Public Health Case Reporting - CSTE TIG Lab Vocabulary Review

May 4th Week – Viral, Parasitic and Non-Infectious Diseases

CRSWg, LMCoP, VMCoP

May 27th, 2010

04/20/23 1

Archive of - 1st ,2nd and 3rd Meeting Lab Vocabulary Review

04/20/23 2

Hyperlink: http://www.phconnect.org/profiles/blogs/call-for-volunteers-review

Scope for 4th Week of CSTE TIG - Lab Vocabulary Review

04/20/23 3

Spreadsheet Overview

04/20/23 4

Note: Includes only the 2nd Week Bacterial Diseases Lab Vocabulary

CSTE Position Statement

CSTE Position Statement not published in the CSTE website for the following conditions:

– St.Louis Encephalitis Virus

Eastern Equine Encephalitis Virus CSTE position statement did not have its accompanying CSTE TIG.

Post the above mentioned CSTE position statements in www.phconnect.org

Need more detailed review of the following CSTE TIG:– Acute Pesticide Poisoning

– Cancer

04/20/23 5

Cyclosporiasis

“Cyclospora organisms or DNA in intestinal fluid/aspirate or intestinal biopsy specimens” – Test Results (SNOMED) – Non-specific as well as specific.– Need to add the following in non-condition specific nominal results value set - “Protozoa, Protozoal spore, Trophozoite, etc..

l

04/20/23 6

Giardiasis

“Giardia trophozoites in stool, duodenal fluid or small bowel biopsy “

Two SNOMED results for a single lab test (LOINC). Need to be formatted and map them appropriately.

04/20/23 7

Malaria

No LOINC or SNOMED mapping in CSTE TIG

04/20/23 8

Riki: RELMA codes: 41447-4; 41448-2; 41449-0; 47085-6 all are ord in BLD and 47260-5 (nom)

Malaria

04/20/23 9

* Need to validate the SNOMED as well as LOINC concepts for its status and find the superseded concept.

Malaria

04/20/23 10

• Could include the Plasmodium hierarchy for more specificity• May need to filter the hierarchy and include only the agents that causes Malaria such as Pl. Vivax, Pl. Malariae, Pl. Ovale, Pl. Falciparum

Small Pox

polymerase chain reaction (PCR) identification of variola DNA in a clinical specimen

polymerase chain reaction (PCR) identification of variola DNA in an isolate from a clinical specimen

04/20/23 11

•CSTE Criteria mapped to the same LOINC and SNOMED codes.•CSTE criteria has detailed information about specimen which may need to obtained outside LOINC code such as SPM segment, specimen source.

Small Pox

04/20/23 12

Varicella

Combination tests– HSV & VZV “HSV+VZV DNA XXX PCR”

A significant rise in serum varicella immunoglobulin G (IgG) antibody level by any standard serologic assay – Specimen 1 & 2– Panel has been included in CSTE TIG which may not be in OBX-3

04/20/23 13

Viral Hemorrhagic Fever (VHF)

Reconcile the CSTE TIG lab criteria with CSTE position statement– Proteinuria

– Platelet count

Need to create a value set with a list of viral agents that was specified in CSTE position statement for VHF:

– Junin virus

– Machupo virus

– Sabia virus

– Lassa virus

– Guanarito virus

– ebolavirus

– marburgvirus

– Crimean-Congo haemorrhagic fever virus

04/20/23 14

West Nile Virus

Stable (less than or equal to a two-fold change) but elevated titer of WNV virus-specific serum antibodies

– No LOINC / SNOMED code, but may repeat the LOINC and SNOMED code from the criteria “Four-fold or greater change in WNV -specific serum antibody titer “

– Riki:• - would be a complex method type - might need more than 1 LOINC, if

decision is made after report, oterwise need to get IMP code

04/20/23 15

Waterborne Disease

No Lab Criteria in CSTE position statement as well as in CSTE TIG. No NND Codes

04/20/23 16

Neuroinvasive & Non-Neuroinvasive diseases

CSTE position statements does not differentiate between Neuroinvasive and Non-neuroinvasive disease but case notification NND codes differentiate between these too.

