Office of Advanced Molecular Detection

National Center for Emerging and Zoonotic Infectious Diseases

Nathelia Barnes, DHSc, MScOffice of Advanced Molecular Detection

ELC- AMD Overview: APHL Seminar

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Agenda

• AMD Program

• ELC-AMD Components

– AMD Capacity

– Workforce Development

– Bioinformatics Resource Support

• 2018-2019 Priorities

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AMD Program

• Advancing molecular technologies in Public Health

– Next Generation Sequencing (NGS)

– Whole Genome Sequencing (WGS)

– Bioinformatics

• Modernizing infectious disease laboratories through AMD capacity building

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AMD Program

• Funding national, state, and local public health programs

– To support capacity and training in microbial genomics and bioinformatics

– Examples: PulseNet, TB, Influenza, Legionella

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AMD Overarching Goals• Improve pathogen identification and detection• Develop new diagnostics to meet evolving public

health needs• Support states to coordinate current and future testing

needs• Implement enhanced, sustainable, integrated

laboratory information systems• Develop tools for the prediction, modeling and early

recognition of emerging infectious diseases

* http://www.cdc.gov/fmo/topic/Budget%20Information/FY-2015-Fact-Sheets/Advanced-Molecular-Detection-Infectious-Disease-Outbreaks.pdf

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AMD in State Public Health Labs• AMD began funding state PHLs in 2014

− Epidemiology and Laboratory Capacity (ELC) cooperative agreement, Attachment D

• State PHLs funded via ELC-AMDYear (ELC FY) Number of Jurisdictions Funded

2014 6

2015 25

2016 46

2017 47

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ELC-AMD: AMD Capacity in States• AMD Capacity component

– Introduce and expand AMD capacity within state and local public health laboratories

• Sequencing equipment

• Sequencing laboratory supplies

• Cloud computing services*

• AMD activities not funded through other programs

*OAMD will consider one-time or short-term expenditures related to transitioning to cloud based services

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ELC-AMD: AMD Capacity in States• Not covered in ELC-AMD Section

– Service contracts

– Routine office costs

– Ongoing infrastructure costs

– Software licenses

– Ongoing cloud based services*

*OAMD will consider one-time or short-term expenditures related to transitioning to cloud based services

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ELC-AMD: AMD Workforce Development

• Established regional training networks

− Develop and implement AMD training to accomplish public health goals

− Basic bioinformatics and wet-lab training

• Collaboration with academic partners

• AMD Capacity building through training

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ELC-AMD: AMD Workforce Development

Objectives

• Develop training to address current workforce needs

• Improve NGS and bioinformatics knowledge and skills

• Increase bioinformatics analytic capacity

• Increase access to bioinformatics training

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Identifying the WorkforceMicrobiologists

• Hands-on wet lab & bioinformatics training including commercial software

• Basic, intermediate, and advanced NGS & bioinformatics training

Epidemiologists

• Applied and practical approaches for AMD data analysis and understanding genomic data

• Basic NGS & bioinformatics background and training

Bioinformaticians

• Basic, intermediate, and advanced bioinformatics training

• Knowledge of IT infrastructure including existing challenges and solutions

Lab Directors

• Basic NGS & bioinformatics training

• Applied and practical approaches for AMD data analysis

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Workforce Development Challenges

• Identifying Challenges

– Knowledge gaps and demands with the current workforce

– Limited expertise within public health workforce

– Identifying resources for training

– Identifying post-training support resources

– Existing IT infrastructure and policies

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Workforce Development: Overcoming Challenges

• Regional AMD training & bioinformatics support networks – Training lead laboratories– Participant training laboratories– Strengthen regional training networks– Collaborate with universities for training– Establish partnerships with genomic centers

• Develop training curriculums based on needs assessments within regional networks

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Workforce Development: Overcoming Challenges

• Standardize Regional Training and Support Network – Training regions consistent with PulseNet regions

• Training lead may be the same or different from the PulseNetArea Lab

– Establish Training Leads for each region to address training resources

– Establish Bioinformatics Resource Leads• Training Lead and Bioinformatic Resrouce Lead may be the

same or different State PHLs within the region

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Practical Approach to AMD Training

AMD Training Approach includes 4 categories

• Manufacturer Training

• Pathogen Specific Training

• General NGS and Bioinformatics Training

• Supplemental Training

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Man

ufa

ctu

rer

Trai

nin

g •Basic

•Hands on

•Wet lab

•Includes basic introduction to bioinformatics tools

•Offered in lab

Path

oge

n S

pe

cifi

c Tr

ain

ing •Hands-on & wet-lab

•Offered by CDC groups

•Examples include PulseNet, GHOST, FSCoE, and others

•May be offered in lab or at CDC

ELC

-AM

D W

ork

forc

e D

evel

op

me

nt •Basic hands-on bioinformatics

•Intremdiate hands-on bioinformatics

•Advanced bioinformatics

•Regional training networks

•Targeted training assessments

•Off-site training

•Interaction with other state PHLs

•Collaboration with academic partners

•Regional Bioinformatics Resource Support Su

pp

lem

enta

l Tra

inin

g •Web-based modules

•Conferences/Workshops

•1-on-1 wet-lab with AMD training leads or CDC groups

•Delivery methods:

•In person: OAMD Bioinformatics Team

•Intra-lab: Train the trainer

•AMD Training leads

•AMD Bioinformatics Resource

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Training lead may be the same or different from the PulseNet Area Lab.Training lead may be the same or different from the Bioinformatics Resource Support.

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ELC-AMD: Bioinformatics Resource Support

• Established regional bioinformatics support networks− Regions consistent with PulseNet regions

− The lab supporting bioinformatics resource may be the same or different from the PulseNet Area Lab within the region

• Build bioinformatics capacity at the state and local level

• Provide training assistance through partnership with Regional Training Lead

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AMD Bioinformatics Resource Support

• Provide technical support and consultation

– Develop a resource to assist states and large localities with bioinformatics analysis

– Develop and implement web-based training based on laboratory needs

– Assist labs with finding solutions to AMD-related informatics issues

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ELC-AMD: Bioinformatics Resource Support

• FY 2017: Pilot program for bioinformatics Resources– Three State PHLs selected

• Colorado, Massachusetts, and Minnesota

• FY 2018– Anticipate funding seven Regional Bioinformatics

Resource Leads

– One Full-time staff per region

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ELC-AMD Summary• AMD Capacity

– Support for purchasing equipment, supplies, and other AMD activities

• AMD Workforce Development– Training Lead

• One training lead per region

• May be the same or different than Bioinformatics Resource Lead

– Training Participants

– Region mirrors PulseNet; may be the same or different than PulseNet Area Lab

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ELC-AMD Summary• AMD Bioinformatics Resource Support

– Funding seven regional bioinformatics support leads

• May be the same or different than Training Lead

– One full-time staff per region

– Region mirrors PulseNet; may be the same or different than PulseNet Area Lab

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• State and local workforce development

• Expansion of AMD Capacity

• Innovation

• Data integration

2018-2019 Priorities

Office of Advanced Molecular Detection

National Center for Emerging and Zoonotic Infectious Diseases

Questions?For more information please contact Centers for Disease Control and Prevention

1600 Clifton Road NE, Atlanta, GA 30333Telephone: 1-800-CDC-INFO (232-4636)/TTY: 1-888-232-6348E-mail: cdcinfo@cdc.gov Web: http://www.cdc.gov/amd

The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.