Draft SOW - 85691.docx

STATEMENT OF WORK

Title: MVPDB Staffing Support for BML, QMS, and Web Developer

SECTION 1 – BACKGROUND

The Centers for Disease Control and Prevention (CDC), National Center for Immunization and Respiratory Diseases (NCIRD), Division of Bacterial Diseases (DBD), Meningitis and Vaccine Preventable Diseases Branch (MVPDB) is dedicated to the prevention and control of meningitis, pertussis, and other vaccine-preventable diseases. The branch works on Neisseria meningitidis, Bordetella spp., Haemophilus influenzae, tetanus and diphtheria. Epidemiologic and laboratory activities encompass characterization of risk factors for disease, outbreak investigations, surveillance, method and tool development, pathogen detection and characterization to monitor anti-microbial resistance (AMR) trends and strain genomics, vaccine evaluations, implementation and evaluation of prevention strategies, and vaccine policy development and assessment, both domestically and globally. Cross-cutting activities on vaccines include developing, implementing and evaluating guidelines for use of vaccines, standardization and quality assurance activities, and characterization of potential vaccine antigens. Staff engages in collaborations with numerous CDC programs, other federal agencies, state health departments and external partners to carry out these activities.

This is a follow-on contract to fill the ongoing need for staffing support for the Bacterial Meningitis Laboratory (BML), Quality Management Systems (QMS) team as well as the Management and Operations (M&O) team. The tasks listed in this acquisition are currently being performed by contract support staff and there is an ongoing need to fill these roles.

SECTION 2 – PURPOSE/OBJECTIVE

The purpose of this contract is to provide technical and administrative support to the Bacterial Meningitis Laboratory (BML), Quality Management Systems (QMS) team and Management and Operations (M&O) team within MVPDB. This will be accomplished by providing support services to achieve the branch objectives.

These support services are divided into eight (8) task areas:

(a) Task 1: Bacterial Meningitis Laboratory (BML) Staffing Support

(b) Task 2: Quality Management Systems (QMS) Staffing Support

(c) Task 3: Program Management Staffing Support

(d) Task 4: Monthly Report

(e) Optional Task 5: Outbreak/Pandemic Support

(f) Optional Task 6: Genomics Microbiologists

(g) Optional Task 7: ABiL Bioinformatics Support

(h) Optional Task 8: Travel

As an independent organization, and not as an agent of the Government, the Contractor shall furnish all of the necessary personnel to provide MVPDB with the technical and administrative support services described below. These services are provided on a labor-hour basis with a not-to-exceed ceiling.

SECTION 3 – SCOPE OF WORK

The scope of work of this project includes staffing support for BML activities, such as: genomic surveillance of bacterial meningitis; evaluation of meningococcal serogroup B vaccines; diagnostics, surveillance and outbreak response for meningococcal and H. influenzae diseases; meningitis diagnostic method development; bioinformatics analysis, tool development, and data management; and characterization of bacterial meningitis pathogens and monitoring of anti-microbial resistance (AMR) trends. Furthermore, Contractor shall participate in the development, implementation and maintenance of the Branch Quality Management System and adherence to applicable guidelines and requirements. Contractor shall also provide expertise in the web development of internal and external facing websites to improve usability and enhance current capabilities. Finally, Contractor shall, as needed, provide support to CDC’s Emergency Operations Center (EOC) and to DBD in outbreak/pandemic situations.

SECTION 4 – TASKS TO BE PERFORMED

Task 1: Bacterial Meningitis Laboratory (BML) Staffing Support

1. Genomic surveillance – Working within the Bacterial Meningitis Laboratory (BML), contractor shall provide technical and intellectual support for the method development and molecular typing systems to improve bacterial meningitis genomic surveillance. Contractor’s responsibilities shall be the following:

a. Support projects to monitor the molecular epidemiology of meningococcal and Haemophilus infuenzae disease, serogroup B meningococcal vaccine antigens, and population genetics of bacterial meningitis pathogens.

b. Provide support for outbreak responses and applied research projects to advance our understanding of meningococcal disease and carriage as well as genomics, strain evolution and transmission, virulence factors, and antibiotic resistance of common bacterial meningitis pathogens.

c. Explore, develop, and implement new molecular and next-generation sequencing methods and systems to assist characterization of common bacterial meningitis pathogens and epidemiological and outbreak investigations.

d. Perform quality control, assembly, and analysis of pathogen genome sequences and management of genome sequence files and database including uploads to National Center for Biotechnology Information (NCBI) or other similar sequence data banks.

e. Analyze, review, revise and/or interpret the data and prepare scientific reports, summaries, presentations, training materials, minutes, summaries, abstracts, manuscripts, and laboratory Standard Operating Procedures (SOPs) and other documents related to research projects, surveillance, and other lab activities.

f. Disseminate scientific findings and information at local, national and international meetings and ensure CDC clearance of disseminated information.

g. Comply with Clinical Laboratory Improvement Amendments (CLIA) and quality and safety regulations as required by CDC.

h. Assist with the establishment of procedures for Quality Assurance (QA) and Quality Control (QC) of sequence data analysis in the context of the specific projects.

