Amendment 1 RFP 75N93022R00015 with Attachment 5.pdf

AMENDMENT #1 RFP No. 75N93022R00015 1

Amendment No. 1 RFP No. 75N93022R00015

“Mycobacterium Tuberculosis Quality Assessment Program”

Solicitation Number: 75N93022R00015

Amendment Number: One (1)

Amendment Issue Date: November 2, 2022

Proposal Due Date/Time: November 30, 2022 at 3:00 PM, EST (Unchanged)

Issued By: Robert Corno

Contracting Officer

OA/DEA/NIAID/NIH/DHHS

5601 Fishers Lane, Room 3D10, MSC 9821 Bethesda, Maryland 20892-9821

Points of Contact: PRIMARY cornorj@niaid.nih.gov Robert Corno, Contracting Officer Phone: 240.669.5151

SECONDARY

isaac.elliott@nih.gov Isaac Elliott, Contract Specialist Phone: 301.761.7447

Please note that we do NOT intend to extend the due date for submission of proposals as a result of this amendment. The date specified for receipt of proposals remains unchanged.

Offerors must acknowledge receipt of this Amendment by identifying the amendment number and the date of the amendment on each copy of the submitted proposal. Failure to receive your acknowledgement may result in the rejection of your proposal. Except as provided herein, all terms and conditions of the solicitation remain unchanged and in full force and effect.

The purpose of this Amendment is to: (1) provide responses to questions from potential offerors, regarding the solicitation; and (2) revise Attachment 5, Additional Business Proposal Instructions and Uniform Cost Assumptions, Section 3.1.e.1. to remove the costing information related to the evaluation of the Akonni Biosystems TruArray MDR-TB assay.

mailto:cornorj@niaid.nih.gov mailto:isaac.elliott@nih.gov

AMENDMENT #1 RFP No. 75N93022R00015 2

RESPONSES TO QUESTIONS FROM POTENTIAL OFFERORS:

Question 1 Regarding Section F.2.a., “During the period of performance of this contract, the Contractor shall provide _____ direct labor Hours.”

Although the RFP calls for 5 FTEs/year, what is the number of hours the government expects to be used per FTE per year?

Response to Question 1 The number of Hours will vary depending on the Contractor’s work year, therefore we state the requirement in terms of FTEs as opposed to hours. Please provide the direct labor hours as it relates to your institutions work year (e.g. 2080, 1830, 1880, 1840, etc…)

Question 2 Regarding Section H.13.b., Does the technical proposal volume need to be 508 compliant?

Response to Question 2 Yes, the technical proposal volume needs to be Section 508 complaint, as does the business proposal volume.

Question 3 Regarding Section H.17., Please clarify the statement below is part of the RFP:

“The data sharing plan submitted by the Contractor is acceptable. The Contractor's data sharing plan, dated TBD is hereby incorporated by reference. The Contractor agrees to adhere to its plan and shall request prior approval of the Contracting Officer for any changes in its plan…”

Response to Question 3 Yes, this is part of the RFP. This is notifying the Offeror that should they be awarded a contract, the data sharing plan submitted will be found acceptable either at peer review or during negotiations and shall be incorporated into the contract by reference. Since we do not know the date the plan is accepted we state To Be Determined (TBD).

Question 4 Regarding Section L.2.b.5., Please clarify missing information from the “Enhancing Reproducibility through Rigor and Transparency” section. This section ends with: Specifically, the offeror shall describe in its technical proposal the information described below:

Response to Question 4

AMENDMENT #1 RFP No. 75N93022R00015 3

The ending statement “Specifically, the offeror shall describe in its technical proposal the information described below”, was added in error so therefore please ignore the ending statement.

Question 5 Regarding Attachment 1, Section II.A.4., Can figures/tables be a smaller font size than the requested 10 to 12 pt. font for the proposal?

Response to Question 5 No, there will be no deviation from the required range in the proposal.

Question 6 Regarding Attachment 5, Section 3.1.f., The following sentence in section F in incomplete:

Repository isolates are to undergo whole-genome and targeted…..

Please clarify if the first paragraph in section F is an incomplete duplication of the paragraph below or a separate assumption for pricing.

Response to Question 6 The first paragraph is a separate assumption for pricing and was incomplete and should include the word “sequencing”, which is missing at the end of the sentence.

