ATTACHMENT_6-Domain_6_Sample_RFTOP.docx

ATTACHMENT 6 SAMPLE TASK ORDER 6

DOMAIN 6: RFTOP 2016-6-Task Order 001 Whole Genome Sequencing for Transmission of Healthcare-Associated Pathogens Studies

Estimated Price Range:

|X| $Over 79,000 to but less than $105,000 Base Award |X| $Over 36,000 to but less than $44,000 Optional Task 1

Proposed Period of Performance: Work shall begin from date of award of the order and shall continue for a period of 14 months. This project is a non-severable project that will be funded fully at the time of award. Funding for Optional Task 1 for 12 month period, Optional Task 2 for 12 month period, and Optional Task for 12 month period will be subject to availability of funds.

Page Suggestion: The Contractor shall limit the proposal for this task order to 10 pages single-spaced pages.

DESCRIPTION OF WORK

1. Background and Need Whole genome sequencing (WGS) has been used to identify and understand the source of healthcare-associated infections (HAI). CDC has identified eliminating HAIs as a winnable battle. The Division of Healthcare Quality Promotion (DHQP) provides the highest quality support to our clinical laboratories and public health partners to identify clinically significant microorganisms in a timely manner and characterize new and novel mechanisms of resistance and the laboratory support to outbreak investigations and conduct applied research studies to assess causation and intervention strategies as a follow-up to outbreak investigations. In addition, DHQP provides epidemiological and laboratory assistance to state and local health departments for approximately 30 cluster investigations of HAI each year. Related outbreak investigations also focus on the detection, investigation, and prevention of HAI and emerging antimicrobial resistance (AR). Our over-arching goal is to develop WGS analysis components that will be deployed to state and regional public health laboratories. To this end, we will evaluate factors impacting HAI and AR in the course of outbreak investigations and surveillance studies; identify appropriate WGS pipelines to assess HAI relatedness and presence of acquired resistance genes; identify genetic variation such as single nucleotide polymorphisms (SNP) or small indels, copy number variants, and relevant mobile genetic elements. For deployment to states and external partners, tools for HAI and AR analysis would then be accomplished using existing PulseNet WGS infrastructure for generation of WGS data and data analysis.

2. Scope of Work The diversity and complexity of HAI pathogens makes molecular typing and characterization of isolates a key part of the CDC support provided to local and state health departments during outbreak investigations. This project will study known acquired antimicrobial resistance determinants, strain characteristics, and genomic sequences of public health importance from the genomic data to develop a streamlined workflow for pathogen characterization and interpretative criteria of WGS data in HAI outbreaks. Specifically, the vendor will be required to:

· Perform whole genome sequencing on up to 800 epidemiologically-linked isolates provided by CDC to determine strain relatedness and assess transmission dynamics within a healthcare system

· Optional task: perform metagenomic stool analysis for up to 50 epidemiologically-linked patient specimens provided by CDC to understand the microbiome metrics associated with transmission and acquisition of HAI pathogens, and identify acquired antimicrobial resistance genes of interest and the changes in bacterial community profiles of patients with gut carriage of enteric multi-drug resistant organisms (MDRO) acquisition.

3. IRB Approval If IRB approval is required for WGS data analysis, the contractor will complete institutional review board (IRB) applications and ensure that the project is reviewed and approved by the appropriate IRBs. If required, the Contractor shall prepare the packages including all forms and attachments for CDC Science Officer approval as needed. The Contractor shall submit the IRB package to their IRB for and receive IRB approval. Copies of IRB approvals from the Contractor shall be provided to the CDC Science Officer.

4. Contractor Furnished Property The contractor shall provide all labor, expertise, materials, supplies and perform all services required to carry out the work under this task order.

