SPECIAL NOTICE
65 -- Assay Kit Delivery and Assay Kit Development for Abbott Molecular/IBIS Biosciences T5000/PlexID System
- Notice Date
- 4/14/2010
- Notice Type
- Special Notice
- NAICS
- 325413
— In-Vitro Diagnostic Substance Manufacturing
- Contracting Office
- Department of Health and Human Services, Food and Drug Administration, Office of Acquisitions and Grants Services, 5630 Fishers Lane, Room 2129, Rockville, Maryland, 20857-0001
- ZIP Code
- 20857-0001
- Solicitation Number
- HHS-FDA-10-1071396
- Archive Date
- 5/6/2010
- Point of Contact
- Tara R. Hobson, Phone: 3018279691, Doreen Williams, Phone: 3018273366
- E-Mail Address
-
Tara.Hobson@fda.hhs.gov, doreen.williams@fda.hhs.gov
(Tara.Hobson@fda.hhs.gov, doreen.williams@fda.hhs.gov)
- Small Business Set-Aside
- N/A
- Description
- Description: Assay Kit Delivery and Assay Kit Development for Abbott Molecular/IBIS Biosciences T5000/PlexID System This is a RFI to determine the availability and capability of small businesses (i.e., certified 8(a), Small Disadvantaged, and HUBZone firms; veteran and service-disabled veteran-owned small businesses, and woman-owned small businesses) for Assay Kit Delivery and Assay Kit Development for Abbott Molecular/IBIS Biosciences T5000/PlexID System. This information is being sought for information and planning purposes only and shall not be construed as a solicitation or as an obligation on the part of the Food and Drug Administration (FDA). No official solicitation exists; therefore, please do not request a copy of a solicitation. If in the future an official solicitation is released, there is no guarantee that sources responding to this will be included on the source list. No telephone inquiries will be accepted. Objectives: The Office of Regulatory Science, in collaboration with the FDA's Office of Regulatory Affairs and the State of North Carolina will be testing a high throughput rapid foodborne bacteria detection and identification system known as the PlexID, which could greatly enhance the FDA's ability to monitor and protect the nations food supply. A hybrid delivery order and task order contract is needed to 1) facilitate the procurement of assay kits for CFSAN and for the collaborating laboratories; 2) facilitate further assay kits development. Draft Scope of Work: 1.) Assay kits for Abbott Molecular/Ibis Biosciences T5000 and PlexID bacterial identification systems. 2) Assays for Abbott Molecular/Ibis Biosciences PlexID bacterial identification system. Part 1. Delivery of assay kits for IBIS T5000 and IBIS PlexID systems. The contractor will deliver kits compatible for use with the Abbott Molecular/IBIS Biosciences T5000 and PlexID bacterial identification systems. These systems are generally capable of the following and the kits supplied must be compatible with these systems, since they will be operational at CFSAN and in the field. These systems use an integrated sample preparation and measurement approach. They use robotics to extract and isolate DNA from samples, followed by transfer to a PCR thermal cycler to amplify the DNA after introduction of particular, and specifically chosen, primers. Once the amplification has been completed, the sample will be robotically handled and cleaned up, followed by analysis using electrospray mass spectrometry. A mass spectrometry measurement of the PCR amplicons gives a detailed organism fingerprint, which provides much more information than a simple yes/no answer provided by probes in real-time PCR; detection is not limited to previously known organisms. The approach can rapidly identify organisms in a mixture without additional sample preparation steps. By adjusting the primer selection, the method can be made general or specific and can rapidly identify mutations (within the amplified region). The approach can handle many different types of samples including: air, soil, water, mucosal swabs and washes, sterile fluids (blood, CSF, urine), hair, teeth, and bone, making it very amenable to food matrices. The approach is also high throughput, allowing for the analysis of 600-1200 samples per 24 hour period. Draft requirements 1. Kits must be compatible with the Abbott Molecular/IBIS Biosciences T5000 or PlexID system. As such they must be have the following specifications a. T5000 kits i. Must consist of a set of 3 plates, 10 sets per kit, with bar codes that can be registered with the data system and database for the T5000 system. Each plate must be of a 96-well format and must be physically compatible with the sample handling robotics of the T5000 system. ii. Each well of plate 1 of each set must have PCR primers that are specific for that well/sample/amplicon combination, in order to generate a PCR amplicon that can be measured by the mass spectrometer and correlated with an overall fingerprint pattern for that target. Appropriate amplification standards (to measure quantity) and PCR mass calibration standards must also be included in each well and must be compatible with the Abbott Molecular/Ibis Biosciences data analysis and database software. Each plate must be compatible with the Mastercycler thermal cycler or equivalent for PCR amplification. iii. The second plate must consist of a cleanup plate consisting of ion exchange resin on magnetic particles. Each well from plate well is transferred to a corresponding well on plate two and the DNA amplicons from stage 1 are de-salted with the ion exchange resin coated magnetic beads. After cleanup, the beads a re pulled to the bottom of the plate and the solution is transferred to plate 3. Each plate must be completely compatible with the T5000 robotics, and must be capable of preparing the amplified DNA, by thorough de-salting, for measurement by the T5000n mass spectrometer. iv. The third plate must be a 96-well plate compatible with the T5000 robotics, must be capable of receiving the liquid sample of prepared amplicon from the second plate and must be barcoded for proper identification by the T5000 system. v. Each kit must contain appropriate