i. Provide recommendations and feedback to Laboratory and Branch personnel on CLIA and QMS regulations for informatics methods for VPD surveillance.

j. Attend CDC, Center, Division, Branch and Lab required trainings

2. Vaccine evaluation – Working within the BML, contractor shall provide technical and intellectual support for the evaluation of meningococcal serogroup B vaccines. Contractor’s responsibilities shall be the following:

a. Develop, designs, and implement scientific projects to understand the genetic diversity and in vitro or in vivo expression level of vaccine antigens among strains of Neisseria species,

b. Develop new methods and systems to improve evaluation and monitoring of vaccine antigens to estimate strain coverage by assessed vaccines.

c. Perform quality control, assembly, and analysis of pathogen genome and RNA sequences and management of genome sequence files and database including uploads to National Center for Biotechnology Information (NCBI) or other similar sequence data banks.

d. Analyze, review, revise, and/or interpret the data and prepare scientific reports, summaries, training materials, minutes, presentations, manuscripts, and laboratory Standard Operating Procedures (SOPs) and other documents related to research projects, surveillance, and other lab activities.

e. Perform a variety of lab experiments such as microbiological methods and whole genome sequencing in support of research projects such as monitoring of genomic epidemiology of bacterial meningitis pathogens and estimating B vaccine coverage.

f. Provide support for outbreak responses and applied research projects to advance our understanding of meningococcal disease and carriage as well as genomics, strain evolution and transmission, virulence factors, and antibiotic resistance of common bacterial meningitis pathogens.

g. Comply with Clinical Laboratory Improvement Amendments (CLIA) and quality and safety regulations as required by CDC.

h. Assist with the establishment of procedures for Quality Assurance (QA) and Quality Control (QC) of sequence data analysis in the context of the specific projects.

i. Provide recommendations and feedback to Laboratory and Branch personnel on CLIA and QMS regulations for informatics methods for VPD surveillance.

j. Attend CDC, Center, Division, Branch and Lab required trainings

3. Meningitis diagnostics, surveillance and outbreak response – Working within the BML, contractor shall provide technical and intellectual support for diagnostics, surveillance and outbreak response for meningococcal and H. influenzae diseases. Contractor’s responsibilities shall be the following:

a. Under senior staff members in the team, perform a variety of lab experiments such as lab diagnostic testing under CLIA, microbiological tests, antimicrobial susceptibility tests, and whole genome sequencing in support of research projects and surveillance programs for bacterial meningitis pathogens.

b. Assist with developing and implementing suitable and customized microbiological, molecular and whole genome sequencing-based methods for diagnostics, surveillance and outbreak investigations, in compliance with CDC laboratory Quality Management System (QMS).

c. Work with team members to coordinate activities related to laboratory supply procurement and specimen management

d. Prepare, maintain and organize biological materials such as bacterial culture stocks, clinical specimens, and bacterial DNA. Must be aware of, and strictly adhere to CDC and Clinical Laboratory Improvement Act (CLIA) requirements.

e. Provide support for outbreak responses and applied research projects to advance our understanding of meningococcal disease and carriage as well as genomics, strain evolution and transmission, virulence factors, and antibiotic resistance of common bacterial meningitis pathogens.

f. Analyze, review, revise, and/or interpret data and prepare scientific reports, Standard Operating Procedures (SOPs), training materials, meeting minutes, summaries, abstracts, manuscripts, presentations, and other documents related to research projects, surveillance, and other laboratory activities.

g. Comply with Clinical Laboratory Improvement Amendments (CLIA) and quality and safety regulations as required by CDC.

h. Assist with the establishment of procedures for Quality Assurance (QA) and Quality Control (QC) of sequence data analysis in the context of the specific projects.

i. Provide recommendations and feedback to Laboratory and Branch personnel on CLIA and QMS regulations for informatics methods for VPD surveillance.

j. Attend CDC, Center, Division, Branch and Lab required trainings

4. Lab method and tool development and improvement – Working within the BML, contractor shall support the meningitis diagnostic method development. Contractor’s responsibilities shall be the following:

a. Regularly review literatures to keep updated with the development of new diagnostics and detection methods for meningitis pathogens (bacterial, viral, fungal etc.)

b. Work closely with stakeholders such as WHO and state health laboratories to explore, develop, validate and implement new detection methods using advanced and emerging technologies to improve the diagnostics, surveillance and outbreak response for diseases caused by meningitis pathogens.

c. Analyze, review, revise, and/or interpret the data and prepares scientific reports, laboratory Standard Operating Procedures (SOPs), training materials, summaries abstracts, manuscripts, presentations, and other documents related to research projects, surveillance and other lab activities.

d. Provide support for outbreak responses and applied research projects to advance our understanding of meningococcal disease and carriage as well as genomics, strain evolution and transmission, virulence factors, and antibiotic resistance of common bacterial meningitis pathogens.

e. Comply with Clinical Laboratory Improvement Amendments (CLIA) and quality and safety regulations as required by CDC.

f. Assist with the establishment of procedures for Quality Assurance (QA) and Quality Control (QC) of sequence data analysis in the context of the specific projects.

g. Provide recommendations and feedback to Laboratory and Branch personnel on CLIA and QMS regulations for informatics methods for VPD surveillance.

