2026-07-30 LabMCoP Meeting Notes

X

Nancy Cornish

CDC

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Manjula Dharmawardhana

CDC

X

Riki Merrick

APHL

X

Christina Gallegos

APHL

-

Amy Liu

Inductive Health / APHL

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Raj Dash

Duke / CAP

X

John Snyder

Pragmatic Terminologies, LLC

X

Andrea Pitkus

UW

X

Kathy Walsh

Labcorp

Rob Hausam

Hausam Consulting

Pam Banning

 3M

Elissa Passiment

Kristina Betz

CDC - NHSN

Jake Bunn

CDC

Marissa McMeen

CDC

Upcoming OOO

• Reminder: We are now using https://aphlinformatics.atlassian.net/wiki/spaces/LMCOPL/calendars and everyone can just keep it updated

  NOTE: you will need to use type “Event” if you do not have a confluence account

Announcements

Andrea

CMS RFI for CLIA Amendments

• Suboptimal specimen

• Blood culture contamination (BCC) (Microbiology):

1. What best practices has the laboratory implemented to reduce and monitor BCC?

2. What challenges does the laboratory face in maintaining low blood culture contamination rates?

We should make a comment to re-instate CLIAC, since data for this RFI came from their recomendations

USCDI V7 has been published

we got Specimen Collection Date/time and collection method added; Specimen Condition now has the correct name

they still have the Healthcare Attributes class, that has the Reason Not Performed and Performance Date/time

Looking in US COre: they have no lab specific ServiceRequest artifact, but the generic one prescribes the use of Lab LOINC for .code and use of Lab test SCT code from the procedure hierarchy (which might exacerbate the isseu of folks wanting to use Procedure to model a Labtest)

SNOMED International proposal for Serologic terms

for when John is here

SNOMED International is purposing to revise content with “Serology” or “Serologic” in the FSN and remove this wording from FSN across clinical findings, procedures, and observable entities. I would like LabMCop team to review and provide any feedback on the topic during the meeting.

Open

Prior discussions: 2026-06-25 LabMCoP Meeting Notes

Next Steps:

• Review the document and email John your suggestions feedback - we can also summarize next week, but please be preprared to have opinions

Salmonella Serotype SNOMED CT code requests

for when John is here

APHL has gotten this request for Salmonella serotype concepts (AIMSSD-14636) - John has mapped another enterics to existing concepts before - there are 219 unmapped, which we need to review:

• findings not organisms

  • appropriate to be in this hierarchy, but need to make new terms

• old organisms - need to map to new names, or find out if still valid - this might need SME input

• provisional names (out of scope, so those could go into APHL namespace extension - check against Vet extension before creatign new content!)

• need Salmonella SME to review concepts:

  • mapped to the same SCT conceptID, but with different names, so if true, they should be added as synonyms

  • may have existing concepts with different name, so it’s the synonym that is missing

  • ensure all mapped terms are correct

Open

There is actually another file with Salmonella serotypes (from OR PHL) Christina is working on (that’s the AIMS ticket linked above - need to find the other AIMS ticket wehre this file is coming from)

Problem is that some of the testing for specific serotypes have qualitative results - those are not part of this file

About a ddecade ago Patti Fields (CDC) had a great spreadsheet with mappings between the formula and serotypes - her preference would be to have folks just use the formula instead of names - potnetially we could reserve SCT coding at the species level (which is what most clinical labs can diagnose) and leave the serotypes just formula?

Before creating any new concepts should check the veterinary extension: : https://vtsl.vetmed.vt.edu/TerminologyMgt/Browser/results.cfm

Next Steps:

Send file to Nancy for checking with Enteric Disease Lab Branch SMEs (DFWED)

Working with DHQP for NHSN reporting

Nancy

Follow up list:

• Urine culture results for HAI requirements

• Gather current means to record bottle volume

  • Biomerieux

    • it records the volume for each bottle, but not coming across with the instrument, no code set, lab has to record it on their own - willing to help

  • SHIELD - no feedback received

• Provide feedback on NHSN IG: https://measures-ci.nhsnlink.org/artifact-listing.html - Submit Jira to GET INFO FROM LAST MINUTES!!!

