RFQ No. 75F40125Q00340 Metagenomics Analysis_r1.pdf

Metagenomics Analysis

Request for Quote (RFQ)

RFQ Number 75F40125Q00340

1 Background

The FDA prioritized modernizing high throughput approaches to antimicrobial resistance (AMR) monitoring across the food supply by awarding funding to a Cross Agency Regulatory Science (CARS) grant proposal entitled: Modernizing methods for high throughput detection and reporting of critically important antimicrobial resistance. This grant will use metagenomic data to describe the antimicrobial landscape for foods, without the need to focus on select pathogens.

As we understand more about transmission of clinically significant AMR, it becomes valuable to extend AMR monitoring beyond genomes of a limited set of well-studied pathogenic microbes (Salmonella, E. coli, Campylobacter, Listeria and Enterococcus), to additional, closely related microbes that persist in human and animal food environments. This supports improved characterization of risks posed by mobile elements in species not traditionally monitored and will help identify selection pressures that may be driving the AMR persistence and transmission.

Another component of modernized monitoring includes profiling metabolic features of microbiomes, instead of just taxonomic features. With metabolic and taxonomic information, we can advance our understanding of both taxonomic and metabolic drivers of AMR.

To support this effort, scientists in the Office of Applied Science (OAS) are pioneering analysis methods that combine functional and taxonomic gene analysis at the same time they identify and link virulence, heavy metal, and AMR genes. Typically, these analyses use different pipelines that are merged for biological inference to support modernized monitoring of clinically significant AMR in food environments. Certain analytic pipelines support taxonomic, functional, virulence, AMR, and many other statistical annotations at the same time, such as the tools created by the Harvard School of Public Health’s Biobakery. These tools are incredibly valuable to FDA research aims and provide valuable reference by which to benchmark FDA pipelines.

The requested contract will allow OAS to get analysis support in this arena to guide development of internal tools, protocols, standard operating procedures (SOPs) which can subsequently be validated and shared publicly via external platforms.

2 Objective

The objective of this order is to acquire: The objective of this order is to acquire the most up to date taxonomic, antimicrobial resistance (AMR), and functional annotations and analyses to support mission critical evaluation of human and animal food safety.

3 Scope

The Contractor shall support and perform bioinformatic analysis of metagenomic data to characterize AMR and functional and taxonomic features of human and animal food and food environments to support public health and food safety initiatives.

4 Period of Performance

The period of performance will be a twelve (12) month base year.

5 Place of Delivery

The primary place of performance shall be at the contractor site.

6 Order Type

The is Firm Fixed Price (FFP) task order.

7 Reporting Requirements/Deliverables

Because of specific tasking in performance of the activities in this Order, the Contractor shall provide the deliverables. Deliverables will include full taxonomic, AMR, and metabolic profiles of metagenomic data from human and animal foods and associated microbiomes. The deliverables may be emailed documents and reports and figures that describe the results of statistical evaluations using MaAsLin2 and 3 (and other relevant tools) of significant differences between human and animal food treatments being examined by OAS.

8 Salient Characteristics

The analysis service or webservice support for Microbiome Multivariate Association with Linear Models (MaAsLin2 and MaAsLin3) is required to provide the most up to date annotation and statistical analysis of microbial taxonomy (virus, fungi, bacteria, protist, eukaryote), functional genes, and AMR genes and can be used to describe comprehensive metabolic, virulence, heavy metal, AMR, and multi-domain taxonomy for FDA datasets describing AMR and food. The service must support analysis of publicly available data (described below) generated by the FDA so that analysis can be run using database and pipeline features. This will support risk assessment and potentially identify significant features of microbiomes that correlate with selection pressures and drivers of AMR.

The following are the requirements that the service shall provide at the minimum:

• Microbiome Multivariate Association with Linear Models (MaAsLin2 and MaAsLin3) analysis of taxonomy and function of microbiomes from short read sequence data

• Annotation of MetaCyc functional pathways for 300 + datasets

• Annotation of Enzymes by the Enzyme commission (the hierarchical, numerical classification system for enzymes based on the chemical reactions that they catalyze)

• Linear discriminate analysis Effect Size (Lefse analysis) to identify biomarkers from features (organisms, genes, or functions that are statistically significantly differentially enriched in one microbial data set contrasted to another

• Contractor shall provide support for technical issues – by virtual meeting - with response time not to exceed 48 hours.

