:
E. coli O157:H7
Validated Application:
Real-Time PCR
Detection Method:
Primer-Probe Detection
PCR Method:
qPCR
For Use With (Equipment):
7500 Fast System
Sample Type (General):
Bacteria, Food & Environmental Samples
Sample Type (Specific):
Any Swab Type, Food, Water Samples
Hot Start:
Built-In Hot Start
Passive Reference Dye:
ROX (Pre-mixed)

The MicroSEQ® E. coli O157:H7 Detection Kit detects E. coli O157:H7 simply, reliably, and rapidly in food samples. The assay uses the polymerase chain reaction (PCR) to amplify a unique microorganism-specific DNA target sequence and a TaqMan® probe to detect the amplified sequence.

Key product features: 

  • Enjoy ease-of-use from a streamlined, lyophilized format and a simple, software guided 3-step process 
  • Get your results quickly with time-to-results in as little as 8 hours for a 25g sample 
  • Genome sequencing using the Applied Biosystems SOLiD™ or 5500 Series Genetic Analyzer platforms helps ensure high specificity 
  • Detect 1-3 colony-forming units (CFU) per 25 grams of food 
  • Get optimal performance on a wide range of food sample and environmental surface types 
  • Eliminate false negatives with internal positive control
  • Validated by the AOAC Research Institute and AFNOR according to ISO 16140 
Target Organism Class:
E. coli
Strain or Genotype:
E. coli O157:H7
Validated Application:
Real-Time PCR
Detection Method:
Primer-Probe Detection
PCR Method:
qPCR
For Use With (Equipment):
7500 Fast System, Centrifuge, StepOne™, Fast Mode, StepOnePlus™, StepOnePlus™, Fast Mode
Sample Type (General):
Bacteria, Food & Environmental Samples
Sample Type (Specific):
Any Swab Type, Bacteria (Hard-to-Lyse), Food, Food (High Lipid Content), Water Samples
Hot Start:
Built-In Hot Start
Passive Reference Dye:
ROX (Pre-mixed)

The MicroSEQ® E. coli O157:H7 Detection Kit detects E. coli O157:H7 simply, reliably, and rapidly in food samples. The assay uses the polymerase chain reaction (PCR) to amplify a unique microorganism-specific DNA target sequence and a TaqMan® probe to detect the amplified sequence.

Key product features: 

  • Enjoy ease-of-use from a streamlined, lyophilized format and a simple, software guided 3-step process 
  • Get your results quickly with time-to-results in as little as 8 hours for a 25g sample 
  • Genome sequencing using the Applied Biosystems SOLiD™ or 5500 Series Genetic Analyzer platforms helps ensure high specificity 
  • Detect 1-3 colony-forming units (CFU) per 25 grams of food 
  • Get optimal performance on a wide range of food sample and environmental surface types 
  • Eliminate false negatives with internal positive control
  • Validated by the AOAC Research Institute and AFNOR according to ISO 16140 
Target Organism Class:
E. coli
Strain or Genotype:
E. coli O157:H7
Validated Application:
Real-Time PCR
Detection Method:
Primer-Probe Detection
PCR Method:
qPCR
For Use With (Equipment):
7500 Fast System, StepOne™, Fast Mode, StepOnePlus™, StepOnePlus™, Fast Mode
Sample Type (General):
Bacteria, Food & Environmental Samples
Sample Type (Specific):
Any Swab Type, Food, Water Samples
Hot Start:
Built-In Hot Start
Passive Reference Dye:
ROX (Pre-mixed)

The MicroSEQ® E. coli O157:H7 Detection Kit detects E. coli O157:H7 simply, reliably, and rapidly in food samples. The assay uses the polymerase chain reaction (PCR) to amplify a unique microorganism-specific DNA target sequence and a TaqMan® probe to detect the amplified sequence.

Key product features: 

  • Enjoy ease-of-use from a streamlined, lyophilized format and a simple, software guided 3-step process 
  • Get your results quickly with time-to-results in as little as 8 hours for a 25g sample 
  • Genome sequencing using the Applied Biosystems SOLiD™ or 5500 Series Genetic Analyzer platforms helps ensure high specificity 
  • Detect 1-3 colony-forming units (CFU) per 25 grams of food 
  • Get optimal performance on a wide range of food sample and environmental surface types 
  • Eliminate false negatives with internal positive control
  • Validated by the AOAC Research Institute and AFNOR according to ISO 16140 
Target organism class
Listeria spp.
Validated application
Real-Time PCR
Detection method
Primer-Probe Detection
PCR method
qPCR
For use with (equipment)
7500 Fast System, StepOne™, Fast Mode, StepOnePlus™, StepOnePlus™, Fast Mode
Sample type (general)
Bacteria, Food & Environmental Samples
Sample type (specific)
Any Swab Type, Food, Water Samples
Hot start
Built-In Hot Start
Passive reference dye
ROX (Pre-mixed)
Reaction speed
Fast

The MicroSEQ® Listeria spp. Detection Kit detects Listeria simply, reliably, and rapidly in food and environmental samples. The assay uses the polymerase chain reaction (PCR) to amplify a unique microorganism-specific DNA target sequence and a TaqMan® probe to detect the amplified sequence.