• Reviewing the Blood culture panel diagram:

  • the blood volume needs to be communicated back to the provider when it is too low

    • this will not be a diagnostic report yet - no testing has started yet and don't want to wait for that

    • this is recorded on the specimen in the LIS, often only as a comment - hard to pull out

    • maybe use an order update message to communicate that volume is too low

• similar note is in the LIS for hemolysed samples

  • if unacceptable for single test ordered => rejection, else rest of testing will be performed and the specimen conditon will be included in the report

  • instruments also now report HIL index - need to figure out how that will be reported / translated into specimen condition

• For NHSN reporting currently asking for vancomyacin resistant E. coli, but in the lab they have the organism and the susceptibility result for the Abx, which requries re-mapping to report

• Does USCDI support comments on results?

  • https://isp.healthit.gov/taxonomy/term/681/uscdi-v7 with the definition using the terms “structured AND unstructured” we think yes

Follow up from AndesVirus codes question

Riki

• John and Riki have reached out to Steven Bradfute to get the low-down on the taxonomy and then figure out how to model the disorder concepts and create submissions for anything new:
  NOTE that for SNOMED CT: The following disorder concepts have been added for the August 2026 International Edition release of SNOMED CT:

  • 1404527009 |Hantavirus cardiopulmonary syndrome caused by Orthohantavirus sinnombreense (disorder)|

  • 1404528004 |Hantavirus cardiopulmonary syndrome caused by Orthohantavirus andesense (disorder)|

  Unfortunately, these concepts will not appear in the U.S. Edition of SNOMED CT until the March 2027 release. The concepts are still valid for use once published in the international edition; it will just be some time before we publish them as part of the U.S. Edition.

  • Had brief discussion about IMO mapping for diagnoses (95% of EHR-s use them) - identified that the IMO cocnept may not always be an equivalent map, so relying on it for cross-mapping in historical records may be problematic

• pathway for requesting CPT codes

• pathway to getting ICD-10-CM codes (when ICD-11 codes exist)

• Overall thoughts on setting up a code request process (across all SDOs) for emergencies (how do we ensure that Emergency Response teams include properly coded reporting in their work?)

  • Division of Laboratory Systems at CDC

  • WHO

  • who decides on offical names for new organisms / tests etc

• include education in the process documentation on where to get concepts that are not yet in the US Edition / offical LOINC releases and how EHR and terminology vendors can support

• Riki reached out to Colleen Kraft at NETEC to follow up on formalizing processes / discussions - will have more info in a few weeks

HPV screening/confirmatory testing workflow

John

Need to find a date with Hanna - John to do!

We’d like to discuss with the group the current modeling and naming policy for procedures connected to detecting HPV and/or pre-cancerous/cancerous cells in the cervical region.
Our national screening program for cervical cancer has recently updated their guidelines for testing and analyzing said tests, and currently the content in SNOMED CT that deals with these tests are defined as always being of a cytologic kind. Meanwhile, our new guidelines defer to a liquid based cell sampling from the cervix that may be used to test for the presence of HPV, and if positive, used for further (cytological) testing to look for pre-cancerous/cancerous cells.
This puts us in a bit of a pickle. The procedure to obtain cell samples is the same for both the HPV test and the cytological test, and the same test tube is used for both analyses. In the cases where the HPV testing is negative, a cytological analysis is never done. Therefore, calling a procedure a “liquid based cytology” when it won’t necessarily be analyzed for cytology seems incorrect.
We want to have a discussion around whether or not we’re the only ones in this predicament, or if we ought to raise the issue to SNOMED International for a thorough review of existing content.
Best regards,
Hanne

From Andrea Pitkus' email: US protocols are usually to reflex to HPV testing with PAP Smears.  Most use liquid based methods such as Thin Prep (brand). Technically, cytopathology is the term used for this area of laboratory testing.  I'm sure Nancy will have more thoughts too.  

Robyn Temple-Smolkin (AMP) email: Our reference lab used to run HPV from ThinPrep or SurePath. Sample would go to the hospital cytopathology lab for preparation of the pap smear then the atypicals were reflexed as sendouts to us for high-risk HPV testing by PCR. The entire ThinPrep/SurePath vial was the specimen we received. We also did CT/NG off this sample when ordered. I believe this is still a very common workflow performed either within one institution or as a sendout, but defer to others' input on newer workflows as I have been away from day-to-day operations since joining AMP. 

prior discussion:

https://www.hologic.com/hologic-products/collection-devices/thinprep-pap-test = example of the collection kit

the collection is the swab/brush/spatula of cells, this is really the collection container though

Here is the labcorp example: https://www.labcorp.com/tests/507385/high-risk-hpv-with-hpv-genotypes-16-and-18-cobas which shows the different colelction methods depending on container used at the bottom