• Contractor shall provide the ability to review previously uploaded and publicly available data to support temporal assessments describing AMR in response policy implementations.

• Technical Support o The vendor shall provide guidance on connectivity issues at no additional charge.

o The vendor shall provide web based (video conference) technical support within

48 hours of request Monday through Friday from 8am to 5pm ET, throughout the period of the service agreement in the event of non-functional analytic pipelines.

9 Authorized Reseller/Servicing Agent

The contractor shall be an authorized reseller and/or servicing agent of the software manufacturer while performing on this order. The quoters shall notify the Contract Specialist/Contracting Officer immediately if this requirement is registered by a reseller with the Original Equipment Manufacturer (OEM).

10 Order of Precedence

The Contractor shall follow the terms and conditions of this order. Should the contractor include any additional terms and conditions resulting in conflicts between this document and the contractor’s document, the order of precedence shall be as specified in FAR Clause 52.212-4 of the order. Any indemnification language indemnifying the contractor of any liability and governing law language in the contractor’s terms and conditions shall be invalid and shall be stricken and removed from this order. Any additional terms and conditions shall not be prohibited by applicable laws and regulations. Any additional terms and conditions identified with a web link and/or incorporated by reference shall be stricken and removed from this order.

11 Inspection and Acceptance

The Government shall review all reporting requirement deliverables in accordance with specifications and standards identified by the FDA COR. Reporting Requirements/Deliverables shall be submitted to the FDA COR in accordance with the delivery schedule. The acceptance of deliverables and satisfactory work performance, required herein, shall be based upon the timeliness and accuracy of the deliverables.

The Contractor shall share information and provide full access to code, constructs, databases, and documentation while delivering integrated, cohesive business and technology services and products. The level of required cooperation in the system or software development and testing processes is unprecedented in FDA’s experience and is central to the success of the endeavor.

Products developed under this contract shall be owned by the Government and shall not be labeled ‘copyright’ or ‘proprietary’ or anything similar that might preempt the desired environment of fluid sharing and partnership.

The FDA will reject nonconforming products and services. The contractor shall correct any deficiencies within thirty (30) calendar days after the government issues the rejection notice. If the contract cannot correct the deficiencies within this time frame, the contractor shall immediately notify the COR or technical POC of the reason for the delay and provide a proposal for corrective action plan within ten (10) business days.

The Contractor shall implement necessary changes within ten (10) business days, or a mutually agreed upon period, from the day of change notification.

The FDA COR shall perform inspection and acceptance of materials and services.

All work products under this order including, but not limited to, source code, executable code, scripts, batch jobs, documentation, notes, and meeting materials are the sole property of the US government.

Inspection and acceptance shall be performed at: 10903 New Hampshire Avenue, Silver Spring, Maryland 20903, or any other elated FDA facility.

12 Contracting Officer Authority

The Contracting Officer (CO) is the sole person authorized to make or approve any changes in any of the requirements of this order and notwithstanding any provisions contained elsewhere in the order, the said authority remains solely with the CO. In the event the contractor makes any changes at the direction of any person other than the CO, the change shall be considered to have been made without authority and no adjustment will be made in the delivery order terms and conditions, including price. The CO shall be the only individual authorized to accept nonconforming work, waive any requirement of the order and modify any term or condition of the order. The CO is the only individual who can legally obligate Government funds.

13 Contracting Officer Representative Authority

The Contracting Officer’s Representative (COR) or Project Officer is not authorized to make any commitments or otherwise obligate the Government or authorize any changes which affect the order price, terms or conditions. The COR/Project Officer is responsible for the technical aspects of the project and serves as technical liaison with the contractor and is responsible for the final inspection and acceptance, and such other responsibilities as may be specified in the order.

14 Invoicing Instructions

The clause at 52.212-4, Contract Terms and Conditions—Commercial Items (NOV 2021), applies to this acquisition with the following addenda:

Instructions for invoicing are indicated below. The instructions may change during the period of performance of the catalog as required.

FDA Electronic Invoicing and Payment Requirements - Invoice Processing Platform (IPP) (Jan 2022)

a. All Invoice submissions for goods and or services must be made electronically through the U.S. Department of Treasury's Invoice Processing Platform System (IPP).

http://www.ipp.gov/vendors/index.htm

b. Invoice Submission for Payment means any request for contract financing payment or invoice payment by the Contractor. To constitute a proper invoice, the payment request must comply with the requirements identified in FAR 32.905(b), "Content of Invoices" and the applicable Payment clause included in this contract, or the clause 52.212-4 Contract Terms and Conditions - Commercial Items included in commercial items contracts. The IPP website address is:

https://www.ipp.gov c.