– West Nile Virus

– Western Equine Encephalitis Virus

– St.Louis Encephalitis Virus

– ? Eastern Equine Encephalitis Virus

04/20/23 17

Western Equine Encephalitis Virus

“Demonstration of WEEV- specific nucleic acid by PCR in a clinical specimen“

– LOINC codes have been requested.

– Riki: use LOINC: 54036-9?

04/20/23 18

Yellow Fever

cross-reactions to other flaviviruses – Negative results

– Need to check the Flavivirus Hierrarchy in SNOMED / LOINC browsers and include those tests in the CSTE TIG.

04/20/23 19

Yellow Fever

?? Any tests for Yellow Fever antigens

04/20/23 20

Yellow Fever

Antibody Titers with specific values and different methods

04/20/23 21

Lead Poisoning

04/20/23 22

Different CSTE criteria with specific Qn values, but same LOINC tests.

Silicosis

04/20/23 23

Imaging & Pathology tests

Acute Pesticide - related illness and Injury

04/20/23 24

Riki: SNOMED Herbicide Value Sets - Why not include all pesticide children under concept 59545008^Pesticide (substance) in the possible results? This list should be reviewed for completeness by SME.

Cancer (1)

04/20/23 25

Cancer (2)

04/20/23 26

LIMSi Feedback- Cindy

04/20/23 27

Common Core Data Elements for Case Reporting and Laboratory Result

Reporting

First iteration of common core data element list appears in CSTE position statement 09-SI-01 “Common Core Data Elements for Case Reporting and Laboratory Result Reporting”

– Actions: provide a process for updating/maintaining common core data set

CRSWg has undergone a review to update the initial list– Consolidated case reporting and laboratory result reporting data elements

– Addressed feedback from CSTE

Scope for the common core data set:– Initial case report from a provider to public health (case reporting)

– Data elements can be applied across all nationally notifiable conditions

04/20/23 28

CategoryData element* = complex data element Definition Case Reporting Notes Laboratory Result Reporting Notes

Test/result Specimen collection date/time

Test/result Study identifier*

useful identifier related to test performed; common term --- lab TIG review

Accession number: may be specimen ID or the order number in the message

Test/result Specimen received date/time

Test/result Specimen type [coded] common term -- lab TIG review specimen origin in PHLIP?

Specimen origin should be an additional data element in the report – coding system / values et is still TBD, will be sent as OBX following SPM segment in a messageCoding system for specimen type either HL70487 or SNOMED CT in specimen hierarchy

Test/result Specimen source site [coded] common term -- lab TIG review specimen origin in PHLIP?

Specimen origin should be an additional data element in the report – coding system / values et is still TBD, will be sent as OBX following SPM segment in a messageCoding system for specimen source site could be either HL7 or SNOMED CT in anatomical structure hierarchy (prefer terms using the “structure of”

Test/result Test ordered [coded]The name of the laboratory test.

Test/result Test performed [coded]

Test/result Test result [coded]The result of the laboratory test.

Test/result Test result, not codedThe result of the laboratory test.

Result that cannot be coded, e.g., a number, a ratio, a text report from a radiologic study, an image

Test/result Result date Test/result Result statusTest/result Reference rangeTest/result UnitsTest/result Performing lab identifier*Test/result Performing lab name Test/result Performing person name* Test/result Specimen sent to PHL 04/20/23 29

Additional Data Elements Considered for Inclusion in Common Core

Quantitative/QualitativeAbnormal flagsPaired serology result

Paired Serology Result (1)

04/20/23 31

Review the e-mail thread

Paired Serology Result (2)

04/20/23 32

Recommendation Letter to CSTE about CSTE TIG Lab Vocabulary

Include Changes that needs to be made in CSTE position Statements Mention the issues that are related to lab domain which would be

addressed by the lab community of practice and SDO (LOINC, SNOMED).

CSTE lab Criteria Interpretation issues Maintenance of the CSTE lab Criteria

– ?? Unique identifier for the lab criteria

– Centralized repository of data elements – Maintained by CSTE

04/20/23 33