h. Attend CDC, Center, Division, Branch and Lab required trainings

5. Bioinformatics support – Working within the BML, contractor shall provide technical and intellectual support for bioinformatics analysis, tool development, and data management to improve bacterial meningitis surveillance and understanding of bacterial diseases. Contractor’s responsibilities shall be the following:

a. Provide bioinformatic support for studies and projects to understand meningitis diseases, pathogen genomics and population genetics, vaccine antigens, antibiotic resistance, virulence of bacterial meningitis pathogens.

b. Provide bioinformatic and informatic support for genomic surveillance and outbreak response to monitor emerging and spreading of meningitis pathogens

c. Perform quality control, assembly, and analysis of pathogen genome and RNA sequences and management of genome and RNA sequence files and database including uploads to National Center for Biotechnology Information (NCBI) or online sequence data banks such as PubMLST.

d. Improve and maintain BML Bacterial Meningitis Genome Analysis Platform (BMGAP) and coordinate data submission and analysis with CDC internal and external partners.

e. Effectively manage and maintain the molecular and whole genome sequencing data on specimens/bacterial isolates collected through surveillance, carriage and other studies

f. Develop, validate, and implement suitable and customized bioinformatics and informatics tools and pipelines to improve data management and analysis, in compliance with CDC laboratory Quality Management System (QMS).

g. Collaborate with partners to provide technical support and consultation on sequencing data interpretation in support of research projects, surveillance and outbreak investigations.

h. Analyze, review, revise, and/or interpret the data and prepares scientific reports, laboratory Standard Operating Procedures (SOPs), training materials, summaries abstracts, manuscripts, presentations, and other documents related to research projects and activities.

6. Antibiotic resistance surveillance – Working within the BML, contractor shall provide laboratory technical and support services for characterization of bacterial meningitis pathogens and monitor their anti-microbial resistance (AMR) trends. Contractor’s responsibilities shall be the following:

a. Perform laboratory tests including antimicrobial susceptibility testing (AST), molecular and microbiological assays, to support AMR surveillance of bacterial meningitis pathogens.

b. Collaborate with other BML members to improve AST and other laboratory methods for bacterial meningitis surveillance.

c. Develop, review and review AST related documents and maintain the AST capacity (procurement, equipment maintenance, onboarding trainings etc.) in BML in compliance with CLSI standards

d. Analyze, review, revise, and/or interpret the data and prepare scientific reports, laboratory Standard Operating Procedures (SOPs), training materials, minutes, summary reports, abstracts, manuscripts, presentations, and other documents related to laboratory testing, training, specimen management, safety and quality.

e. Provide support for outbreak responses and applied research projects to advance our understanding of meningococcal disease and carriage as well as genomics, strain evolution and transmission, virulence factors, and antibiotic resistance of common bacterial meningitis pathogens.

f. Comply with Clinical Laboratory Improvement Amendments (CLIA) and quality and safety regulations as required by CDC.

g. Assist with the establishment of procedures for Quality Assurance (QA) and Quality Control (QC) of sequence data analysis in the context of the specific projects.

h. Provide recommendations and feedback to Laboratory and Branch personnel on CLIA and QMS regulations for informatics methods for VPD surveillance.

i. Attend CDC, Center, Division, Branch and Lab required trainings

7. Bioinformatics support for global portfolio – Working within the BML, contractor shall provide technical and intellectual support for bioinformatics analysis, tool development, and data management to improve bacterial meningitis surveillance and understanding of diseases. Contractor’s responsibilities shall be the following:

a. Provide bioinformatic support for studies and projects to understand meningitis diseases, pathogen genomics and population genetics, vaccine antigens, antibiotic resistance, virulence of bacterial meningitis pathogens.

b. Provide bioinformatic and informatic support for genomic surveillance and outbreak response to monitor emerging and spreading of meningitis pathogens

c. Perform quality control, assembly, and analysis of pathogen genome and RNA sequences and management of genome and RNA sequence files and database including uploads to National Center for Biotechnology Information (NCBI) or online sequence data banks such as PubMLST.

d. Improve and maintain BML Bacterial Meningitis Genome Analysis Platform (BMGAP) and coordinate data submission and analysis with CDC internal and external partners.

e. Effectively manage and maintain the molecular and whole genome sequencing data on specimens/bacterial isolates collected through surveillance, carriage and other studies

f. Develop, validate, and implement suitable and customized bioinformatics and informatics tools and pipelines to improve data management and analysis, in compliance with CDC laboratory Quality Management System (QMS).

g. Collaborate with partners to provide technical support and consultation on sequencing data interpretation in support of research projects, surveillance and outbreak investigations.

h. Analyze, review, revise, and/or interpret the data and prepares scientific reports, laboratory Standard Operating Procedures (SOPs), training materials, summaries abstracts, manuscripts, presentations, and other documents related to research projects and activities.