Question 7 The RFP does not include any language concerning requirements for major vs. minor subcontractors. Should subcontractors submit a full proposal or is only pricing required?

Response to Question 7 Under section “Note to Offerors” pages 72 and 73, part 12 article f, “A complete cost proposal in the same format as the offeror’s cost proposal.” A full cost proposal as the offeror will be required.

The RFP does not include any language concerning requirements for major vs. minor subcontractors. Should subcontractors submit a full proposal or is only pricing required?

Per Section L – Instructions, Conditions, and Notices to Offerors, paragraph 2 Instructions to Offerors, subparagraph C. Business Proposal Instructions, item 12 Subcontractors, states the below:

If subcontractors are proposed, please include a commitment letter from the subcontractor detailing:

a. Willingness to perform as a subcontractor for specific duties (list duties).

b. What priority the work will be given and how it will relate to other work.

c. The amount of time and facilities available to this project.

d. Information on their cognizant field audit offices.

e. How rights to publications and patents are to be handled.

AMENDMENT #1 RFP No. 75N93022R00015 4

f. A complete cost proposal in the same format as the offeror's cost proposal.

Question 8 Regarding Attachment 3., Section 3.A.1., There is mention of PT panels as well as quality control material (QCM) in this section. However, these are used for 2 distinct purposes. Would the government please define how each is expected to be used for this laboratory support?

Response to Question 8 The term Quality Control Materials (QCMs) as appears in the indicated section is used as a general term for any materials that may be used to construct a proficiency testing panel.

Question 9 Regarding Attachment 3., Section 3.A.4., How will laboratories be assessed, and will training be study-specific?

Response to Question 9 As the SOW states that: “New and established Labs will be assessed by another NIAID resource for ability to conduct operations according to Good Clinical Laboratory Practices (GCLP). Any deficiencies observed by such assessment, as well as the need for training to be provided by the TBQA, will be conveyed to the TBQA by the Government. Training may be for protocol-specific requirements.

Question 10 Regarding Attachment 3., Section 3.B.1., Could the government confirm that where it states that the contractor may "facilitate single or multiple lab studies" for new assays, it can be done with both domestic and international laboratories, and that it will be possible to publish results?

Response to Question 10 Single site or multi-site evaluations facilitated by the TBQA may take place in the U.S. or outside the U.S. Yes, you can publish results, providing its in accordance with contract.

Question 11 Regarding Attachment 3., Section 3.C., Is the purpose of obtaining isolates and non sputa specimens for QCM to create a biobank as well? If so, is it possible for non-consortia labs to obtain these materials as well?

Response to Question 11 The RFP indicates the following “Establish and maintain a dynamic collection of distinct clinical MTB isolates.” Other types of materials do not necessarily need to be captured in a biobank, rather need to be accessible to the TBQA in order to accomplish its tasks. Materials may be obtained from any source the TBQA deems appropriate.

Question 12

AMENDMENT #1 RFP No. 75N93022R00015 5

Regarding Attachment 3., Section 3.E., Would the government please explain the existing FISMA-compliant website that is mentioned in this section?

Response to Question 12 The NIAID has another contractor that houses this type of information on the pSMILE.org website. We will provide more information after the award.

Question 13 Must our university have the expertise with all the MTB assay methodologies mentioned in Attachment 3 in-house within its own workforce, or can subcontractors fulfill this requirement?

Response to Question 13 The Contractor can work with subcontractors to fulfill this requirement.

Question 14 Our university has contacted the manufacturers of the RFP-specified systems and assays and many are unavailable in the US. How are we supposed to get access to these? Does that preclude a US entity from being awarded the contract? Can our university find a foreign subcontractor with access to these systems?

1. Attachment 5, 3.1.e.1.: the Akonni Biosystems TruAssay MDR-TB assay. The president of Akonni has informed us that the company is under reorganization and has paused all commercial production activities.

Response to Question 14 If you are unable to obtain quotes directly from the manufacturer, proposing a subcontractor who can obtain such information is an option. This does not preclude a U.S. entity from being awarded the contract, for the incumbent contractor is a domestic entity. Yes, you can find a foreign subcontractor with access.

1. We are revising Attachment 5, Section 3.1.e.1. to remove the costing information related to the evaluation of the Akonni Biosystems TruArray MDR-TB assay.

