MODIFICATION
B -- Genotyping of M. Tubercuosis Isolates
- Notice Date
- 4/15/2013
- Notice Type
- Modification/Amendment
- NAICS
- 541380
— Testing Laboratories
- Contracting Office
- Department of Health and Human Services, Centers for Disease Control and Prevention, Procurement and Grants Office (Atlanta), 2920 Brandywine Road, Room 3000, Atlanta, Georgia, 30341-4146
- ZIP Code
- 30341-4146
- Solicitation Number
- 2013-57215
- Archive Date
- 5/14/2013
- Point of Contact
- WIKIKI HENTON, Phone: 7704882621
- E-Mail Address
-
kfv5@cdc.gov
(kfv5@cdc.gov)
- Small Business Set-Aside
- Total Small Business
- Description
- This is a Small Business Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding: (1) the availability and capability of qualified small business sources; (2) whether they are small businesses; HUBZone small businesses; service-disabled, veteran-owned small businesses; 8(a) small businesses; veteran-owned small businesses; woman-owned small businesses; or small disadvantaged businesses; and (3) their size classification relative to the North American Industry Classification System (NAICS) code for the proposed acquisition. The NAICS Code for this acquisition is 541380 - Testing Laboratories; annual receipts or $14.0M. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. An organization that is not considered a small business under the applicable NAICS code should not submit a response to this notice. Background. This procurement is entitled Genotyping of M. Tubercuosis Isolates. Genotyping (also referred to as DNA fingerprinting) of M. tuberculosis isolates using restriction fragment length polymorphism (RFLP) analysis with the insertion sequence IS6110 was introduced in 1990. Application of this technique to outbreaks investigated by the Division of Tuberculosis Elimination demonstrated the utility of strain typing for support of epidemiologic investigations and suggested this technology should be available to TB control programs nationwide. Because of the complexity of the technique and the limited number of isolates to be typed, it was decided that implementation in a small number of regional laboratories would be most efficient, which began in 1992. To further assess the utility of large scale typing, the National Tuberculosis Genotyping and Surveillance Network (NTGSN) was established in 1996. NTGSN included seven Sentinel Surveillance Sites and seven Regional DNA Fingerprinting Laboratories (hereinafter refered to as Regional Laboratories). The NTGSN conducted a prospective study of fingerprinting of isolates in the seven surveillance sites during calendar years 1996-2000. During this period, the Regional Laboratories provided genotyping services to their assigned regions in addition to performing genotyping of isolates from the Sentinel Surveillance Sites. The results of the NTGSN project confirmed the utility of universal, prospective genotyping for TB control and support the establishment of universal genotyping in the US. The project also highlighted limitations of the standard IS6110 RFLP method, including the slow turnaround time for results, high cost, limited throughput, and difficulties in analysis of complex fingerprint patterns. To overcome these difficulties, newer, rapid methods have been introduced for primary genotyping. Spoligotyping and MIRU-VNTR are PCR based typing methods that require minimal amounts of culture material, are conducive to high throughput analysis, have a fast turnaround time and provide a high level of discrimination. These methods have been used to provide universal genotyping services in the US. The National TB Genotyping Service consists of two laboratories which were selected by a competitive process in response to a request for proposal. The first contract provided for the genotyping of up to 5,000 isolates per year per laboratory during the time period September 2003 - September 2008 and a second contract continued the support of genotyping for the time period September 2008 - September 2013. As of January 2013, over 70,000 isolates have been submitted to these laboratories by TB control programs for genotyping. For those clusters of isolates that require further discrimination, the standard IS6110-RFLP method is available upon request as a secondary typing method. The service has been shown to be useful to the TB control programs by identifying numerous previously unidentified outbreaks, by defining limits of suspected outbreaks, and by detecting instances of false positive cultures. The TB Genotyping Information Management System (TB GIMS) is a web based system developed by CDC to provide TB control programs with tools to manage and analyze genotyping data as well as to integrate genotyping information with the National TB Surveillance System. Submission of isolates for genotyping is now one of the TB Indicators used to evaluate TB control programs. Purpose and Objectives. The purpose of this contract is to establish regional laboratories to provide genotyping of Mycobacterium tuberculosis isolates in support of state and local tuberculosis (TB) control programs within the United States and research activities of the CDC Division of Tuberculosis Elimination (DTBE) and the Tuberculosis Epidemiologic Studies Consortium (TBESC). The goal will be to provide genotyping for one isolate from each newly diagnosed, culture-positive case of TB in the US. Project requirements. Scope of Work: The contractor shall, as an independent organization and not as an agent of the United States Government, furnish all the necessary services, qualified personnel, material, equipment, and