Task 1: Start Up Meeting

· The Contractor shall arrange and conduct an initial meeting (either in person or by teleconference) with the CDC Science Officer and other relevant staff within 4 weeks of the effective date of the task order. The purpose of the meeting will be to discuss critical contract performance milestones, to delineate roles and responsibilities, and to establish communication protocols. Each task and deliverable will be reviewed, and specific dates and timelines will be assigned for each.

· The Contractor shall submit an agenda for the above meeting within 1 day of the effective date of the task order.

Task 2: Regular Communication with COR/CDC Science Officer.

· Contactor will participate in up to one conference call per month with CDC personnel, plus additional calls will be scheduled as needed.

· Contactor will respond to emails and telecommunications within 2 days of event.

Task 3: Quarterly Progress Reports

· Contractor shall prepare and submit a quarterly progress report containing a summary of project activities and status updates on invoices.

Task 4: Perform WGS on a total of 500-800 epidemiologically-linked isolates (to be provided)

· Generate WGS data to minimum average sequence depth of 40x coverage; Deposit raw reads to National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).

Task 5: Strain Typing

· Confirm organism identification, purity, strain typing (per conventional organism-appropriate multilocus sequence typing (MLST)) from WGS data.

Task 6: Detection of AR Genes and Plasmids

· Identify acquired antimicrobial resistance genes of interest, number and type of replicons from WGS data.

Task 7: Transmission Analysis

· Provide single nucleotide polymorphism (SNP) matrices and phylogenetic trees of isolates belonging to same species and MLST type from WGS data.

Optional Task 1: Metagenomic stool analysis of up to 50 epidemiologically-linked patient specimens (to be provided)

· Generate shotgun meta-genomic sequence data from stool of epidemiologically-linked patients; Deposit raw reads to NCBI SRA.

· Provide composition and metabolic analysis of stool metagenome; identify acquired antimicrobial resistance genes of interest, number and type of replicons.

· Deposit WGS and/or Metagenomic data in public repository, specifcally raw reads to NCBI SRA.

Task 8: Final Report

· At the conclusion of the project, contractor shall provide summary including all isolates sequenced under this agreement in electronic spreadsheet or word format.

Deliverables Summary Table

The following deliverables shall be provided to the COR/CDC Science Officer no later than the dates specified below:

Frequency Due Date

Responses to emails and telecommunications within 2 days of receipt.

Metagenomic analysis

Deposit WGS and/or metagenomic data in public repository

Generate shotgun meta-genomic sequence data from stool of epidemiologically-linked patients; Deposit raw reads to NCBI SRA

Provide composition and metabolic analysis of stool metagenome; identify acquired antimicrobial resistance genes of interest, number and type of replicons

Deposit raw reads to NCBI SRA

5. General Information

A. Place of Performance: The work to be performed under this contract will be performed at the Contractor’s facility and associated academic, healthcare or research facilities as required.

B. Type of Contract:This will be a Firm Fixed Price (FFP) contract.

C. Contractor Travel: Contractor will not be required to travel during the performance of this contract for data collection. Travel is not required in this Task Order.

D. Data Rights: 52.227-14 Rights in Data-General, Alternate IV (Dec 2007). As prescribed in 27.409(b)(5), substitute the following paragraph (c)(1) for paragraph (c)(1) of the basic clause: (c) Copyright—(1) Data first produced in the performance of the contract. Except as otherwise specifically provided in this contract, the Contractor may assert copyright in any data first produced in the performance of this contract. When asserting copyright, the Contractor shall affix the applicable copyright notice of 17 U.S.C. 401 or 402, and an acknowledgment of Government sponsorship (including contract number), to the data when such data are delivered to the Government, as well as when the data are published or deposited for registration as a published work in the U.S. Copyright Office. For data other than computer software, the Contractor grants to the Government, and others acting on its behalf, a paid-up, nonexclusive, irrevocable, worldwide license for all such data to reproduce, prepare derivative works, distribute copies to the public, and perform publicly and display publicly, by or on behalf of the Government. For computer software, the Contractor grants to the Government and others acting on its behalf, a paid-up, nonexclusive, irrevocable, worldwide license for all such computer software to reproduce, prepare derivative works, and perform publicly and display publicly (but not to distribute copies to the public), by or on behalf of the Government.