1. The Agency will enroll the Contractors new to IPP. The Contractor must follow the IPP registration email instructions for enrollment to register the Collector Account for submitting invoice requests for payment. The Contractor Government Business Point of Contact (as listed in SAM) will receive Registration email from the Federal Reserve Bank of St. Louis (FRBSTL) within 3 - 5 business days of the contract award for new contracts or date of modification for existing contracts.

2. Registration emails are sent via email from ipp.noreply@mail.eroc.twai.gov. Contractor assistance with enrollment can be obtained by contacting the IPP Production Helpdesk via email to IPPCustomerSupport@fiscal.treasury.gov or phone (866) 973-3131.

3. The Contractor POC will receive two emails from IPP Customer Support, the first email contains the initial administrative IPP User ID. The second email, sent within 24 hours of receipt of the first email, contains a temporary password. You must log in with the temporary password within 30 days.

4. If your company is already registered to use IPP, you will not be required to re-register.

5. If the Contractor is unable to comply with the requirement to use IPP for submitting invoices for payment as authorized by HHSAR 332.7002, a written request must be submitted to the Contracting Officer to explain the circumstances that require the authorization of alternate payment procedures.

d. Invoices that include time and materials or labor hours Line Items must include supporting documentation to (1) substantiate the number of labor hours invoiced for each labor category, and (2) substantiate material costs incurred (when applicable).

e. Invoices that include cost-reimbursement Line Items must be submitted in a format showing expenditures for that month, as well as contract cumulative amounts. At a minimum the following cost information shall be included, in addition to supporting documentation to substantiate costs incurred.

• Direct Labor - include all persons, listing the person's name, title, number of hours worked, hourly rate, the total cost per person and a total amount for this category.

• Indirect Costs (i.e., Fringe Benefits, Overhead, General and Administrative, Other In directs)- show rate, base and total amount.

• Consultants (if applicable) - include the name, number of days or hours worked, daily or hourly rate, and a total amount per consultant.

• Travel - include for each airplane or train trip taken the name of the traveler, date of travel, destination, the transportation costs including ground transportation shown separately and the per diem costs. Other travel costs shall also be listed.

• Subcontractors (if applicable) - include, for each subcontractor, the same data as required for the prime Contractor.

• Other Direct Costs - include a listing of all other direct charges to the contract, i.e., office supplies, telephone, duplication, postage; and

• Fee - amount as allowable in accordance with the Schedule and FAR 52.216-8 if applicable.

f. Contractor is required to attach an invoice log addendum to each invoice which shall include, at a minimum, the following information for contract administration and reconciliation purposes:

(a) list of all invoices submitted to date under the subject award, including the following:

(1) invoice number, amount, & date submitted

(2) corresponding payment amount & date received

(b) total amount of all payments received to date under the subject contract or order

(c) and, for definitized contracts or orders only, total estimated amounts yet to be invoiced for the current, active period of performance.

g. Payment of invoices will be made based upon acceptance by the Government of the entire task or the tangible product deliverable(s) invoiced. Payments shall be based on the Government certifying that satisfactory services were provided, and the Contractor has certified that labor charges are accurate.

h. If the services are rejected for failure to conform to the technical requirements of the task order, or any other contractually legitimate reason, the Contractor shall not be paid, or shall be paid an amount negotiated by the CO.

i. Payment to the Contractor will not be made for temporary work stoppage due to circumstances beyond the control of U.S. Food and Drug Administration such as acts of God, inclement weather, power outages, and results thereof, or temporary closings of facilities at which Contractor personnel are performing. This may, however, be justification for excusable delays.

j. The Contractor agrees that the submission of an invoice to the Government for payment is a certification that the services for which the Government is being billed, have been delivered in accordance with the hours shown on the invoices, and the services are of the quality required for timely and successful completion of the effort.

k. Questions regarding invoice payments that cannot be resolved by the IPP Helpdesk should be directed to the FDA Employee Resource and Information Center (ERIC) Helpdesk at 301-827- ERIC (3742) or toll-free 866-807-ERIC (3742); or, by email at ERIC@fda.hhs.gov. Refer to the Call-in menu options and follow the phone prompts to dial the option that corresponds to the service that's needed. All ERIC Service Now Tickets will either be responded to or resolved within 48 hours (2 business days) of being received. When emailing, please be sure to include the contract number, invoice number and date of invoice, as well as your name, phone number, and a detailed description of the issue.

