Genny Barkocy-Gallagher, Ph.D.CDC Infectious Diseases LIMS Coordinator

APHL Annual MeetingJune 6, 2010

CDC and PHLIP

CDC Infect ious Diseases and PHLIP

Infect ious Diseases laboratories at CDC Organization Activities

LIMS Current state Governance

Interoperability Organization Proposed architecture Challenges Next Steps

Proposed Organizat ional Structure-Infect ious Disease Laboratories

Office of Infect ious 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 laboratories

Laboratories implementing common LIMS 15 Divisions, 28 branches (proposed) 90+ laboratories

CDC Infect ious Disease Laboratories

Most are divided as pathogen-specific and/or laboratory-specific Examples

• Salmonella, Streptococcus, antimicrobial susceptibility, serology

Usually a broad range of overlapping act ivit ies 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

LIMS Implementat ion- Customizat ion

Extensive development Project started before SUNRISE version of STARLIMS was available Over 800 changes developed to date

• Exampleso Batch operationso Results entry by multi-testo Collection of all types of sample/specimen information

• e.g., for ecto-parasites: host animal, owner, GIS coordinates, link to patient, etc.

o 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

State of CDC Infect ious Diseases STARLIMS(Feb., 2010)

37 ‘live’ labs

364 act ive users

~3K defined tests

~200K specimen records

~500K aliquot records

~1.2M result records

~80K specimen attachments

Governance- LIMS and PHLIP(Infect ious Diseases)

Work Group Laboratory Division representatives Provides unified laboratory input

Steering Committee Center Associate Directors for Laboratory Science

• NCHHSTP, NCIRD, NCEZID (proposed), CGH Office of Infectious Diseases Senior Advisor for Laboratory Science

and for Informatics Work Group chair Program manager and program coordinator Provides high-level guidance

Data Sharing within CDC-Beyond Infect ious Diseases LIMS

Specimen storage system

Unknowns or other specimens potent ially shared with

Nat ional Center for Environmental Health (NCEH)

Shipping system

Epidemiology/surveillance programs

Emergency Operat ions Center (EOC), response teams

Interoperability-CDC External Electronic Data Sharing

Internat ional (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

Collaborat ive surveillance data generat ion (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)

Laboratory Response Network (LRN) Tightly defined scope Currently uses Results Messenger to exchange data and report To use the same internal CDC architecture as PHLIP

Interoperability-CDC and External Data Sharing via PHLIP

Diagnost ic/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 report ing (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

The CDC Electronic Connect ion-Office of Surveillance, Epidemiology, and

Laboratory Services (proposed)

Includes (among others) (proposed) Laboratory 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.

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

U.S. Public Health Interoperability

StatePublic HealthDepartment

CDCSurveillance/ResponsePrograms

CDCLaboratory(s)

State Public HealthLaboratory

ClinicalLaboratory

Laboratory reporting

Test order & results exchange

Surveillance & case reportingdata exchange

Supported InternationalLaboratories

State Public HealthLaboratory

EHR

CollaboratingSurveillanceLaboratories

InternationalLaboratories &Programs

PHLIP Challenges within CDC

NotE. coli

Salmonellapositive

E. coliReference Lab

Campylobacter/HelicobacterReference Lab

SalmonellaReference Lab

AntimicrobialSusceptibilityLab

Salmonellasp.

Signed:Dir, SRL

MIC resultsSigned:Dir, ASL

Salmonellasp. &MIC

ResultsSigned:

Dir, SRL & Dir, ASL

Test order:E. coli

Central ReceivingLab

Test Order: Unknown Respiratory Agent

Anthrax Serology

RespiratoryVirology

Influenza Serology Influenza

Virology

PathologyLaboratoryChlamydia/

LegionellaReferenceLaboratory

StreptococcusReferenceLaboratory

HemophilusInfluenzaReference Laboratory

BordetellaReferenceLaboratory

Anthrax ReferenceLaboratory

BioterrorismRapid ResponseAnd AdvancedTechnologyLaboratory(BRRAT)

ChemicalAgent Testing?(NCEH)

Report

AntimicrobialSusceptibilityReferenceLaboratory

Test order:Unknown

Respiratory agent

CentralReceivingLaboratory

CDC’s Next Steps for PHLIP (p.1)

Infect ious 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 labo Patient: submitter, state, surveillance

Define test orders and corresponding results Interface with PHITPO Interoperability Architecture Continue to provide SMEs- vocabulary, laboratory

CDC’s Next Steps 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

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: www.atsdr.cdc.gov

Acknowledgements

James Tolson, Infect ious Diseases LIMS Program Manager and PHLIP Project Manager

Jennifer McGehee & Emory Meeks, PHITPO Laboratory Services Team Infect ious Diseases PHLIP Team Infect ious Diseases STARLIMS Team Infect ious Diseases and PHITPO Leadership

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