E. Confidentiality of Information: Work on this project may require that personnel have access to Privacy Information. Personnel shall adhere to the Privacy act, Title 5 of the U.S. Code, Section 552a and applicable agency rules and regulations. The user agency will identify and provide direction and guidance for safeguarding all information subject to the Privacy Act. Reports and case files containing individual personal information are confidential. The CDC is not authorized to release individual case reports, and access to individual case data is strictly controlled. The contractor personnel are required to work with case records as well as databases. It is a requirement that the data remain in a controlled access environment.

F. Section 508: Section 508 of the Rehabilitation Act of 1973 (29 U.S.C. 794d) helps to ensure that federal employees with disabilities have access to, and use of, the information and data they need to do their jobs. Furthermore, this law ensures that members of the public with disabilities have the ability to access government information and services. Regardless of format, all Web content or communications materials produced for publication on or delivery via CDC Web sites - including text, audio or video - must conform to applicable Section 508 standards to allow federal employees and members of the public with disabilities to access information that is comparable to information provided to persons without disabilities. All contractors (including subcontractors1) or consultants responsible for preparing or posting content intended for use on a CDC-funded or CDC-managed Web site must comply with applicable Section 508 accessibility standards, and where applicable, those set forth in the referenced policy or standards documents below. Remediation of any materials that do not comply with the applicable provisions of 36 CFR Part 1194 as set forth in the SOW or PWS, shall be the responsibility of the contractor or consultant retained to produce the Web-suitable content or communications material. Checklists for various file formats are available at http://www.hhs.gov/web/508/index.html.

The following Section 508 provisions apply to the content or communications material identified in this SOW or PWS: 36 CFR 1194.21 (for software and programmatic elements in websites), 36 CFR 1194.22 (for documents and websites), and 36 CFR 1194.24 (for video and multimedia content) References: HHS Policy for Section 508 Electronic and Information Technology (E&IT) (January 2005): http://www.hhs.gov/od/Final_Section_508_Policy.html HHS Section 508 Web site: http://508.hhs.gov/ HHS ASPA Web Communications Division Web site: http://www.hhs.gov/web/policies/index.html US General Services Administration (GSA) Section 508 Web site: http://www.section508.gov/index.cfm 1 Prime contractors may enter into subcontracts in the performance of a Federal contract, but the prime remains obligated to deliver what is called for under the contract.

G. Security compliance:

The below information complies with HHSA Security compliance requirements for E-Government Act of 2002 (FISMA 2002) and Federal Information Security Modernization Act of 2014 (FISMA 2014)

Security Compliance If the contractor will host or create an information system on behalf of the CDC, provide IT services to the CDC, or provide IT products to the CDC, then the contractor must comply with the applicable IT security references below. We provide the following information to assist in the preparation of documents necessary for the Security Assessment and Authorization (SA&A) of an Information System. The FISMA 2014, (Federal Information Security Modernization Act of 2014) and the below federal policies dictate the framework for assuring information security for data systems operated by or on behalf of the Federal government. These are summarized below.

