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Hello Leigh,
1. One variable I didn’t read in your message was how your LIS or LIMS handles microbiology cultures. Did you look at the outbound OBX in HL7 to see the pattern? Another way to see the pattern if they’ve exported the directory into a list for Excel is to sort the table by the result interface code identifier. Some systems only hold CULT, MIEX and SUSC result elements for each order. The system would use those three result fields over and over again when building the different types of cultures performed. You’d see that in the Excel sort (many rows of CULT bunched together with the different orders to the left of each row).
BLDC (Blood Culture) = CULT, MIEX and SUSC
URC (Urine Culture) = CULT and SUSC
AFBC (Acid Fast Bacillus Culture) = CULT, MIEX and SUSC (although different type of stain and certainly different antibiotics)
If your system uses the same result fields over and over across all the cultures, you’d want to use
CULT – 41852-5 Microorganism or agent identified in Specimen
MIEX – 11546-9 Microscopic observation [Identifier] in Specimen by Other stain
SUSC – 23658-8 Other antibiotic [Susceptibility]
On the order side in this same system, the lab could use the specific LOINC code for Blood culture, Urine culture and AFB culture.
BLDC (Blood Culture) = 600-7 Bacteria identified in Blood by Culture
URC (Urine Culture) = 630-4 Bacteria identified in Urine by Culture
AFBC (Acid Fast Bacillus Culture) = one of the source-specific Mycobacteria sp identified by Culture
The susceptibility is an add on entry if positivity threshold of the culture is reached; it contains it’s own OBR and OBX records in HL7.
2. Most systems don’t allow LOINC changing on the fly for unexpected results. If yeast can grow on the media and the order was for Urine Culture, the LOINC code is premapped at 630-4 (expecting bacterial results most of the time) and hopefully the lab has their organism table mapped to SNOMED CT codes for the genus or genus/species of the organism detected.
3. Your last question on Culture and Sensitivity of wound with Gram Stain needs to have the consideration of #1 above. Does the system have different result fields for different gram stains?
6462-6 would be correct for a Wound culture. The stain answer hinges on the LIS build for gram stains (only one or many source specific). It could be either 664-3 Microscopic observation [Identifier] in Specimen by Gram Stain OR 10357-2 Microscopic observation [Identifier] in Wound by Gram Stain
Overall when mapping a Microbiology Department, you should be finding a pattern of the build which greatly assists in deciding to go very granular or being forced by the LIS to be very general (non-specific). LOINC will support either use case. I often suggest people start a LOINC project by mapping Micro to get comfortable. Remember to run a quick audit with each LOINC release AND be sure to be notified when a new Micro entry is built in your system in order to get LOINC embedded. Good luck with your project!
Very glad to help. Just volunteering to help shape the attributes. We still rely on you, Francois, to make the submission with the denoted publications.
All the best,
Pam
Hello again Francois,
A few other thoughts on this:
1. The method of microscopy.light.hpf could account for the .HPF instead of in the component, but I think using a method of Prussion Blue stain is more descript. It may be considered a given that in studying erythroblasts we are on the higher objective lens.
2. In order to get the # granules (Type) into the component, you may want to consider Siderocytes.Type I/100 Erythroblasts as the component. The four qn terms might look like this:
Siderocytes/100 Erythroblasts:NFr:Pt:Bld:Qn:Prussian Blue stain
Siderocytes.Type I/100 Erythroblasts:NFr:Pt:Bld:Qn:Prussian Blue stain
Siderocytes.Type II/100 Erythroblasts:NFr:Pt:Bld:Qn:Prussian Blue stain
Siderocytes.Type III/100 Erythroblasts:NFr:Pt:Bld:Qn:Prussian Blue stain
Thank you for the stimulating conversation; I never had the opportunity to run this assay in my past experiences.
Hello Francois,
I only located siderocytes and various normoblasts (basophilic, orthochromic or polychromatophilic) in LOINC 2.69. The Haematologica article is a great reference; I wonder if you have another one that describes the type I, II and III when you request their creation.
All the best,
Pam Banning
Hello Bram,
The key in a local system is whether there are different LIS entries for antibiotics used in typical MIC vs Slow growing MIC OR the system has the capability to use the order and antibiotic to store the different LOINC choices.
If there’s only one local code for Amikacin, whether it’s MIC, Kirby Bauer, Slow growing, etc then the site would need to use the methodless susceptibility term.
I’m very glad to see the past entries of the Forum are helpful!