Key product features:

  • Enjoy ease-of-use from a streamlined, lyophilized format and a simple, software guided 3-step process 
  • Get your results quickly with time to results of less than 3 hours after sample enrichment (27-31 hours total) 
  • Detect 1-3 colony-forming units (CFU) in 25 grams of food or in environmental samples 
  • Get optimal performance on a wide range of food sample and environmental surface types 
  • Eliminate false negatives with internal positive control 
Target organism class
Listeria spp.
Validated application
Real-Time PCR
Detection method
Primer-Probe Detection
PCR method
qPCR
For use with (equipment)
7500 Fast System, Centrifuge, KingFisher™ Flex, MagMAX™ Express-96 Deep Well Magnetic Particle Processor, StepOne™, Fast Mode, StepOnePlus™, StepOnePlus™, Fast Mode
Sample type (general)
Bacteria, Food & Environmental Samples
Sample type (specific)
Any Swab Type, Food, Water Samples
Hot start
Built-In Hot Start
Passive reference dye
ROX (Pre-mixed)
Reaction speed
Fast

The MicroSEQ® Listeria spp. Detection Kit detects Listeria simply, reliably, and rapidly in food and environmental samples. The assay uses the polymerase chain reaction (PCR) to amplify a unique microorganism-specific DNA target sequence and a TaqMan® probe to detect the amplified sequence. This system comes with a PrepSEQ™ Nucleic Acid Extraction Kit.

Key product features:

  • Enjoy ease-of-use from a streamlined, lyophilized format and a simple, software guided 3-step process 
  • Get your results quickly with time to results of less than 3 hours after sample enrichment (27-31 hours total) 
  • Detect 1-3 colony-forming units (CFU) in 25 grams of food or in environmental samples 
  • Get optimal performance on a wide range of food sample and environmental surface types 
  • Eliminate false negatives with internal positive control 
Target organism class
Listeria spp.
Validated application
Real-Time PCR
Detection method
Primer-Probe Detection
PCR method
qPCR
For use with (equipment)
7500 Fast System, Centrifuge, StepOne™, Fast Mode, StepOnePlus™, StepOnePlus™, Fast Mode
Sample type (general)
Bacteria, Food & Environmental Samples
Sample type (specific)
Any Swab Type, Bacteria (Hard-to-Lyse), Food, Food (High Lipid Content), Water Samples
Hot start
Built-In Hot Start
Passive reference dye
ROX (Pre-mixed)
Reaction speed
Fast

The MicroSEQ® Listeria spp. Detection Kit detects Listeria simply, reliably, and rapidly in food and environmental samples. The assay uses the polymerase chain reaction (PCR) to amplify a unique microorganism-specific DNA target sequence and a TaqMan® probe to detect the amplified sequence. This system comes with a PrepSEQ™ Nucleic Acid Extraction Kit.

Key product features:

  • Enjoy ease-of-use from a streamlined, lyophilized format and a simple, software guided 3-step process 
  • Get your results quickly with time to results of less than 3 hours after sample enrichment (27-31 hours total) 
  • Detect 1-3 colony-forming units (CFU) in 25 grams of food or in environmental samples 
  • Get optimal performance on a wide range of food sample and environmental surface types 
  • Eliminate false negatives with internal positive control 
Target organism class
L. monocytogenes
Validated application
Real-Time PCR
Detection method
Primer-Probe Detection
PCR method
qPCR
For use with (equipment)
7500 Fast System, StepOne™, Fast Mode, StepOnePlus™, StepOnePlus™, Fast Mode
Sample type (general)
Bacteria, Food & Environmental Samples
Sample type (specific)
Any Swab Type, Food, Water Samples
Hot start
Built-In Hot Start
Passive reference dye
ROX (Pre-mixed)
Reaction speed
Fast

This kit is recommended for users who have already purchased the starter kit but would like to perform more tests. The MicroSEQ® Listeria monocytogenes Detection Kit detects Listeria monocytogenes simply, reliably, and rapidly in food samples. The assay uses the polymerase chain reaction (PCR) to amplify a unique microorganism-specific DNA target sequence and a TaqMan® probe to detect the amplified sequence. 