OMB Circular A-130 (https://www.whitehouse.gov/omb/Circulars_a130_a130trans4/) establishes policy for the management of Federal information resources, pursuant to a number of laws and regulations, including the Paperwork Reduction Act of 1980 (amended in 1995), the Computer Security Act of 1987, and other laws. Circular A-130 requires all federal information systems to have security plans, emergency response capabilities, designated individuals who are responsible for security, security awareness training, and regular review of the system. Appendix III of Circular A-130, entitled “Security of Federal Automated Information Resources,” establishes a minimum set of controls to be included in Federal automated information security programs; assigns Federal agency responsibilities for the security of automated information; and links agency automated information security programs (such as the DHHS AISSP) with OMB Circular No. A-123 The Federal Information Security Management Act of 2002 (P.L. 107-347) (FISMA) (http://csrc.nist.gov/drivers/documents/FISMA-final.pdf ) and the Federal Information Security Modernization Act of 2014 (P.L. 113-283) (FISMA 2014) (https://www.congress.gov/113/plaws/publ283/PLAW-113publ283.pdf) requires each agency to develop, document, and implement an agency-wide information security program to safeguard information and information systems that support the operations and assets of the agency, including those provided or managed by another agency, contractor (including sub-contractor), or other source. The National Institute of Standards and Technology (NIST) has issued a number of publications that provide guidance in the establishment of minimum security controls for management, operational, and technical safeguards needed to protect the confidentiality, integrity, and availability of a Federal information system and its information.

Pursuant to Federal and HHS Information Security Program Policies the following standards and guidelines apply:

1. FIPS Publication 200, Minimum Security Requirements for Federal Information and Information Systems (http://csrc.nist.gov/publications/fips/fips200/FIPS-200-final-march.pdf),

1. FIPS Publication 199, Standards for Security Categorization of Federal Information and Information Systems (http://csrc.nist.gov/publications/fips/fips199/FIPS-PUB-199-final.pdf),

1. NIST Special Publication 800-18, Guide for Developing Security Plans for Federal Information Systems (http://csrc.nist.gov/publications/nistpubs/800-18-Rev1/sp800-18-Rev1-final.pdf),

1. NIST Special Publication 800-60, Guide for Mapping Types of Information and Information Systems to Security Categories Vol. 1 (http://csrc.nist.gov/publications/nistpubs/800-60-rev1/SP800-60_Vol1-Rev1.pdf) and Vol. 2 (http://csrc.nist.gov/publications/nistpubs/800-60-rev1/SP800-60_Vol2-Rev1.pdf),

1. NIST Special Publication 800-37, Guide for Applying the Risk Management Framework to Federal Information Systems: A Security Life Cycle Approach (http://nvlpubs.nist.gov/nistpubs/SpecialPublications/NIST.SP.800-37r1.pdf),

1. NIST Special Publication 800-53, Security and Privacy Controls for Federal Information Systems and Organizations (http://nvlpubs.nist.gov/nistpubs/SpecialPublications/NIST.SP.800-53r4.pdf),

1. NIST Special Publication 800-63, Electronic Authentication Guideline (http://nvlpubs.nist.gov/nistpubs/SpecialPublications/NIST.SP.800-63-2.pdf).

The System Security Plan (SSP) is part of the Security Assessment and Authorization (SA&A) process required by the FISMA 2014 and NIST Special Publication 800-18, 800-37 and will include selected mandatory controls required by NIST Special Publication 800-53, Volume I & II. The successful contractor in conjunction with the NCEZID Information System Security Officer (ISSO) will submit SA&A documentation to the CDC Chief Information Security Officer (CISO). The successful completion of the SA&A documents will result in an award of an Authority To Operate. Based on guidance in FIPS 199 and NIST SP 800-60 the system will be assigned an overall security category (SC) of LOW or MODERATE based on (confidentiality, LOW/MODERATE), (integrity, LOW/MODERATE), and (availability, LOW/MODERATE) impact levels. These impact levels will be initially determined by the NCEZID ISSO and confirmed by the CDC Certifying Authority as part of the SA&A process.