clean-up reagents for each step in the analysis process, and must contain appropriate instrument calibrants where necessary. b. PlexId kits i. Must consist of a set of 2 plates, 10 sets per kit, with bar codes that can be registered with the data system and database for the PlexID system. Each plate must be of a 96-well format and must be physically compatible with the sample handling robotics of the PlexID system ii. Each well of plate 1 of each set must have PCR primers that are specific for that well/sample/amplicon combination, in order to generate a PCR amplicon that can be measured by the mass spectrometer and correlated with an overall fingerprint pattern for that target. Appropriate amplification standards (to measure quantity) and PCR mass calibration standards must also be included in each well and must be compatible with the Abbott Molecular/Ibis Biosciences data analysis and database software. The plate must be of a size and format compatible with a Tecan liquid handling system, a Mastercycler thermal cycler or equivalent for PCR amplification, and must be compatible with the robotics of the PlexID system.. iii. The second plate must be a 96-well plate compatible with the PlexID robotics, must be capable of receiving the liquid sample of prepared amplicon from the first plate (after cleanup by an intermediate stage that intergral to the PlexID robotics and must be barcoded for proper identification by the PlexID system. c. All kits i. Must be barcoded in such a way as to be compatible with the T5000 or PlexID system, respectively. As such, the barcode must specify the assay type and well layout so that the operating system can correlate the results for a particular well with the identification pattern that is part of that assay. ii. Standard assay kits must be available for the T5000 and the PlexID in the following formats: 1. Bacterial surveillance (general bacterial surveillance across broad classes) 2. High sensitivity bacterial surveillance (detection of and identification of low levels of broad classes of bacteria) 3. Detection of vibrio cholerae and vibrio parahaemolyticus 4. Detection of influenza viruses iii. Beta test kits (and future standard kits should they proceed beyond the development stage) must be available in the following formats 1. Detection and identification of the foodborne pathogens E. coli, Salmonella spp, Shigella spp, and Listeria spp. 2. Future beta test kits (and future standard kits, if developed) to include a. Salmonella serotyping b. Enteric disease plates iv. Kits must be available in quantities (1-10 kits per order) sufficient to allow for the government to respond to research needs and foodborne outbreaks as methods based on the T5000 or PLexID become standard methods. The ability to order from one location (CFSAN) and drop ship to other locations must be part of the ordering and delivery process. v. Vendor must specify a maximum estimated shipping cost per kit (to CFSAN in College Park, MD, Raleigh, NC or Irvine, CA). Part 2. Draft Statement of Work for development of custom assays for the T5000 and PlexId systems Overview: The Office Regulatory Science has recently purchased a three new multiplexed DNA amplification and detection systems for the rapid detection and identification of organisms, particularly bacteria. This system is manufactured by Abbott Molecular and is known as the PlexID system. This system will be used at CFSAN, at the FDA/ORA LosAngeles district lab (Irvine) and in a collaborative effort at the North Carolina State Laboratory. There are many food safety problems, particularly those related to the foodborne illnesses caused by pathogenic bacteria, which require the rapid detection and identification of the microorganism that is responsible for the outbreak. Such identification can be used to determine the course of appropriate treatment, and can be used in tracing back the outbreak to its origin so that the causes can be evaluated and prevented. The PlexID rapid DNA detection and identification system also allows for the identification of changes within an organism and would allow for the identification of the emergence of new strains. Other applications may include the rapid amplification and measurement of DNA for fish species identification and the rapid characterization of allergens in foods using DNA-based identification. The precursor for the PlexID, the T5000, is already being used in bacterial surveillance studies and in microbial ecology studies related to the outbreak of Salmonella in tomatoes. The system uses an integrated sample preparation and measurement approach. It uses specifically chosen PCR primers to amplify DNA targets extracted from samples. Once the amplification has been completed, the sample is robotically handled and cleaned up, followed by analysis using electro-spray mass spectrometry. A mass spectrometry measurement of the PCR amplicons gives a detailed organism fingerprint, which provides much more information than a simple yes/no answer provided by probes in real-time PCR; detection is not limited to previously known organisms. The approach can rapidly identify organisms in a mixture without additional sample preparation steps. By adjusting the primer selection, the method can be made general or specific and can rapidly identify mutations (within the amplified region). The approach can handle many different types of samples including: air, soil, water, mucosal swabs and washes, sterile fluids (blood, CSF, urine), hair, teeth, and bone, making it very amenable to food matrices. The approach is also high throughput, allowing for the analysis of 600-1200 samples per 24 hour period. General Requirements: Further development of the PlexID system will be required to fully utilize its capabilities for FDA related issues. Foremost among the problems that the PlexID could rapidly address, with additional development, is the problem of foodborne pathogen typing including species identification of Salmonella. Shigella, E. coli, and Listeria. Current beta test