  • Enjoy ease-of-use from a streamlined, lypholized format and a simple, software guided 3-step process 
  • Get your results quickly with time to results of less than 3 hours after sample enrichment (less than 27 hours total) 
  • Detect 1-3 colony-forming units (CFU) per 25 grams of food 
  • Get optimal performance on a wide range of food sample types 
  • Eliminate false negatives with internal positive control 
  • Validated by the AOAC Research Institute 
Target Organism Class:
L. monocytogenes
Validated Application:
Real-Time PCR
Detection Method:
Primer-Probe Detection
PCR Method:
qPCR
For Use With (Equipment):
7500 Fast System, Centrifuge, StepOne™, Fast Mode, StepOnePlus™, StepOnePlus™, Fast Mode
Sample Type (General):
Bacteria, Food & Environmental Samples
Sample Type (Specific):
Any Swab Type, Bacteria (Hard-to-Lyse), Food, Food (High Lipid Content), Water Samples
Hot Start:
Built-In Hot Start
Passive Reference Dye:
ROX (Pre-mixed)
Reaction Speed:
Fast

The MicroSEQ® Listeria monocytogenes Detection Kit Starter Kit is recommended for first time users in laboratories that routinely prepare up to 100 samples a day. It detects Listeria monocytogenes simply, reliably, and rapidly in food samples. The assay uses the polymerase chain reaction (PCR) to amplify a unique microorganism-specific DNA target sequence and a TaqMan® probe to detect the amplified sequence. 

  • Enjoy ease-of-use from a streamlined, lypholized format and a simple, software guided 3-step process 
  • Get your results quickly with time to results of less than 3 hours after sample enrichment (less than 27 hours total) 
  • Detect 1-3 colony-forming units (CFU) per 25 grams of food 
  • PrepSEQ™ Rapid Spin Sample Preparation Kit included
  • Get optimal performance on a wide range of food sample types 
  • Eliminate false negatives with internal positive control 
  • Validated by the AOAC Research Institute 
Target organism class
Salmonella spp.
Validated application
Real-Time PCR
Detection method
Primer-Probe Detection
PCR method
qPCR
For use with (equipment)
7500 Fast System, StepOne™, Fast Mode, StepOnePlus™, StepOnePlus™, Fast Mode
Sample type (general)
Bacteria, Food & Environmental Samples
Sample type (specific)
Any Swab Type, Food, Water Samples
Hot start
Built-In Hot Start
Passive reference dye
ROX (Pre-mixed)
Reaction speed
Fast

This kit is recommended for users who have already purchased the starter kit but would like to perform more tests. The MicroSEQ® Salmonella spp. Detection Kit detects Salmonella spp. simply, reliably, and rapidly in food samples. The assay uses the polymerase chain reaction (PCR) to amplify a unique microorganism specific DNA target sequence and a TaqMan® probe to detect the amplified sequence. 

  • Enjoy ease-of-use from a streamlined, lypholized format and a simple, software guided 3-step process 
  • Get your results quickly with time to results of less than 3 hours after sample enrichment (less than 27 hours total) 
  • Detect 1-3 colony-forming units (CFU) per 25 grams of food 
  • Get optimal performance on a wide range of food sample types 
  • Eliminate false negatives with internal positive control 
  • Validated by the AOAC Research Institute 
arget Organism Class:
Salmonella spp.
Strain or Genotype:
Salmonella spp.
Validated Application:
Real-Time PCR
Detection Method:
Primer-Probe Detection
PCR Method:
qPCR
For Use With (Equipment):
7500 Fast System, KingFisher™ Flex, MagMAX™ Express-96 Deep Well Magnetic Particle Processor, StepOne™, Fast Mode, StepOnePlus™, Fast Mode
Sample Type (Specific):
Any Swab Type, Food, Water Samples
Product Size:
96 assays

The MicroSEQ Salmonella Species Detection Starter Kit with PrepSEQ Nucleic Acid Extraction Kit is recommended for those needing to prepare and analyze hundreds of food or environmental samples per day. The Starter Kit detects Salmonella species simply, reliably, and rapidly using the polymerase chain reaction (PCR) to amplify a unique microorganism-specific DNA target sequence and a TaqMan probe to detect the amplified sequence. The MicroSEQ Salmonella Species Detection Kit is optimized for use with the PrepSEQ Nucleic Acid Extraction Kit. For ease of ordering, we have combined a 96 reaction MicroSEQ SalmonellaSpecies Detection Kit with a 100 reaction PrepSEQ Nucleic Acid Extraction Kit and offer it here as a single product.