END OF AMENDMENT NO. 1, RFP No. 75N93022R00015

ATTACHMENT 5: ADDITIONAL BUSINESS PROPOSAL INSTRUCTIONS

AND UNIFORM COST ASSUMPTIONS

Mycobacterium tuberculosis (MTB)

Quality Assessment Program (TBQA)

RFP No. 75N93022R00015

In addition to the format requirements for the Business Proposal that are contained in Section L of the solicitation, the information presented in this section of the RFP is intended to provide uniform cost assumptions and business clarifications.

Offerors are advised to give careful consideration to the Statement of Work, all reference material provided as attachments, the Technical Evaluation Criteria, and, the RFP as a whole, in the development of your proposal. The information requested in these instructions should be used as a guide for the development and formatting of your Business Proposal. Offerors should consider and include the information requested here, as well as any other information which will benefit the proposal.

BUSINESS PROPOSAL – TABLE OF CONTENTS

SECTION 1 – PROPOSAL COVER SHEET (use form NIH 2043 identified in Section J of the solicitation)

SECTION 2 – COST OR PRICE SUPPORT

Section L of the RFP specifies the minimum documentation requirements for cost data and all cost related support. All related documentation should be included in a clearly marked section of the proposal.

SECTION 3 – UNIFORM COST ASSUMPTIONS

1) Technical Cost Assumptions

a. For costing activities related to monitoring the ability of Labs to perform MTB assays, assume that PT programs provided by the TBQA will be continued throughout the duration of the contract. For any PT panels created by the TBQA, assume the cost of collection, processing and characterization of QCMs to be used for PT panel preparation and shipping at appropriate conditions to Labs, data retrieval and analysis and reporting of results. Assume the annual cost of the following:

1. Providing a PT program with panels shipped twice a year to 15 non-US Labs twice a year, to monitor the Nipro Genoscholar PZA-TB II assay performance of these Labs.

2. Participation of 30 non-U.S. Labs in the SmartSpot Quality (https://www.smartspotq.com/) GeneXpert MTB/RIF PT program, including the cost of panels and their shipment panel shipment to Labs.

b. For costing activities related to supporting method validation at Labs, assume the cost of annually providing:

1. Five (5) Labs in Brazil with a 10-sample validation panel consisting of MTB and nontuberculous mycobacterial materials needed to validate the Hain MTBDRsl assay at the Labs.

2. Five (5) Labs in South Africa with a 10-sample validation panel, including 5

MTB isolates resistant to moxifloxacin with Minimal Inhibitory Concentration (MIC) of >1.0ug/ml, for validation using the MGIT method.

c. For cost purposes related to Lab assistance, guidance and training, assume the following on an annual basis:

1. Conduct three 10-day visits to Labs, one in South Africa, one in Brazil, and one in India, each requiring 1 Contractor staff.

2. Attend two 2-day User Group meetings in Washington DC, each requiring the attendance of 2 Contractor staff.

d. For costing purposes related to capacity building of a new Lab, assume the cost of supporting one Lab every year in Vietnam, including a 10-day visit to the Lab.

e. For costing activities related to evaluations of MTB technologies and specimen processes, assume the annual cost to conduct in-house (Contractor’s laboratory) of the following:

1. Evaluation of the GenoScreen Deeplex Myc-TB method.

2. Assessment of optimal conditions for processing gastric aspirates for MTB culturing, including variables related to neutralization, processing timeframes and transport temperature.

3. Assessment of optimal processing methods for recovering MTB from Cerebral

Spinal Fluid (CSF) using the GeneXpert Ultra method, including variables related to sample volume, sample to reagent buffer ratio, storage conditions and length of storage.

f. For cost purposes related to acquisition and characterization of QCMs needed for preparation of proficiency testing panels and for method evaluation studies, assume the annual cost of establishing, as needed, maintaining and replenishing a collection of 50 distinct MTB drug-resistant isolates representative of resistances to both first-and second-line anti-TB drugs and containing common genetic mutations associated with resistance; and 30 MTB drug-sensitive isolates. Isolates shall include representatives of the MTB complex. Repository isolates are to undergo whole-genome and targeted sequencing.

Establishment, as needed, maintenance and replenishment of a collection of 50 distinct MTB drug-resistant isolates representative of resistances to both first- and https://www.smartspotq.com/ second-line anti-TB drugs and containing common genetic mutations associated with resistance; and 30 MTB drug-sensitive isolates. Isolates shall include representatives of the MTB complex. Repository isolates are to undergo whole-genome and targeted sequencing and be characterized for resistance to currently available TB drugs by various methods.

g. Maintenance services for equipment at the TBQA laboratory needed to support activities described in the SOW.

