We are moving forward in implementing LOINC in Oman and would like to clarify few issues we encountered during the mapping process.
Culture Test Order Codes… In our LIS we have different culture tests based on the type of specimen. For example, ‘Urine Culture’, ‘Sputum Culture’ etc. We could not find all of these tests in the LOINC database with similar name. We have found two ways of mapping such tests.
Option 1 : -Map the order tests to respective ‘Bacteria identified’ codes in LOINC. For example, ‘Urine Culture’ to ‘630-4 Bacteria identified in Urine by Culture’. ‘Sputum Culture’ to ‘6460-0 Bacteria identified in Sputum by Culture’
Option 2 : All the routine culture will be ordered as a 6463-4 (Bacteria identified in Unspecified specimen by Culture) and the specimen type will not be part of the code ( will be mentioned separately in HL7 OBR). As we need to mention specimen/site type separately in HL7 message, is there any other issue in mapping all Routine Culture tests to a single LOINC?
So please give your opinion. Is this the way culture orders should be mapped? Or is there any other better way? Please share your experience and knowledge.
Hello and thank you for asking about microbiology culture tests. If our clients’ systems have unique local order codes to support being tied to separate LOINC codes, I would suggest option #1. Most of our clients use this option, augmented with the organism specific screens/cultures for Strep pyogenes, MRSA, E Coli O157, etc.
One situation to ascertain beforehand is that the routine blood culture does only identify bacteria, in order to use the “Bacteria Identified” series of LOINC codes. If the cultures will also identify fungi, viruses, or non-bacteria, there is LOINC code 11475-1 Microorganism identified:Prid:Pt:XXX:Nom:Culture and
for the non-cultures there is 41852-5 Microorganism or agent identified:Prid:Pt:XXX:Nom:
Where there is not an appropriate LOINC code for the specimen source from your listing, post the individual display names here, and we’ll try to help you before determining if it’s necessary to submit a new request to Regenstrief.
If our clients’ systems use only one code for cultures, one code for stains, etc, we will use option #2 to map to LOINC. The granularity of the messaging and the resulting repository is further restricted by not having a full complement of specific LOINC codes. But until those client’s LIS vendors build their micro systems to support this, the clients cannot move forward in meaningful use.
Best Regards,
Thank you Ms. Pam Banning for the information on Culture Test mapping.
I also would like to know how Histopathology Tests are mapped in LOINC. We have two different LIS in our organization.
In System 1, the Histo tests are coded based on the tissue/site type. For example ‘Biopsy - Appendix’, ‘Biopsy - Kidney’ etc.
In System 2, there is only one test called ‘Histopathology Examination’ and the requesting clinician has to mention the sites/tissues separately.
I could not get any information from the manual or from internet about coding of Histo tests in LOINC. So please share your knowledge.
Thank you very much for the reply. Following are few culture tests that we could not map to LOINC. Please advice.
EAR SWAB CULTURE
EYE SWAB CULTURE (Similar to 609-8 (Bacteria identified in Eye by Aerobe culture) but method as ‘Culture’)
Hydrocele Fluid Culture
PEADIATRIC BLOOD CULTURE
Middle Ear Fluid Culture
Vitreous fluid Culture
Anterior Chamber Fluid Culture
Corneal Ring (Donor) Culture
Corneal Ring (Recipient) Culture
Nasal Swab Culture
Vaginal Culture - (Similar to 11261-5. But method as ‘Culture’)
There are few Microscopy tests also that we could not map. for eg. ‘Bile Microscopy’,
‘Sinus Microscopy’,
‘Anterior Chamber Fluid Microscopy’,
‘Vitreous fluid Microscopy’,’ Corneal Scrapping Microscopy’,
‘Middle Ear Fluid Microscopy’,
‘Pericardial Fluid Microscopy by Gram Stain’,
‘Hydrocele Fluid Microscopy’,
‘Amniotic Fluid Microscopy’ etc.
Would suggest there be a subject matter expert from your laboratory to assist in choosing some mappings. As mentioned in the LOINC Guide, the intent of LOINC is to serve as an additional Observation Name, and to accompany the local display in the HL7 message.
EAR SWAB CULTURE - unless your lab offers more than aerobic bacteria searches, 608-0 should suffice
EYE SWAB CULTURE (Similar to 609-8 (Bacteria identified in Eye by Aerobe culture) but method as ‘Culture’) - would opt for 609-8 unless other microorganisms are included in the search
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Hydrocele Fluid Culture -
PEADIATRIC BLOOD CULTURE
Middle Ear Fluid Culture
Vitreous fluid Culture
Anterior Chamber Fluid Culture
Corneal Ring (Donor) Culture
Corneal Ring (Recipient) Culture
For each of the above, would use either the larger eye or ear structure, and let the local report display that accompanies LOINC describe the more specific anatomic part. Same for Pediatric vs Adult designations.
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Nasal Swab Culture - use either nose or nasopharnyx as the specimen type; doublecheck with lab on what they collect. Aerobic or anaerobic culture types should also be confirmed by the subject matter expect in the lab.
Vaginal Culture - (Similar to 11261-5. But method as ‘Culture’), would use 11261-5, until other microorganisms may also be reported.
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There are few Microscopy tests also that we could not map. for eg. ‘Bile Microscopy’,
‘Sinus Microscopy’,
‘Anterior Chamber Fluid Microscopy’,
‘Vitreous fluid Microscopy’,’ Corneal Scrapping Microscopy’,
‘Middle Ear Fluid Microscopy’,
‘Pericardial Fluid Microscopy by Gram Stain’,
‘Hydrocele Fluid Microscopy’,
‘Amniotic Fluid Microscopy’ etc.fahadfax
would use the Microscopic Observation component series for these microscopy tests; go with either the specific stain they use on that assay, such as
664-3 Microscopic observation:Prid:Pt:XXX:Nom:Gram stain, or
27112-2 Microscopic observation:Prid:Pt:Body fld:Nom:Gram stain
for the substructures of the ear or eye, would use the larger structure name.
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We also use the 48767-8 Annotation comment to portray either a special request from the provider on what to look for or what the sample is, in addition to serving as a note from the lab back to the provider on what was looked for or performed. Sometimes the lab compendium will include a “Special Request” field that the provider can attach to any order. The description in RELMA for this code is “This is an observation code indicating that a particular observation represents a free text annotation comment that can be appended to some other observation such as a lab result.”