OE15-15010302SUPP17 Project Plans.docx

Attachment 1 – Project Areas Appendix A. Public Health Laboratory Strengthening and Leadership Project Name: Continued Support for the Implementation and Upgrade of the Public Health Laboratory System Database (PHLSD) Project Activity Contact Information: John RIdderhof / jcr0@cdc.gov Approximate Amount of Supplemental Funding Available: $100,000 Project Description: The Public Health Laboratory System Database (PHLSD) and the anticipated National PHL Test Directory, were developed by APHL and DLS, in response to requests from PHL leadership, and with the objective to provide a resource for laboratory information management. The database is on its second version and is developed on MS SharePoint to have dual functionality as a database and a directory, be easy-to-use, and be accessible for laboratories with varying technological expertise and support. Data entry will be incentivized by immediately providing useful and shared information to state and local PHLs, but APHL will own the tool and will be able to continually modify and maintain the tool in a cost-effective manner. The database has been rolled out, and marketing efforts are ongoing to onboard PHLs. The requested funding will continue support for a SharePoint contractor ($60K), a Laboratory SME ($15K) contractor for test list upgrades, support subcommittee activities to guide upgrades ($25K), and enable data analyses and data access policy efforts. The funding will help to enhance PHL capacity as they leverage the database as a tool for regulatory compliance, preparedness, and information management.

Mid-Term Outcomes Improves laboratory methods, systems, and informatics capacity Increases laboratory effectiveness in response to public health needs, including emergencies Assures CLIA standards and good laboratory practices are followed by PHLs and are promoted to clinical laboratories performing tests of public health importance.

Long-Term Outcome Creates sustainable and resilient PHLs that effectively and efficiently adapt to evolving public health needs

Appendix B. Public Health Preparedness and Response Project Name: Market Analysis of Regional Clinical Laboratory Systems to Support Public Health Response Project Activity Contact Information: Jasmine Chaitram / zoa6@cdc.gov Approximate Amount of Supplemental Funding Available: $200,000 (One-time funding) Project Description: The Zika virus outbreak identified a need to proactively find clinical diagnostic laboratories throughout the US that could provide additional surge capacity to the LRN and public health laboratories. Although relevant data are available from the records required under the Clinical Laboratory Improvement Amendments of 1988 (CLIA), there is currently no comprehensive understanding of which certified clinical diagnostic laboratories in the US are technically able and would be willing to work with public health partners to provide surge laboratory testing during an emergency. Further, each laboratory’s ability and willingness will likely vary according to the threat. CDC/CSELS/DLS is working with professional laboratory organizations and large commercial lab entities to establish relationships in advance of the next major public health event. CDC/CSELS/DLS is also interested in partnering with APHL to explore other large regional laboratory systems that exist with sufficient capacity and willingness to work with state health departments and the federal government during emergencies.

Mid-Term Outcome Increases laboratory effectiveness in response to public health needs, including emergencies

Long-Term Outcome Protects the public from public health threats

Project Name: Logistical Support for Shipments of Clinical Samples from TB Patients for Rifampin Drug Levels Project Activity Contact Information: Angela Starks /eog0@cdc.gov Approximate Amount of Supplemental Funding Available: $5,000.00 Project Description: DTBE has developed a plan to evaluate serum drug levels of rifampin, the most important first-line drug used to treat TB, in diabetic patients. The purposes of the evaluation are to understand the variability of rifampin levels in diabetics with varying stages of diabetes for the purposes of improving patient outcomes with optimized dosing. Treating patients correctly is critical to prevent ongoing transmission and prevent morbidity and mortality associated with this devastating disease.

For completion of the project, APHL would coordinate logistical support for shipment of clinical specimens from 3 public health laboratories in collaboration with local TB clinics. APHL would support shipment of two clinical specimens from ~90 patients at these sites to a national reference laboratory for testing. APHL would not be engaged in the project beyond this logistical support.

Mid-Term Outcomes Increases laboratory effectiveness in response to public health needs, including emergencies Improves public health laboratory detection and response programs

Long-Term Outcomes Reduces incidence and prevalence of preventable diseases and public health threats Creates sustainable and resilient PHLs that effectively and efficiently adapt to evolving public health needs

Project Name: Expanding Regional Networks of Public Health Laboratories Project Activity Contact Information: John RIdderhof / jcr0@cdc.gov Approximate Amount of Supplemental Funding Available: $270,000 Project Description: DLS-guided regional network activities and consultations have influenced 14 states to form 2 new consortia and two CDC programs to adopt a regional approach to supporting testing services. Further steps are required to: 1) expand and align state-directed and CDC-program supported regional network structure to further address consistent access to PHL services; and 2) work with public health law institutes to research and establish a scalable multi-state MOU that addresses legal concerns surrounding state-directed test sharing, CDC-directed interstate test referral, and development of multistate PHL COOP plans. A small proportion of funds may also be used to incentivize—largely through travel support—the creation of additional state-directed consortia so that the US moves toward a more comprehensive model of regional networks.