Hologic ThinPrep package insert page: https://www.hologic.com/package-inserts/diagnostic-products/thinprep-pap-test

Try to see, if Jenna from Arup can be available then, too

Call adjourned - below not discussed

11:58 AM EDT

Question on Karius Testing

Riki/Christina

Next Steps:

• review the list of results and figure out where current gaps in organism hierarchy are AND identify the substance concepts that are still missing in SCT - need 93 concepts in organism hierarchy, many more in substance, so suggest for now to request the organism concepts and work on the substance hierarchy over time (later)

• do education to get LIS and EHR-s and surveillance systems to support more than one hierarchy for results - bring this to the SHIELD Standards and Vocab WG:

  • organism

  • qualifer

  • clincial findings

  • substance

• let Karius know that in the future we will have substance concepts, but it is going to be a little while

• Choices for LOINC:

  • new LOINC with different system based on: https://loinc.org/103566-6/ - will ask if they want 2, one for cell-free plasma and one for BAL, or if one for specimen would be enough, since they are sending the specimen type (however the orgnaism list is different between the 2, so potentially 2 LOINCs might be better.

  • new LOINC based on https://loinc.org/97601-9 with nominal scale.

Specimen CMT - Hosting Options

Riki

Any Updates on FU with:

Clinical Architecture: They could create conceptMap based on the content model they built, need to follow up about FHIR server usage

ONC: Pull up email from Carmela

Specimen CMT terms

Christina

Review collection method concepts (initiated by USCDI valueset creation: https://hackmd.io/38xa1BZ7TjaPMao6LJHuCA#Proposal ):

retired concepts:

24139008 Endoscopy of urinary bladder (procedure)
176178006 Diagnostic cystoscopy (procedure)
397394009 Bronchoalveolar lavage (procedure)
1388791008 Urine collection after prostatic massage (procedure)
1571000284107 Arterial sampling catheter procedure (procedure)
78181000284104 Cornea impression (procedure)

not in procedure hierachy:

258429002 Rectal scrape specimen
261665006 Unknown

Using preferred name, not FSN (these should not be an issue in the final version, since FSN or preferred name would be pulled based on the concept code, correct?):

122462000 Drainage procedure
14766002 Aspiration
232595000 Bronchoscopic lavage

Reflex testing in FHIR follow up

Andrea

Andrea is working on a reflex workflow layout to check how the orders / grouping and specimen reject might work: - look at minutes from last week: 2026-07-02 LabMCoP Meeting Notes

CMT Governance process

CMT proposed maintenance process

Start writing this up on this confluence page: Specimen CMT Update Process

Questions from Zulip thread that should be covered by the process we come up with here:

1. Requests for terms used in practice that are not yet in the Cross Map Table?

2. Requests for any corrections or needed updates to terms?

3. What type of version control will be leveraged for releases and major/minor updates?

4. How do you plan to incorporate SNOMED CT Release Updates into Cross Map updates/releases?

5. At what frequency will updates occur? For example, will you process SCT updates once yearly and have a subsequent Cross Map release yearly with changes or more or less often?

6. How do you communicate differential changes between releases? Is a differential file produced or is it expected that users will be able to find changes on their own?

7. What type of customer support for downloads is expected? Will the release entity provide or is it expected of the site hosting the content for download? Both need to work colLABoratively to ensure no blockers arise for users/consumers.

User Guide starter Specimen Cross-Mapping-Table (Specimen CMT)

Follow up items

• Riki’s Follow up - none of these got done yet

  • Contact United Network for Organ Sharing for input on donor terms (pre-coordinated or not?) =

    • ISBT 128 | ICCBBA | Technical Documents

      • https://www.isbt128.org/_files/ugd/1a7593_edfd176861c94dca94c34eff8fa3ad0d.pdf - for organs

    • Riki has some contact now with European bloodbank and biobanks = Home - BBMRI-ERIC working with the folks that define their minimum data set: MIABIS - BBMRI-ERIC - these folks shared the follwoing for the reject reason topic, but it seems they differentiate between source site and the organ: #1 Standard PREanalytical Code Version 4.0 - (version 3.0 is here: https://cdn.ymaws.com/www.isber.org/resource/resmgr/isber_2019/pdf/standard_preanalytical_code_.pdf) and also Robin for US

    Clinical Archtecture unmapped LOINCs:

    • Riki should check up with Charlie to see, if he knows where the LOINCs using the shorname in the description come from - as that is discouraged

  • Riki to set up her VSAC authoring log in

  • For wound modeling (see 2023-11-30 LabMCoP Meeting Notes ) create a few pre-coordinated specimen terms

    • to cover the wound causes as children under: 119365002 | Specimen from wound (specimen)

    • another child term for aspirate under 445611000124106 | Specimen from bite wound (specimen), since that is preferred over the existing swab

Lab tests as procedures or orderables

Do we still need this?

