2024-05-02 LabMCoP Meeting Notes

Date

02 May 2024

Attendees

Present	Name	Organization
X	Nancy Cornish	CDC
X	Manjula Gama-Ralalage	CDC
X	Riki Merrick	APHL
X	Christina Gallegos	APHL
X	Amy Liu	Inductive Health / APHL
-	Raj Dash	Duke / CAP
X	John Snyder	National Library of Medicine (SNOMED CT)
	Andrea Pitkus	UW
X	Kathy Walsh	Labcorp
	Rob Hausam	Hausam Consulting
	Doug York	APHL
	Pam Banning	3M

Discussion topics

Topic	Discussed?	Notes
Updates	Yes	No topics or updates. Review specimen cross mapping table Discuss reporting Biomarkers to Cancer registries with Sandy Jones - we will send another meeting invite for May 16th.
Upcoming OOO	Yes	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
Previous Action Items		Nancy Follow up: EDTA Stopper top EDTA sufficient or do we need to specify K2 or K3? Nancy can review the list in SNOMED from John Need to check on completeness against the Anne/Nancy list (compare with ARUP) Nancy/Anne’s list is 10 years old - may not want to compare with this outdated list and use ARUP and Labcorp lists Raj: I found this at a phlebotomy certification course website: What Color Tubes Are Used for Which Tests in Phlebotomy – PhlebotomyU Here's a nice one-pager (University of Colorado Health): https://www.testmenu.com/universityhospital/TestDirectory/SiteFile?fileName=sidebar\CLNLAB-2020-03-13-Blood-Tube-Color-Chart.pdf Cleveland Clinic: Blood Collection Tubes - Collection \| Cleveland Clinic Laboratories https://phlebotomygeeks.yolasite.com/resources/PRINT OUT COMMON TUBES.pdf but color is manufacturer dependent, which is why we named the tubes by the additives there are container types in SNOMED under 706049005 \|Blood tube (physical object)\| Have a start here: https://aphlinformatics.atlassian.net/wiki/download/attachments/2018312270/ContainertypesListRikiEmailed20171013.xlsx?api=v2 K1 or K2 might be important to differentiate We should leave the top color out of it, since that is manufacturer specific Contact United Network for Organ Sharing for input on donor terms (pre-coordinated or not?) = Contact - UNOS Nancy reached out to Scott A. Brubaker (he/him/his) at the FDA. He suggested to reach out to UNOS and complete an online form: Contact - UNOS ISBT 128 \| ICCBBA \| Technical Documents Scott’s response: “When the SNOMED representative referred to the existence of “donor codes,” they might be referring to the ISBT-128 coding standard that’s managed by ICCBBA. Please see their website: ISBT 128 \| ICCBBA, and navigate to view their technical documents: ISBT 128 \| ICCBBA \| Technical DocumentsFDA’s regulations for human cells, tissues, and cellular and tissue-based products (HCT/Ps) in 21 CFR part 1271 require assignment of a “distinct identification code” to facilitate tracking HCT/Ps (see 21 CFR 1271.290(c)) but I don’t believe this is relevant to your question.” Might be a topic for SNOMED International We may need to reach out to laboratories/industry to see if the donor codes are needed (we need to show that these codes are needed.) Amy follow up - check if she has all of these nasal sinus fluid definition surgical insertion site peritonealDialysisTunnelSite surgical insertion site peritonealDialysisSite Riki’s Follow up: liquid-based cytology specimen vial = https://us-request.ihtsdotools.org/#/requests/preview/354843?fromList=truehttps://request.ihtsdotools.org/#/requests/edit/786429 submit a code for formalin10 work with John new term for pacemaker insertion site sample in SCT there are only swabs for insertion sites (line, drain, chest tube, vascular catheter) - this should be fixed we should model it after 435971000124108 \| Body fluid specimen from peritoneal dialysis insertion site (specimen) and require method, which should be aspirate 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 IDSA has a guidelines for wound cultures (deep and superficial - related to surgical wounds) - link sent to Amy 460621000124104 \|Superficial surgical incision wound (morphologic abnormality)\| - created in US extension in 2019. Is this needed? If so, then LabMCoP/APHL should promote it to SNOMED International to retain US SNOMED identifier. John submitted this to be promoted: https://request.ihtsdotools.org/#/requests/edit/959920?fromList=true SNOMED guidance related to morphological abnormality: Morphologic Abnormalities vs. Findings - SNOMED CT Editorial Guide - SNOMED Confluence
Specimen CMT - review of terms with questions	Yes	5/2/2024: Gastric Tube - do not use term (not appropriate for culture) Broad term. There are different types of gastric tubes (i.e., nasogastric tube, tube that goes through the abdominal wall, etc.) you do not want to culture them or the site culture stomach secretions for babies with TB (constantly coughing and swallowing sputum) Use gastricfluid_gastronomytube or gastricfluid_nastogastricdrainage terms Preferred term would be GastricFluid_Drainage TubingTip (IV catheter) - do not use term generic term - we have other related terms must be collected sterile is this a device sample (before being used)? (i.e., environmental sample) UrineCatheter generic term - is it referring to indwelling catheter? pull in same fields as catheterTip_IndwellingCatheter Wound_PostSurgical encourage aspirates, discourage swabs collect only if there is cardinal signs of infection: redness, swelling, heat, and pain use surgical wound SCT code: (112633009 \|Surgical wound (morphologic abnormality)\| - it implies surgery had taken place ArterialBlood_PeripheralArterialCatheter_PosteriorTibialArtery Do we include source site and spatial orientation or specimen? drawing blood from arterial catheter is not encouraged It should be fully coordinated. SPM-10: 13363002 \|Structure of posterior tibial artery (body structure)\|
CALL ADJOURNED	Yes	@ 1:00pm ET
Specimen CMT pilot implementers	No	Review where we are: Vendor Connections no update
Specimen CMT - Hosting Options	No	How can we publish the content in the dB? Allow access somehow to query the dB as access or excel or csv Using FHIR conceptMap similar to Conceptmap-example-specimen-type - FHIR v6.0.0-cibuild - based on this profile: ConceptMap - FHIR v6.0.0-cibuild riki.merrick to ask Eric if he still has that or how he built it: ANSWER FROM ERIC: if you look in the xml source Conceptmap-example-specimen-type.xml - FHIR v6.0.0-cibuild . you can see how it is mapped. I am not sure if you mean the table rendering or creating the concept map from a spreadsheet or CSV file. The FHIR build tool did the table rendering for that mapping, I think I entered the data by hand, or Grahame did it. It would not be hard to create a script to create a concept map from an excel or csv file if needed. The table needs to be large enough to make it worthwhile though. you could even create formula cells in the spreadsheet to generate the XML or json for each item. and then copy to a text editor and append to the Metadata fields. There will be a call Clinical Architecture on May 3rd to discuss moving specimen CMT to Symedical Manjula will take a look at the concept map
Specimen CMT - education	No
Specimen CMT - tracking implementation impact Setting baseline Define metrics	No
Specimen CMT - Compare to NHS Medical Terminology testing	No
LOINC to SNOMED CT mapping	No
Reporting Biomarkers to Cancer registries	No	National Program of Cancer Registries (NPCR) \| CDC Sandy Jones will put together a one-pager - Nancy will reach out
Future projects for this call after CMT	No	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 (i.e., Specimen Condition table, etc.)