· The need for multistate MOUs to facilitate test service sharing has been identified in multiple forums. Additionally the PHEP coag requires PHLs to have formal or informal agreements with other agencies to maintain services as part of COOP. However, past assessments (Policy Guide for PHL test service sharing, 2014, APHL/CDC) and ongoing network deliberations note that there are almost no existing MOUs that specifically enable service sharing as preparedness for any event. The Institutes for Public Health Law indicated interest and ability but required a funding agreement to pursue legal research and implementation of a model multistate MOU with state’s general counsels. $120,000

· APHL, with CDC support, has published two reports outlining the benefits and many activities supported by existing state directed regional networks. To date, key findings include the value of regional networks in COOP and preparedness since they involve close relationships, communication and sharing of information on specific testing services that might be shared in an emergency or other situation. All networks also involve workforce with extensive sharing of training and workshops in addition to one conducting a regional emerging leader program to develop staff. Last is the benefit of improving state to state and state to clinical electronic test orders and results reporting (ETOR) for quality, speed and interoperability. Further evaluation is needed to assist with further evidence about the benefits for states participating in networks in addition to identifying best practices. $50,000

· APHL has an important role to provide in supporting travel, meeting costs, sharepoint, information and facilitation as a key partner participating and supporting regional networks externally with processes that are difficult for individual states to conduct. $100,000 Mid-Term Outcomes Promotes competent, collaborative, and practice-ready PHL workforce Improves laboratory methods, systems, and informatics capacity Increases laboratory effectiveness in response to public health needs, including emergencies

Long-Term Outcomes Protects the public from public health threats Creates sustainable and resilient PHLs that effectively and efficiently adapt to evolving public health needs

Project Name: National Coordination of Next Generation Sequencing (NGS) Quality Efforts to Improve Implementation of NGS in Public Health Laboratories Project Activity Contact Information: Collette Fitzgerald Leaumont / chf3@cdc.gov Approximate Amount of Supplemental Funding Available: $1,575,000 (one-time funding) Project Description: Currently Next Generation Sequencing (NGS) is being broadly implemented across both CDC programs and state and local public health laboratories. There are many challenges associated with implementing a transformative technology, such as NGS, and there is no comprehensive plan to develop and implement an NGS Quality Management System to ensure reliable and high quality data for incorporation into nationwide disease surveillance systems and other public health functions to improve population health outcomes. In May 2016, APHL convened three focus groups to discuss challenges and potential solutions surrounding the implementation and use of NGS technologies. These solutions, in combination with and expanding upon the quality efforts of the CDC NGS Quality Workgroup and Review Board and intersecting with the Tri-agency (FDA, CMS, CDC) endeavors to identify NGS quality and regulatory challenges, CDC proposes to develop and implement a quality management system framework for NGS using the 12 Quality System essentials (QSE’s) within CLSI’s established Quality Framework.

More than just building the foundation of the QMS system, we will develop a comprehensive roadmap on practical implementation of NGS QMS intended for CDC and state public health laboratory partners. Specifically, we will develop a quality approach to NGS by:

· Establishing Quality Management System requirements based in part using the 12 QSE framework and cross-walking of available professional organizations’ NGS guidelines

· Developing a CLIA validation guide for laboratories to implement an NGS-based test

· Developing an externally facing communication platform, to share and disseminate QMS development efforts and documents, and host subject-specific workgroups across laboratory groups both inside and outside CDC

· Developing competency-based training curriculum for NGS quality requirements for CDC and state public health laboratory partners

· Building and disseminating tools to standardize implementation of NGS QMS across laboratories. Providing centralized technical assistance for NGS QMS to ensure comprehensive implementation and alignment between CDC programs.

· Facilitating shared NGS quality best practices intersecting across NGS laboratory users, bio-informaticians, quality mangers, and epidemiologists.

Evaluation efforts will consist of, at a minimum, evaluating successes and challenges in developing requirements and a roadmap for implementing NGS QMS, and competencies required and achieved, assessing needs across all stakeholders to ascertain iterative needs, lessons learned, and best practices in supporting nation-wide disease surveillance needs and other public health applications.

Mid-Term Outcomes Improves laboratory methods, systems, and informatics capacity Increases laboratory effectiveness in response to public health needs, including emergencies Improves public health laboratory detection and response programs Assures CLIA standards and good laboratory practices are followed by PHLs and are promoted to clinical laboratories performing tests of public health importance

Long-Term Outcomes Reduces incidence and prevalence of preventable diseases and public health threats Creates sustainable and resilient PHLs that effectively and efficiently adapt to evolving public health needs Revises standards for the PHL system resulting in a more efficient, higher quality, and safe PHL system