8. Global meningitis surveillance – Working within the Meningitis and Vaccine Preventable Diseases Branch (MVPDB), Contractor shall provide laboratory support for global meningitis surveillance.

a. Serve as a country focal point to coordinate, monitor and evaluate the implementation of activities to reinforce the laboratory systems in BML-supported countries

b. Have a full understanding of global bacterial meningitis epidemiology and molecular epidemiology, laboratory systems, and testing algorithms in BML-supported countries

c. Coordinate communications, meetings, visits between CDC internal and external partners

d. Support CDC-led External Quality Assurance program, perform retesting of specimens from the assigned countries, prepare and share data reports, and develop action plans to address any issues related to EQA.

e. Conduct follow-up visits or provide onsite trainings/technical assistance to improve laboratory capacity, develop country specific work plans, and address meningitis surveillance and outbreak related issues in BML-supported countries

f. Coordinate, develop, and conduct national or regional laboratory assessments and trainings in international settings to improve laboratory capacity for bacterial disease surveillance

g. Lead/participate in diagnosis assays development to improve bacterial pathogen detection and characterization

h. Prepare and manage materials and documents including progress reports, summaries, SOPs, training materials, laboratory budget, and job aids

i. Be responsible for procurement of laboratory equipment, supplies and reagents to ensure timely testing for meningitis case confirmation in collaborator countries

j. Collaborate with CDC internal and external partners to support meningitis rapid diagnostic test development and global genomic surveillance network

k. Review, revise, and/or prepares SOPs, training materials, grants, contracts, agency agreement, minutes, summaries, reports, abstracts, manuscripts, presentations, and documents related to bacterial meningitis surveillance and applied research.

Task 2: Quality management systems (QMS) Staffing Support

1. Laboratory quality liaison – Assigned to the Meningitis and Vaccine Preventable Diseases Branch (MVPDB) Quality Management Team. Contractor shall participate in the development, implementation and maintenance of the Branch Quality Management System, as well as adherence to applicable guidelines and requirements. Contractor’s responsibilities shall be the following:

a. Participate in the development, implementation and maintenance of the Branch Quality Management System and adherence to applicable guidelines and requirements established by Clinical Laboratory Improvement Amendments (CLIA), the Food and Drug Administration (FDA) and the International Organization for Standardization (ISO).

b. Provide direct laboratory support for the implementation of quality system activities:

(a) Prepare schedules for, and monitor equipment calibration and preventive maintenance activities.

(b) Coordinate equipment maintenance with vendors as applicable.

(c) Maintain records (training, equipment, monitoring records, NCEs etc.) in accordance with quality standards.

(d) Assist laboratories with documentation and investigation of nonconformances.

(e) Prepare schedules for, and monitor competency assessments and proficiency testing.

c. Under the direction of the Branch Quality Team, work directly with laboratory staff to implement and ensure quality system requirements are met.

d. Perform document control activities as assigned by the quality team lead.

e. Assist branch quality team in performing periodic internal quality audits.

f. Assist branch quality team in development and collation of data for branch quality management reviews.

g. Work with branch quality team to ensure that all aspects of the branch QMS are developed, documented, implemented and maintained.

h. Analyze, review, revise, and/or interpret the data and prepare scientific reports, laboratory Standard Operating Procedures (SOPs), training materials, minutes, summary reports, abstracts, manuscripts, presentations, and other documents related to laboratory testing, training, specimen management, safety and quality.

i. Assist in placing orders, receiving and ensuring that packing slips are maintained/uploaded and all relevant trackers are updated.

j. Manage in-processing of reagents and supplies, assist in QC and labeling, and with the supplies and reagents inventory.

k. Assist/manage disposal of expired/hazardous waste.

2. (Optional) Laboratory Quality Specialist - Assigned to the Meningitis and Vaccine Preventable Diseases Branch (MVPDB) Quality Management Team. Contractor shall participate in the development, implementation and maintenance of the Branch Quality Management System, as well as adherence to applicable guidelines and requirements. Contractor’s responsibilities shall be the following:

a. Participate in the maintenance of the Branch Quality Management System and adherence to applicable guidelines and requirements established by Clinical Laboratory Improvement Amendments (CLIA), the Food and Drug Administration (FDA) and the International Organization for Standardization (ISO).

b. Provide direct laboratory support for the implementation of quality system activities:

(a) Monitor equipment calibration and preventive maintenance activities.

(b) Coordinate equipment maintenance with vendors as applicable.

(c) Maintain records (training, equipment, monitoring records, NCEs etc.) in accordance with quality standards.

(d) Assist laboratories with documentation and investigation of nonconformances.

(e) Monitor competency assessments and proficiency testing.

c. Under the direction of the Branch Quality Team, work directly with laboratory staff to implement and ensure quality system requirements are met.

d. Assist branch quality team in performing periodic internal quality audits.

e. Assist branch quality team in development and collation of data for branch quality management reviews.

f. Work with branch quality team to ensure that all aspects of the branch QMS are developed, documented, implemented and maintained.

g. Analyze, review, revise, and/or interpret the data and prepare scientific reports, laboratory Standard Operating Procedures (SOPs), training materials, minutes, summary reports, abstracts, manuscripts, presentations, and other documents related to laboratory testing, training, specimen management, safety and quality.

h. Assist in placing orders, receiving and ensuring that packing slips are maintained/uploaded and all relevant trackers are updated.

i. Manage in-processing of reagents and supplies, assist in QC and labeling, and with the supplies and reagents inventory.

j. Assist/manage disposal of expired/hazardous waste.

