Logical Observation Identifiers Names and Codes (LOINC​®​)

Guide for Using

LOINC Microbiology Terms
VERSION 1.1

Edited by: Swapna Abhyankar, MD

Mary Zabriskie, MLS(ASCP)
David Baorto, MD, PhD
Daniel Vreeman, PT, DPT, MS, FACMI

Questions and Comments: [email protected]

Website: loinc.org

THIS WORK WAS SUPPORTED BY THE

U.S. FOOD AND DRUG ADMINISTRATION
CONTRACTS HHSF223201710178P AND HHS223201810268P.

COPYRIGHT © 2019 REGENSTRIEF INSTITUTE, INC. ALL RIGHTS RESERVED.

Table of Contents
1 Introduction 7
1.1 Background about LOINC 7
1.2 Scope of this Guide 8
1.3 Organization of this Guide 8
1.4 Utilizing existing LOINC mappings 10
1.4.1 Reference laboratories’ mappings 10
1.4.2 In vitro diagnostics (IVD) vendors 10
1.4.3 National health systems 10
1.5 Feedback and Future versions of this Guide 11

2 Conventions used in this guide 12

2.1 Part types and names 12
2.2 Part type and name tables 12
2.3 OBX segments 13
2.4 LOINC code and name pairs 15
2.5 Key points and Evolving models 15
2.6 Citations 15

3 Microscopic examination 16
3.1 Light microscopy 17
3.1.1 Microscopy to identify the characteristics or type of organism present 17
3.1.2 Microscopy to identify the presence or absence of a specific organism 18
3.2 Stains 18
3.2.1 Stains that help identify the characteristics or type of organism present 19
3.2.2 Stains that help identify the presence of a specific organism 20
3.3 Wet/KOH Preparations 21
3.3.1 Wet or KOH preparations that help identify the type of unknown organism 21
3.3.2 Wet or KOH preparations that help identify the presence of a suspected organism 22
3.4 Thick and thin films 23
3.5 Ova and parasite (O&P) 24

4 Cultures 26
4.1 Specimen-specific requirements 27
4.2 Routine culture to detect and identify an unknown organism 29
4.3 Organism-specific culture to identify the presence or species of a suspected organism 30
4.3.1 Presence or absence of a suspected genus or species 31
4.3.1.1 Screening cultures for drug-resistant organisms 31
4.3.2 Detecting and identifying the specific species of suspected organism 32

Guide for Using LOINC Microbiology Terms ​• 2

 4.4 Colony counts 33

5 Susceptibility testing 35
5.1 Phenotypic susceptibility testing 35
5.1.1 Bacterial or fungal phenotypic susceptibility testing 37
5.1.2 Susceptibility testing for slow-growing bacteria 38
5.1.3 Viral phenotypic susceptibility testing 39
5.1.4 Susceptibility thresholds based on type of infection (“Breakpoints”) 40
5.2 Phenotypic testing for resistance enzymes 41
5.3 Genotypic resistance testing 42
5.3.1 Bacterial molecular resistance testing 44
5.3.1.1 Identifying the presence or absence of a resistance gene 44
5.3.1.2 Identifying the presence or absence of a resistance-conferring mutation 45
5.3.1.3 Identifying the specific resistance-conferring mutation found 46
5.3.2 Predicted susceptibility based on molecular testing 47

6 Antigen tests 48
6.1 LOINC Methods for antigen testing 48
6.2 Identifying the presence or absence of a suspected organism 49
6.3 Identifying the specific subtype of a suspected organism 50
6.4 Quantitative antigen tests 50

7 Nucleic acid tests 52

7.1 Choosing LOINC terms with the correct Component 52
7.2 LOINC Methods for nucleic acid tests 53
7.3 Identifying the presence or absence of a suspected organism 54
7.4 Identifying the subtype or species of a suspected organism 55
7.5 Multiplex assays 56
7.6 Quantitative assays 58
7.6.1 Real-time PCR 58
7.6.2 Viral loads 58
7.6.2.1 Viral load reported as copies/volume 60
7.6.2.2 Viral load reported as units/volume 60

8 Serology testing 61
8.1 LOINC Components for antibody testing 62
8.1.1 Specifying the antibody class in the Component 62
8.1.2 Measuring acute and convalescent antibodies and vaccine efficacy 63
8.2 LOINC Methods for antibody testing 63
8.3 Testing for the presence or absence of antibodies to a specific organism 65
8.4 Quantitative antibody testing 66

Guide for Using LOINC Microbiology Terms ​• 3

 8.5 Reporting the interpretation of a serologic test panel 67

9 Mapping Qualitative Result Values 69

9.1 Linking LOINC Answer Lists to LOINC terms 70
9.2 LOINC Answers and SNOMED CT concepts 73
9.3 Ordinal result values 73
9.4 Nominal result values 74
9.5 Uncertain result values 75
9.6 Flavors of null 75

10 Choosing the right LOINC term (“mapping”) 77

10.1 Minimum test information necessary to map 77
10.1.1 Analyte, Specimen, and Method 77
10.1.2 Sample results 78
10.1.3 Units of measure 78
10.2 Additional useful data 78
10.2.1 List of abbreviations used by your laboratory in its test names 78
10.2.2 Frequency data 79
10.3 Mapping tools 79
10.3.1 Regenstrief LOINC Mapping Assistant (RELMA) 79
10.3.2 Online search application 79
10.4 General mapping principles 80
10.5 Part-specific mapping principles 82
10.5.1 Component 82
10.5.1.1 Types of antibodies 83
10.5.1.2 Microorganism antigens versus genetic targets 83
10.5.1.3 “&” versus “+” 83
10.5.2 Property and Scale 84
10.5.3 Time Aspect 86
10.5.4 System 87
10.5.5 Method 88
10.6 Mapping an assay approved for multiple specimens and resulting styles 88

11 Putting it all together 91

11.1 Scenario 1 - Sepsis evaluation for two-week-old infant with fever 91
11.2 Scenario 2 - Determining the cause of likely infectious diarrhea 95
11.3 Scenarios 3, 4, and 5 - multiple reporting options described in the package insert for a
single test kit 98
11.3.1 Scenario 3 - Multiplex assay for HIV 99
11.3.2 Scenario 4 - Single kit that can be used for screening and quantitative evaluation 100

Guide for Using LOINC Microbiology Terms ​• 4

 11.3.3 Scenario 5 - Immunoblot assay that produces multiple related results that have to be
interpreted together 100

12 Mapping validation, maintenance, and publication 103

12.1 Validating your mappings 103
12.2 Maintaining your mappings 104
12.3 Mapping publication 106
12.3.1 Publishing your mappings 106
12.3.2 LIVD specification for vendor to LOINC mappings 106
12.3.3 Future considerations for centralized LIVD mapping publication 107

Appendix A - Resources 108

About LOINC 108
LOINC Users’ Guide 108
LOINC website 108
Videos to learn more about LOINC 108
Journal publications 108
Mapping and Validation 109
Introduction to Mapping 109
RELMA Users’ Manual 109
LOINC Essentials 109
LOINC Premium Membership program 109
Journal Publications 109
Related standards 110
UCUM 110
HL7 v2 110
HL7 CDA 110
HL7 FHIR 110