Appendix E. Workforce Development Project Name: NLTN Sentinel Laboratory Training Project Activity Contact Information: Rick Parry / rtp0@cdc.gov Approximate Amount of Supplemental Funding Available: $120,000 Project Description: The National Laboratory Training Network (NLTN) in support of APHL Cooperative Agreement activities will engage in several projects to update, improve and enhance the skills of laboratorians performing testing that addresses BT, CT and all hazard threat events. Critical biosafety and biosecurity requirements continue to evolve, especially post the recent Ebola and Zika events. It will be urgently important for public health laboratories to maintain highly skilled and training workforce ready to respond to all threats. Working in close collaboration with the CDC health scientist, subject matter experts and the CDC DLS Training Branch, NLTN will provide relevant and timely training on biosafety, biosecurity, ad emergency response laboratory procedures to the public health and clinical laboratory communities. Examples of activities to be addressed through this agreement include Packaging and Shipping of Division 6.2 materials training, online rule-out-or-refer training modules, virtual exercises to assess retention of rule-out-or-refer skills, basic microbiology, and basic molecular biology skills. Training will be offered in a variety of online and classroom formats. All training will be evaluated to determine effectiveness sin achieving learning objectives, impact, and to inform a continual improvement process.

Mid-Term Outcome Increases laboratory effectiveness in response to public health needs, including emergencies

Long-Term Outcome Protects the public from public health threats

Project Name: APHL Laboratory Fellowship Project Activity Contact Information: Kate Glynn / mjg6@cdc.gov Approximate Amount of Supplemental Funding Available: $800,000 Project Description: State and local public health laboratories are a critical component of the national public health laboratory system, but face chronic challenges in attracting and retaining a qualified workforce. Service learning fellowship programs are an effective means to attract qualified individuals into training to advance their skills and serve as an entry point for a career in public health. The proposed project address workforce development challenges in-state and local public health laboratories by supporting workforce capacity building through competency-based, applied learning fellowships. APHL is funded to manage a group of fellowships on multiple disciplinary tracks (e.g., infectious disease, environmental health).

The proposed activity in this supplement is to support bringing on APHL Laboratory fellows under the newly revised infectious diseases fellowship program to be placed in assignments in state or local public health laboratories. Specifically, APHL will recruit, select, and match fellows to state or local public health laboratories for a one-year fellowship (potentially extendable to two years). They will recruit and select laboratories to serve as host sites for fellow assignments. They will onboard fellows and arrange for placement in the assigned laboratories. They will train fellows both in a competency -based curriculum (e.g., that addresses topic areas such as biosafety, informatics, and QMS, including CLIA compliance) and through the structured implementation of a service-learning fellowship, monitoring.

Expected outcomes for the activity include:

· Qualified fellows placed in qualified state or local public health laboratories and complete fellowship

· Training curriculum is competency-based and acquisition of competencies is exhibited by fellows

· Service of fellows contributes to public health mission of agency where assigned

· Graduating fellows take positions in public health laboratories

Project Name: Workforce Development/National Center for Public Health Laboratory Leadership Project Activity Contact Information: Renee Ned-Skyes / rin1@cdc.gov Approximate Amount of Supplemental Funding Available: $220,000 Project Description: The proposed projects will address workforce development challenges in a number of areas, mainly competency implementation and leadership training and development.

A. Competency Adoption and Implementation ($160,000) -- Through the previous APHL cooperative agreement, the organization worked with CDC to develop the first-ever comprehensive set of laboratory competencies. The proposed activities are to further competency adoption and implementation in state/local public health laboratories (PHLs), to include:

· Mini-grants to state/local public health laboratories for the development and implementation of competency-based career ladders and/or paths.

· The provision of technical assistance and the development of guidance to help individual state/local public health laboratories, including regional networks of PHLs, perform competency-based training needs assessments (TNAs). The assessments can be performed at an individual laboratory, state-wide, or regional level, as appropriate. The work should include aiding laboratories in progressing from the identification of broad, competency-based training needs to the development of actionable guidance or strategies to address gaps in specific topic areas. A summary report, guidance document, and/or TNA template should be developed as a national resource. Activity may also include plans to evaluate impact of the competency-based TNAs.

· The development of behavioral statements for competency domains, which will facilitate staff competency assessment and evaluation across the public health laboratory system. The behavioral statements can be incorporated into a competency assessment tool.

B. Leadership ($60,000)

· A formal evaluation of APHL’s Emerging Leader Program to assess strengths and areas for improvement. To include evaluation of the program’s structure, content, and costs/return on investment.

· The National Center for Public Health Laboratory Leadership’s coaching program:

-- The development of training for the coaches to improve coach readiness and performance -- A formal evaluation of the coaching program to inform programmatic improvements Mid-Term Outcomes Promotes competent, collaborative, and practice-ready PHL workforce Improves laboratory methods, systems, and informatics capacity

Long-Term Outcome Creates sustainable and resilient PHLs that effectively and efficiently adapt to evolving public health needs

Appendix F. Laboratory Informatics Capacity

Project Name: Laboratory Informatics Curriculum and Tools to Strengthen Workforce and Capabilities Project Activity Contact Information: Simon Adebola / vmb7@cdc.gov John Ridderhof / jcr0@cdc.gov Approximate Amount of Supplemental Funding Available: $300,000 Project Description: To advance Public Health Laboratory capacity for efficient practice, information sharing, and electronic data exchange, we are proposing a continuation of two key ongoing activities. These activities were introduced in response to needs described by PHL stakeholders, and have both been developed in a collaborative fashion with continual engagement with SMEs from the informatics, institutional research and workforce committees of the APHL. Advancing these activities will increase both the quality and adoption of the two resources by PHLs—resulting in a stronger system.