The successful contractor is responsible for providing pertinent security information to the NCEZID ISSO and Security Staff and assisting in completing the below CDC SA&A documents to include Annual Assessments, Annual Business Continuity Plan, Re-Certifications and applicable significant/non-significant change requests. Appropriate security templates will be provided to the successful Contractor by the NCEZID Security Staff. Completed documents will be sent by the NCEZID Security Staff to the CDC Chief Information Security Office (CISO) for review, approval and subsequent issuance of an Authority To Operate (ATO)

1. Baseline System Information (BSI)

1. Privacy Impact Assessment (PIA)

1. System Security Plan (SSP)

1. Business Continuity Plan (BCP)

1. Risk Assessment Report (RAR)

The Contractor shall respond to the following seven security–associated requirements in the application:

0. Position Sensitivity Designations CDC requires a Public Trust Level 5 for the following The following position sensitivity designations and associated clearance and investigation requirements apply under this licensing contract:

Level 5: Public Trust - Moderate Risk (Requires Suitability Determination with NACIC, MBI or LBI). Licensor employees assigned to a Level 5 position with no previous investigation and approval shall undergo a National Agency Check and Inquiry Investigation plus a Credit Check (NACIC), a Minimum Background Investigation (MBI), or a Limited Background Investigation (LBI).

Upon award, the Licensor will be required to submit a roster of all staff (including sub-contractor staff) working under the contract that will have the ability to access NCEZID sensitive information from the system. .

Non-Disclosure Agreements The Contractor and any sub-Contractors or employees are forbidden from sharing any technical or logistical information they may gain in conjunction with matters related to this task order that could jeopardize the physical or information security of CDC or its employees, projects, or information systems.

The following apply to Licensor employees and their subcontractors associated with the project:

1. Personnel may not begin work under the contract until the contractor has submitted the employee roster and non-disclosure agreements as described above.

1. Personnel without necessary background investigations will not have access to sensitive project data.

1. Violation of these conditions may lead to termination of the contract.

It is the Contractor's responsibility to ensure that all employees have met CDC and federal requirements, such as, for example, completion of background checks, before gaining or utilizing access to CDC information technology resources.

0. Privacy Compliance Licensor in conjunction with CDC Center ISSO shall conduct and maintain an initial Privacy Impact Assessment (PIA) as defined by Section 208 of the FISMA 2014. Periodic reviews shall be conducted by the system owner, with assistance from the CDC Center ISSO and contractor, to determine if a major change to the system has occurred, and if a PIA update is needed.

0. Contractor’s Official Responsible for Information Security The contractor shall include in the “Information Security” part of the Technical Proposal the name and title of its official who will be responsible for all information security requirements shall the contractor be selected for an award.

0. Rules of Behavior The contractor’s employees and subcontractors shall comply with the HHS Information Technology General Rules of Behavior.

0. Information Security Training HHS policy requires that contractors and subcontractors shall receive security training commensurate with their responsibilities for performing work under the terms and conditions of their contractual agreements. The successful contractor shall be responsible for assuring that each employee, including subcontractors, has completed the HHS Computer Security Awareness Training course (or another course designated by CDC) prior to performing any contract work, and thereafter completing the HHS-specified annual refresher course during the period of performance of the contract. This would be provided at the Contractor's expense and would be the Contractor's responsibility to plan and arrange.

The successful contractor shall maintain a listing of all individuals who have completed this training and shall submit this listing to the Science Officer.

0. HSPD-12 Compliance Federal Information Processing Standard 201 (FIPS-201) (vii) compliant, Homeland Security Presidential Directive 12 (HSPD-12) card readers shall: (a) be included with the purchase of servers, desktops, and laptops; and (b) comply with FAR Subpart 4.13, Personal Identity Verification.

As part of the Federal HSPD-12 directive, all information systems deployed within/outside of any federal infrastructure must be able to support HSPD-12 compliant Personal Identity Verification (PIV) of federal employees and contractors. The government has complied with HSPD-12 by issuing PIV cards with embedded digital certificates to all users of federal information systems. In accordance with this directive, all Contractors providing hardware and software to the federal government are now required to ensure that these PIV cards will integrate with their software and hardware at the application level. Contractor must be able to implement and support PIV card integration.

0. Encryption

All sensitive CDC-funded data stored on desktop computers used on behalf of HHS shall be secured either through a FIPS 140-2 compliant encryption solution or through adequate physical security and operational controls at the desktop’s residing location.