Chat:

Nancy @ 12:22pm: What is Gastric Fluid Analysis? –Purpose, Procedure, Result (http://anavara.com )

Kathy @ 12:23pm : Definition: Gastric culture is a test to check a child's stomach contents for the bacteria that cause tuberculosis (TB).How the Test is Performed: A flexible tube is gently placed through the child's nose and into the stomach. The child may be given a glass of water and asked to swallow while the tube is inserted. Once the tube is in the stomach, the health care provider uses a syringe to remove a sample of the stomach contents. The tube is then gently removed through the nose. The sample is sent to a lab. There, it is placed in a special dish called a culture medium and watched for the growth of bacteria. https://www.ucsfbenioffchildrens.org/medical-tests/gastric-culture

Nancy @ 12:38pm: Clinical Practice Guidelines for the Diagnosis and Management of Skin and Soft Tissue Infections: 2014 Update by IDSA (http://idsociety.org )

John @ 12:42pm: 112633009 |Surgical wound (morphologic abnormality)|

Nancy @ 12:47 (email): Clinical Practice Guidelines for the Diagnosis and Management of Skin and Soft Tissue Infections: 2014 Update by IDSA
VII. What Is the Preferred Management of Surgical Site Infections?

Suture removal plus incision and drainage should be performed for surgical site infections (strong, low).
Adjunctive systemic antimicrobial therapy is not routinely indicated, but in conjunction with incision and drainage may be beneficial for surgical site infections associated with a significant systemic response (Figure 2), such as erythema and induration extending >5 cm from the wound edge, temperature >38.5°C, heart rate >110 beats/minute, or white blood cell (WBC) count >12 000/µL (weak, low).
A brief course of systemic antimicrobial therapy is indicated in patients with surgical site infections following clean operations on the trunk, head and neck, or extremities that also have systemic signs of infection (strong, low).
A first-generation cephalosporin or an antistaphylococcal penicillin for MSSA, or vancomycin, linezolid, daptomycin, telavancin, or ceftaroline where risk factors for MRSA are high (nasal colonization, prior MRSA infection, recent hospitalization, recent antibiotics), is recommended (strong, low). See also Tables 2 and 3.
Agents active against gram-negative bacteria and anaerobes, such as a cephalosporin or fluoroquinolone in combination with metronidazole, are recommended for infections following operations on the axilla, gastrointestinal tract, perineum, or female genital tract (strong, low). See also Table 3.

John @ 12:55pm: 13363002 |Structure of posterior tibial artery (body structure)|

Recording:

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