3.4 Microbiology

3.4.1 Microbiology cultures

The inherent complexity in reporting microbiology culture results presents unique challenges for the goal of standardized observation names.

3.4.1.1 Result status

The result status (Preliminary, Final) should not be reported as a separate observation or as part of the name. It should be reported in the Result Status field (OBR-25) of the HL7 OBR segment.

3.4.1.2 Specimen

The specimen type (Serum, Blood, Urine, etc.) will be indicated in the HL7 OBR segment with the Specimen Source field (OBR-15), but may also be represented in the name.

Details of specimen collection will usually be noted as OBX segments or comment segments that accompany the culture result message. The observation identifier for the OBX segment will have the fully specified name of “Specimen collection description:Find:Pt:*:Nom” and the Observation Sub-ID field will be used to order or group sets of observations. That is, if the material was collected by swabbing a wound of the right upper arm, multiple OBX segments would be created, each with the name “Specimen collection description:Find:Pt:*:Nom” and the Observation Results fields of the OBX segments would contain respectively “Swab,” “Right,” “Arm,” and “Wound.” (The granularity of the actual terms used in the specimen description is at the discretion of the user. Thus, “Right Arm Wound” as the value of a single OBX segment could be used in place of the three codes described in the previous sentence.)

3.4.1.3 Descriptive results

Descriptions of measurement and culture growth will be noted as separate OBX segments that accompany the culture result message. The name of the observation identifier will provide the context of the observation. For instance, the name for a quantitative test of bacteria in a specimen would be:

Colony count:Num:Pt:XXX:Qn:VC

Descriptions of Gram stain findings will be noted as OBX segments that accompany the culture result message. The name of the observation identifier will be:

Microscopic observation:Prid:Pt:XXX:Nom:Gram stain

The result values that could be reported with this test (which is a multiple-choice, multiple answer type or observation) might include one or more of the following:

• Epithelial cells
• Gram-positive cocci in chains
• Many Gram-negative diplococci

3.4.1.4 Culture results

The organisms identified in a culture will be sent as result values in OBX segments. LOINC provides codes to identify the observation, but not for identifying the names of organisms that would appear as result values (i.e. in OBX-5). SNOMED CT is an appropriate source for these organism concepts.

While “Throat Culture” is the source of the culture inoculum, it is also a label that indicates what kind of media was inoculated and the other techniques used in the laboratory. So, it is a short hand for a kind of method and such will be recorded as the Method part of the name. Thus, “Throat Culture”, “Blood Culture”, and “Clostridium difficile Culture” all represent labels for how a culture was performed.

The LOINC naming model for routine cultures is:

Bacteria identified:Prid:Pt::Nom:Culture

Example names include:

Bacteria identified:Prid:Pt:Bld:Nom:Culture

Bacteria identified:Prid:Pt:Burn:Nom:Culture

Bacteria identified:Prid:Pt:Stool:Nom:Culture

The LOINC names for cultures are based on the expected observations they generate, e.g. “bacteria identified” or “virus identified”. For most routine cultures the users are looking for bacteria. However, in some cases a routine culture may also grow out some fungi like yeasts. Such observations can also be reported under the same test code. But, since the culture would not be optimized for growing out fungi we have a bacteria-focused name.

It is worth emphasizing these culture terms are intended for use as both as orders and observations despite having a more result-oriented name. Furthermore, as a matter of good clinical practice, most laboratories perform susceptibility testing on any significant isolate on a reflex basis. So there is no need for codes that say “culture and sensitivity” because it is implied. Thus, an order for:

17928-3 Bacteria identified in Blood by Aerobe culture

would likely trigger several workflow steps, including bottle blood culture, bacteria isolation, identification, and antimicrobial susceptibility testing.

LOINC names for Methods of staining a sample/material directly (where many descriptive observations are possible) include:

Microscopic observation:Prid:Pt:XXX:Nom:Gram stain

Microscopic observation:Prid:Pt:XXX:Nom:Dry mount

Microscopic observation:Prid:Pt:XXX:Nom:India ink preparation

Microscopic observation:Prid:Pt:XXX:Nom:Trichrome stain

Microscopic observation:Prid:Pt:XXX:Nom:Giemsa stain

Names for results of staining procedures performed on organisms that are growing in culture will use Isolate as the System (sample type). For example:

Fungus identified:Prid:Pt:Isolate:Nom:Fungal subtyping

Names for organism-specific cultures:

Brucella sp identified:Prid:Pt:Bld:Nom:Organism specific culture

Bordetella pertussis:PrThr:Pt:Thrt:Ord:Organism specific culture

Chlamydia sp identified:Prid:Pt:Gen:Nom:Organism specific culture

Legionella sp identified:Prid:Pt:Sputum:Nom:Organism specific culture

Note if a test applies to a specific species of organism, the Component should include the genus AND species (at least). If the measure applies to a series of species in the same family the string “sp” must be included. If it applies to as subgroup of the genus, then that subgroup should be named.

Names for Method for general class of organism:

Fungus identified:Prid:Pt:Wound:Nom:Culture

Bacteria identified:Prid:Pt:CSF:Nom:Culture

Again, the Result Value of these tests would be either organism names or other statements of culture outcome. The table below contains valid values of the culture result from the HL7 OBX segment:

Table 15: Example Culture Results

3.4.2 Property values for culture terms

Presence or Identity (Prid) as a Property should be used when the value of a test can identify one set of alternative infectious agents. If the culture is for herpes virus and the culture can have results of herpes virus 1, herpes virus 2, etc., then Prid is the right Property. If the culture is for herpes virus and the answer is positive/negative or yes/no, then the Property should be presence (PrThr) and the Scale ordinal (Ord).

3.4.3 Microorganism identification based on nucleic acid targets

PCR-based testing for the presence of microorganisms is becoming more common. Early on, we received requests for and created codes with Components such as Acinetobacter baumannii DNA or Influenza virus RNA. More recently, we have received requests for tests that detect bacteria, viruses, and other pathogens based on a specific genetic target. Thus, LOINC now contains terms with more specific Components such as Clostridium difficile toxin A+B (tcdA+tcdB) genes and Zika virus envelope (E) gene.

As genetic testing continues to evolve, distinguishing the specific analyte (i.e. the genetic target) will be important for understanding the differences between tests, interpreting the results, and guiding further testing. Therefore, we will continue to create new LOINC codes that specify the gene targets, and ask requesters of new LOINC codes to supply this information. This specificity is important for bacterial identification, but also for other pathogens.