coding of molecular diagnostic test

Could anyone elaborate on how to code molecular diagnostic tests in microbiology. ie we currently use an in house pcr assay to detect Campylobacter in stool. The molecular test detects only Campylobacter species associated with diarrhea but does not detect all Campylobacter species. What code shall we use or request. The same question holds for the combined shigella-EIEC PCR. Basis o f this question is that a lot of these test are custom and they sometimes detect groups of microorganisms crossing species an genus barriers.

We have recently decided to include the gene name(s) in the component along with the organism name when the gene is specific for one species or genus or the word “bacterial” when the gene crosses different species.

For example:

  • Staphylococcus aureus enterotoxin B (seb) gene (PROPOSED)
  • Bacterial aminoglycoside resistance (aacA) gene
  • Bacterial shiga-like toxin 1 (STX1) gene

    Hope this helps

My questeion is slightly more complicated. In this regard there are two different kind of PCR test. The gene solution only works when a PCR is designed to detect every copy of the gene (cross species or genus). ie primers are designed on a conserved region within a gene. In the case of our campylobacter pcr, primers are designed on a less conserved region of the genome in such a way that it is specific for a certain subset of campylobacter sp. (those associated with diarrea). Therefore it is not correct to describe the test as gene specific since copies of the same gene in different species are not detected.

Can you give me a little more detail about the gene you are looking at - what makes it the “diarrhea-producing Campy species only”? And if it is not in the conserved region of the gene, then how do you know you are not missing some due to mutation, that still cause diarrhea, but won’t come up - or does Campy not mutate very frequently (sorry I work with Influenza a lot)? May be with a little more information I could help.

The campylobacter PCR targets the 16S gene that is present in all bacteria. However the primers are designed in such a way that it only detects a specific subset of campylobacter species. (The PCR is not yet published so I can’t provide more detail at the moment).

A different PCR that illustrates the question is the Aspergillus PCR. This PCR is based on an intergenic region since the diversity within genes is not high enough to make even a genus specific PCR (eukaryotes make far less mistakes during DNA replication). Therefore it does not even target a gene so including the gene name is not possible. Different PCR’s are currently in use that all target an intergenic region with different primer sets. The different PCRs differ in their specificity. Some not only detect specific Aspergillus species but also some Penicillium species. Our PCR is Aspergillus fumigatus specific but does not detect other Aspergillus sp. How can we code both pcr’s within LOINC?

Might it be an idea to include the primers used within LOINC since PCRs using different primer sets are most likely to have different specificities and sensitivities and therefore require an unique LOINC code.

Anyone? I really need some answers on this issue!

It appears that no existing LOINC code fits your purpose, so I suggest that you submit a request for new terms. Please review Appendix D of the LOINC User’s guide for guidance on how to request new terms.