Appendix B - Requesting new LOINCs 111

How to submit 111
Required information 111
Reminders about common issues in lab term requests 112
Format for submissions 112
Online request form 112
RELMA submission 113
Excel file submission 113
Sending submission files to Regenstrief Institute 113

Appendix C - LOINC Primer 114

Six major Parts of a LOINC concept 114

Guide for Using LOINC Microbiology Terms ​• 5

Orders, Observations, and Results 116
Orders versus Observations 116
Observations versus Results 119
LOINC Components and Properties for microbiology assays 120
Component 120
Property and Scale 121
Qualitative results 121
Quantitative results 122
Qualitative results versus the interpretation of quantitative results 123

Guide for Using LOINC Microbiology Terms ​• 6

1 Introduction
1.1 Background about LOINC
Logical Observation Identifiers Names and Codes (LOINC®) is a freely available international
standard for identifying health measurements, observations, and documents. LOINC facilitates the
storage, exchange, and pooling of results for clinical care, outcomes management, and research by
providing a set of standard names and identifiers that can be used across heterogeneous computing
environments. LOINC is used by people and organizations of many kinds, including hospitals and
other providers, public health agencies, researchers, third-party payers, and organizations
responsible for quality assurance and utilization review. LOINC is used inside health information
technology (IT) applications such as Electronic Health Record (EHR) systems, Laboratory
Information Systems (LIS) and Laboratory Information Management Systems (LIMS), where LIS
systems are typically utilized in clinical care settings and LIMS in research or public health
laboratories, and other health applications. Between systems, LOINC codes are used in conjunction
with existing information exchange standards, such as HL7 v2, FHIR, and CDA, CEN TC251, ISO
TC215, ASTM, and DICOM.

LOINC was first published in 1995, and over the last 25 years has had significant growth and
adoption across domains including laboratory, physiological measurements, radiology, standardized
survey instruments, clinical documents, and nursing management and assessment. New LOINC
versions are published twice yearly, usually in June and December, and contain new content as well
as edits to previously published content.

At present, LOINC is used in more than 170 countries, and over 30 countries, including the United
States, have adopted LOINC as a national standard. U.S. federal regulations mandate the use of
LOINC codes through the "Promoting Interoperability" incentive programs for electronic health
records (formerly referred to as "meaningful use"), which require LOINC for laboratory test result
reporting. And in June 2018, the U.S. Food and Drug Administration (FDA) published Guidance
that supports the adoption of LOINC for in vitro diagnostic (IVD) tests, the distribution of LOINC
codes by IVD vendors, and the inclusion of LOINC codes for IVD tests in product labeling.1

1
Logical Observation Identifiers Names and Codes for In Vitro Diagnostic Tests. Guidance for
Industry and Food and Drug Administration Staff. Silver Spring, MD: U.S. Food and Drug
Administration; 2018. Available from:
https://www.fda.gov/ucm/groups/fdagov-public/@fdagov-meddev-gen/documents/document/ucm
610636.pdf

Guide for Using LOINC Microbiology Terms ​• 7

1.2 Scope of this Guide
The purpose of this guide is to help users select LOINC terms for clinical microbiology and
infectious diseases laboratory tests according to best practices. The audience for this guide is vendors
of ​in vitro​ diagnostic (IVD) assays, laboratory professionals and others tasked with mapping
laboratory catalogs to LOINC, and anyone needing guidance on choosing the appropriate LOINC
term for an individual assay within the fields of microbiology and infectious diseases.

The primary focus of this mapping guide is observation values that are reported to a patient record;
limited information about mapping lab orders is also presented. Other use cases (e.g. specific
chemical tests or culture media used to identify isolates from a positive blood culture) are not fully
addressed at this time, but will likely be included in future versions. Next-generation sequencing
assays (which could be the subject of a whole guide itself) are out of scope.

This guide includes information about how to select LOINC terms for tests that detect a variety of
microorganisms (such as groups of bacteria, viruses and fungi as well as specific organisms) by
different methods, including culture, microscopy, immunoassay and molecular methods. It includes
tests that are resulted in different ways, including qualitative and quantitative measurements, as well
as those for which the result may evolve over time from preliminary to final. It also includes
serological testing for antibodies to microorganisms, even though such assays are not strictly in the
microbiology domain.

Lastly, LOINC continues to evolve following changes in laboratory medicine as well as lessons
learned regarding the best practices for reporting, storing, and aggregating laboratory data. In some
cases, LOINC terms that represented the preferred way of reporting 15 or 20 years ago may not
necessarily be the best concepts to use today based on current understanding. In such cases, we still
present information about mapping to such concepts in this guide, but with a usage note titled
“Evolving model” that describes the mapping strategy that is no longer preferred along with
recommendations for which codes to use based on current best practices.

1.3 Organization of this Guide

Chapter 2 describes the formatting conventions used in this document; a review of these
conventions will be useful for understanding the content in the remaining chapters.

Chapters 3 through 8 cover assays that evaluate:

● Physical aspects of a microorganism, such as stains;

● Organism growth, such as aerobic culture and organism-specific culture;

Guide for Using LOINC Microbiology Terms ​• 8

 ● Susceptibility of an organism to a particular antimicrobial;
● The presence of an organism-specific antigen;
● The presence of organism-specific genetic material; and
● The antibody response to a particular organism, which is used to diagnose vaccine response,
or acute, chronic, or prior infection.

In the assay-specific chapters, we include information about the specific methodology and how the
different LOINC axes (i.e., LOINC P​ arts)​ should be valued for various types of results. For different
types of assays and results, different P​ arts​ have specific values. For example, ordinal results are
represented using a LOINC term with ​Scale​ ​Ord​, and specific stains have ​Method​ names that include
the type of stain. We also include examples of LOINC terms that represent each type of result within
that methodology, as well as example HL7 v2 OBX segments that demonstrate how the result could
be reported electronically. The HL7 v2 format is used for these examples because v2 is widely used in
laboratory result reporting and may be familiar to readers, whereas other standards such as Clinical
Document Architecture (CDA) and Fast Healthcare Interoperability Resources (FHIR) are not as
commonly used (in the United States) for laboratory reporting at this time.

This Guide also includes mapping and other information that are not assay-specific. Chapters 9
through 12 cover:

● Information about mapping qualitative result values;

● General and part-specific mapping principles, as well as guidelines for IVD vendors;
● Case studies or scenarios that are intended to help users synthesize the information found in
the previous chapters. In these scenarios, various examples are provided that incorporate
several different types of assays or reporting styles; and
● Recommendations for mapping validation, maintenance, and publication.

For readers who would like more information about LOINC or mapping principles, we have
provided several appendices at the end of this guide. Appendix A includes additional resources for
learning more about LOINC, mapping and validation, and related standards. Appendix B has
detailed information about requesting new LOINC terms. And Appendix C is a LOINC primer that
describes the 6 primary LOINC axes (​Parts)​ , typical ​Component​ and​ Property/​ S​ cale​ constructs for
microbiology, as well as the definitions and differences between orders, observations, and results.