All mobile devices, portable media and transfer data files that contain CDC- data shall have full-disk encryption using FIPS 140-2 compliant algorithms.

6. Government Furnished Property, Equipment, and Services Not Applicable

7. Payment Terms

Payment will be made quarterly and subject to receipt of deliverables in accordance with the payment schedule established herein and in accordance with FAR 52.232-25. Prompt Payment, which states that the due date for making invoice payments shall be the 30th day after the designated billing office (see block 21 of the order) has received a proper invoice from the vendor or the 30th day after Government acceptance of the services provided by the vendor, whichever is later.

Base Period

Quarter 1

Quarter 2

Quarter 3

Quarter 4

Optional Task 1

Quarter 1

Quarter 2

Quarter 3

Quarter 4

Optional Task 2

Quarter 1

Quarter 2

Quarter 3

Quarter 4

Optional Task 3

Quarter 1

Quarter 2

Quarter 3

Quarter 4

8. Special Clearances:

|_| OMB

procedures. Based upon the scope of this contract, the SOW must include the appropriate language to address the following IT security topics: Standard for Security Configurations; Standard for Encryption Language; and Security requirements for Federal Information technology Resources.

SPECIAL CLAUSES:

HHSAR 352.224-70, Privacy Act (Dec 2015) This contract requires the Contractor to perform one or more of the following:

(This contract requires the Contractor to perform one or more of the following: (a) design; (b) develop; or (c) operate a Federal agency system of records to accomplish an agency function in accordance with the Privacy Act of 1974 (Act) (5 U.S.C. 552a(m)(1)) and applicable agency regulations. The term system of records means a group of any records under the control of any agency from which information is retrieved by the name of the individual or by some identifying number, symbol, or other identifying particular assigned to the individual. Violations of the Act by the Contractor and/or its employees may result in the imposition of criminal penalties (5 U.S.C. 552a (i)).The Contractor shall ensure that each of its employees knows the prescribed rules of conduct in 45 CFR part 5b and that each employee is aware that he/she is subject to criminal penalties for violation of the Act to the same extent as Department of Health and Human Services employees. These provisions also apply to all subcontracts the Contractor awards under this contract which require the design, development or operation of the designated system(s) of records (5 U.S.C. 552a(m)(1)). The contract work statement: (a) Identifies the system(s) of records and the design, development, or operation work the Contractor is to perform; and (b) specifies the disposition to be made of such records upon completion of contract performance.

HSSAR 352.270-4a Notice to Offerors, Protection of Human Subjects (December 18, 2015)

(a) The Department of Health and Human Services (HHS) regulations for the protection of human subjects, 45 CFR part 46, are available on the Office for Human Research Protections (OHRP) website at: http://www.hhs.gov/ohrp/index.html.

These regulations provide a systematic means, based on established ethical principles, to safeguard the rights and welfare of human subjects participating in research activities supported or conducted by HHS.

(b) The regulations define a human subject as a living individual about whom an investigator (whether professional or student) conducting research obtains data or identifiable public information through intervention or interaction with the individual, or identifiable private information. In most cases, the regulations extend to the use of human organs, tissue, and body fluids from individually identifiable human subjects as well as to graphic, written, or recorded information derived from individually identifiable human subjects. 45 CFR part 46 does not directly regulate the use of autopsy materials; instead, applicable state and local laws govern their use.

(c) Activities which involve human subjects in one or more of the categories set forth in 45 CFR 46.101(b)(1)-(6) are exempt from complying with 45 CFR part 46. See http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.html.

(d) Inappropriate designations of the noninvolvement of human subjects or of exempt categories of research in a project may result in delays in the review of a proposal.

