Microbiology mapping

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    Leigh Lemons

    I have a few questions regarding mapping of cultures and sensitivity with and without gram stains.

    In the Microbiology guide for using Loinc terms it seems that you can map to Bacterial identified even if you identify a yeast of fungus or virus if identified. I read somewhere else that in that case you should report out Microorganism identified. I am new at this process and need some assistance. We also have codes for cultures with and without gram stain would they be linked to same loinc code or would you link to culture and the stain if it contains a gram stain.

    They order blood culture  loinc 600-7 and if fungus grows they would report it. Is that appropriate

    They order Culture and Sensitivity of wound with Gram Stain should it be coded as 6462-6 and 664-3?


    Thanks for any assistance


    Pam Banning

    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!


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