3. (Optional) Laboratory Quality Specialist - Assigned to the Meningitis and Vaccine Preventable Diseases Branch (MVPDB) Quality Management Team. Contractor shall participate in the development, implementation and maintenance of the Branch Quality Management System, as well as adherence to applicable guidelines and requirements. Contractor’s responsibilities shall be the following:

a. Participate in the maintenance of the Branch Quality Management System and adherence to applicable guidelines and requirements established by Clinical Laboratory Improvement Amendments (CLIA), the Food and Drug Administration (FDA) and the International Organization for Standardization (ISO).

b. Provide direct laboratory support for the implementation of quality system activities:

(a) Monitor equipment calibration and preventive maintenance activities.

(b) Coordinate equipment maintenance with vendors as applicable.

(c) Maintain records (training, equipment, monitoring records, NCEs etc.) in accordance with quality standards.

(d) Assist laboratories with documentation and investigation of nonconformances.

(e) Monitor competency assessments and proficiency testing.

c. Under the direction of the Branch Quality Team, work directly with laboratory staff to implement and ensure quality system requirements are met.

d. Assist branch quality team in performing periodic internal quality audits.

e. Assist branch quality team in development and collation of data for branch quality management reviews.

f. Work with branch quality team to ensure that all aspects of the branch QMS are developed, documented, implemented and maintained.

g. Analyze, review, revise, and/or interpret the data and prepare scientific reports, laboratory Standard Operating Procedures (SOPs), training materials, minutes, summary reports, abstracts, manuscripts, presentations, and other documents related to laboratory testing, training, specimen management, safety and quality.

h. Assist in placing orders, receiving and ensuring that packing slips are maintained/uploaded and all relevant trackers are updated.

i. Manage in-processing of reagents and supplies, assist in QC and labeling, and with the supplies and reagents inventory.

j. Assist/manage disposal of expired/hazardous waste.

Task 3: Web development – Contractor shall provide expertise in the web development of internal and external facing websites.

A. Web development for Management and Operations (M&O)

a. Providing expertise in the design and layout of graphical user interfaces for internal and external facing sites.

b. Ensuring compliance with CDC and HHS security and system development and development standards.

c. Leveraging technology to recommend technical solutions to web design challenges.

d. Collaborating with appropriate developers and providing sufficient information for designing, building, and maintaining sites.

e. Developing, assessing, and communicating website usage analytics.

f. Designing and developing MVPDB SharePoint site, which includes workflow development and document management and sharing.

g. Designing and developing Power BI dashboards, visuals, and maps

h. Developing and managing excel documents that utilize power query editor

i. Providing training and instruction to MVPDB staff as needed regarding the use and or development of SharePoint site components.

Task 4: Monthly Report – Contractor shall prepare and submit monthly technical progress reports in narrative form, which shall contain technical results of the work accomplished during the reporting period. This report shall be in sufficient detail to disclose all work started and results achieved during the reporting period; an indication of any current problems, which may impede performance; the proposed corrective action; and the work forecast for the next period. This document shall report progress and planning so as to correspond with the work schedule contained in the Center approved program plan.

1. Format: delivered electronically in MS Word.

2. Due date: by the 5th calendar day of each month

3. Deliver to: Contracting Officer’s Representative (COR) Heena Mikoleit

Final Report – Upon completion of all work under the contract, the Contractor shall prepare and submit to the Government a final report covering in detail all the work accomplished under the contract. The final report shall document and summarize the entire contract work and shall include recommendations and conclusions based on the experience and results obtained. The final report shall include tables, graphs, photos, and diagrams in sufficient detail to comprehensively explain the results achieved under the contract. The report shall also include an analysis of salient findings, a presentation of general conclusions, and any guidance or recommendations deemed pertinent for future consideration by the MVPDB.

1. Format: delivered electronically in MS Word

2. Due date: Final report due no later than by the end of the period of performance

3. Deliver to: COR Heena Mikoleit

Optional Task 5: Outbreak/Pandemic Support – Contractor shall provide support to CDC’s Emergency Operations Center (EOC) and to DBD in outbreak/pandemic situations.

1. The following sub-tasks apply to all categories of labor (any task listed within task areas 1 through 3) provided under this contract, including categories of labor aligned to optional tasks, if exercised:

a. Provide support to the CDC EOC for agency response activities when the EOC is activated.

b. Provide support for CDC pandemic activities.