(e) In accordance with 45 CFR part 46, offerors considered for award shall file an acceptable Federal-wide Assurance (FWA) of compliance with OHRP specifying review procedures and assigning responsibilities for the protection of human subjects. The FWA is the only type of assurance that OHRP accepts or approves. The initial and continuing review of a research project by an institutional review board shall ensure that: the risks to subjects are minimized; risks to subjects are reasonable in relation to anticipated benefits, if any, to subjects, and the importance of the knowledge that may reasonably be expected to result; selection of subjects is equitable; and informed consent will be obtained and documented by methods that are adequate and appropriate. Depending on the nature of the research, additional requirements may apply; see http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.html#46.111 for additional requirements regarding initial and continuing review. HHS regulations for the protection of human subjects (45 CFR part 46), information regarding OHRP registration and assurance requirements/processes, and OHRP contact information is available at the OHRP website (at http://www.hhs.gov/ohrp/assurances/index.html).

(f) Offerors may consult with OHRP only for general advice or guidance concerning either regulatory requirements or ethical issues pertaining to research involving human subjects. ONLY the contracting officer may offer information concerning a solicitation.

(g) The offeror shall document in its proposal the approved FWA from OHRP, related to the designated Institutional Review Board (IRB) reviewing and overseeing the research. If the offeror does not have an approved FWA from OHRP, the offeror must obtain an FWA before the deadline for proposal submission. When possible, the offeror shall also certify the IRB’s review and approval of the research. If the offeror cannot obtain this certification by the time of proposal submission they must include an explanation in their proposal. Never conduct research covered by 45 CFR part 46 prior to receiving certification of the research’s review and approval by the IRB.

(End of provision)

HHSAR 352.270-4b Protection of Human Subjects (December 18, 2015)

(a) The Contractor agrees that the rights and welfare of human subjects involved in research under this contract shall be protected in accordance with 45 CFR part 46 and with the Contractor’s current Federal-wide Assurance (FWA) on file with the Office for Human Research Protections (OHRP), Department of Health and Human Services. The Contractor further agrees to provide certification at least annually that the Institutional Review Board has reviewed and approved the procedures, which involve human subjects in accordance with 45 CFR part 46 and the Assurance of Compliance.

(b) The Contractor shall bear full responsibility for the performance of all work and services involving the use of human subjects under this contract and shall ensure that work is conducted in a proper manner and as safely as is feasible. The parties hereto agree that the Contractor retains the right to control and direct the performance of all work under this contract. Nothing in this contract shall create an agency or employee relationship between the Government and the Contractor, or any subcontractor, agent or employee of the Contractor, or any other person, organization, institution, or group of any kind whatsoever. The Contractor agrees that it has entered into this contract and will discharge its obligations, duties, and undertakings and the work pursuant thereto, whether requiring professional judgment or otherwise, as an independent Contractor without creating liability on the part of the Government for the acts of the Contractor or its employees.

(c) Contractors involving other agencies or institutions in activities considered to be engaged in research involving human subjects must ensure that such other agencies or institutions obtain their own FWA if they are routinely engaged in research involving human subjects or ensure that such agencies or institutions are covered by the Contractors’ FWA via designation as agents of the institution or via individual investigator agreements (see OHRP website at: http://www.hhs.gov/ohrp/policy/guidanceonalternativetofwa.pdf).

(d) If at any time during the performance of this contract the Contractor is not in compliance with any of the requirements and or standards stated in paragraphs (a) and (b) above, the Contracting Officer may immediately suspend, in whole or in part, work and further payments under this contract until the Contractor corrects the noncompliance. The Contracting Officer may communicate the notice of suspension by telephone with confirmation in writing. If the Contractor fails to complete corrective action within the period of time designated in the Contracting Officer’s written notice of suspension, the Contracting Officer may, after consultation with OHRP, terminate this contract in whole or in part.

(End of clause)

HHSAR 352.270-12 Needle Exchange (December 18, 2015) The Contractor shall not use any funds obligated under this contract to carry out any program of distributing sterile needles or syringes for the hypodermic injection of any illegal drug.