2) Other Meetings – cost assumptions

a. Assume travel costs for one Contractor staff to present data each year at one 3-day meeting in England

b. Assume travel costs for one Contractor staff to present data each year at a one 2-day meeting in Los Angeles, USA.

c. Assume the administrative costs of one contract initiation meeting of one-day duration at the Contractor’s site as well as one annual site visit of one-day duration by the COR and other NIAID personnel designated by the COR. The Contractor will not be responsible for travel costs for the COR nor NIAID personnel.

3) Government Furnished Property

Government Furnished Property is offered for this acquisition.

No Government Furnished Property is offered for this acquisition.

The purchase of Government Furnished Property will not be authorized as a direct charge under the resultant contract.

SECTION 4 – TYPE OF CONTRACT AND ESTIMATE OF EFFORT

Please note that All Offerors are required to propose on all Options 1-40.

It is anticipated that a term (level of effort) type contact will be awarded as a result of this solicitation. The period of performance will be for one year beginning approximately October 16, 2023. The requirement will be the delivery of 5.00 full time equivalents (FTEs) per year for the base period (Year 1) and 5.00 FTEs per year for Options 1-6 (Years 2-7). PLEASE NOTE: The number of FTEs includes the effort of subcontractors and consultants.

Labor Category Years 1 – 7 (Base Period and Options 1- 6)

Principal Investigator (PI) 0.10 Project Director/Manager 0.50

Biostatistician 0.10 Senior Scientist 0.20

QA and safety Compliance 0.10 Medical technologist 0.80 Research Technician 3.20

Total 5.00

While the total level of effort provided above is a requirement, the labor mix is the Government’s estimate and should not be considered restrictive for proposal purposes. Offerors should propose the labor mix they consider most appropriate for satisfactory completion of the work.

Options 1-6: Extend the Term of the Contract: The Government may exercise Options to extend the term of the contract beyond the base period (Year 1), annually for a total contract period of up to 7 years. Assume that the scope and types of activities as outlined in the Statement of Work for the base requirement would be continued for each succeeding annual contract period. The requirement will be the delivery of 5.00 full time equivalents (FTEs) per year for the base period (Year 1) and 5.00 FTEs per year for Options 1-6 (Years 2-7). PLEASE NOTE: The number of FTEs includes the effort of subcontractors and consultants.

Options 7 through 27, to Increase Level of Effort for Additional Labs: The Government may exercise Options for an increased level of effort that may result from unanticipated increases in demand for the activities supported by the base requirements of this contract. During the course of the contract, it may be necessary to incorporate additional Labs to support NIAID-supported clinical trials. Such an increase would require an increase in the Contractor's effort activities to be activated, at the discretion of the Government, as an Option. Each Option of this type will implement work commensurate with the addition of 5 Labs. If the Government elects to exercise this Option, the Contractor shall provide an additional 1.0 FTE. One Option for adding new Labs may be exercised once per year during any year of the contract, beginning with Year 2 of the contract, to a total of 21 options during the life of the contract, as follows: Year 2 (Option 7), Year 3 (Options 8 & 9), Year 4 (Options 10, 11, 12), Year 5 (Options 13, 14, 15, 16), Year 6 (Options 17, 18, 19, 20, 21), and Year 7 (Options 22, 23, 24, 25, 26, 27). The period of performance of an Option for Increased Services will not exceed the term of the base year or the Option year in which the Option is exercised.

The labor mix provided below is to be used as an example only for the level of effort for Options 7 through 27. The following tables provide a breakdown of Options per year and the anticipated level of effort for each:

Labor Category Yr 2 Yr 3 Yr 4 Yr 5 Yr 6 Yr 7 Project Director 0.05 0.05 0.05 0.05 0.05 0.05

Research Technician 0.95 0.95 0.95 0.95 0.95 0.95 Total 1.0 1.0 1.0 1.0 1.0 1.0

While the total level of effort provided above is a requirement, the labor mix is the Government’s estimate and should not be considered restrictive for proposal purposes. Offerors should propose the labor mix they consider most appropriate for satisfactory completion of the work.