The laboratory informatics curriculum was developed based on earlier work on the PHL informatics self-assessment, and the Competency Guidelines. Gaps were identified in both informatics capacity, and the availability of training resources and programs to address this need. This informatics curriculum and its component modules will help address these gaps by providing publicly accessible online training targeted at laboratory staff and information technology personnel, with the aim of teaching informatics concepts as practiced within the laboratory setting. The introductory modules focus on basic informatics concepts, and it is intended that these will be followed by additional modules to address capacity needs as identified by PHL informatics SMEs and APHL.

Requested funding will help in developing training resources on topics such as LIMS and other Data Management Systems, Data Quality, Data Standards, Data Systems Integration, Project and Change Management, etc. CDC support to this effort will ensure that there are resources available to grow the workforce and address the turnover in laboratory informatics capacity. ($200,000) The Public Health Laboratory System Database (PHLSD), developed by APHL and DLS, contains a list of laboratory tests and equipment provided as a resource for laboratory information management. PHLs that complete the database will have access to a complete list of tests and equipment about other laboratories, and can use these to support test reporting for surveillance, and service sharing for preparedness and response. PHL stakeholders have requested that this test list be linked to standardized nomenclature for laboratory testing. LOINC and SNOMED are widely-accepted standards for reporting tests and results, and are part of the Meaningful Use regulations on interoperability of healthcare systems. The requested funding will initiate a process for linking the PHLSD test list with look-up tables for corresponding LOINC and SNOMED codes to accelerate and improve consistency of ELR. The PHL would receive an automated report listing the appropriate codes for each clinical test performed. This activity, in addition to providing a publicly-available resource, will also provide a basis for test code harmonization with significant impact on the quality of laboratory test reporting across public health. ($100,000) Mid-Term Outcomes Promotes competent, collaborative, and practice-ready PHL workforce Improves laboratory methods, systems, and informatics capacity

Long-Term Outcome Creates sustainable and resilient PHLs that effectively and efficiently adapt to evolving public health needs

Project Name: Messaging Support for Multiple Surveillance Systems Project Activity Contact Information: Michele Hoover / mhoover@cdc.gov Approximate Amount of Supplemental Funding Available: $1,500,000 Project Description: This project proposes to provide funding that will allow the submission of Nationally Notifiable Disease (NND) data to CDC, jurisdictions often are required to send their data, which are housed in a single system, through a number of separate, often duplicative, data streams. Implementing HL7 messaging for transmitting surveillance data will reduce this burden on state public health departments by eliminating redundant data collection systems, will increase interoperability and standardization of electronic data exchange, and will improve data quality for national disease surveillance. This project will build upon current investments in HL7 data message exchange to serve multiple NND programs across three CDC centers and reduce state burden.

Mid-Term Outcome Improves laboratory methods, systems, and informatics capacity

Long-Term Outcome Reduces incidence and prevalence of preventable diseases and public health threats

Project Name: Electronic Disease Notification Data (EDN) for Vaccinated Refugees Using HL7 Messages Project Activity Contact Information: dlv8@cdc.gov / Yoni Haber Approximate Amount of Supplemental Funding Available: $50,000 (one-time funding only) Project Description: Since inception of this program, more than 100,000 U.S.-bound refugees have been vaccinated, accounting for more than 700,000 documented vaccine doses. These refugees are then settled into different states where the public health agencies need to have access to medical history data, including vaccination history. The goal of the project is to send vaccination information into state immunization registries by using HL7 messages, making refugee vaccination information available to a wider medical community and limiting revaccination.

Mid-Term Outcomes Improves laboratory methods, systems, and informatics

Long-Term Outcomes Reduces incidence and prevalence of preventable diseases and public health threats

Appendix G. Newborn Screening and Genetics Project Name: Newborn Screening and Genetics/Newborn Screening Fellows Project Activity Contact Information: Amy Mowbray / htm3@cdc.gov Approximate Amount of Supplemental Funding Available: $412,000 (one-time funding only) Project Description: Newborn screening laboratories are increasingly using molecular detection technologies to better identify and improve treatment for newborns with heritable diseases. As laboratories adopt next generation sequencing technologies, they produce large amounts of valuable data but currently possess limited bioinformatics capacity to adequately analyze it.

This project proposes to expand the Newborn Screening and Genetics Program’s fellowship activities to place Bioinformatics fellows in at least four newborn screening laboratories. These fellows will help increase bioinformatics Capability in the newborn screening system.