Recommendation by SNOMED is that the Observable entity hierarchy be used for both ordering and resulting. 

As for the technique hierarchy, that in no way is intended to be used for either ordering or resulting laboratory tests.  Those concepts are used to model both observables and procedures.  

SNOMED LOINC extension: https://browser.loincsnomed.org/?perspective=full&conceptId1=363787002&edition=MAIN/LOINC/2025-09-21&release=&languages=en

The problem is that major EHR-s vendors have set up CPOE using Procedures for orders to initiate a workflow (that creates the triggering event in the system) - that’s where the push-back comes from.

There is a CPT to SNOMED CT mapping (as a paid mapping available from AMA), but no LOINC mapping.

Can we reach out to CAP Informatics, ADLM Informatics and ASCLS Informatics to get their take on where Lab tests should live

We had said we would work through the Colonoscopy example:

Reference links:

clinical guidelines: Official journal of the American College of Gastroenterology | ACG

Quality Indicators: Official journal of the American College of Gastroenterology | ACG

• For CAP cancer reporting is using SNOMED CT - would be good to look which they chose to represent the performed lab test

There is this question in the LOINC Community: https://forum.loinc.org/t/assistance-creating-a-value-set-for-all-loinc-procedure-concepts/2993

it is related to this US Core FHIR Change request: https://jira.hl7.org/browse/FHIR-54415

Answer to this one is that in USCDI Procedure (https://isp.healthit.gov/taxonomy/term/781/uscdi-v6) does not list LOINC as applicable Vocab standard in any verion, so remove it.

Often folks think of lab tests as procedures, because they can be ordered in CPOE (and outsidde the US, in the UK for example that’s how folks have modeled those, which is why LOINC was adding more of the high level order codes in 2.81 release, so we still should tackle the LOINC community question.

John was working on creatign an intesnional valueset definition based on class + type and maybe a few other attributes

European Semantic work

Link to the German FHIR IG around suceptibility testing:

https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsimplifier.net%2Fguide%2Fars-implementation-guide%3Fversion%3Dcurrent&data=05%7C02%7Criki.merrick%40aphl.org%7Ce11e8daf7f2d4827d07808ddcac8861c%7C434e0aedef824568a0493b17adc08ddd%7C1%7C0%7C638889684844672822%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=kZJRoBl2tMQzWQoYVkaRnEUaaBxepA9sAIu1myDQMyo%3D&reserved=0

Semantic Example section: https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsimplifier.net%2Fguide%2FARS-Implementation-Guide%2FHome%2FSemantics%3Fversion%3Dcurrent&data=05%7C02%7Criki.merrick%40aphl.org%7Ce11e8daf7f2d4827d07808ddcac8861c%7C434e0aedef824568a0493b17adc08ddd%7C1%7C0%7C638889684844702198%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=qQH%2Ff5xwG0O8DvNE4rbjZineXBhY%2BiOWmN047DRthNQ%3D&reserved=0

Confluence page:

Ask if Rob can keep us updated

Specimen CMT pilot implementers

• Review where we are: Vendor Connections

Specimen CMT - education

• Need education for providers and IT folks that helps with set up of the EHR-S / LIS configuration -this can be supported / accomplished? with the Implementaiton Guide we could write

• if we have a use case of how a patient is impacted on their journey through the healthcare system - CAP created a nice video that showed how patient care was affected by incorrect data https://infobeta.cap.org/shield/

Specimen CMT - tracking implementation impact

• Setting baseline

• Define metrics

Future projects for this call after CMT

• In general the call is intended as a forum for ANY messaging related issues to work out.

• In the past we have

  • reviewed containers re-vive that - and how does that interact with devices (UDI identification?)

  • review code systems around additives (HL70371 and SCT substance and product hierarchies)

  • started work on cross-mapping between HL7 method codes and SNOMED CT procedure / technique concepts

    • American College of Surgeons is working on procedure protocol and synoptic data elements / surgical synoptic reports - we could work with them together on that

  • Look at other HL7 tables that we would want to migrate SCT: Collection method is now USCDI element, review proposed value set: https://hackmd.io/38xa1BZ7TjaPMao6LJHuCA#Proposal