1. Infectious Diseases Labs and LOINC Coding Stephen Soroka, NCEZID/OD June 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
Few Programs go across all Centers.

4. OID/CGH Lab Organization
Every year ,000 specimens received into CDC for testing
,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
Few Programs go across all Centers.

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
Purpose is to show that one system is the backbone but many systems make up the 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 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 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