Public Health Laboratory Interoperability Project (PHLIP) The Vocabulary Harmonization Process APHL Association of Public Health Laboratories Ulrike Merrick, MPH John Carroll, MBA Michelle Meigs, BS Coordinating Center for Infectious Disease, Centers for Disease Control and Prevention CCID, CDC Wenkai Li, MD 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

Presentation Objectives Flavors of electronic messaging Overview of PHLIP Vision Scope Participants Structure Goals Harmonization Process Timeline, Achievements and Future Plans Tools, Deliverables and Decisions

Flavors of Electronic Messaging Electronic Laboratory Messaging (ELM): All lab related electronic data exchange - PHLIP is starting with PHL to PHL Electronic Lab Reporting (ELR): Reportable disease related result from all labs (hospital, PHL, commercial) to state EPI & NND related results from PHD to CDC Electronic Case Reporting (ECR): Reportable disease related patient information from physician to state EPI (includes lab results) – NND related de-identified cases to CDC (from state EPI)

Related Definitions 1 Reportable (CSTE): Condition required by local/state law to be reported to respective public health departments by laboratorians, physicians and other entities. Notifiable (CSTE): Condition voluntarily reported from state health departments to CDC. Nationally Notifiable Condition (NNC): Condition should be under surveillance by reports of individual cases, include infectious diseases, chronic conditions, injuries, etc. Nationally Notifiable Disease (NND): Those diseases that must be reported to the CDC as part of the NNDSS CSTE Position Statement ID08-EH-01, accessed on 7/29/2008:

PHLIP Electronic Laboratory Messaging Electronic Lab Surveillance Messaging (ELSM): NND related results from SPHLs to CDC Epi Electronic Test Order and Result (ETOR): Test requests and results between SPHLs and CDC Test requests and results to submitter (local) Test requests and results between SPHLs for value use cases: COOP (Continuity of Operations Plan) Surge Reference Tests

PHLIP Vision Achieve bi-directional laboratory data exchange State public health labs (SPHL) with CDC labs SPHLs with local partners Which will Improve data quality and accessibility Improve data sources for active surveillance Develop and test future system approaches

PHLIP Scope

PHLIP Participants Public Health Labs California* Colorado Florida Iowa Minnesota Nebraska Virginia CDC CCID Labs National Organizations: CDC Coordinating Center for Infectious Diseases (CCID) CDC National Center for Public Health Informatics (NCPHI) Association of Public Health Laboratories (APHL) * California is currently on hold for implementation

1. 1.Harmonization of Vocabulary and Messaging Guides Implementation of Production Level Messages Building Collaboration and Cross Project Fertilization. The Three Pieces To PHLIP

PHLIP Structure Executive Committee (governance level guidance)

PHLIP Structure Executive Committee (governance level guidance) Steering Committee (technical level guidance)

PHLIP Structure Executive Committee (governance level guidance) Steering Committee (technical level guidance) Work Groups (producing deliverables) Vocabulary and Messaging (V&M) Messaging Implementation State-to-State (PH Lab WG) Public Health Data Exchange (PHD Ex) RNR-Hub Implementation

PHLIP Goals Pilot sustainable architecture for laboratory data exchange: Peer to peer for starters Route-not-Read (RnNR) hubs - regional exchanges Send and receive HL7 Test Results from states to CDC (v2.3.1) with migration to v2.5.1 Send and receive HL7 Test Order and Test Result from State to State Send and receive HL7 Test Order and Test Result between States and CDC

PHLIP Goal - Harmonization Collection of information about all tests performed and related reported results Agreement on the library of tests Arrangement in a hierarchical fashion Assignment of standard vocabulary (LOINC for tests and SNOMED-CT for results) Deliverable: the Test Category Spreadsheet For each Nationally Notifiable Disease (NND):

PHLIP Vocabulary Harmonization Tasks NND selection based on high volume tests across current PHLIP states Example workflow and data for a new NND After Lab SME work group meeting, all states submit data (workflow & test metadata) Data is compiled into the category sheet and all tests harmonized Review compiled test category sheet with suggested LOINC and SNOMED codes

PHLIP Vocabulary Harmonization Tasks (cont.) Once category sheet is approved: Keep LOINC / SNOMED codes Assign PHLIP codes where standard codes are missing/not available Create encoding guidelines Create sample message Provide access to centrally managed vocabulary (currently PHIN VADS)

Timeline

Harmonized NNDs To Date Influenza and related respiratory viruses* Mycobacterium tuberculosis and related species Diphtheria (Corynebacterium diphtheriae) Pertussis (Bordetella pertussis and related species) Enterics: Salmonella spp., Shigella spp., Shigella toxin- producing Escherichia coli (STEC), Campylobacter spp., Vibrio spp. HIV Genital Chlamydia trachomatis Treponema pallidum Neisseria gonorrhoeae Neisseria meningitidis

Challenges The “devil is in the details” Both messaging and vocabulary standards leave significant room for interpretation Breadth and depth of expertise is required Messaging, Vocabulary, Laboratory, IT Collaboration takes time Technical limitations Competing priorities Infrastructure is evolving HL7 Vocabulary Laboratory IT Courtesy: NHIN-Connects_2008_03_06.ppt

PHLIP Swimlanes

Reusable Resources The PHLIP Toolkit 1. 1.Collaboration Portal (Sharepoint) 2. 2.Test Data Collection Sheet 3. 3.Test Category Sheet 4. 4.Encoding Guidelines 5. 5.Mapping Workbook 6. 6.HL7 implementation Guide 7. 7.The PHLIP primer

Sharepoint

Test Metadata Collection Sheet

Information Collected Agent (supra-family, family, genus, species) Specimen type (XXX, ISLT) Test class: Nucleic acid detection Test type: Probe, PCR (Conventional, Real-time) Specific target: Whole sequence, partial sequence Product: Manufacturer, specific product Is test ‘stand-alone’, ‘panel’ Is ‘result’ reported? What is reported? Raw result, interpretation, conclusion, summary conclusion?