15 Order Level Terms and Conditions

The full text of a clause or provision may be accessed electronically at https://www.acquisition.gov/; except the HHSAR clause deviations which is provided in full text herein.

FAR Clauses

FAR

CLAUSE

NO.

DESCRIPTION DATE

52.203-19 Prohibition on Contracting with Entities that Require Certain Internal Confidentiality Agreements

Jan 2017

52.204-27 Prohibition on a Byte Dance Covered Application Jun 2023 52.212-4 Contract Terms and Conditions Nov 2023 52.227-14 Rights in Data-General May 2014

52.217 – 8 Option to Extend Services (Nov 1999)

The Government may require continued performance of any services within the limits and at the rates specified in the contract. These rates may be adjusted only because of revisions to prevailing labor rates provided by the Secretary of Labor. The option provision may be exercised more than once, but the total extension of performance hereunder shall not exceed 6 months. The Contracting Officer may exercise the option by written notice to the Contractor at any time within prior to the expiration of the contract.

(End of Clause)

52.252-6 Authorized Deviations in Clauses (Nov 2020)

(a) The use in this solicitation or contract of any Federal Acquisition Regulation (48 CFR Chapter

1) clause with an authorized deviation is indicated by the addition of "(DEVIATION)" after the date of the clause.

(b) The use in this solicitation or contract of any HHSAR Class Deviation (48 CFR Chapter 3) clause with an authorized deviation is indicated by the addition of "(DEVIATION)" after the name of the regulation.

(End of Clause)

HHSAR Clauses

352.232-71 Electronic Submission of Payment Requests (Feb 2022)

(a) Definitions. As used in this clause- Payment request means a bill, voucher, invoice, or request for contract financing payment with associated supporting documentation. The payment request must comply with the requirements identified in FAR 32.905(b), "Content of Invoices" and the applicable Payment clause included in this contract.

(b) Except as provided in paragraph (c) of this clause, the Contractor shall submit payment requests electronically using the Department of Treasury Invoice Processing Platform (IPP) or successor system. Information regarding IPP, including IPP Customer Support contact information, is available at www.ipp.gov or any successor site.

(c) The Contractor may submit payment requests using other than IPP only when the Contracting Officer authorizes alternate procedures in writing in accordance with HHS procedures.

(d) If alternate payment procedures are authorized, the Contractor shall include a copy of the Contracting Officer's written authorization with each payment request.

(End of Clause)

352.239-79 Information And Communication Technology Accessibility (Feb 2024) (Deviation)

(a) Pursuant to Section 508 of the Rehabilitation Act of 1973 (29 U.S.C. 794d), as amended by the Workforce Investment Act of 1998, all information and communication technology (ICT) supplies, products, platforms, information, documentation, and services support developed, acquired, maintained or delivered under this contract or order must comply with the Revised 508 Standards, which are located at 36 C.F.R. 1194.1 and Appendices A, B, and C, and are available at https://www.access-board.gov/ict/.

Information about Section 508 is available at https://www.hhs.gov/web/section- 508/index.html.

(b) Additional Section 508 accessibility standards applicable to this contract or order may be identified in the specification, statement of work, or performance work statement. If it is determined by the Government that ICT supplies, products, platforms, information, documentation, and services support provided by the Contractor do not conform to the described accessibility standards in the contract, remediation of the supplies, products, platforms, information, documentation, or services support to the level of conformance specified in the contract will be the responsibility of the Contractor at its own expense.

(c) In the event of a modification(s) to this contract or order, which adds new ICT supplies or services or revises the type of, or specifications for, supplies, products, platforms, information, documentation, or services support, the Contracting Officer shall require that the Contractor submit a completed HHS Section 508 Accessibility Conformance Checklist (see https://www.hhs.gov/web/section-508/accessibility- checklists/index.html) or an Accessibility Conformance Report (ACR) (based on the Voluntary Product Accessibility Template (VPAT) see https://www.itic.org/policy/accessibility/vpat), and any other additional information necessary to assist the Government in determining that the ICT supplies or services conform to Section 508 accessibility standards. If it is determined by the Government that ICT supplies, products, platforms, information, documentation, and services support provided by the Contractor do not conform to the described accessibility standards in the contract, remediation of the supplies, products, platforms, information, documentation, or services support to the level of conformance specified in the contract will be the responsibility of the Contractor at its own expense.

