Infectious Diseases Labs and LOINC Coding Stephen Soroka, NCEZID/OD June 25, 2014

1. Infectious Diseases Labs and LOINC CodingStephen Soroka, NCEZID/ODJune 25, 2014 Office of the Director National Center for Emerging and Zoonotic Infectious Diseases

2. Agenda • Background to OID/CGH, a systems perspective • Recent history • ELIMS • Current status • Understanding OID/CGH lab test orders and tests • Gaps and Challenges of LOINC coding in OID/CGH

3. OID/CGH Lab Organization • 4 National Centers • NCEZID, NCIRD, NCHHSTP, CGH • 16 Divisions with Labs • 32 Lab Branches • 90+ Infectious Diseases Laboratories

4. OID/CGH Lab Organization • Every year 50-100,000 specimens received into CDC for testing • 200-500,000 tests performed in Infectious Diseases (ID) laboratories • Numbers vary by year • Not all tests are reported • IT Systems for managing specimens, data, and tests vary widely in ID

5. Recent Lab History (Systems Perspective) • Early 2000s: High profile events demonstrated the need for labs to collectively organize and manage lab data. Few labs utilized anything beyond MS Excel/Access • 2004: A Laboratory Information Management System was selected, STARLIMS v9 (SLv9). A lab-by-lab implementation approach was taken • 2009: 40+ labs were given customized implementations into SLv9, leading to system performance issues, difficulty in data sharing, and long lab implementations • Late 2000s: Other labs have also developed systems. Siloed approaches to specimen and data management

6. Recent Lab History (Systems Perspective) • 2010: A LIMS Blue Ribbon Panel recommended an enterprise approach to implementing LIMS within the ID labs. • 2011: A strategic approach for implementing an enterprise LIMS (ELIMS) was developed. The plan calls for standardization of data management and lab workflows (management of specimen testing). This is in contrast to previous lab-by-lab custom implementations. • 2012: ID selected STARLIMS v10 (SLv10) as the foundation for ELIMS. • 2013: ID ELIMS development initiated.

7. Centralization and Standardization • Implementation of an enterprise Laboratory Information Management System (ELIMS) • To support and centralize lab workflows and data • Culture shift from silo to enterprise • Benefits • Process Automation • Systems Integration ELIMS • Specimen Management • Quality Improvements in data accuracy, security, and access • Establishes a common/core data model across the labs • Improves data sharing with internal/external partners • Allows for establishment of ETOR

8. ELIMS Solution

9. ELIMS Current State • 42 ID laboratories have been implemented and are active Units in SLv9. • By end of FY14, all ID labs (~93) will be accessioning specimens into ELIMS through SLv10 • Systems integration with SLv9 • Establishes an Enterprise lab data model • Future development work includes standard workflows, electronic reporting, and other lab-specific functionality • Some labs still use custom developed systems • Many SQL-based, Access front end systems • Some systems maintained by 1 developer • Interoperability is still not on the ELIMS radar • Attempts were made with SLv9 • ELIMS development based on future utilization of ETOR

10. Enterprise Accomplishments • Improved the specimen submission process for samples submitted to CDC: • new 50.34 form (an electronically fillable, barcoded specimen submission form); • online infectious diseases laboratory test directory; • new ‘one-stop shop’ website. • SLv9 laboratories have the ability to issue standardized, encrypted PDF reports electronically • Demonstrated the importance of standardized data during a recent Anthrax Lab Surge Exercise (2013) • Real-time data sharing with EOC • Efficient data integration with epidemiological data

11. Specimen Submission Form

12. Why is all of this important to know? • Without ELIMS, silo approaches to interoperability were the way forward • A lack of a standardized system would mean different lab requirements (i.e. 90+ different ETOR guides) • Difficult to standardize/code data across labs • Who would monitor for appropriate SNOMED/LOINC codes? • What system(s) would labs use? • Standardizing the specimen submission process and establishing ELIMS allowed CDC to create its first ID Test Directory

13. Test Directory for the Infectious Diseases Laboratories • Identified by SPHLs as an area of improvement • List of CDC Test Orders • Required when specimens are submitted to CDC • Supplemental information supplied with orders • Key contact information, pre-approvals • Test descriptions, turn around time, required volume • Available online and orderable through the 50.34 Form • Laboratory-defined test orders • 350+ test orders • Similar in concept to test panels

14. Test Directory for the Infectious Diseases Laboratories • Test Orders are flexible • Not directly linked to any tests • Allows labs ability to choose tests based on different scenarios • Test orders development process did not collect tests per order • ELIMS does not link orders with tests • ID Test Orders and Tests are not LOINC coded • Why? • It was new; many changes since going live • Time and budget • Limited SME support • Should they be coded? Well…yes! • Benefits to LOINC codes are known in this WG

15. Gaps and Challenges to LOINC Coding ID Test Orders and Tests • Most labs lack knowledge of LOINC/SNOMED • While many labs lack knowledge, they are the ones who know their tests and need to review codes with those who assign them • Not all labs will care about coding • Linkage between Test Orders and actual tests performed does not currently exist • Development work needed within ELIMS • Low in priority on the ELIMS roadmap • Decreased budget over the past few years led to lost interoperability resources on the ELIMS team

16. Gaps and Challenges to LOINC Coding ID Test Orders and Tests • LOINC coding need SNOMED coding • Capturing proper data elements for tests • Result values, interpretations need coding as well • ELIMS results data model in progress • Effort requires OID leadership buy-in • Progress can be impeded by lack of leadership support

17. Potential Solutions to LOINC Coding ID Test Orders and Tests • Well-organized agency wide implementation plan for LOINC coding ID tests is needed • Coordination across CIOs is fundamentally necessary • OID leadership needs buy-in and oversight • Educating staff on benefits of coding and interoperability • Promote and support the concept and importance of harmonization, standardization, and collaboration • An enterprise process/guide for getting new codes or retiring codes should be established • Should CDC have a central group for getting SNOMED/LOINC codes? Do they now? • The knowledge of a few shared to the whole • Establish Test Orders (i.e. LOINC panels) not directly linked to actual test performed • Implementation becomes more simplified, though still not easy

18. Summary and Discussion Points • LOINC coding ID test orders and tests is necessary • Education for buy-in would be ideal • Lab involvement is necessary • Makes for a lengthy process; • Few are fully aware of coding standards • Who to involve from the lab? • Must consider other competing factors • ELIMS implementation • QMS implementation • Routine lab work • Need a CDC-defining a coding process