Mid-Term Outcomes Promotes competent, collaborative, and practice-ready PHL workforce Improves laboratory methods, systems, and informatics capacity Increases laboratory effectiveness in response to public health needs, including emergencies Improves public health laboratory detection and response programs

Long-Term Outcomes Reduces incidence and prevalence of preventable diseases and public health threats Creates sustainable and resilient PHLs that effectively and efficiently adapt to evolving public health needs

Appendix H. Food Safety Project Name: Food Safety: WGS or Enteric Pathogen Training/Meeting and InFORM Support Project Activity Contact Information: Racquel Williams / iic3@cdc.gov Approximate Amount of Supplemental Funding Available: $145,000 Project Description: Identify training needs and provide training opportunities for PHL staff and executive leadership.

Support foodborne disease outbreak response training of laboratorians and other local and state officials through the Epi-Ready Team Training Courses and other training courses

Support training of laboratorians in the detection, categorization and identification of foodborne organisms and the diagnosis of foodborne disease

Provide training for laboratorians and other local and state officials on whole genome sequencing (WGS) or detection, categorization and identification of other enteric pathogen. Anticipated Available for this activity: $45,000

Support travel for laboratorians and other local and state officials to trainings/meetings. Anticipated Available Funding for this activity: $100,000

Mid-Term Outcomes Promotes competent, collaborative, and practice-ready PHL workforce Improves laboratory methods, systems, and informatics capacity Increases laboratory effectiveness in response to public health needs, including emergencies Improves public health laboratory detection and response programs

Long-Term Outcome Creates sustainable and resilient PHLs that effectively and efficiently adapt to evolving public health needs

Appendix I. Infectious Diseases

Project Name: Influenza Laboratory Strengthening Pandemic Preparedness H7N9 identification and Characterization Project Activity Contact Information: Chris Duggar & Dr. Dan Jernigan / cnd8@cdc.gov Approximate Amount of Supplemental Funding Available: $2,500,000

Project Description: Influenza Pandemic Preparedness and Laboratory Capacity Strengthening:

Human infections with avian influenza A (H7N9) virus were first reported in China in March 2013. Epidemics of human infections with H7N9 viruses in China have occurred each winter since 2013. The current annual epidemic – the fifth – is different from previous because of the unusually high number of human infections and the identification of some strains of the virus with mutations that make them highly pathogenic to poultry. In collaboration with HHS staff in China and counterparts in the Chinese National Health and Family Planning Commission, HHS is actively monitoring the situation and increasing our domestic and global preparedness planning in the event the virus spreads further.

· U.S. CDC Influenza Division, CDC Atlanta, are working closely with the APHL and Member States to monitor the occurrence of human infections of Influenza in and around Agricultural settings A(H7N9), A(H5Nx), etc.

· Above and beyond the current Sequencing, AMD, and Cloud activities we aim to increase the number of viruses characterized and reported through MGS labs and Reference labs.

Mid-Term Outcomes

· Improves laboratory methods, systems, and informatics capacity

· Increases laboratory effectiveness in response to public health needs, including emergencies

· Improves public health laboratory detection and response programs

Long-Term Outcomes

· Reduces incidence and prevalence of preventable diseases and public health threats

· Reduces morbidity and mortality equitably delivered throughout the United States and the world

· Protects the public from public health threats

Project Name: AMD – URDO: MA DPH Project Activity Contact Information: Jonas Winchell / zdx2@cdc gov Beth Laney / dyb6@cdc.gov Approximate Amount of Supplemental Funding Available: $270,000 Project Description: Implementation of comprehensive multipathogen detection strategies during respiratory disease outbreaks is critical as many viral and bacterial respiratory infections initially manifest with similar clinical features yet may require pathogen-specific interventions, including vaccination, prophylaxis, or other infection control practices, to halt the spread of disease. Rapid and accurate determination of etiology is also important for guiding appropriate and responsible use of antivirals and antibiotics and mitigating the impact of newly emerging and potentially unanticipated respiratory threats.

Patient specimens collected during outbreak responses will be evaluated using a targeted resequencing approach that will provide more comprehensive detection and characterization of respiratory agents during outbreak investigations. This approach uses the SmartChip NGS Target Enrichment system (Wafergen Biosystems) to generate a ligation-free, Seq-ReadyTM amplicon library from clinical specimens that can be sequenced on the Illumina MiSeq to obtain targeted amplicon reads. This will allow for broader pathogen detection, including novel or emerging pathogens, as well as characterization of relevant features that may be actionable for halting outbreak progression.

Goals (CDC and PHL partners)

· Validated state partner health labs by creating a common PT panel to run at the two state sites and CDC. Results obtained at all three sites were comparable.

· Transferred the assay development SOP to the state partner labs and assisted them on assay design and development.

· Validated Wafergen technology by sending PT samples for amplification on the SmartChip system and sequencing at both Wafergen and CDC.

· Implementation of bioinformatics workflows on SciComp high-performance computing environment to recover pathogen-specific characterization assays with next generation sequencing data.

· Developed a web based visual analytic prototype tool to assist with data analysis of next generation sequencing data for pathogen-specific detection assays.

· Develop CLC Genomics workflow to analysis pathogen-specific detection assay next generation sequencing data for state PHL.

· Purchase the Wafergen SmartChip machine for CDC and the partnering state public health labs.