Optional Task 6: Genomics Microbiologists – Contractor shall provide technical and intellectual support for the method development and molecular typing systems to improve bacterial meningitis genomic surveillance

1. Genomics Microbiologist IV

a. Support projects to monitor the molecular epidemiology of meningococcal and Haemophilus infuenzae disease, serogroup B meningococcal vaccine antigens, and population genetics of bacterial meningitis pathogens.

b. Provide support for outbreak responses and applied research projects to advance our understanding of meningococcal disease and carriage as well as genomics, strain evolution and transmission, virulence factors, and antibiotic resistance of common bacterial meningitis pathogens.

c. Explore, develop, and implement new molecular and next-generation sequencing methods and systems to assist characterization of common bacterial meningitis pathogens and epidemiological and outbreak investigations.

d. Perform quality control, assembly, and analysis of pathogen genome sequences and management of genome sequence files and database including uploads to National Center for Biotechnology Information (NCBI) or other similar sequence data banks.

e. Analyze, review, revise and/or interpret the data and prepare scientific reports, summaries, presentations, training materials, minutes, summaries, abstracts, manuscripts, and laboratory Standard Operating Procedures (SOPs) and other documents related to research projects, surveillance, and other lab activities.

f. Disseminate scientific findings and information at local, national and international meetings and ensure CDC clearance of disseminated information.

g. Comply with Clinical Laboratory Improvement Amendments (CLIA) and quality and safety regulations as required by CDC.

h. Assist with the establishment of procedures for Quality Assurance (QA) and Quality Control (QC) of sequence data analysis in the context of the specific projects.

i. Provide recommendations and feedback to Laboratory and Branch personnel on CLIA and QMS regulations for informatics methods for VPD surveillance.

j. Attend CDC, Center, Division, Branch and Lab required trainings

2. Genomics Microbiologist IV

a. Support projects to monitor the molecular epidemiology of meningococcal and Haemophilus infuenzae disease, serogroup B meningococcal vaccine antigens, and population genetics of bacterial meningitis pathogens.

b. Provide support for outbreak responses and applied research projects to advance our understanding of meningococcal disease and carriage as well as genomics, strain evolution and transmission, virulence factors, and antibiotic resistance of common bacterial meningitis pathogens.

c. Explore, develop, and implement new molecular and next-generation sequencing methods and systems to assist characterization of common bacterial meningitis pathogens and epidemiological and outbreak investigations.

d. Perform quality control, assembly, and analysis of pathogen genome sequences and management of genome sequence files and database including uploads to National Center for Biotechnology Information (NCBI) or other similar sequence data banks.

e. Analyze, review, revise and/or interpret the data and prepare scientific reports, summaries, presentations, training materials, minutes, summaries, abstracts, manuscripts, and laboratory Standard Operating Procedures (SOPs) and other documents related to research projects, surveillance, and other lab activities.

f. Disseminate scientific findings and information at local, national and international meetings and ensure CDC clearance of disseminated information.

g. Comply with Clinical Laboratory Improvement Amendments (CLIA) and quality and safety regulations as required by CDC.

h. Assist with the establishment of procedures for Quality Assurance (QA) and Quality Control (QC) of sequence data analysis in the context of the specific projects.

i. Provide recommendations and feedback to Laboratory and Branch personnel on CLIA and QMS regulations for informatics methods for VPD surveillance.

j. Attend CDC, Center, Division, Branch and Lab required trainings

Optional Task 7: Applied Bioinformatics Laboratory (ABiL) Bioinformatics SME Support - The Contractor shall provide analysis of data generated by Advanced Molecular Detection (AMD) methods, including but not limited to data generated by the MinION, Illumina platforms, and PacBio. The contractor shall create data systems to allow analyses, perform both basic descriptive analyses as well as more complex modeling, and generate reports for scientific meetings and publications. The scientists shall develop bioinformatic solutions for performing MinION NGS in the field, including data analysis and data transfer to CDC and other partner labs. The Contractor shall design and implement computational algorithms that analyze NGS data (MionION and /or Illumina and/or PacBio) specifically for DBD pathogens, along with metagenomics sequencing projects and will be responsible for constructing and troubleshooting data analysis pipelines within a Linux environment.

1. ABiL Bioinformatics Support

a. Developing and maintaining Standard Operating Procedures and protocols for analysis of MinION, Illumina, and possibly PacBio generated sequences.

b. Develop and maintain a database of NGS generated by these platforms

c. Perform complex data analysis and provide oral or written reports, as instructed

d. Write code and use existing software to fully analyze data.

e. Ensure all data and metrics meets Quality Management Standards for NGS results

f. Provide results to other scientists within CDC when requested

g. Preparation of scientific reports and manuscripts

h. Be able to effectively communicate technical elements of bioinformatics to other staff scientists and upper management

i. Provide training and/or assistance to junior bioinformatics scientists

j. Provide succinct algorithms for analyzing complex data

k. Develop and implement tools for analyzing metagenomic data

l. Develop workflows that can be used inside CDC laboratories, and PH partner labs

m. Construct multi-faceted pipelines for NGS data analysis

2. ABiL Bioinformatics Support

a. Developing and maintaining Standard Operating Procedures and protocols for analysis of MinION, Illumina, and possibly PacBio generated sequences.

b. Develop and maintain a database of NGS generated by these platforms

c. Perform complex data analysis and provide oral or written reports, as instructed

d. Write code and use existing software to fully analyze data.

e. Ensure all data and metrics meets Quality Management Standards for NGS results

f. Provide results to other scientists within CDC when requested

g. Preparation of scientific reports and manuscripts

h. Be able to effectively communicate technical elements of bioinformatics to other staff scientists and upper management

i. Provide training and/or assistance to junior bioinformatics scientists

j. Provide succinct algorithms for analyzing complex data

k. Develop and implement tools for analyzing metagenomic data

l. Develop workflows that can be used inside CDC laboratories, and PH partner labs

m. Construct multi-faceted pipelines for NGS data analysis

Optional Task 8: Travel - Travel will support all activities described above in the scope of work for meningitis surveillance activities, and emergency and outbreak response. Travel may also be necessary for site visits in conjunction with both domestic and global activities, as well as for attending and/or presenting at scientific conferences.