Have a great day,
Pam
Lab LOINC Committee Chair
Hi Brittany,
My opinion only would be to include something of the process of isolating spermatozoa from the diluting urine after being redirected to the bladder? It’s not like the testes creating the semen made them in the urine instead. The delivery mechanism (a muscle lapse?) didn’t close off the bladder to urethra track, causing the semen to be directed to the bladder. So it is an unusual collection point. Maybe try system Urine.retrograde semen in your submission?
I’m not sure if Regenstrief keeps track of all rejected terms; seems like 3M did try to get them submitted back in 2014-16 era.
Hi Christopher!
I just received this message from ARUP:
I have reviewed this request and searched for an appropriate LOINC code for Mucorales by PCR . The LOINC code I would recommend is 92253-4 “Microorganism identified in Isolate or Specimen by Molecular genetics method”. I will be making the change on our test 3000352 Mucorales by PCR and the updated code will be visible in 2 to 3 business days.
Kind Regards,
J. Chad Campbell, MBA, M (ASCP)cm
Hello Itay!
I have forwarded your request to an Epic representative who attends LOINC meetings. Will pass along any information provided.
Best regards,
Pam
Hello Francois,
We have a colleague and friend in common! Riki Merrick is the lead of our Lab Community of Practice, and I understand you are her IHE PaLM co-chair. She started emailing responses with you, but for the sake of the Forum, I’ll insert a link to the Specimen Cross Mapping table and a note of current development.
The latest version of the specimenCMT is on Manjula’s (CDC) computer in a dB format – we are working through the good old spreadsheet that has outstanding questions on the LabMCoP calls on Thursdays, COVID permitting. That spreadsheet is on the APHL sharepoint site:
Riki is working with SNOMED International on getting to host the final product.
Best regards, Pam
Hello Francois! LOINC’s intent is not to be the sole source of all possible information, including source and methodology. It is intended to work alongside other standards.
Two thoughts from the specimen arena: 1. A lot of work has been performed on a Specimen Cross Mapping table through the American Public Health Laboratories’ Lab Community of Practice workgroup. This table incorporates other portions of the HL7 message format to provide additional information. This is augmentary to the LOINC specimen attribute of Body Fluid. You can find some information on it at https://www.cdc.gov/labhit/paper/2016-standardization-of-laboratory-test-coding—phi-conference.pdf If you are interested in seeing the latest release of the Specimen CMT, I will locate that for you.
2. The LOINC term 31208-2 Specimen source identified is the most commonly used LOINC term. This demonstrates laboratories using one additional field to portray more information about the specimen used in this assay.
If your site is not using HL7 or a laboratory information system, the above options may not help record a specimen such as “fluid from an ovarian cyst”.
Best regards & Happy New Year!
Hello Francois! LOINC’s intent is not to be the sole source of all possible information, including source and methodology. It is intended to work alongside other standards.
Two thoughts from the specimen arena: 1. A lot of work has been performed on a Specimen Cross Mapping table through the American Public Health Laboratories’ Lab Community of Practice workgroup. This table incorporates other portions of the HL7 message format to provide additional information. This is augmentary to the LOINC specimen attribute of Body Fluid. You can find some information on it at https://www.cdc.gov/labhit/paper/2016-standardization-of-laboratory-test-coding—phi-conference.pdf If you are interested in seeing the latest release of the Specimen CMT, I will locate that for you.
2. The LOINC term 31208-2 Specimen source identified is the most commonly used LOINC term. This demonstrates laboratories using one additional field to portray more information about the specimen used in this assay.
If your site is not using HL7 or a laboratory information system, the above options may not help record a specimen such as “fluid from an ovarian cyst”.
Best regards & Happy New Year!
Hi Christopher,
We always recommend asking the performing lab for the LOINC code. I’m going to forward your message to their LOINC team, and they will get back to you. Thank you for asking!
Pam
Hi Christopher!
My recollection is that buccal swab collections for genetic testing are included in BLD/TISS systems. The individual cells provide the DNA used for testing.
Thanks for asking,
Pam Banning
Hello Malarkodi,
The next release content may be seen through loinc.org/prelease and loinc.org/submissions/queue with a status of Done. I can see one SARS coronavirus 2 spike protein RBD Ab.neut (96603-6)
Literature does reveal immunity effective differences between the spike and nucleocapsid proteins of SARS coronavirus 2. At this moment, submissions from the industry have not been made for new terms at a more specific Component to this level of detail. The team is working with industry and US government to plan for more development in the future.
Stay tuned!
Pam Banning
Lab LOINC co-chair