facilities to perform the services required in the contract, except for equipment specifically listed in the statement of work as provided by CDC. Technical Requriements. The contractor shall perform the following tasks: Task 1.0/ Communication: Communicate with public health laboratories and TB control programs in their assigned region via telephone, fax, and e-mail, to allow prior notice of shipment of cultures, confirmation of receipt of cultures, transmittal of results, and consultation on shipments. Provide physical security measures for maintenance of confidentiality of patient data. Task 2.0/Submissions: Provide input on CDC established protocols at protocol discussion meeting for the submission of isolates for genotyping from submitting laboratories which include prior notification of shipment to contractor, submission form, proper containers and labeling, and enforce these protocols by rejecting any improperly prepared submission and providing consultation on proper submissions to submitting laboratory. Task 3.0/Process submitted samples for genotyping: The following subtasks shall be completed by the contractor: Subtask 3.1/Frozen stocks: Receive and log M. tuberculosis isolates for genotyping. Prepare two subcultures of each isolate. One subculture (0.5 mL) will be transferred to CDC no later than 90 calendar days after receipt of isolate. Maintain frozen subcultures (-70C) and a computerized inventory of isolates for duration of contract. Frozen subcultures shall be destroyed at conclusion of contract. The shipment of M. tuberculosis cultures must comply with all regulations of the U.S. Department of Transportation for the shipment of Category A Infectious Substances (www.dot.gov). Shipping charges and containers will be the responsibility of the contractor. Subtask 3.2/DNA Preparations: Prepare small scale DNA samples for rapid PCR-based assays. Retain frozen DNA samples (-20C) and maintain a computerized inventory. An aliquot (0.05 mL) will be transferred to CDC no later than five (5) days after receipt of isolate. Frozen samples will be maintained for five (5) years from the date of receipt of the corresponding isolates and will be transferred to CDC, if requested. All DNA samples will be transferred to CDC at the contract completion; shipping charges will be the responsibility of the contractor. DNA samples shall be prepared using the CDC protocol. Alternative protocols may be submitted to CDC along with validation of the protocol to provide DNA of sufficient quality for the spoligotyping and MIRU-VNTR (subtask 3.4) assays. Subtask 3.3/MIRU-VNTR: Perform mycobacterium interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) typing by amplification of MIRU loci by PCR followed by automated analysis on a capillary electrophoresis sequencing instrument (references attached). MIRU-VNTR analysis shall be conducted using the CDC protocol. Alternative protocols may be submitted to CDC along with validation of the protocol. Analyze data using CDC provided Microsoft Excel spreadsheets; confirm results with visual inspection of data. Training for all methods will be provided by CDC. No reagents will be provided by CDC. Subtask 3.4/Reports: Prepare and upload genotyping reports to TB GIMS by importing results from excel spreadsheets into a CDC provided Microsoft Access database. Training for all methods will be provided by CDC. Contractor shall upload MIRU-VNTR result to TB GIMS no later than 15 days of receipt of isolate. Task 4.0/IS6110 typing: Prepare purified DNA samples for IS6110 RFLP analysis and perform IS6110 typing by standard agarose gel electrophoresis, blotting, and hybridization methods on requested isolates. IS6110 typing will be performed as needed only after the results of the PCR-based typing are obtained and will only be performed on those isolates belonging to a PCR cluster in that jurisdiction. The decision to IS6110 type will be based on request by the relevant TB control program or by request of CDC. It is anticipated that less than 10% of submitted isolates will require IS6110 typing. IS6110 typing will be completed and results reported to the requesting program within 45 working days after the decision is made to perform typing. Contractor shall analyze results of IS6110 typing by pattern matching using computer software (Bionumerics). Patterns will only be compared to the patterns of those isolates belonging to the same PCR genotype cluster as defined by spoligotype and MIRU-VNTR pattern. Image files of specific IS6110 fingerprint patterns will be submitted to CDC when requested via e-mail. Training in these methods will not be provided by CDC. CDC will provide IS6110 marker. Task 5.0/Data review: Provide to the CDC project officer copies of the output data files and the excel files from MIRU-VNTR and the genotyping Microsoft Access database on a monthly basis. All data should be stored on CD-ROM and be made to reach the CDC no later than 10 days after the end of the month. After review of data, repeat typing of any isolate will be at the discretion of the CDC Project Officer. Task 6.0/Quality Assurance: Subtask 6.1/Contractor's Quality Control Plan (QCP): The contractor will be required to provide a QCP. At a minimum, this program shall consist of retyping 3% of isolates each month. The contractor will provide CDC with a report of the QCP results including a description and resolution of discrepant results within 30 days of the end of the month. Subtask 6.2/External Quality Assessment Program: The contractor shall participate in on going external quality assessments (EQA) of MIRU-VNTR genotyping. This program will consist of MIRU-VNTR typing of up to 30 DNA samples provided each year by CDC. The contractor will provide CDC with a report of the results within 60 calendar days of receipt of the EQA DNA samples. Task 7.0/Genotyping Methods and Project Meetings: Subtask 7.1/Genotyping Methods Meeting: Contractor is required to participate in a meeting held to provide training on the genotyping methods to be used in the contract. Meeting will be two days in length and will be held at a CDC facility in Atlanta, GA. Contractor employees travel costs are the responsibility of the contractor. Subtask 7.2/ Protocol Discussion Meeting: All assigned contractor personnel will be required to participate in a protocol discussion meeting at the beginning of the contract period. It is anticipated that this meeting will be three hours in length and will be held via teleconference. Subtask 7.3/Annual Meetings: All assigned contractor personnel will be required to participate in annual meetings of all contractors and CDC personnel. It is anticipated that these meetings will be three hours in length and will be held via teleconference. Task 8.0/Maintenance of Government furnished property: It is the responsibility of the contractor to insure that the equipment furnished by the Government is fully operational at all times during the contract performance period. Contractor shall provide a maintenance/service agreement for an ABI 3130XL capillary electrophoresis instrument and maintain this agreement at all times during the contract performance period. A copy of the original agreement and all updates to the original agreement shall be provided to the CDC project officer within one month of activation. Anticipated period of performance. Base Period: 9/21/2013 - 9/22/2014 Option Period 1: 9/21/2014 - 9/22/2015 Option Period 2: 9/21/2015 - 9/22/2016 Option Period 3: 9/21/2016 - 9/22/2017 Option Period 4: 9/21/2017 - 9/22/2018 Other important considerations. None. Capability statement /information sought. All respondents must provide, as part of their responses, a capability statement. The capability statement must include the following: 1. Technical and Business Content: - information regarding respondents': (a) staff expertise, including their availability, experience, and formal and other training; (b) current in-house capability and capacity to perform the work; (c) prior completed projects of similar nature; (d) corporate experience and management capability; and (e) examples of prior completed Government contracts, references, and other related information; and - information regarding respondents' ability to perform in a Biosafety Level 3 (BSL-3) laboratory that meets the minimum following criteria: a) Facility: Restricted access to the laboratory with a series of two self-closing doors: Seams, walls, and ceiling are sealed and easy to clean and decontaminate; Laboratory exhaust air is not re-circulated to any other area of the building; a hands-free sink is available for hand washing; an eyewash station is available; the laboratory is equipped with a Class II-A1 or II-A2 Biological Safety Cabinet (BSC) that is re-certified annually; and b) Standard Microbiological Practices: A risk assessment for working with TB in the laboratory has been completed; a TST or IGRA program is available and testing is done at least annually; a biosafety manual specific for the laboratory is available; testing personnel are knowledgeable about hazards of working with TB and demonstrate proficiency in laboratory procedures; BSL-3 Personal Protective Equipment (PPE) is used based on risk assessment of laboratory procedures and practices; all procedures involving manipulation of viable TB strains are conducted in a BSC or other physical containment devices; decontamination of laboratory waste must be available in the facility, preferably within the laboratory (e.g., autoclave, chemical disinfection, or other validated decontamination method); and - technical and business content shall not exceed 10 pages. 2. Cover Page and Table of Content: - information regarding respondents' DUNS number, organization name, address, point of contact including names, titles, addresses, telephone and fax numbers, and e-mail addresses, and size and type of business (e.g., 8(a), HUBZone, etc.) pursuant to the applicable NAICS code; and - Cover Page and Table of Contents shall not exceed 2 pages. 3. Formatting and Delivery Instructions: - information shall be provided electronically only (telephone and facsimile responses will NOT be accepted); - information should be provided in Microsoft Word (.doc) or Adobe PDF, font size must be greater than 10 pitch, paper size must be 8 ½ X 11, margins must be greater than or equal to 1.0, spacing should be single or double space; and - one copy of the response is required. All sources sought Capability Statments must be delivered via email to the Contracting Officer, Wikiki Henton. Ms. Henton's email address is kfv5@cdc.gov. The Notice number (2013-57215) shall be in the email Subject Line. Disclaimer and Important Notes. This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation. Confidentiality. No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s)."
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/CDCP/PGOA/2013-57215/listing.html)
- Place of Performance
- Address: Contractor's Facility, United States
- Record
- SN03036532-W 20130417/130415234410-93ee1f5cf2027fae6fae3a5dc8a23259 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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