plate development is underway and should be completed soon, but future modifications may be necessary as new information becomes available. This is a critical application that would significantly enhance FDA's forensic and investigatory microbiology capability and enable more rapid trace-back when new outbreaks occur. Other problems that will be addressed by the PlexID, but will require further development, include the problem of Salmonella serotyoping, a currently tedious process requiring weeks for completion that is critical for identifying the source of bacterial foodborne outbreaks. Finally, there are new emerging problems, such as the appearance of new strains of E.coli outside the O157:H7 serotype most commonly associated with human illness. New assays will have to be developed to target all enteric disease producing E. coli, not just the O157:H7 group. To do this, the capability is required to develop new assays for the PlexID, followed by beta kit testing and deployment. Draft Specific Requirements under this Procurement: A. Initial assay development 1. FDA scientists will work with the vendor to assemble information, based on genetic information available from on-line data bases, newly sequenced genomes and other appropriate sources within and outside the public domain, to generate DNA sequences that, if incorporated into the T5000/PlexID analysis scheme, should provide the appropriate level of differentiation and identification necessary for the designated problem. The vendor will use appropriate software tools to determine whether the information available is suitable to proceed with assay development that will fit with the T5000/PlexID approach. 2. The vendor will use this genetic information to design primer pairs that will generate PCR amplicons appropriate for the PlexID biosensor. The vendor will then develop a prototype kit suitable for testing as part of the PlexID system. These kits will include the appropriate primer pairs, PCR standards, and mass calibration standards. The vendor will be required to have the capability to modify the database used by the PlexID system in order to be able to use the results from the prototype kit in the initial experimental evaluation phase, which will verify correct identification of the bacteria in question. The vendor will produce enough prototype kits (up to 10) that they can be sufficiently tested in the vendor's laboratories and at CFSAN, in close collaboration with CFSAN scientists. 3. The costs for parts 1 and 2 will be combined together when the vendor is making a proposal for the work. Should the initial testing and prototype development not justify further development of beta test kits, then the task can be modified to allow for more prototype development, or a new task can be developed based on new or existing information. 4. In some cases, CFSAN may do the assay development and prototype development in its own laboratories. In this case, the vendor will be asked to modify the PlexID database to incorporate the CFSAN-developed assay. B. Draft Beta test kit development and delivery 1. Upon completion of prototype testing, the vendor will generate a specified number of beta test kits for use at CFSAN at a specified price per kit. The beta kits will be based upon the results of the initial assay development/prototype testing. The vendor will be required to develop no fewer than 10 kits to allow for a sufficient production run, and the vendor will agree to supply a sufficient number of kits to allow for thorough testing at CFSAN (up to 30). Should the vendor have no plans to turn the kits into a commercial product, the vendor must be able to continue to supply the same beta kits in future production runs, as designated by future task orders. 2. If the vendor so desires, the beta kits can be moved to a standard price list so that they can be obtained through delivery orders, credit card purchases or any other standard procurement process, for use not only be the FSDA/CFSAN, but anyone else the vendor deems appropriate. 3. In some cases, CFSAN may do the assay development and prototype development in its own laboratories. In such cases, the vendor may be requested to bid on production of beta test kits based on CFSAN specifications We may anticipate a firm fixed price type IDIQ contract for five years. Viable parties shall provide the following: Part A. Capabilities and Technical Experience - Provide a capability statement describing how your company would provide Assay Kit Delivery and Assay Kit Development as provided in the Draft Scope of Work. Part B. Size of Business- Please provide your business size and submit copies of any documentation such as letters or certificates to indicate the firm's status. Part C. Organizational Conflict of Interest (OCI) - If any, provide disclosure of business activities of your company, your affiliates, your team members and affiliates of your team members which create either a conflict of interest or the appearance of a conflict of interest in the Assay Kit Delivery and Assay Kit Development. Part D. Cost Estimate - Provide a cost estimate for the equipment and maintenance agreement/service with the equipment for 4 option years. Part E. Small Business - Describe your ability to meet the requirements in accordance with 52.219.14 - Limitation on Subcontracting. Responses shall be:  identified with the RFI number ;  no more than ten (10) pages in length;  not submit marketing materials;  submitted to the email as indicated above. FDA makes no implied or in fact contract by issuing this RFI. Acknowledgement of receipt of responses will not be made, nor will respondents be notified of the FDA's view of the information received. Do not send any material that requires a non-disclosure agreement or that may be business sensitive. Responses received that include a non-disclosure agreement or identify information that is business sensitive will not be accepted. Responses to this notice will not be returned.
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