1. Site-Visit Travel: Domestic and International

a. Microbiologists may travel on 2-3 Domestic and 1-2 International site visits per year may be required to improve public health capacity for meningitis diagnosis.

b. Domestic trips may be 1-7 days in duration and international trips may be 10-12 days in duration.

c. Travel will be billed at cost and in accordance with Federal Travel Regulation (FTR).

d. All requests for federally reimbursable travel will be pre-approved by the Contracting Officer’s Representative (COR) in advance. Funding for travel will be added to the contract via bilateral modification. The Contractor shall limit travel costs to those authorized by the Federal Travel Regulation (FTR).

2. Conference Travel:

a. Bioinformaticians, Microbiologists and Quality Management Staff may travel to attend conferences may be required to convey protocol improvements or updates in domestic N. meningitidis or H. influenzae surveillance, including changes in dominant serogroups/serotypes/specific strains/antimicrobial resistance. Sharing these findings with the public health and scientific communities improves awareness and in doing so may improve public health outcomes. It also may encourage additional surveillance and research work to better understand the circulating strains, transmission, and resistances.

b. Conference Approval Management Systems (CAMS) approval is required in advance of anticipated travel and obligation of funds

3. Outbreak Response:

a. Microbiologists may travel to assist in outbreak response may be required as outbreaks occur; for example, if a state lab requests assistance in their identification protocols.

SECTION 5 – GOVERNMENT FURNISHED PROPERTY

The Government shall furnish adequate workspace at the Government site for Contractor personnel and provide desktop computers with all software required to support this project. The Government shall provide desks, chairs, cabinet space, telephones, and customary office supplies. Laptop computers shall be furnished when needed.

SECTION 6 – PLACE OF PERFORMANCE

Contractor shall perform services at CDC facilities located at 1600 Clifton Road NE, Atlanta, GA, 30329, within NCIRD/DBD/MVPDB.

SECTION 7 – TRAVEL

Travel will be in accordance with / and not to exceed the Federal Travel Regulation rates. Travel costs need to be approved in advance by the COR. The contractor shall be required to provide their travel policy to the Government for review.

Travel does include conferences. Conference Approval Management Systems (CAMS) approval is required in advance of any travel for conferences. If the need for conference travel occurs, the contract will be modified to separately add funding.

SECTION 8 – DELIVERABLES/REPORTING SCHEDULE

Contractor shall provide a total of 12 monthly status reports in a 12-month period to contain, at a minimum, the following information:

1. A brief description of requirements the Contractor is currently performing;

2. Accomplishments during the reporting period and significant events regarding the contract;

3. Deliverables submitted or progress on deliverable products;

4. Any current or anticipated problems and solutions proposed; and

5. A brief summary of activities planned for the next reporting period.

SECTION 10 – PERIOD OF PERFORMANCE

Base Period: September 30, 2024 to September 29, 2025 Option Period One: September 30, 2025 to September 29, 2026 Option Period Two: September 30, 2026 to September 29, 2027 Option Period Three: September 30, 2027 to September 29, 2028 Option Period Four: September 30, 2028 to September 29, 2029

SECTION 11 – ADDITIONAL REQUIREMENTS

Information Security and Privacy

(a) Baseline Security Requirements.

(1) Applicability. The requirements herein apply whether the entire contract or order (hereafter “contract”), or portion thereof, includes either or both of the following:

(i) Access (Physical or Logical) to Government Information: A Contractor (and/or any subcontractor) employee will have or will be given the ability to have, routine physical (entry) or logical (electronic) access to government information.

(ii) Operate a Federal System Containing Information: A Contractor (and/or any subcontractor) will operate a federal system and information technology containing data that supports the HHS mission. In addition to the Federal Acquisition Regulation (FAR) Subpart 2.1 definition of “information technology” (IT), the term as used in this section includes computers, ancillary equipment (including imaging peripherals, input, output, and storage devices necessary for security and surveillance), peripheral equipment designed to be controlled by the central processing unit of a computer, software, firmware and similar procedures, services (including support services), and related resources.

(2) Safeguarding Information and Information Systems. In accordance with the Federal Information Processing Standards Publication (FIPS) 199, Standards for Security Categorization of Federal Information and Information Systems, the Contractor (and/or any subcontractor) shall:

(i) Protect government information and information systems in order to ensure:

(A) Confidentiality, which means preserving authorized restrictions on access and disclosure, based on the security terms found in this contract, including means for protecting personal privacy and proprietary information;

(B) Integrity, which means guarding against improper information modification or destruction, and ensuring information non-repudiation and authenticity; and

(C) Availability, which means ensuring timely and reliable access to and use of information.