· Continue assay development and validation for the remaining targets. Begin in earnest the development of the 16S and viral family markers, engaging various CDC and partner SMEs on feasible approaches and interpretation algorithms.

· Implement CLC Genomics workflow for state PHL to analyze 16S targets

· Combine pathogen specific detection and characterization bioinformatics workflows into a single standardized bioinformatics process on SciComp computing environment.

· Begin bioinformatics development for both 16S and viral family database queries; Construct a computational activation script that initiates the 16S, pathogen-specific detection, and pathogen-specific characterization bioinformatics analyses workflows

· Develop CLC Genomics workflow to analysis pathogen-specific characterization assay next generation sequencing data for state PHL.

· Work with SciComp and DBD bioinformatics personal to host web based visual analytic prototype tool for internal use for all CDC laboratories working with metagenomics data sets.

· Establish data transfer mechanism using APHL Cloud computing environment for external partners.

· Add additional functionality to visual analytic tool to report pathogen-specific characterization assays Mid-Term Outcomes

· Increases laboratory effectiveness in response to public health needs, including emergencies

· Improves public health laboratory detection and response programs Long-Term Outcomes

· Reduces incidence and prevalence of preventable diseases and public health threats

· Reduces morbidity and mortality equitably delivered throughout the United States and the world

· Protects the public from public health threats

Project Name: AMD URDO: MN DPH Project Activity Contact Information: Jonas Winchell / zdx2@cdc gov Beth Laney / dyb6@cdc.gov Approximate Amount of Supplemental Funding Available: $270,000

Project Description: Implementation of comprehensive multipathogen detection strategies during respiratory disease outbreaks is critical as many viral and bacterial respiratory infections initially manifest with similar clinical features yet may require pathogen-specific interventions, including vaccination, prophylaxis, or other infection control practices, to halt the spread of disease. Rapid and accurate determination of etiology is also important for guiding appropriate and responsible use of antivirals and antibiotics and mitigating the impact of newly emerging and potentially unanticipated respiratory threats.

Patient specimens collected during outbreak responses will be evaluated using a targeted resequencing approach that will provide more comprehensive detection and characterization of respiratory agents during outbreak investigations. This approach uses the SmartChip NGS Target Enrichment system (Wafergen Biosystems) to generate a ligation-free, Seq-ReadyTM amplicon library from clinical specimens that can be sequenced on the Illumina MiSeq to obtain targeted amplicon reads. This will allow for broader pathogen detection, including novel or emerging pathogens, as well as characterization of relevant features that may be actionable for halting outbreak progression.

Key Goals (CDC and PHL partners)

· Validated state partner health labs by creating a common PT panel to run at the two state sites and CDC. Results obtained at all three sites were comparable.

· Transferred the assay development SOP to the state partner labs and assisted them on assay design and development.

· Validated Wafergen technology by sending PT samples for amplification on the SmartChip system and sequencing at both Wafergen and CDC.

· Implementation of bioinformatics workflows on SciComp high-performance computing environment to recover pathogen-specific characterization assays with next generation sequencing data.

· Developed a web based visual analytic prototype tool to assist with data analysis of next generation sequencing data for pathogen-specific detection assays.

· Develop CLC Genomics workflow to analysis pathogen-specific detection assay next generation sequencing data for state PHL.

· Purchase the Wafergen SmartChip machine for CDC and the partnering state public health labs.

· Continue assay development and validation for the remaining targets. Begin in earnest the development of the 16S and viral family markers, engaging various CDC and partner SMEs on feasible approaches and interpretation algorithms.

· Implement CLC Genomics workflow for state PHL to analyze 16S targets

· Combine pathogen specific detection and characterization bioinformatics workflows into a single standardized bioinformatics process on SciComp computing environment.

· Begin bioinformatics development for both 16S and viral family database queries; Construct a computational activation script that initiates the 16S, pathogen-specific detection, and pathogen-specific characterization bioinformatics analyses workflows

· Develop CLC Genomics workflow to analysis pathogen-specific characterization assay next generation sequencing data for state PHL.

· Work with SciComp and DBD bioinformatics personal to host web based visual analytic prototype tool for internal use for all CDC laboratories working with metagenomics data sets.

· Establish data transfer mechanism using APHL Cloud computing environment for external partners.

· Add additional functionality to visual analytic tool to report pathogen-specific characterization assays Mid-Term Outcomes

· Improves laboratory methods, systems, and informatics capacity

· Increases laboratory effectiveness in response to public health needs, including emergencies

· Improves public health laboratory detection and response programs

Long-Term Outcomes

• Reduces incidence and prevalence of preventable diseases and public health threats • Protects the public from public health threats

Project Name: AMD – Legionella: MA DPH Project Activity Contact Information: Jonas Winchell / zdx2@cdc gov Beth Laney / dyb6@cdc.gov Approximate Amount of Supplemental Funding Available: $75,000 Project Description: Legionnaires ’ Disease (LD) is a severe and potentially fatal form of pneumonia that can occur in susceptible individuals exposed to contaminated man-made water sources. During outbreaks of LD, it is crucial to identify and mitigate the environmental source of infection. High quality, reproducible, and rapid molecular methods such as genome sequencing can be used to match clinical and environmental isolates of Legionella and help stop an outbreak, limiting the potential for new infections. The purpose of this project is to develop and deploy the analysis tools needed to perform this testing using a standardized approach across laboratories.