(d) If this is an Indefinite-Delivery type contract, a Blanket Purchase Agreement or a Basic Ordering Agreement, the task/delivery order requests that include ICT supplies, products, platforms, information, documentation, or services support will define the specifications and accessibility standards for the order. In those cases, the Contractor shall be required to provide a completed HHS Section 508 Accessibility Conformance Checklist (see https://www.hhs.gov/web/section-508/accessibility-checklists/index.html) or an ACR (based on the VPAT see https://www.itic.org/policy/accessibility/vpat), and any other additional information necessary to assist the Government in determining that the ICT supplies, products, platforms, information, documentation, or services support conform to Section 508 accessibility standards. If it is determined by the Government that ICT supplies and services provided by the Contractor do not conform to the described accessibility standards in the provided documentation, remediation of the supplies, products, platforms, information, documentation, or services support to the level of conformance specified in the contract will be the responsibility of the Contractor at its own expense.

(e) The contractor shall identify to the Contracting Officer any perceived exception or exemption to Section 508 requirements.

(End of clause)

FDA Condition – Language for Insertion in Acquisition Documents Based on the Change to Disable Macros in Microsoft Office Documents from Outside Sources Be advised that FDA does not accept documents which contain the use of macros. When submitting documents via email, DO NOT include .exe, .mso, or any other executable file types that could potentially trigger email security protections (i.e. email blocks, quarantine). Document submissions required throughout the award period(s) shall not have macro enabled functionality and any document delivered having that functionality will be deemed delinquent, if not corrected prior to the due date.

INSTRUCTIONS

Quoters shall submit all quotes with the following:

a) The quote shall provide product pricing for the webservice subscription listed in the RFQ.

The quoter must be an authorized reseller or manufacturer/provider for the brand name quoted items in the schedule on the date of the quote submission. The quoter must provide documentation that shows it is an authorized reseller of the brand name.

Period for Acceptance of Quotes: The quoter agrees to hold prices firm for sixty (60) calendar days after the quote due date.

Quotes that do not submit based on requirements stated above may be deemed non-responsive.

All responsible sources may submit a quote, which if timely received, shall be considered.

The quote and any questions shall reference solicitation number 75F40125Q00340.

All quotes must be submitted via SAM on or before September 23, 2025 by 5:00 PM EST. All quotes must be submitted via SAM on or before the due date and time indicated on the solicitation in SAM.

It is the quoter’s responsibility to monitor SAM for the release of any amendments to the request for quote.

Quoters that fail to submit all required information in accordance with the instructions, or reject the terms and conditions of the solicitation, may be excluded from consideration.

The quoter shall submit all electronic documents for Microsoft Office suite products without the use of “macros”. When submitting proposals via email, DO NOT include .exe, .mso, or any other executable file types that could potentially trigger email security protections (i.e. email blocks, quarantine). If the offeror or applicant submits documents that contain macros, macro referenced files, and/or executable files, the Government will not be able to view or open such documents and the submission will be considered non-responsive to the solicitation. No additional time will be given to a quoter to correct the document submission and the Government will not inform the quoter that their submission is non-responsive prior to award. It is the quoter’s responsibility to ensure all electronic documents are submitted without the use of macros.

Point of Contacts: Steven Gagnon at Steven.Gagnon@fda.hhs.gov

v. Basis for Award:

The Government anticipates awarding a Firm Fixed Price (FFP) delivery order resulting from this solicitation to the responsible quoter whose quote meets the requirements stated in this solicitation and is the lowest priced quote received in response to this solicitation. Therefore, award will be made to quoter whose quote is determined to be Lowest Price Technically Acceptable (LPTA).

A written notice of award or acceptance of an offer mailed or otherwise furnished to the successful quoter within the time for acceptance specified in the offer, shall result in a binding contract without further action by either party. Before the offer's specified expiration time, the Government may accept an offer (or part of an offer), whether or not there are negotiations after its receipt, unless a written notice of withdrawal is received before award.

vi. Evaluation

The following factors shall be used to evaluate quotes that were submitted timely through

SAM:

1) Submitted all schedule items for each brand in accordance with the solicitation.

2) Is an authorized distributor/reseller or manufacturer/provider for the quoted items based on the information provided.