CDC and PHLIP. Genny Barkocy-Gallagher, Ph.D. CDC Infectious Diseases LIMS Coordinator. APHL Annual Meeting June 6, 2010

Transcription

1 CDC and PHLIP Genny Barkocy-Gallagher, Ph.D. CDC Infectious Diseases LIMS Coordinator APHL Annual Meeting June 6, 2010

2 CDC Infectious Diseases and PHLIP Infectious Diseases laboratories at CDC Organization Activities LIMS Current state Governance Interoperability Organization Proposed architecture Challenges Next Steps

3 Proposed Organizational Structure- Infectious Disease Laboratories Office of Infectious Diseases Deputy Director for Infectious Diseases, Rima Khabbaz, M.D. Provides strategic leadership to CDC s infectious disease National Centers National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (NCHHSTP) National Center for Immunization and Respiratory Diseases (NCIRD) National Center for Emerging and Zoonotic Infectious Diseases (NCEZID) (proposed) Center for Global Health Includes parasitic diseases and global (non-u.s.) AIDS laborat ories Laboratories implementing common LIMS 15 Divisions, 28 branches (proposed) 90+ laboratories

4 CDC Infectious Disease Laboratories Most are divided as pathogen-specific and/or laboratory-specific Examples Salmonella, Streptococcus, antimicrobial susceptibility, serology Usually a broad range of overlapping activities within a laboratory Diagnostic/Reference, Surveillance, Public Health Research, R&D, Production/Manufacturing, etc. Overlapping specimens, personnel, workflows, etc. Diverse operational needs Varying size 3 to >20 lab members One to multiple teams Widely different data management needs

5 LIMS Implementation- Customization Extensive development Project started before SUNRISE version of STARLIMS was available Over 800 changes developed to date Examples o o o o Batch operations Results entry by multi-test Collection of all types of sample/specimen information e.g., for ecto-parasites: host animal, owner, GIS coordinates, link to patient, etc. Patient-level approval and specimen-level approval Change management Global vs. lab-specific functionality Studies and outbreaks module Sharing of specified data across laboratories- limited

6 State of CDC Infectious Diseases STARLIMS (Feb., 2010) 37 live labs 364 active users ~3K defined tests ~200K specimen records ~500K aliquot records ~1.2M result records ~80K specimen attachments

7 Governance- LIMS and PHLIP (Infectious Diseases) Work Group Division representatives Provides unified laboratory input Steering Committee Center Associate Directors for Science NCHHSTP, NCIRD, NCEZID (proposed), CGH Office of Infectious Diseases Senior Advisor for Science and for Informatics Work Group chair Program manager and program coordinator Provides high-level guidance

8 Data Sharing within CDC- Beyond Infectious Diseases LIMS Specimen storage system Unknowns or other specimens potentially shared with National Center for Environmental Health (NCEH) Shipping system Epidemiology/surveillance programs Emergency Operations Center (EOC), response teams

9 Interoperabilit y- CDC External Electronic Data Sharing International (proposed) CDC labs administer proficiency tests to supported labs CDC participates in international surveillance and case reporting (WHO Collaborating Center for several diseases) System(s) to be determined Collaborative surveillance data generation (proposed) Share capacity between CDC and collaborating or contract laboratories for large projects Sometimes ends up in patient chart/ehr Potentially using PHLIP system in the future (TBD) Response Network (LRN) Tightly defined scope Currently uses Results Messenger to exchange data and report To use the same internal CDC architecture as PHLIP

10 Interoperabilit y- CDC and External Data Sharing via PHLIP Diagnostic/reference test order and results exchange (ETOR) Share CDC laboratory expertise and surge capacity Currently paper-based system between submitters (usually state public health laboratories) and CDC Would end up in patient chart/ehr Surveillance and case reporting (ELSM) Nationally Notifiable Diseases that are reported directly to CDC from state public health laboratories Also supports outbreak/event response by CDC Can overlap with international surveillance and case reporting Can link with ETOR-- laboratory results may have been obtained at CDC via reference testing Likely to be reflected in patient chart/ehr

11 The CDC Electronic Connection- Office of Surveillance, Epidemiology, and Services (proposed) Includes (among others) (proposed) Science Policy and Practice Program Office (LSPPPO) Proposed to be the programmatic home for PHLIP. Public Health Informatics and Technology Program Office (PHITPO) Proposed to provide the architecture for data sharing between systems internally and interoperability with external partners. Internal systems, such as Infectious Diseases LIMS, must also work to interface with this architecture. Primary mission (proposed) To provide scientific service, expertise, skills, and tools in support of CDC s national efforts to promote health; prevent disease, injury, and disability; and prepare for emerging health threats.

12 Proposed CDC Interoperability Architecture (courtesy of Jennifer McGehee, CDC/ OSELS/ PHITPO)

13 U.S. Public Health Interoperabilit y Clinical EHR St at e Public Health St at e Public Health St at e Public Health Department reporting Test order & results exchange CDC (s) Supported International Laboratories Collaborating Surveillance Laboratories CDC Surveillance/ Response Programs International Laboratories & Programs Surveillance & case reporting data exchange

14 PHLIP Challenges within CDC Test order: E. coli Cent ral Receiving Lab Salmonella sp. & MIC Result s Signed: Dir, SRL & Dir, ASL E. coli Reference Lab Not E. coli Salmonella sp. Signed: Dir, SRL Salmonella Reference Lab MIC results Signed: Dir, ASL Campylobacter/ Helicobacter Reference Lab Salmonella positive Antimicrobial Susceptibility Lab

15 Chlamydia/ Legionella Reference Hemophilus Influenza Reference Test order: Unknown Respirat ory agent Test Order: Unknown Respiratory Agent Anthrax Serology Pathology Antimicrobial Susceptibility Reference Cent ral Receiving Anthrax Reference Respirat ory Virology Streptococcus Reference Influenza Serology Report Bordetella Reference Bioterrorism Rapid Response And Advanced Technology (BRRAT) Influenza Virology Chemical Agent Testing? (NCEH)

16 CDC s Next Steps for PHLIP (p.1) Infectious Diseases Plan internal specimen/sample flows with data flows for electronic messaging Document business rules Non-human specimen/sample information needs Process issues, e.g., urgent specimen testing may begin before all patient/specimen information is received Error-handling, e.g., broken specimens, etc. Organizing and capturing appropriate identifiers o Specimen: submitter, state, CDC, internal lab o Patient: submitter, state, surveillance Define test orders and corresponding results Interface with PHITPO Interoperability Architecture Continue to provide SMEs- vocabulary, laboratory

17 CDC s Next St eps for PHLIP (p. 2) PHITPO Get buy-in and approval for proposed laboratory interoperability architecture Develop remaining components Interface with Infectious Diseases LIMS Continue to provide SMEs- messaging, vocabulary, interoperability, security LSPPPO Define organizational structure and governance Establish PHLIP program office

18 Acknowledgements James Tolson, Infectious Diseases LIMS Program Manager and PHLIP Project Manager Jennifer McGehee & Emory Meeks, PHITPO Services Team Infectious Diseases PHLIP Team Infectious Diseases STARLIMS Team Infectious Diseases and PHITPO Leadership For more information please contact Centers for Disease Control and Prevention 1600 Clifton Road NE, Atlanta, GA Telephone, CDC-INFO ( )/TTY: Web: The findings and conclusions in this presentation are those of the author and do not necessarily represent the views of the Centers for Disease Control and Prevention