CDC, with PHL partners, will fully support wgMLST for typing Legionella pneumophila (Lp) by providing external access to computational resources required to detect alleles. Currently the Lp wgMLST database contains 4,472 alleles and an expanded allele database is being designed based on complete Lp genome sequences (generated using the PacBio instrument) of a diverse panel of strains representing multiple serogroups and a subset of different STs. Pilot testing of the wgMLST approach will be expanded outside of 2 external partner labs currently collaborating to assist in the develop of this system (New York State Department of Health, Massachusetts Department of Public Health.)

Key Goals: (CDC and PHLs)

· Pilot test wgMLST analysis using 50 Lp isolates sequenced at 2 external labs (New York State and Massachusetts) and CDC to evaluate reproducibility of allele calling and clustering analysis.

· Generate expanded wgMLST allele database using a diverse panel of high quality reference sequences.

· Evaluate methods for extraction of SBT alleles from genome sequences to allow backward compatibility with traditional molecular typing.

· Develop an internal reporting tool for communicating AMD results using R Shiny server hosted on Scicomp infrastructure

· Develop bioinformatic tools to extract serotype (ex. Lp1-Lp17) information from genome sequences

· Expand pilot testing to approximately 5 or more state and local public health laboratories using an expanded wgMLST database and permitting external access to CDC computational resources for wgMLST allele calling

· Perform wgMLST proficiency testing with external partner laboratories using a set of blinded Lp isolates.

· Conduct genome sequencing on LD outbreak isolates collected during current Epi-Aids

Mid-Term Outcomes Improves laboratory methods, systems, and informatics capacity Increases laboratory effectiveness in response to public health needs, including emergencies Improves public health laboratory detection and response programs

Long-Term Outcomes Reduces incidence and prevalence of preventable diseases and public health threats Protects the public from public health threats Project Name: AMD – Legionella: NY DPH Project Activity Contact Information: Jonas Winchell / zdx2@cdc gov Beth Laney / dyb6@cdc.gov Approximate Amount of Supplemental Funding Available: $75,000 Project Description: Legionnaires’ Disease (LD) is a severe and potentially fatal form of pneumonia that can occur in susceptible individuals exposed to contaminated man-made water sources. During outbreaks of LD, it is crucial to identify and mitigate the environmental source of infection. High quality, reproducible, and rapid molecular methods such as genome sequencing can be used to match clinical and environmental isolates of Legionella and help stop an outbreak, limiting the potential for new infections. The purpose of this project is to develop and deploy the analysis tools needed to perform this testing using a standardized approach across laboratories.

CDC, with PHL partners, will fully support wgMLST for typing Legionella pneumophila (Lp) by providing external access to computational resources required to detect alleles. Currently the Lp wgMLST database contains 4,472 alleles and an expanded allele database is being designed based on complete Lp genome sequences (generated using the PacBio instrument) of a diverse panel of strains representing multiple serogroups and a subset of different STs. Pilot testing of the wgMLST approach will be expanded outside of 2 external partner labs currently collaborating to assist in the develop of this system (New York State Department of Health, Massachusetts Department of Public Health.)

Key Goals: (CDC and PHLs)

· Pilot test wgMLST analysis using 50 Lp isolates sequenced at 2 external labs (New York State and Massachusetts) and CDC to evaluate reproducibility of allele calling and clustering analysis.

· Generate expanded wgMLST allele database using a diverse panel of high quality reference sequences.

· Evaluate methods for extraction of SBT alleles from genome sequences to allow backward compatibility with traditional molecular typing.

· Develop an internal reporting tool for communicating AMD results using R Shiny server hosted on Scicomp infrastructure

· Develop bioinformatic tools to extract serotype (ex. Lp1-Lp17) information from genome sequences

· Expand pilot testing to approximately 5 or more state and local public health laboratories using an expanded wgMLST database and permitting external access to CDC computational resources for wgMLST allele calling

· Perform wgMLST proficiency testing with external partner laboratories using a set of blinded Lp isolates.

· Conduct genome sequencing on LD outbreak isolates collected during current Epi-Aids Mid-Term Outcomes Improves laboratory methods, systems, and informatics capacity Increases laboratory effectiveness in response to public health needs, including emergencies Improves public health laboratory detection and response programs

Long-Term Outcomes Reduces incidence and prevalence of preventable diseases and public health threats Protects the public from public health threats

Project Name: ID: BioInformatics Fellow Project Activity Contact Information: Melissa Olsen-Rasmussen / mxr2@cdc.gov Approximate Amount of Supplemental Funding Available: $121,738

Project Description: APHL will continue to support, coordinate and maintain two (2) post-masters fellows from the 2016 cohort of the CDC/APHL Bioinformatics in Public Health Fellowship Program. This support will include one (1) postmasters fellow in the Pertussis and Diphtheria Laboratory (NCIRD/DBD) and one (1) post-masters fellow in the Enteric Diseases Laboratory Branch (NCEZID/DFWED). In this capacity, APHL will facilitate the payment of stipends, ensure the ongoing maintenance of their health insurance coverage and other benefits, provide ongoing professional development opportunities for these fellows and continue to monitor fellowship deliverables from the 2016 cohort.