KEY POINT

See Appendix A-C at the end of this guide for: A) recommended resources; B) how to
request new LOINC terms; and C) information about LOINC Parts, specific modeling for
microbiology and discussion about orders, observations, and results.

Guide for Using LOINC Microbiology Terms ​• 9

1.4 Utilizing existing LOINC mappings
Before starting a new mapping effort, hospital and private labs should investigate whether any
LOINC mappings for their tests have previously been published. Two primary resources for such
mappings are instrument or assay vendors and reference laboratories.

1.4.1 Reference laboratories’ mappings

In the United States, many large reference laboratories, including Mayo Medical Laboratories,
ARUP Laboratories, LabCorp, and Quest Diagnostics, publish the LOINC mappings for each test in
their online catalog, typically on the individual page for each lab test. Although it is always a good
idea to double-check mappings published by other organizations, these reference laboratory
mappings are a great resource to help get you started. Keep in mind, however, that not all
laboratories perform the same test or report results in the same way, so you should review the details
provided by the reference laboratory to make sure the test is the same as the one you are mapping.

1.4.2 In vitro diagnostics (IVD) vendors

Many IVD vendors have mapped, or are in the process of mapping, their orders and test results to
LOINC terms. Some vendors publish these mappings publicly, but more often the specific maps for a
particular device are available to customers who purchase that device. Before you begin mapping,
you should speak to your IVD representative to find out if any LOINC mappings are available, but
keep in mind that the list provided by the vendor will likely cover all approved uses of the test kit,
not just the ones implemented in your laboratory. In the future, as IVD vendors begin to use the
LIVD format to publish the LOINC codes associated with each of their test results (see the section
about the LIVD specification in Chapter 12 “Mapping validation, maintenance, and publication”),
integrating LOINC mappings from multiple vendors should become more streamlined.

1.4.3 National health systems

In some countries, including Austria, Belgium, Canada, France, Portugal, the Netherlands, and
others, resources are available at a national level. Such resources include databases with constrained
subsets of LOINC terms that are applicable within the context of that country, and lists of
observations and their associated LOINC terms. Several countries also publish mappings from their
national billing codes to LOINC.

Lastly, LOINC content and documentation have been t​ ranslated​ into many languages, courtesy of
volunteer translators, which may help in mapping efforts outside of the U.S.

Guide for Using LOINC Microbiology Terms ​• 10

1.5 Feedback and Future versions of this Guide
As microbiology laboratory testing evolves over time, we anticipate publishing periodic updates that
will include new LOINC content and mapping best practices. When such updates are needed, they
will likely be published in conjunction with one of the twice yearly LOINC releases. The exact
review process for such updates and future publications has not yet been decided. However, if you
have comments, proposed edits, or other suggestions for future versions of this Guide, you are
welcome to submit them using our​ d​ edicated feedback site​. If you have questions or need help
unrelated to this guide, please contact us via the​ ​Contact LOINC​ page.

Guide for Using LOINC Microbiology Terms ​• 11

2 Conventions used in this guide
The following typographical conventions are used throughout this guide. Please consult this key to
better understand the significance of the formatting that is used.

2.1 Part types and names

The types of LOINC P​ arts​, such as ​Component​ and P​ roperty,​ are capitalized and set in an italicized
typeface. The names of LOINC P​ arts​ that appear in LOINC term names, such as U ​ rine​ and ​Ord​, are
capitalized and set in a bold typeface. If you would like more information regarding the relationship
between LOINC terms and LOINC P​ arts​, please refer to Appendix C “LOINC primer”.

2.2 Part type and name tables

For each type of test that is described, there is a table that shows how each ​Part​ should be named for
a representative LOINC term. If a particular P​ art​ type is limited to a constrained set of appropriate
names, that P​ art​ type and all members of the constrained set will be given in a blue row. The​ Parts
that are not constrained to a limited set are in white rows with a curly brace notation to generally
indicate how that ​Part​ will be named.

The table below illustrates this format using molecular microorganism detection as an example.
LOINC terms for molecular assays that detect whether or not a specific organism is present always
have P
​ rThr​ as the ​Property,​ ​Ord​ as the ​Scale,​ and one of the names shown in the M ​ ethod​ row as the
Method​, so the ​Property,​ ​ Scale​, and ​Method​ rows are blue. The ​Component a​ lways includes the words
gene, DNA, RNA, or rRNA but the microorganism name can vary, so this row is white, with the
variable part given in curly braces. The ​Time Aspect​ and S​ ystem​ can vary, so these rows are white and
contain the curly brace notation.

Component {Name of microorganism} gene or DNA or RNA or rRNA

Property PrThr

Time {Time value}

Aspect

System {Specimen type}

Scale Ord

Guide for Using LOINC Microbiology Terms ​• 12

 Method Molgen

Probe

Probe.amp.sig

Probe.amp.tar

Non-probe.amp.tar

For more information about how to align the test results in your system with the correct LOINC
Part​ value, for example, which ​Property​ and S​ cale​ are appropriate for tests resulted as a titer versus
those resulted as ordinal strings (“Detected”, “Negative”), see Chapter 10 “Choosing the right LOINC
term (“mapping”)” and Appendix C “LOINC primer”.

2.3 OBX segments

Example HL7 v2 OBX segments are included throughout the subsequent chapters and are
distinguished with a fixed-width typeface in a bordered box, as shown below. As previously
mentioned, the HL7 v2 format rather than CDA or FHIR is used to provide messaging examples
because at the current time, v2 is widely used in laboratory result reporting. The LOINC code in
each example links to the web page with details for that term.

OBX|1|NM|​8014-3​^Rubella virus IgG Ab [Units/​volume] in Serum^LN^RUB IGG^Rubella IgG

Serum^L||18|IU/mL|<10|P|...

The table below provides a brief overview of the field definitions in an HL7 OBX segment to help
you understand the examples in the guide. Note that the examples are simplified for readability and
do not represent the full OBX structure. For more information, please refer to the appropriate HL7
234
v2 and related specifications. , ,

The relevant fields for quantitative and qualitative results are as follows:

Quantitative result:
OBX|1|2|3.1^3.2^3.3^3.4^3.5^3.6|4|5|6|7|8|...
Qualitative result:

2
HL7 V2 Standard: ​http://www.hl7.org/implement/standards/product_brief.cfm?product_id=185
3
HL7 V2 Lab Results Interface (LRI) for US Realm:
http://www.hl7.org/implement/standards/product_brief.cfm?product_id=329
4
Integrating the Healthcare Enterprise (IHE) Pathology and Laboratory Medicine (PaLM) Technical
Framework Supplement - Laboratory Analytical Workflow (LAW):
http://www.ihe.net/Technical_Frameworks/#PaLM

Guide for Using LOINC Microbiology Terms ​• 13

 OBX|1|2|3.1^3.2^3.3^3.4^3.5^3.6|4|5.1^5.2^5.3^5.4^5.5^5.6||7|8|...