(End of Clause

CONTRACTING OFFICER REPRESENTATIVE:

TBD

SCIENCE OFFICER:

TBD

9. Technical Evaluation Criteria

Award: This task order will be awarded to the contractor whose proposal is considered to be the most advantageous to the Government, price and other factors identified below considered. Technical factors will be more important in the evaluation than price. The Government will not make an award at a significantly higher overall cost to the Government to achieve only slightly superior performance.

Contractors with demonstrated experience performing both required and optional tasks are preferred. Contractors with specific expertise in performing optional tasks 8 and 9 shall emphasize this capacity, which will be taken into consideration to offset a lack of demonstrated experience performing tasks 5 – 7.

Technical Evaluation for this RFTOP is as follows:

A. Technical Plan (10):

1. The contractor shall provide:

a. Detailed plan of their approach for providing the required services, including details that have been specified. This discussion shall be in the contractor’s own words; not a restatement of the listed requirements.

b. Demonstrated knowledge of genome sequencing and WGS analyses for typing and characterization of HAI pathogens, assessing pathogen transmission, as well as generation of metagenomic data and its interpretation, if applicable.

c. Demonstrated ability to obtain data of optimum quality for NCBI submission.

2. Criteria will be evaluated according to the extent that they reflect a clear understanding of the subject areas to be accomplished and on the soundness, practicality, and feasibility of the contractor’s technical approach for providing the services required for this task order.

B. Similar Experience (10):

1. Contractor shall demonstrate:

a. Experience performing next-generation whole genome sequencing and bioinformatics analysis for the purpose of studying transmission of HAI/AR pathogens in outbreak and endemic settings, examining bacterial genomes for strain typing and presence of acquired resistance genes, and examining genomes for novel resistance mechanisms. The contractor shall provide documentation of such experience by providing a bibliography of peer-reviewed articles for which one or more authors are employed by the prime vendor. Larger numbers of relevant peer reviewed articles will be evidence of greater experience.

2. Additionally, for the optional tasks, the contractor shall demonstrate:

a. Experience performing next-generation metagenomic sequencing and bioinformatics analysis for the purpose of determining alpha and beta diversity of gut microbiome, and providing composition and metabolic analysis of bacteria. The contractor shall provide documentation of such experience by providing a bibliography of peer-reviewed articles for which one or more authors are employed by the prime vendor. Larger numbers of relevant peer reviewed articles will be evidence of greater experience.

C. Staffing and Management Plan (10):

1. The contractor shall provide a detailed statement of staffing and management approach for managing the work outlined in these task areas by demonstrating their understanding of the labor requirements listed in this study. Contractor shall include:

a. resumes from key personnel outlining the credentials and background of key management, professional, and technical personnel to be used for these task areas, including the percent time on this and other projects;

b. a detailed plan that describes current staff available for these task areas and how the team will interface with CDC, as well as descriptions the Offeror’s approach to rapidly obtain and/or replace qualified staffing resources to support the contract;

c. a clear delineation of staff authorities and line of responsibility with special emphasis on relationships with subcontractors, other Contractors, and CDC partners;

d. a detailed description of how conflicts are managed;

e. a measurement of fiscal responsibility and accountability paying particular attention to the deliverable timeline in this task order.

2. The contractor’s proposal will be evaluated according to the soundness, practicality, and feasibility of the contractor’s staffing and management plan for this task order. Ideal staffing to successfully accomplish the tasks of this acquisition:

a. Project Manager with sufficient time devoted to overseeing the implementation of the project. This person shall have experience using WGS methods, and metagenomics methods if applicable.

b. Bioinformatics staff with demonstrated understanding of SNP analysis, AR detection, and metagenomics analysis if applicable

c. Technical staff trained in generation of high quality WGS data, and shotgun metagenomics data if applicable

SHEPheRD RFTOP 2016-6-001