Option 1 Year 2

Option 2 Year 3

Option 3 Year 4

Option 4 Year 5

Option 5 Year 6

Option 6 Year 7

10/16/24 – 10/15/25

10/16/25 – 10/15/26

10/16/26 – 10/15/27

10/16/27 – 10/15/28

10/16/28 – 10/15/29

10/16/29 – 10/15/30

Option 7 Option 8 Option 10 Option 13 Option 17 Option 22

1.0 1.0 1.0 1.0 1.0 1.0

Option 9 Option 11 Option 14 Option 18 Option 23

1.0 1.0 1.0 1.0 1.0 Option 12 Option 15 Option 19 Option 24

1.0 1.0 1.0 1.0 Option 16 Option 20 Option 25

1.0 1.0 1.0 Option 21 Option 26

1.0 1.0 Option 27 1.0

For costing Options 7-27 for additional Labs, assume that for each option the TBQA will annually:

1. Provide PT oversight support to five (5) Labs in India.

2. Support the validation of the Hain MTBDRsl assay at 2 Labs in India

3. Conduct one 10-day visit to a Lab in India, requiring 1 Contractor staff.

Options 28 through 33, to Increase Level of Effort for Use of a CLIA Certified Lab:

During the course of the contract, it may become necessary to use new and novel immunologic assays in clinical trials where results will be used for clinical decisions within the trial. This will necessitate the use of a CLIA certified laboratory for late-stage validation of the assay and for clinical testing. If necessary, this will be provided through the exercise of options to this contract. Should the Government elect to exercise these options, the Contractor shall provide resources for the unanticipated increase in work volume by 1.0 FTE for each option exercised. One option may be exercised per year in Years 2 through 7.

The period of performance of an Option for increased level of effort for this purpose will not exceed the term of Option year in which the Option is exercised. The percentage of effort includes the effort of subcontracts and consultants.

For costing Options 28 - 33 for use of a CLIA certified Lab to perform MTB testing, assume that each Option will require the addition 1.0 FTE. The labor mix provided below is to be used as an example only for the level of effort for Options 28 through 33.

Labor Category Yr 2 Yr 3 Yr 4 Yr 5 Yr 6 Yr 7 Project Director 0.05 0.05 0.05 0.05 0.05 0.05

Clinical Lab Technician/Medical

Technologist

0.90 0.90 0.90 0.90 0.90 0.90

Research Technician 0.05 0.05 0.05 0.05 0.05 0.05 Total 1.0 1.0 1.0 1.0 1.0 1.0

While the total level of effort provided above is a requirement, the labor mix is the Government’s estimate and should not be considered restrictive for proposal purposes. Offerors

Options 34 through 40, for Addition of Expertise: During the course of the contract, it may be necessary to provide contract services for non-MTB pathogens that would directly support NIAID research on high priority public health emergency needs. Such services may include the development of new, or optimization of existing, diagnostic tests and sample collection techniques, development of SOPs and training materials, and testing of study samples. Should the Government elect to exercise these options, the Contractor shall provide resources for the unanticipated increase in work volume by 1.2 FTEs for each option exercised.

For costing Options 34-40 for addition of expertise, assume that each Option will require the addition of 1.20 FTEs. The labor mix provided below is to be used as an example only for the level of effort for Options 34 through 40.

Labor Category Yr 1 Yr 2 Yr 3 Yr 4 Yr 5 Yr 6 Yr 7 Project Director 0.05 0.05 0.05 0.05 0.05 0.05 0.05

Clinical Lab Technician/Medical

Technologist

0.90 0.90 0.90 0.90 0.90 0.90 0.90

Biostatistician 0.05 0.05 0.05 0.05 0.05 0.05 0.05 Research Technician 0.20 0.20 0.20 0.20 0.20 0.20 0.20

Total 1.20 1.20 1.20 1.20 1.20 1.20 1.20 While the total level of effort provided above is a requirement, the labor mix is the Government’s estimate and should not be considered restrictive for proposal purposes. Offerors

Additionally, assume that each Option will include the optimization of one (1) diagnostic method and associated sample collection techniques, as well as development of SOPs and training materials.

SECTION 5 - TABLE OF CONTENTS FOR DOCUMENTATION REQUIRED UNDER

SECTION L OF THE SOLICITATION

Refer to Section L of the solicitation for documentation requirements. All relevant documentation should be included in a clearly marked section of the proposal.