Table: OBX segment field definitions for both quantitative and qualitative results​.

Field Sub-field Definition

Sequence of a single OBX segment in the series of OBX segments

that are associated with a given OBR segment. Note that this
OBX-1 1
sequence number has no meaning outside of the HL7 message that
contains it.

Data type of the result given in this segment. In this example, the
OBX-2 2
result is quantitative, so the data type is NM (numeric).

3.1 Observation identifier

OBX-3 is a triplet of 3.2 Observation name

values separated by
the ^ character that 3.3 Observation coding system
can be optionally
repeated to represent 3.4 Observation identifier in a second coding system
an observation in two
coding systems 3.5 Observation name in a second coding system

3.6 Second observation coding system

Observation Sub-Id, which is used to distinguish multiple results

reported under one observation identifier in OBX-3 and to link
related results. For example, this field is used when multiple
OBX-4 4
organisms are identified in a single culture to track the status of
each individual result and to associate each organism with its
corresponding susceptibility results.

5 Quantitative result
OBX-5 carries either 5
a single quantitative 5.1 Qualitative result code
value or, if qualitative,
a triplet that can be 5.2 Qualitative result text
optionally repeated,
5.3 Qualitative result coding system
e.g., for reporting
observation values
5.4 Qualitative result code in a second coding system
using both the local
code system and a
5.5 Qualitative result text in a second coding system
standard code system
5.6 Second qualitative result coding system

OBX-6 6 Units of measure for a quantitative result

5
All of the examples in this guide use LOINC Answer codes for qualitative results; due to licensing
restrictions, this guide does not yet include SNOMED CT codes. However, we recommend using
SNOMED CT codes for qualitative results in countries that are licensed to do so.

Guide for Using LOINC Microbiology Terms ​• 14

 OBX-7 7 Reference range

Interpretation code, such as P (positive), H (high), and N (normal).

OBX-8 8
See HL7 v2 Table 0078 for a complete list.

2.4 LOINC code and name pairs

Example pairs of LOINC code and Long Common Name (LCN) are presented in a sans-serif typeface
like the following. The LOINC code links to the web page with details for that term. Note that the
LCN is italicized, both when the LOINC code and name pairs are presented separately (as below) as
well as when they are included within a paragraph of text.

10729-2​ Trypanosoma sp identified: Prid: Pt: Bld: Nom: Microscopy.light

LCN: ​Trypanosoma sp identified in Blood by Light microscopy

2.5 Key points and Evolving models

Specific points that need special attention will be offset using a style as follows.

KEY POINT

Result: “Positive” or “Negative” → LOINC ​Scale​ = Ord

Result: 3 mg/dL, interpretation is “Positive” or “Negative” → LOINC ​Scale​ = Qn

In addition, information about specific LOINC models that have evolved or continue to evolve over
time will be offset using this style:

EVOLVING MODEL

LOINC terms with specific detection limit ​Methods​ are no longer recommended for use.
Instead, we encourage reporting individual results using a more generic code along with
a second LOINC (​87706-8​ ​Laboratory device Detection limit)​ to report the detection limit
as a separate observation.

2.6 Citations
We cite various articles, websites, and online resources in this guide. All citations and URLs were
verified at the time this guide was published. Scientific articles are referenced with their PubMed
identification numbers and linked to the entry at P​ ubMed.gov​.

Guide for Using LOINC Microbiology Terms ​• 15

3 Microscopic examination
Microscopic examination includes many different types of tests, including light microscopy without
special pre-processing, darkfield microscopy, stains, and different slide preparations, such as “wet
prep”, potassium hydroxide (KOH), and smears. In LOINC, there are primarily two types of terms
in this general class of tests: 1) those for identifying the absence or, if present, characteristics or type
of microorganism (​Property​ ​Prid​, ​Scale​ ​Nom​); and 2) those for identifying the presence or absence of
a specific organism (​Property​ ​PrThr​, ​Scale​ ​Ord​). The following table summarizes the typical naming
pattern in LOINC for different types of microscopic exams.

Table: Comparison of different microscopic exams and their LOINC naming patterns

Type of result Component Property Scale Method

Absence or, if present, the Microscopic Prid Nom {Name of stain}

characteristics or identity of observation Wet preparation
an unknown organism {Thick smear or thin smear}

Microscopy to identify the {Name of organism Prid Nom Microscopy.light

absence or, if present, type or class of organism}
or subtype of a suspected
organism

Presence or absence of a {Name of organism} PrThr Ord Microscopy.light

suspected organism {Name of stain}
Wet preparation
KOH preparation

Wet preparation to identify {Bacterium, amoeba Prid Nom Wet preparation

the type of bacterium, or fungus} identified
amoeba or fungus that is
present

O&P exam Ova & parasites Prid Nom {Name of stain or other
identified methodology}

KEY POINT

Property​ ​PrThr​, ​Scale​ ​Ord​ = presence or absence of an analyte, including presence or

absence based on some predetermined threshold
Property​ ​Prid​, ​Scale N
​ om​ = absence, or, if the analyte is present, its specific identity

Guide for Using LOINC Microbiology Terms ​• 16

The following sections cover how to choose appropriate LOINC terms for different types of more
common microscopic exams.

3.1 Light microscopy

For tests that identify microorganisms by light microscopy without specific staining, the LOINC
term typically includes the name of the organism or class of organism in the ​Component,​ and
Microscopy.light​ as the ​Method.​ Microscopy may be used to identify the presence or absence of a
microorganism in a specimen, or to identify the characteristics or type of organism present, if any.
Light microscopy is used to identify organisms such as bacteria, fungi, and parasites. Viruses, which
are usually too small to be seen by basic light microscopy, may be detected using electron
microscopy; however, the use of electron microscopy in the microbiology domain is not common,
especially given the availability and automation of other methods such as immunoassay and
molecular techniques.

3.1.1 Microscopy to identify the characteristics or type of

organism present
Microscopy can be used to directly observe specimens under the microscope to determine whether
or not a specific class or species of organism is present and if so, the identity of the organism. Such
tests are represented in LOINC by the following naming pattern:

Component {Class or name of organism} identified

Property Prid

Time Aspect {Time value}

System {Specimen type}

Scale Nom

Method Microscopy.light

Examples:
10729-2​ Trypanosoma sp identified: Prid: Pt: Bld: Nom: Microscopy.light
LCN: ​Trypanosoma sp identified in Blood by Light microscopy

OBX|1|CE|​10729-2​^Trypanosoma sp identified in Blood by Light

microscopy^LN|1|LA11883-8^Not detected^LN|||...

