2026-08-13 LabMCoP Meeting Notes

X

Nancy Cornish

CDC

X

Manjula Dharmawardhana

CDC

X

Riki Merrick

APHL

X

Christina Gallegos

APHL

-

Amy Liu

Inductive Health / APHL

-

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

X

Charlotte Lane

CDC

Blake Dinsmore

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

Salmonella Serotype SNOMED CT code requests

for when John is here

APHL has gotten this request for Salmonella serotype concepts (AIMSSD-14636) - 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

Discussion today:

Brief introduction to interoperability and SNOMED CT in particular:

Open

and

Open

• SNOMED CT has different editions:

  • International is the basis for all

  • US creates an edition from International Edition (published monthly) and the US extension (published twice a year to reduce update requriements on implementers

  • APHL has namespace, which is using the US edition as a starting point - currenlty working out new publication means, since PHaaaaiNVADS is going away (used to publish there twice a year) - this gets concepts that are either not as commonly used in US or may not need persisitence for a long time (like SARS-CoV-2 lineages for the latter we get maybe 1-2 requests per month; other requests are less frequent, but could be more substantive like this Salmonella serovar addition, where we decide in consultation with NLM where to create the concepts)

• Walking through the SNOMED CT browser: https://snomedbrowser.org/?perspective=full&conceptId1=404684003&edition=MAIN/SNOMEDCT-US/2026-03-01&release=&languages=en

  • organism hierarchy is primitive (only relationships in the same hierarchy) - can filter on just it on the left navigation bar

  • follows the linnean classification, which is based on phenotypic relationships

  • best tabs to review are summary and details (which shows the US english Fully Specified Name (FSN) = the one with the semantic tag identifying the hierarchy, in this case (organism) as well as other synonyms

  • For FSN SNOMED CT uses the LPSN (https://lpsn.dsmz.de/ ) as authoritative source, so there may be cases, where that has changed since the term was created, we’d like to kow about that

• some concepts are pre-coordinated with clinically relevant attributes like resitance factors, but they are often not how the lab reports those

  • this means that the organism name is combined with the finding of resistance to a specific antibiotic for example Methicillin-resistant Staphylococcus aureau (MRSA) - the lab usually would report this as organism identifies = Staphlyococcus aureas and Methicilin Suscptibility as resistant (post-coordinated)

• important to know the test that was performed (identified by LOINC) to know which coded result answers to attach:

  • organism specific LOINC => qualitative ordinal answers = SCT from qualifier hierarchy

  • method specific LOINC => qualitative nomial answers = SCT from organism hierarchy

Do we know more about the testing? We can ask, assume this is phenotypic, not genomic, but will find out, if they are doing full serotyping, or only sero grouping and how many other serovar attributes were tested

Charlotte mentioned a paper on comparison of phenotype to genotype for Salmonella serotypes is pretty close - assume this is it: https://journals.asm.org/doi/10.1128/aem.01746-19

Goal of the review is to get exact maps - if not possible, identify as a gap, so we can create new content - will decide if in international, US or APHL namespace

also identify any issues with current FSN / missing synonyms, so we can clean up the hierarchy in SCT

Next Steps:

• Reach out to OR to get more details on the testing performed

• share slides with Charlotte

Question on Karius Testing

Riki/Christina

Background documentation:

Clinical Guidance on the Use of Next Generation Sequencing (NGS) Tests for Infectious Diseases

https://kariusdx.com/ - see our solution for pathogen lists (that’s also what is in the Excel file):

cell-free plasma: https://kariusdx.com/our-solution/pathogens?product=spectrum

BAL: https://kariusdx.com/our-solution/pathogens?product=bal

Next Steps:

• Request specimen concept for cell-free plasma (as a child of plasma)

• 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) - will add these to US edition

  • have to decide what to do about the mixed organisms - in this case these are OR concepts, due to detection limitations of the method used - similar to some Biomerieux terms Xavier brought to SHIELD a while back (have not gotten to those)

    • regardless of which hierarchy these mixed terms go, we’ll add each organism indivdually also, if not already available

    • per the editorial policy these should be findings, BUT clinical and reference labs don’t usually include terms from findings hierarchy in their tables, so might have to put in organism hierarchy, if that would affect ability by commercial labs to report to PH

    • if we put in organism hierarchy, definetly would need to be in US extension, not international

    • should check with Virginia Tech how they are handling these in the vet extension (Riki has not checked that for these concepts - will do prior to asking John to add)

• 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 organism list is different between the 2, so potentially 2 LOINCs might be better, especially since they have 2 different products; Riki prefers this one, since currently they use the LOINC part code https://loinc.org/LP437401-5 in OBX-3

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

Call adjourned

12:05 PM EDT - below not discussed

Announcements

Andrea

• CMS RFI for CLIA Amendments

• https://www.federalregister.gov/documents/2026/07/16/2026-14327/medicare-and-medicaid-programs-cy-2027-payment-policies-under-the-physician-fee-schedule-and-other CMS RFI starts on page 298/719 = Request for Information (RFI) on Duplicate Laboratory Testing, Imaging, and Result Sharing and Interoperability

Do we want to comment in any way?

Emergency support for reportable conditions reporting in emergencies

Riki

• Goal is to set up a code request process (across all SDOs) for emergencies - not just US, but international (how do we ensure that Emergency Response teams include properly coded reporting in their work?) - include edcuational materials on where to find emergency release content (before offical release) / EOC is activated after specific threshold of an outbreak (need to have the information of what triggers that)

• Organizations / people to get this completed:

  • Division of Laboratory Systems at CDC - Beth Schweitzer, Manjula, Jasmine Chaitram

  • WHO

  • APHL - Chris Mangal

  • NETEC - Colleen Kraft (more responsible for clinical care of infected patients - may not be the right avenue)

  • FDA - no current contact - does NLM or CDC have any?

  • SDOs:

    • LOINCs - Regenstrief - Eza

    • organism and diagnosis codes (via SNOMED CT) - this could be authored in APHL extension, once stable name can then be evaluated for promotion into international (or US, depending on need) - NLM - John / Raja

    • ICD-10-CM - no good process for requesting content (talk to IMO) and CMS; ICD-11 (WHO) - also retrospectively would need to be added to older versions for countries that are still on those versions (CMS is the conduit for ICD)

• Development of new organism / new methods: CDC → PHL → commercial labs LDT and IVD vendors with FDA review for EUA or 510k

Update today:

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

HPV screening/confirmatory testing workflow

John

Need to find a date with Hanna - John will offer up the 8/20 and 8/27 calls

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

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 SHIELD FDA BAA Year 2

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