This requirement specifically addresses the maintenance of these two post-masters fellows from the 2016 BPHFP cohort. Post-doctoral and post-masters fellows admitted into the 2017 cohort are addressed elsewhere.

Mid-Term Outcomes Promotes competent, collaborative, and practice-ready PHL workforce Improves laboratory methods, systems, and informatics capacity

Long-Term Outcomes Creates sustainable and resilient PHLs that effectively and efficiently adapt to evolving public health needs

Project Name: Addressing the Public Health Threat of Culture Independent Diagnostic Tests (CIDT) Project Activity Contact Information: John Besser / jtw8@cdc.gov Approximate Amount of Supplemental Funding Available: $100,000 Project Description: The project involves the organization of up to four meetings addressing the public health threat of CIDT. The two first meetings will be organized in Atlanta before 6/30/2017. Possibly two follow-up meeting will be organized the following year.

The laboratory surveillance depends on the availability of cultures. An increasing number of molecular panels that do not yield at culture have been FDA approved in recent year and are increasingly replacing culture for foodborne pathogens in the clinical laboratories. The meeting are follow-up on ongoing activities by APHL: 1. In 2013, CDC with public health partners initiated a project to identify optimal methods to recover Salmonella and Shiga toxin-producing E. coli from CIDT positive specimens; these standards methods have been identified and validated but not published, yet; a meeting with public health partners will be organized with the goal of agreeing on how to implement the methods in public health laboratories and discuss the need to develop standard methods for culturing other pathogens from CIDT positive specimens, and 2. A follow-up to a successful meeting organized in 2012 to raise awareness and develop solutions to the challenges that adoption of CIDTs by clinical laboratories presents for CDC surveillance programs. The conference increased awareness of the issues throughout CDC and other government agencies, engaged partners, spawned programs at CDC (EDLB, OAR, EIP, etc.), and informed a number of publications about CIDT issues; the current project involves the organization of a smaller follow-up conference to assess progress and direction, to generate new ideas; the outcomes of this meeting will be two-fold: a) to identify gaps in current planning efforts in an discussion between key collaborators at FDA (device licensure), CLIA, private health insurers, Kit manufacturers, CDC and APHL legal advisors, APHL, CSTE, and state health representatives, and b) to inform EDLB scientists of new developments and strategies to aid in their research. Additionally, other programs at CDC struggling with the same problem will benefit from the discussion and cross-fertilization.

If funds are available targeted follow-up meetings will be organized the following year.

Mid-Term Outcomes Promotes competent, collaborative, and practice-ready PHL workforce Improves laboratory methods, systems, and informatics capacity Increases laboratory effectiveness in response to public health needs, including emergencies Improves public health laboratory detection and response programs Long-Term Outcomes Protects the public from public health threats Creates sustainable and resilient PHLs that effectively and efficiently adapt to evolving public health needs

Project Name: Strengthening Lab Capacity to Detect STDs That Contribute to Infertility Project Activity Contact Information: Tranita Anderson / tkg1@cdc.gov Approximate Amount of Supplemental Funding Available: $75,000 Project Description: Due to limited program and laboratory capacity on many of the islands, the true burden of asymptomatic HIV and other sexually transmitted infections (STDs) − including viral hepatitis − is not fully understood. However, from 2009 through 2012, a burden of STD assessment was conducted using CDC PCR testing of population-based samples of largely asymptomatic persons in Guam, Palau and Yap (FSM). The evaluation found very high prevalence of chlamydia (> 25%) and moderate prevalence of gonorrhea (3-5%) among men and women 15 to 35 years of age. These data suggest that all six island states, which currently rely on syndromic STD management, likely have high prevalence of chlamydia and at least moderate prevalence of gonorrhea. Additionally, based largely upon prenatal screening, most jurisdictions have high case rates of syphilis, including congenital syphilis, compared with the U.S.

mainland. Although HIV rates appear to be low in the USAPI jurisdictions, high STD prevalence is a concern because of the association of various infections with adverse reproductive health outcomes, perinatal morbidity and mortality, anogenital and liver cancers and potential increased risk for acquisition and transmission of HIV. Additionally, the Pacific states are at risk for importation of highly resistant strains of gonorrhea, as gonococcal resistance to available antibiotics tends to emerge out of East and Southeast Asian nations, the home of origin of a large proportion of workers and tourists to these six Pacific Island states.

Laboratory testing capacity is limited as USAPI grantees face high shipping cost, and delayed procurement processes leading to stock-out and service gaps.