Guide for Using LOINC Microbiology Terms ​• 17

3.1.2 Microscopy to identify the presence or absence of a
specific organism
Microscopy can also be used to identify the presence or absence of a suspected (known) organism.
Such tests are represented in LOINC as follows:

Component {Class or name of organism}

Property PrThr

Time Aspect {Time value}

System {Specimen type}

Scale Ord

Method Microscopy.light

Example:
20457-8​ Fungi.filamentous: PrThr: Pt: Urine sed: Ord: Microscopy.light
LCN: ​ Fungi.filamentous [Presence] in Urine sediment by Light microscopy

OBX|1|CE|​20457-8​^Fungi.filamentous [Presence] in Urine sediment by Light

microscopy^LN|1|LA11882-0^Detected^LN|||...

3.2 Stains
LOINC includes terms for a variety of stains that aid in the identification of microorganisms. The
type of stain is indicated in the ​Method​.

Microorganisms are naturally colorless. By adding color to a fixed smear, specific characteristics of
the organism such as morphology or cell wall properties become visible. These characteristics help
to identify the organism that is present. Examples of common stains and how they are used include:

● Acid-fast stains i​ dentify bacteria with long-chain fatty acids that are resistant to crystal
violet stain and other basic dyes;
● Gram stains​ are used to classify bacteria as Gram positive or Gram negative based on their
cell wall staining pattern;
● Nucleic acid stains​ bind to DNA and/or RNA and, depending on the stain, may
distinguish between the two and also differentiate single-stranded from double-stranded
nucleic acids;

Guide for Using LOINC Microbiology Terms ​• 18

 ● Methylene blue stains​ highlight the morphology of fusiform bacteria and spirochetes
from oral infections;
● Capsule stains​ identify encapsulated organisms such as Cryptococcus neoformans;
● Immune stains​ are used to identify specific antigens on microorganisms.

LOINC contains two primary types of stain terms: 1) those that utilize staining patterns to
determine the type of organism present, if any; and 2) those that identify the presence or absence of
a suspected organism.

3.2.1 Stains that help identify the characteristics or type of

organism present
Often, a patient sample is suspected to contain a microorganism based on the clinical context (e.g.
fever, sepsis). Staining the sample helps confirm whether or not an organism is present, as well as
the type of organism. For such tests, the LOINC ​Component​ is M
​ icroscopic observation​, because
the test result describes what is seen under the microscope when a particular stain is used. These
LOINC terms are named with the pattern shown in the table below:

Component Microscopic observation

Property Prid

Time Aspect {Time value}

System {Specimen type}

Scale Nom

Method {Name of stain}

Examples:
11480-1​ Microscopic observation:Prid:Pt:Urine:Nom:Acid fast stain
LCN: ​Microscopic observation [Identifier] in Urine by Acid fast stain

11476-9​ Microscopic observation:Prid:Pt:Gast fld:Nom:Acid fast stain

LCN: ​Microscopic observation [Identifier] in Gastric fluid by Acid fast stain

27112-2​ Microscopic observation:Prid:Pt:Body fld:Nom:Gram stain

LCN: ​Microscopic observation [Identifier] in Body fluid by Gram stain

OBX|1|CE|​11480-1​^Microscopic observation [Identifier] in Urine by Acid fast

stain^LN|1|LA20996-7^Mycobacterium tuberculosis^LN||...

Guide for Using LOINC Microbiology Terms ​• 19

 KEY POINT

The ​Component​ for terms used to identify the characteristics or type of organism present
using a stain is always ​Microscopic observation​.

3.2.2 Stains that help identify the presence of a specific

organism
When a specific (known) organism is suspected, stains that identify characteristics specific to that
organism may be used to confirm its presence. In this case, the LOINC C ​ omponent​ is the name of
suspected specific organism, rather than Microscopic observation, because the test result indicates
whether or not that organism is present rather than the characteristics seen under the microscope.
For such tests, the LOINC name follows this pattern:

Component {Name of organism}

Property PrThr

Time Aspect {Time value}

System {Specimen type}

Scale Ord

Method {Name of stain}

Examples:
23597-8​ Dermatophilus congolensis:PrThr:Pt:Exudate:Ord:Methylene blue
LCN: ​Dermatophilus congolensis [Presence] in Exudate by Methylene blue stain

20781-1​ Cryptosporidium sp:PrThr:Pt:Stool:Ord:Acid fast stain

LCN: ​Cryptosporidium sp [Presence] in Stool by Acid fast stain

OBX|1|CE|​23597-8​^Dermatophilus congolensis [Presence] in Exudate by Methylene blue

stain^LN||LA11882-0^Detected^LN||...

Guide for Using LOINC Microbiology Terms ​• 20

3.3 Wet/KOH Preparations
In addition to stained fixed smears, organisms can be identified by examining wet preparations. Wet
preparations are drops of liquid specimen that are viewed directly under the microscope. Stains can
be added to help enhance the characteristics of the organisms. A wet preparation can also use
potassium hydroxide (KOH) mixed with a specimen such as skin, hair, nails, or sputum to visualize
fungal hyphae and yeast cells.

Similar to staining tests, wet and KOH preparation terms fall into two categories: 1) nominal tests
that are looking for the absence or, if present, specific identity of an organism, and 2) ordinal tests
looking for the presence or absence of a specific organism.

3.3.1 Wet or KOH preparations that help identify the type of

unknown organism
Wet and KOH preparations can be used to determine the general class of microorganism present,
such as bacterium, amoeba or fungus, or, when the general class is known, the species of organism
within that class. Observations that report the presence and/or broad class of an unknown organism
by examining a wet preparation contain the C ​ omponent​ of ​Microscopic observation​. In contrast,
when the general class is known from prior information, the class is reflected in the ​Component​, for
example, ​Amoeba identified​ or ​Bacteria identified​.

LOINC naming patterns for both types of observations are given in the two tables below.

Component Microscopic observation

Property Prid

Time Aspect {Time value}

System {Specimen type}

Scale Nom

Method Wet preparation

KOH preparation

Component {Class of organism} identified

Property Prid

Guide for Using LOINC Microbiology Terms ​• 21

 Time Aspect {Time value}

System {Specimen type}

Scale Nom

Method Wet preparation

Examples:
6470-9​ Microscopic observation:Prid:Pt:Stool:Nom:Wet preparation
LCN: ​Microscopic observation [Identifier] in Stool by Wet preparation

68383-9​ Microscopic observation:Prid:Pt:Body fld:Nom:KOH preparation

LCN: ​Microscopic observation [Identifier] in Body fluid by KOH preparation

10733-4​ Trypanosoma sp identified:Prid:Pt:Bld:Nom:Wet preparation

LCN: ​Trypanosoma sp identified in Blood by Wet preparation

OBX|1|CE|​6470-9​^Microscopic observation [Identifier] in Stool by Wet

preparation^LN|1|LA28390-5^Enterobius vermicularis^LN||...