(ii) Provide security for any Contractor systems, and information contained therein, connected to an HHS network or operated by the Contractor on behalf of HHS regardless of location. In addition, if new or unanticipated threats or hazards are discovered by either the agency or contractor, or if existing safeguards have ceased to function, the discoverer shall immediately, within one (1) hour or less, bring the situation to the attention of the other party.

(iii) Adopt and implement the policies, procedures, controls, and standards required by the HHS Information Security Program to ensure the confidentiality, integrity, and availability of government information and government information systems for which the Contractor is responsible under this contract or to which the Contractor may otherwise have access under this contract. Obtain the HHS Information Security Program security requirements, outlined in the HHS Information Security and Privacy Policy (IS2P), by contacting the CO/COR or emailing fisma@hhs.gov.

(iv) Comply with the Privacy Act requirements and tailor FAR clauses as needed.

(3) Information Security Categorization. In accordance with FIPS 199 and National Institute of Standards and Technology (NIST) Special Publication (SP) 800-60, Volume II: Appendices to Guide for Mapping Types of Information and Information Systems to Security Categories, Appendix C, and based on information provided by the ISSO, CISO, or other security representative, the risk level for each Security Objective and the Overall Risk Level, which is the highest watermark of the three factors (Confidentiality, Integrity, and Availability) of the information or information system are the following:

Confidentiality: [] Low [X] Moderate [ ] High Integrity: [] Low [X] Moderate [ ] High Availability: [] Low [X] Moderate [ ] High Overall Risk Level: [] Low [X] Moderate [ ] High

Based on information provided by the ISSO, Privacy Office, system/data owner, or other security or privacy representative, it has been determined that this solicitation/contract involves:

[X] No PII [ ] Yes PII

Personally Identifiable Information (PII). Per the Office of Management and Budget (OMB) Circular A-130, “PII is information that can be used to distinguish or trace an individual's identity, either alone or when combined with other information that is linked or linkable to a specific individual.” Examples of PII include, but are not limited to the following: social security number, date and place of birth, mother‘s maiden name, biometric records, etc.

PII Confidentiality Impact Level has been determined to be: [X] Low [ ] Moderate [ ] High

(4) Controlled Unclassified Information (CUI). CUI is defined as “information that laws, regulations, or Government-wide policies require to have safeguarding or dissemination controls, excluding classified information.” The Contractor (and/or any subcontractor) must comply with Executive Order 13556, Controlled Unclassified Information, (implemented at 3 CFR, part 2002) when handling CUI. 32 C.F.R. 2002.4(aa) As implemented the term “handling” refers to “…any use of CUI, including but not limited to marking, safeguarding, transporting, disseminating, re-using, and disposing of the information.” 81 Fed. Reg. 63323. All sensitive information that has been identified as CUI by a regulation or statute, handled by this solicitation/contract, shall be:

(i) marked appropriately;

(ii) disclosed to authorized personnel on a Need-To-Know basis;

(iii) protected in accordance with NIST SP 800-53, Security and Privacy Controls for Federal Information Systems and Organizations applicable baseline if handled by a Contractor system operated on behalf of the agency, or NIST SP 800-171, Protecting Controlled Unclassified Information in Nonfederal Information Systems and Organizations if handled by internal Contractor system; and

(iv) returned to HHS control, destroyed when no longer needed, or held until otherwise directed. Destruction of information and/or data shall be accomplished in accordance with NIST SP 800-88, Guidelines for Media Sanitization.

(5) Protection of Sensitive Information. For security purposes, information is or may be sensitive because it requires security to protect its confidentiality, integrity, and/or availability. The Contractor (and/or any subcontractor) shall protect all government information that is or may be sensitive in accordance with OMB Memorandum M-06-16, Protection of Sensitive Agency Information by securing it with a FIPS 140-2 validated solution.

(6) Confidentiality and Nondisclosure of Information. Any information provided to the contractor (and/or any subcontractor) by HHS or collected by the contractor on behalf of HHS shall be used only for the purpose of carrying out the provisions of this contract and shall not be disclosed or made known in any manner to any persons except as may be necessary in the performance of the contract. The Contractor assumes responsibility for protection of the confidentiality of Government records and shall ensure that all work performed by its employees and subcontractors shall be under the supervision of the Contractor. Each Contractor employee or any of its subcontractors to whom any HHS records may be made available or disclosed shall be notified in writing by the Contractor that information disclosed to such employee or subcontractor can be used only for that purpose and to the extent authorized herein.

The confidentiality, integrity, and availability of such information shall be protected in accordance with HHS and CDC policies. Unauthorized disclosure of information will be subject to the HHS/CDC sanction policies and/or governed by the following laws and regulations:

(i) 18 U.S.C. 641 (Criminal Code: Public Money, Property or Records);

(ii) 18 U.S.C. 1905 (Criminal Code: Disclosure of Confidential Information); and

(iii) 44 U.S.C. Chapter 35, Subchapter I (Paperwork Reduction Act).

(7) Internet Protocol Version 6 (IPv6). All procurements using Internet Protocol shall comply with OMB Memorandum M-05-22, Transition Planning for Internet Protocol Version 6 (IPv6).

(8) Government Websites. All new and existing public-facing government websites must be securely configured with Hypertext Transfer Protocol Secure (HTTPS) using the most recent version of Transport Layer Security (TLS).