Influenza Category sheet

Influenza Encoding Guidelines

Influenza Mapping Workbook

PHLIP Primer - Quotes

Vocabulary & Messaging WG

LOINC Code Availability

‘Sub-LOINC Codes’ Campylobacter spp.: H 2 S Production LOINC code: ‘H 2 S Production’ Multiple methods detect H 2 S production Methods differ in sensitivity Accurate species identification: method dependent Methodology critical Need ‘Sub-LOINC’ method-specific code

Method-Specific Codes ‘Sub-LOINC Codes’ = ‘PHLIP’ Codes

Report Related Definitions Result – The raw observed result comes from direct test observation that could be descriptive or quantifiable Interpretation – The interpretation of the result reported for a single test

Report Related Definitions cont. Conclusion – The conclusion derives from the results and interpretations of multiple tests of a specific type for a single agent (at the genus level or below) like PCR Summary Conclusion - The summary conclusion based on the results of multiple test of different types for a single agent or multiple agents

Example reports

Other PHLIP vocabulary Panel: Collection of tests performed on the same sample, using the same method, but looking for different organisms Example: Respiratory Virus Panel PCR: LOINC# Resp virus DNA+RNA Pnl XXX PCR Influenza virus A Influenza virus B Adenovirus Parainfluenza virus Types 1-3 Respiratory Syncitial Virus Battery: PHLIP defines it as a grouping of tests for ordering convenience – these tests are performed together, can be different methods, can look for same organism.

PHLIP Decisions Clinical specimen = XXX: Use LOINCs with system = "XXX" (information will be in a different part of the message), unless exclusively done on one type of specimen (e.g. serum). Isolates = ISLT: Reference testing - Use LOINCs with system = ISLT to distinguish between isolates and clinical specimen. Use LOINC to the fullest extent possible for test method: For more granular method metadata use OBX-17, unless that information is required for ordering the correct test. Example: PHLIP code for Real-time PCR, because LOINC method = target amplified probe

Use explicit terms, for example: TB culture implies smear and culture PHLIP term is Smear, Isolation and Identification Established hierarchical relationships between high level and granular level, built on ideas from Steven Steindel et.al. "Introduction of a Hierarchy to LOINC to Facilitate Public Health Reporting" (PMID: for Introduction of a hierarchy to LOINC to facilitate public health reporting; Steindel S, Loonsk JW, Sim A, Doyle TJ, Chapman RS, Groseclose SL.; Proc AMIA Symp. 2002;:737-41) Allow for aggregating tests for single high level orders (battery). Highest level includes pathogens with similar occurrence. Example: Respiratory Viruses for Influenza PHLIP Decisions cont.

How to report cultures Culture = Isolation and Identification in PHLIP Battery of tests that leads to report of organisms name. Example: Virus Isolation: Culture to isolate Confirmatory identification tests: PCR, HAI or DFA Report summary conclusion of organism name or no organism found LOINC needs to be PRID with nominal scale PHLIP will not distinguish medium type used for culture in the method. Use of selective medium is associated with LOINC method of "organism specific culture“ – limits organisms allowed to be reported to Genus named in component.

PHLIP Result Harmonization Long-term goal is to standardize the results and document the reasoning Follow up with Food & Drug Admin. (FDA), Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathologists (CAP) about legal issues So far proposed: PCR:use detected instead of positive, use not detected instead of negative. PCR & DFA: use inconclusive instead of indeterminate

Questions? Contact Michelle Meigs: or Riki Merrick:

Glossary APHLAssociation of Public Health Laboratories CCID Coordinating Center for Infectious Disease CCHISCoordinating Center for Health Information and Service CDC Centers for Disease Control and Prevention CLIAClinical Laboratory Improvement Amendments CSTECouncil of State and Territorial Epidemiologists DFADirect Fluorescent Antibody DMB Data Messaging Broker EHR Electronic Health Record ECR Electronic Case Reporting ELI Enterprise Laboratory Interface ELR Electronic Laboratory reporting EPA Environmental Protection Agency FIM Federated Identity Management FDA Food and Drug Administration HL7 Health Level 7 LIMS Laboratory Information Management System LIMSi LIMS Integration LOINCLogical Observation Names and Codes LRN Laboratory Response Network NAHLNNational Animal Health Laboratory Network NCPHI National Center for Public Health Informatics NEDSSNational Electronic Disease Surveillance System NHIN National Health Information Network NND Nationally Notifiable Disease OID Object Identifier PCRPolymerase Chain Reaction PHII Public Health Informatics Institute PHINMSPublic Health Information Network Messaging Service PHINVADS Public Health Information Network Vocabulary Access and Distribution System PHL Public Health Laboratory PRIDPresence or Identification (LOINC term) PHR Personal Health Record RnR Route-not-Read SPHD State Public Health Department SPHL State Public Health Lab STAT Specimen Triaging and Tracking Laboratory (CDC)