3.3.2 Wet or KOH preparations that help identify the

presence of a suspected organism
When a specific (known) class or species of organism is suspected to be present, wet preparations
can identify characteristics specific to that organism, which would confirm its presence. Again,
because the observation result is the presence or absence of a particular organism, the LOINC
Component​ is the name of that organism. For such tests, the LOINC names will follow this pattern:

Component {Name of organism}

Property PrThr

Time Aspect {Time value}

System {Specimen type}

Scale Ord

Method Wet preparation

KOH preparation

Guide for Using LOINC Microbiology Terms ​• 22

Examples:
23520-0​ Trypanosoma evansi:PrThr:Pt:Asp:Ord:Wet preparation
LCN: ​Trypanosoma evansi [Presence] in Aspirate by Wet preparation

55303-2​ Fungus:PrThr:Pt:Skin:Ord:KOH preparation

LCN: ​Fungus [Presence] in Skin by KOH preparation

55320-6​ Yeast:PrThr:Pt:Bronchial:Ord:KOH preparation

LCN: ​Yeast [Presence] in Bronchial specimen by KOH preparation

OBX|1|CE|​55303-2​^Fungus [Presence] in Skin by KOH preparation^LN||LA20667-4^None

seen^LN|...

3.4 Thick and thin films

Thin and thick films are smears made from blood, and are used to identify any parasite. These
smears are used most often in the context of malaria. The thick film can be a drop of blood on a glass
slide or the thick section of a stained blood smear. The thin film is the feathery edge of a stained
blood smear or a small amount of blood spread over a larger area of the slide. A thick film is often
used to screen for the presence of parasites, while the thin film helps differentiate the specific species
of parasite (e.g. Plasmodium falciparum) present.

LOINC terms for thin and thick films are named with the following pattern:

Component {Class or name of organism} identified

Property Prid

Time Aspect {Time value}

System {Specimen type}

Scale Nom

Method Thin film

Thick film

Examples:
10664-1​ Filaria identified:Prid:Pt:Bld:Nom:Thin film
LCN: ​Filaria identified in Blood by Thin film

Guide for Using LOINC Microbiology Terms ​• 23

637-9​ Plasmodium sp identified:Prid:Pt:Bld:Nom:Thick film
LCN: ​Plasmodium sp identified in Blood by Thick film

OBX|1|CE|​637-9​^Plasmodium sp identified in Blood by Thick

film^LN||LA18496-2^Plasmodium falciparum^LN|...

Note that there are a few LOINC terms with the M ​ ethods​ ​Malaria smear ​and M ​ alaria thin smear
that we are in the processing of updating in order to align with the model described above. There are
also some parasitology terms that follow the general light microscopy model described above, such as
51587-4​ ​Plasmodium sp [Presence] in Blood by Light microscopy​, to report the presence of any
Plasmodium species, and ​32206-5​ Plasmodium sp identified in Blood by Light microscopy​, to report the
specific species of Plasmodium that was identified, that may be used when the specific type of smear
is not specified.

3.5 Ova and parasite (O&P)

Ova and parasite (O&P) examinations are done on stool samples to identify organisms that may be
infecting the lower digestive tract. Organisms frequently found in O&P preparations include Giardia
spp., Cryptosporidium spp., and Entamoeba histolytica. Several different techniques are used when
examining an O&P slide, including stains such as trichrome, Wright, and iron hematoxylin stain, as
well as other methodologies including Baerman and McMaster. Such techniques are identified in the
Method ​of the LOINC name.

LOINC names for O&P exam observations follow this pattern:

Component Ova & parasites identified

Property Prid

Time Aspect {Time value}

System {Specimen type}

Scale Nom

Method {Name of stain}

Examples:
43227-8​ Ova & parasites identified:Prid:Pt:Stool:Nom:Trichrome stain
LCN: ​Ova and parasites identified in Stool by Trichrome stain

10702-9​ Ova & parasites identified:Prid:Pt:Stool:Nom:Immune stain

Guide for Using LOINC Microbiology Terms ​• 24

LCN: ​Ova and parasites identified in Stool by Immune stain

OBX|1|CE|​43227-8​^Ova and parasites identified in Stool by Trichrome

stain^LN|1|LA28390-5^Enterobius vermicularis^LN|...

Guide for Using LOINC Microbiology Terms ​• 25

4 Cultures
In clinical microbiology, cultures are used to identify and quantify microorganisms in a patient
specimen in order to determine the etiology of an infection and optimize treatment. A specimen
such as blood, body fluid, or tissue is inoculated onto a nutrient-rich medium and incubated in an
optimal environment (temperature and oxygen or carbon dioxide) for the suspected organism to
grow. When the presence of an organism is suspected but the type not known, different types of
cultures are typically done in parallel, including aerobic, anaerobic, and fungal. These primary
cultures may be followed up by more specific culture methods that encourage the growth of certain
organisms and prevent the growth of others, by chemical assays that identify the specific organism
present based on physical properties, or a combination of the two.

Cultures may be done for reasons outside of routine patient care, such as for propagating cell lines
and preservation for future research and quality control. Such use cases are outside of the scope of
this guide.

In the LOINC name, the type of culture is specified in the ​Method​. Examples include:

● Culture,​ which is a generic M

​ ethod​ that could encompass any of the other culture types;
● Aerobic culture​, which is optimized for organisms that are aerobic (i.e., grow in the
presence of oxygen);
● Anaerobic culture​, which is optimized for organisms that are anaerobic (i.e., do not
require oxygen for growth and may not survive if oxygen is present); and
● Organism-specific culture​, which contains nutrients that optimize the growth of a
specific organism and also inhibitors that prevent the growth of competing organisms.

Note that at the current time, a single code for a routine or organism-specific culture is
recommended for reporting the preliminary result (e.g., from a blood bottle culture or a plated
specimen) and identification. Historically, all of these steps have been included in the laboratory
workflow under the “culture” umbrella, and individual results for each step have not been reported
to or stored in the patient’s EHR record. LOINC does contain some concepts to represent these
individual steps; they are not included in the present version of this guide, but may be added in
future editions.

Guide for Using LOINC Microbiology Terms ​• 26

 KEY POINT

A single LOINC term for a routine culture is used to report the preliminary result (e.g., from
a blood bottle culture or a plated specimen) and organism identification as each of these
steps occurs. Separate terms are used for Gram stain and susceptibility results. See the
first sample scenario in Chapter 11 for an example.

4.1 Specimen-specific requirements

Cultures can be performed on a wide variety of sample types; the most common include blood, CSF,
urine, stool, respiratory, wound, and genital. Specimens such as blood and CSF are normally sterile
(do not contain any microorganisms), while others, such as stool or genital swab specimens,
naturally contain an assortment of microorganisms and therefore necessitate specific culture
techniques designed to isolate the suspected pathological organism. The typical pathologic
microorganisms found in a sample vary depending on the sample type. For example, a stool
specimen is likely to harbor different pathogens than a CSF or respiratory specimen.

In almost all cases, LOINC terms do not distinguish specimen-specific techniques in the M ​ ethod,​
because the S​ ystem​ provides information about the specimen for which the culture is optimized. For
example, the term ​625-4​ ​Bacteria identified in Stool by Culture​ is used to represent a culture optimized
for the growth of pathogens in stool, and ​6331-3​ C ​ ampylobacter sp identified in Stool by Organism
specific culture f​ or a culture that specifically promotes the growth of Campylobacter species in stool.
In both cases, the LOINC M ​ ethod​ does not specify the details of how the culture is optimized for such
growth, because these details are laboratory-specific and unnecessary for interpreting the culture
result. The one exception is certain respiratory cultures, a few of which have specific M ​ ethods​ such as
Respiratory culture​.