Key features

  • Enjoy ease-of-use from a streamlined, lyophilized format and a simple, software-guided 3-step process
  • Time-to-results of less than 3 hours after sample enrichment (less than 19 hours total)
  • Eliminate false negatives with internal positive control
  • Detect 1–3 colony-forming units (CFU) per 25 grams of food
  • Universal PCR cycling conditions for all MicroSEQ pathogen detection kits
  • Validated by the AOAC Research Institute
Target organism class
Salmonella spp.
Validated application
Real-Time PCR
Detection method
Primer-Probe Detection
PCR method
qPCR
For use with (equipment)
7500 Fast System, Centrifuge, StepOne™, Fast Mode, StepOnePlus™, StepOnePlus™, Fast Mode
Sample type (general)
Bacteria, Food & Environmental Samples
Sample type (specific)
Any Swab Type, Bacteria (Hard-to-Lyse), Food, Food (High Lipid Content), Water Samples
Hot start
Built-In Hot Start
Passive reference dye
ROX (Pre-mixed)
Reaction speed
Fast

The MicroSEQ® Salmonella spp. Detection Kit Starter Kit with PrepSEQ™ RapidSpin Sample Preparation Kit – Extra Clean enables the detection of Salmonella spp. simply, reliably, and rapidly in food samples using the Applied Biosystems® 7500 Fast Real-Time PCR System. It is recommended for first time users in laboratories that routinely prepare up to 100 samples a day and prefer a spin column-based workflow. This starter kit combines the PrepSEQ RapidSpin Sample Preparation Kit – Extra Clean with a MicroSEQ Salmonella spp. Detection Kit for ease of ordering. The benefits of this workflow include:

  • Enjoy ease-of-use from a streamlined, lypholized format and a simple, software guided 3-step process 
  • Get your results quickly with time to results of less than 3 hours after sample enrichment (less than 27 hours total) 
  • Detect 1-3 colony-forming units (CFU) per 25 grams of food 
  • Get optimal performance on a wide range of food sample types 
  • Eliminate false negatives with internal positive control 
  • Validated by the AOAC Research Institute 
Detection Method:
Primer-Probe Detection
Product Line:
RapidFinder™
Product Size:
96 reactions
Shipping Condition:
Wet Ice

The Applied Biosystems™ RapidFinder™ STEC Confirmation Assay is part of a complete, validated screening and confirmation workflow enabling TaqMan™ real-time PCR detection of the Shiga toxin-producing E. coli (STEC) O157:H7 and Big 6 non‐O157:H7 serogroup (O26, O45, O103, O111, O121, and O145) in a variety of beef products. Samples assessed as positive using the RapidFinder STEC Screening Assay are further tested using this RapidFinder STEC Confirmation Assay. All reactions include an internal positive control (IPC) and ROX™ passive reference.

Detection Method:
Primer-Probe Detection
Product Line:
RapidFinder™
Product Size:
96 reactions
Shipping Condition:
Wet Ice

The Applied Biosystems™ RapidFinder™ STEC Screening Assay is part of a complete, validated screening and confirmation workflow enabling TaqMan™ real-time PCR detection of the Shiga toxin-producing E. coli (STEC) O157:H7 and Big 6 non‐O157:H7 serogroup (O26, O45, O103, O111, O121 and O145) in a variety of beef products. The RapidFinder STEC Screening Assay was co-developed with the USDA-ARS and contains 96 complete qPCR assays targeted to screen for Shiga toxin 1 and 2 (stx1/stx2), eae, and potential O157:H7 presence. The assay is designed to be inclusive of all know allelic variants of stx and eae, including stx2g and stx2f. All reactions include an internal positive control (IPC) and ROX™ passive reference. Samples assessed as negative require no further testing. Samples assessed as positive must be further tested using the RapidFinder™ STEC Confirmation Assay.

Microbial Identification: Bacterial and Fungal ID using MicroSEQ® System

Thermo Fisher ScientificThermo Fisher Scientific is the world leader in serving science, with revenues of more than $24 billion and approximately 70,000 employees globally. Our mission is to enable our customers to make the world healthier, cleaner and safer. We help our customers accelerate life sciences research, solve complex analytical challenges, improve patient diagnostics, deliver medicines to market and increase laboratory productivity. Through our premier brands – Thermo Scientific, Applied Biosystems, Invitrogen, Fisher Scientific and Unity Lab Services – we offer an unmatched combination of innovative technologies, purchasing convenience and comprehensive services.
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