Questions on assigning LOINC codes in microbiology

Good afternoon,

I have some questions regarding the best way to approach assigning LOINC codes for Microbiology. We will be using Bedrock (Cerner Millennium). I’m wondering if anyone has had some experience they can share.

Here are my questions:

1.For orderables that include both a culture and gram stain: (Ex. CSF culture and gram) Should I assign that orderable 2 LOINC codes? (one LOINC code for the gram stain and one for the culture)

2. Choosing a Method Type: There are a variety of method types to choose from (Culture, aerobic culture, respiratory culture, etc). Would there be anything wrong with assigning all cultures with a method type of “Culture” and “Organism Specific culture” or is it better to be more specific when you can?

3. Assigning an Organism Type: The organism type choices are: Bacteria, Yeast, Fungus, Mycobacteria. How do I choose? In most Micro cultures any of those things could be isolated. For example, a Blood culture…My guess is that I would choose Bacteria Identified (since it is mainly a bacterial culture) but what are the implications on the other end if a Yeast is what grew? We don’t want to report out incorrect information. I have the option of reporting out ‘Microorganism identified’ rather than ‘Bacteria identified’ but if I choose that I will lose the source information for the culture as the only source choice for ‘Microorganism identified’ is ‘XXX’. Is the source mapped somewhere else? and if so, how?

4. Report type: We have 2 options for report type: ‘Gram stain’ or ‘Non-stain report’. How should I assign ‘stains’ that are not ‘gram stains’ (KOH, AFB, etc). I guess I would assign them as Non-stain?

5. How does LOINC work for negative cultures? We wouldn’t want these sent across with a LOINC code saying “bacteria identified” if they didn’t grow. Is it the positive flag on a culture that triggers this?

I apologize if these questions are basic. I am a microbiologist (not a computer specialist) just trying to get a better understanding of how LOINC works for Micro cultures. Any feedback would be appreciated. Thanks

I will give my opinion on your questions and allow others to chime in:

  1. Not clear on what you mean by assinging two LOINCs to the orderable, but if you are going to result both the culture results and the gram stain, (which is the usual practice, no?), the result set will contain two LOINC terms representing the culture and the gram stain. Bottom line is that whatever you are going to report, you need a corresponding LOINC code. If the processes are just part of an overall analysis and only the final result is reported, then you do not need the intermediate codes.

  2. Choose a method type that fully specifies what method you used, but no more. For example, “organism specific culture” implies that you are looking for one particular organism type and no others. These will often have a result set of “detected”, “not detected” or a nominal list of species of a particular bacterial genus. Aerobic cultures will have a nominal result set of organisms that can be cultured aerobically (thus no Clostridium sp. or other anaerobes). To my mind this would also include facultative aerobes. Culture is the least specific and more flexible in reporting the method used and implies that you actually tried to grow the organism, but not the specific method of growth.

  3. If you would be reporting any yeast or fungal growth out of a blood culture, then “Microorganism identified” wouldbe the most appropriate. Again, the LOINC you choose depends ont he value set for the results. You cannot (should not) use a LOINC code for “bacteria identified” and then report out a fungal organism. As for the source, the specimen information may be transmitted in a number of other places (e.g. OBR-15 or the SPM segment).

  4. This sounds like a limitation of your system as opposed to a limitation of LOINC. Stains are stains and you shouldn’t report a non-stain report for a stain result.

  5. LOINC works the same way for negative cultures as for positive, except that the result indicates a failure to detect an organism. This is dependent on the result value set that you have for the LOINC observation. It is perfectly fine to say “Bacteria identified = none (negative)”

    Hope this helps,


That is very helpful. Thank you so much for your post.

I have one more question regarding #3.

I found the following on the LOINC website FAQ (from 7/28/2008):

“Question: The LOINC terms in Microbiology appear to be based on what is identified, which can’t be known a priori. How should I map my culture terms?

Answer: The LOINC model for routine cultures is “Bacteria identified:Prid:Pt::Nom:Culture”, where = urine, stool, blood, etc.

So, for example, a routine urine culture, would be mapped to this code:

630-4:Bacteria identified:Prid:Pt:Urine:Nom:Culture

Long Common Name: Bacteria identified in Urine by Culture

For most routine cultures the users are looking for bacteria. Such cultures may also grow out some fungii, and if so they too would also be reported under this test name. But, the cultures would not be optimized for growing out fungi hence our bacteria-focused name.”

This seems to contradict using a generic ‘Microorganism identified’ response in cases where things other than Bacteria may be reported out.

I have also seen suggestions to assign multiple LOINC codes to single order catalog item. For example, in the case of a blood culture (where bacteria, fungus, yeast, and/or mycobacteria may be reported out) the suggestion was to assign like this:

600-7: Bacteria identified:Prid:Pt:Bld:Nom:Culture AND

601-5: Fungus identified:Prid:Pt:Bld:Nom:Culture AND

533-0 Mycobacteria identified:Prid:Pt:Bld:Nom:OrganismSpecificCulture

Is there a right or a wrong way to approach this? Or is it just personal preference?

Any feedback would be appreciated. Thanks

It’s not so much personal preference of the person mapping, it’s the individual intent of the performing laboratory. We take it from the laboratory’s approach to their media setup for a particular order, and what they normally report out. If a local code, such as UR CULT is only looking for bacteria in a urine culture, the 600-7 code fits.

If a laboratory has a local code for immunosuppressed patients, such as BURN CULT, and they set up media for bacteria, fungus and mycobacteria all under the one local code, then the Microorganism identified approach fits better. 11475-1

Hope this helps!

Thanks for the reply.

Our main intent, using the example of Blood culture, would be to isolate bacteria. We do not routinely add fungal or mycobacteria media. However, we occasionally see yeast, fungus and even mycobacteria grow out of these routine cultures. Although we are primarily looking for bacteria, we do report out whatever may grow.

Since these are mainly bacterial cultures would it be appropriate to use the ‘Bacteria identified’ code?

Or is it more appropriate to use ‘Microorganism identified’ since there may be things other then bacteria that will be reported out from the culture?

If you are using routine culture media, it is appropriate to use the “Bacteria identified” terms.

We are in the process of testing some of the LOINC codes that we have built for Microbiology and have run into a problem. Our system (Cerner) is only able post a LOINC code for cultures that have an organism ‘linked’ within our online workcard. It will not post a LOINC code for negative cultures or any cultures with positive responses written in the culture report.

My understanding was that LOINC codes should post for all cultures (both positive and negative) and that the culture report text would appear in the HL7 message. Are my expectations wrong? Shouldn’t LOINC codes be posted for all tests that were ordered not just for tests that have an organism present. Is this a limitation of our system or were my expectations incorrect?

Any help would be appreciated.