Although LOINC terms for different types of samples look similar in terms of the construction of
the C
​ omponent​ and ​Method,​ there are differences in the spectrum of suspected microorganisms named
in the C
​ omponent a​ nd the specific culture M
​ ethods a​ ssociated with each. The first table below provides
examples of various specimens and the typical LOINC culture ​Method​s used with each; the second
includes specimens and the typical pathogens that may be isolated from each using organism-specific
culture.

LOINC ​System Common LOINC culture ​Methods

Blood Culture
Aerobic culture
Anaerobic culture
Organism specific culture

Guide for Using LOINC Microbiology Terms ​• 27

Bone Aerobic culture

Burn Culture

CSF Culture
Organism specific culture
Shell vial culture

Genital Culture
Aerobic culture
Organism specific culture

Respiratory Aerobic culture

Organism specific culture
Respiratory culture

Stool Culture
Organism specific culture

Urine Culture
Organism specific culture

Wound Culture
Aerobic culture
Anaerobic culture

LOINC ​System Typical pathogens named in the LOINC

Component

Blood Leishmania species

Leptospira species

Cerebrospinal fluid Borrelia species

Neisseria meningitidis
Enterovirus

Genital Neisseria gonorrhoeae

Chlamydia trachomatis
Streptococcus agalactiae
Trichomonas species

Respiratory Influenza virus

Legionella species
Mycobacterium species

Stool Campylobacter species

Clostridioides difficile
Escherichia coli O157:H7
Salmonella enteritidis
Yersinia species

Guide for Using LOINC Microbiology Terms ​• 28

 Urine Trichomonas vaginalis
Escherichia coli
Enterococcus species
Cytomegalovirus

4.2 Routine culture to detect and identify an

unknown organism
Cultures are used to determine whether microorganisms are growing in a patient sample, such as
blood or urine, and to identify the genus and species of organism if present.

Routine cultures are commonly used to look for bacteria, and thus would be named with the
Component​ ​Bacteria identified.​ As discussed in the introduction to this Chapter, a single code for a
routine culture is used to report the results of the bottle culture, bacterial isolation, and
identification. Several results may be reported over time with changing statuses, such as
“Preliminary” and “Final”, but using a single code helps tie these results together. Gram stain and
susceptibility testing results are reported using separate LOINC codes but are typically linked to the
primary culture result, for example, by using the OBX-4 Observation sub-ID field in an HL7 v2
message. OBX-4 is also used when multiple organisms grow on a single culture to both distinguish
the individual results as well as link each organism to its associated Gram stain and susceptibility
results.

Sometimes fungi will grow on a routine culture. If so, most laboratories would report these results
under the same test name. The LOINC name simply reflects that such a culture is not optimized for
growing out fungi; having “bacteria” in the name does not prohibit reporting whatever organism
grows.

LOINC terms that represent cultures for detecting and identifying unknown organisms are named
with the following pattern:

Component Bacteria identified

Fungus identified

Virus identified

Property Prid

Time Aspect {Time value}

System {Specimen type}

Guide for Using LOINC Microbiology Terms ​• 29

 Scale Nom

Method {Type of culture}

Examples:
17928-3​ Bacteria identified:Prid:Pt:Bld:Nom:Aerobic culture
LCN: ​Bacteria identified in Blood by Aerobe culture

569-4​ Fungus identified:Prid:Pt:CSF:Nom:Culture

LCN: ​Fungus identified in Cerebrospinal fluid by Culture

14451-9​ Virus identified:Prid:Pt:Eye:Nom:Culture

LCN:​ Virus identified in Eye by Culture

OBX|1|CE|​17928-3​^Bacteria identified in Blood by Aerobe culture^LN|1| LA19246-0^

Staphylococcus aureus^LN||...

KEY POINT

If an unexpected organism grows on a culture optimized for a different type of organism,

such as growth of a fungus on a routine aerobic bacterial culture, the result would still be
reported using the term for the test that was done, in this case, ​17928-3​ ​Bacteria identified
in Blood by Aerobe culture​. The fact that the result is a fungus does not change the fact that
the assay was optimized for bacteria, which is what the LOINC name reflects.

4.3 Organism-specific culture to identify the

presence or species of a suspected organism
When a specific organism is suspected to be present, a culture medium and environment that is
optimized for the growth of that organism in a particular type of sample is used to selectively
encourage its growth. Rather than having different LOINC M ​ ethods​ to represent every type of
culture medium and growth environment for every sample type, such cultures are represented by the
LOINC M ​ ethod​ ​Organism specific culture​. The specific organism that is suspected is named in the
Component,​ and the sample in the S​ ystem​. Together, this pattern conveys that the culture was
optimized for the growth of a specific organism in a specific specimen. Organism-specific cultures
can be used to determine: 1) whether or not a suspected organism is present; or 2) to determine the
specific species or subtype of the suspected organism.

The same principle applies for organism-specific cultures as for routine cultures when an unexpected
organism is found. The LOINC term reflects what a given culture is optimized for, but if a different

Guide for Using LOINC Microbiology Terms ​• 30

organism grows, it may be reported using the same code, either as a generic result such as “Moderate
fungal growth” if the identity cannot be determined, or as the specific identity. If further testing is
done to determine the organism’s identity, then the generic result is still reported using the original
code, and the specific identity is reported using the appropriate code(s) for the follow-up test(s).

4.3.1 Presence or absence of a suspected genus or species

LOINC terms for cultures that determine the presence or absence of a suspected genus or species of
organism are named with the following pattern:

Component {Name of organism}

Property PrThr

Time Aspect {Time value}

System {Specimen type}

Scale Ord

Method Organism specific culture

Examples:
45095-7​ Chlamydia trachomatis:PrThr:Pt:Genital:Ord:Organism specific culture
LCN: ​Chlamydia trachomatis [Presence] in Genital specimen by Organism specific culture

562-9​ Clostridioides difficile:PrThr:Pt:Stool:Ord:Organism specific culture

LCN:​ Clostridioides difficile [Presence] in Stool by Organism specific culture

48741-3​ Bordetella pertussis:PrThr:Pt:Nph:Ord:Organism specific culture

LCN: ​Bordetella pertussis [Presence] in Nasopharynx by Organism specific culture

OBX|1|CE|​45095-7​^Chlamydia trachomatis [Presence] in Genital specimen by Organism

specific culture^LN|1|LA11882-0^Detected^LN||...

4.3.1.1 Screening cultures for drug-resistant organisms

Screening cultures are a type of organism-specific culture that are performed to identify patients that
may be colonized with drug-resistant organisms for the purpose of infection control. Such cultures
may be done using nasal or anal swabs to facilitate appropriate isolation and patient cohorting when
a patient is admitted to a healthcare facility.

LOINC terms for screening cultures are named with the following pattern:

Guide for Using LOINC Microbiology Terms ​• 31

 Component Bacteria.{Name of drug class} resistant sp identified

{Name of genus or species}.{Name of drug class}

resistant

{Name of genus or species}.{Name of drug class}

resistant isolate

Property PrThr

Prid

Time Aspect {Time value}

System {Specimen type}

Scale Ord

Nom

Method Organism specific culture

Examples:
73834-4​ Bacteria.carbapenem resistant identified:Prid:Pt:Anal:Nom:Organism specific
culture
LCN: ​Bacteria.carbapenem resistant identified in Anal by Organism specific culture

63480-8​ Pseudomonas aeruginosa.multidrug resistant

isolate:PrThr:Pt:XXX:Ord:Organism specific culture
LCN: ​Pseudomonas aeruginosa.multidrug resistant isolate [Presence] in Unspecified specimen by
Organism specific culture

4.3.2 Detecting and identifying the specific species of

suspected organism
Organism-specific cultures can also be used to further specify the suspected microorganism, if
present. LOINC terms for organism-specific cultures that determine the specific species of organism
present are named with the following pattern:

Component {Name of organism} sp identified

Property Prid

Time Aspect {Time value}

Guide for Using LOINC Microbiology Terms ​• 32

 System {Specimen type}

Scale Nom

Method Organism-specific culture

Examples:
20955-1​ Salmonella sp identified:Prid:Pt:Stool:Nom:Organism specific culture
LCN: ​Salmonella sp identified in Stool by Organism specific culture

43979-4​ Aspergillus sp identified:Prid:Pt:XXX:Nom:Organism specific culture

LCN: ​Aspergillus sp identified in Unspecified specimen by Organism specific culture

38394-3​ Legionella sp identified:Prid:Pt:Urine:Nom:Organism specific culture

LCN: ​Legionella sp identified in Urine by Organism specific culture

OBX|1|CE|​20955-1​^Salmonella sp identified in Stool by Organism specific

culture^LN|1|LA21329-0^Salmonella typhi^LN|...

4.4 Colony counts

A colony count represents the number of colonies for each organism identified that are growing in a
culture. Colony counts help determine the clinical significance of the culture result. For example,
low colony counts of multiple bacteria would point to a picture of contamination, whereas a high
colony count of a single organism would indicate true infection.

LOINC terms for colony counts are named with the following pattern:

Component Colony count

Fungus colony count

Property NCnc*

ACnc

Num

* most common

Time Aspect {Time value}

System {Specimen type}

Guide for Using LOINC Microbiology Terms ​• 33

 Scale Qn

Method Culture

Examples:
19090-0​ Colony count:NCnc:Pt:Urine:Qn
LCN: ​Colony count [#/volume] in Urine

19101-5​ Fungus colony count:NCnc:Pt:XXX:Qn:Culture

LCN: ​Fungus colony count [#/volume] in Unspecified specimen by Culture

OBX|1|NM|​19090-0​^Colony count [#/volume] in Urine^LN|1|596|/mL|...

Guide for Using LOINC Microbiology Terms ​• 34

5 Susceptibility testing
Two primary types of susceptibility testing are phenotypic and genotypic testing. The difference
between genotyping and phenotyping susceptibility testing is that the genotyping method results in
a prediction of susceptibility whereas phenotyping is a direct measure of whether an organism can
grow in the presence of an antimicrobial. A third type of testing categorized as susceptibility testing
is testing for specific resistance enzymes themselves.

5.1 Phenotypic susceptibility testing

Phenotypic susceptibility testing is used to determine which antimicrobials will kill a microorganism
and at what concentrations they will do so. The isolated microorganism is incubated with the
antimicrobial(s) being tested and the appropriate culture media. If the microorganism grows, it is
resistant to the drug; if growth is inhibited, it is susceptible, and the specific pattern of growth and
inhibition can be used to determine the antimicrobial concentration at which the organism is
susceptible. For example, a bacterium may be resistant to a low concentration of a particular
antibiotic but susceptible to higher concentrations.

6 7 8
Various agencies, including the FDA and CLSI in the U.S. and EUCAST in Europe, publish
guidelines for the threshold at which a given organism should be susceptible to a specific antibiotic
for the purpose of clinical care. Using a hypothetical example, consider that a particular antibiotic
kills a specific organism at a concentration of 100 ug/mL or above. If the highest safe concentration
for patient dosing is 5 ug/mL, then that antibiotic cannot be used because the organism is not
susceptible at a concentration of 5 ug/mL.

LOINC terms for susceptibility testing have the name of the antibiotic in the ​Component​. Drug names
in LOINC are almost always specified with the generic name. To facilitate searching, the LOINC
database typically includes the brand name in its list of related names.

The following table lists the primary ​Methods​ used in susceptibility testing:

6
Microbiology Data for Systemic Antibacterial Drugs — Development, Analysis, and Presentation
Guidance for Industry. Silver Spring, MD: U.S. Food and Drug Administration; 2016. Available from:
https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/U
CM182288.pdf
7
M100: Performance Standards for Antimicrobial Susceptibility Testing, 27th Edition. Wayne, PA:
Clinical and Laboratory Standards Institute; 2017.
8
Clinical Breakpoints [Internet]. Basel (Switzerland): The European Committee on Antimicrobial
Susceptibility Testing. Available from: ​http://www.eucast.org/clinical_breakpoints/

Guide for Using LOINC Microbiology Terms ​• 35

 LOINC ​Method Description

Agar (Disc) diffusion A standardized inoculum density from a culture isolate is applied to an agar
plate. Discs of absorbent material to which specific concentrations of
(Kirby-Bauer) antibiotic have been added are placed on the agar. The agar plate is incubated
to allow the isolate to grow on the plate in the presence of the antibiotic. If an
area surrounds the disc where growth of the organism has been inhibited, the
organism may be susceptible to the antibiotic on the disc. The diameter of the
zone of inhibition surrounding the disc can be measured and compared to
standards to determine if the organism is susceptible, intermediate, or
9
resistant to the antibiotic.

MIC (minimum A standardized density of an isolated organism is inoculated 1) into a series of

inhibitory increasing dilutions of antibiotic in culture broths or 2) on increasing dilutions
concentration) of antibiotic incorporated into agar plates, and allowed to incubate. The
concentration of the lowest dilution of antibiotic where no growth of the
organism being tested is visible is the minimum inhibitory concentration (MIC)
of the drug. The MIC is typically reported as ug/mL.

Gradient strip A small strip is impregnated with an antimicrobial drug that has an increasing
concentration from one end of the strip to another. The concentrations of the
(e.g. E-test​™) antibiotic are marked along the strip. The strip is placed on the agar surface
that has been inoculated by a standardized density of the isolated organism
being tested. The MIC of the antimicrobial is determined by the intersection of
the border where microbial growth is inhibited and the concentration of
10
antimicrobial designated on the strip. The gradient strip test is a form of MIC
testing.​6

MLC (minimum The minimum lethal concentration (MLC) is used to determine the minimum
lethal concentration) bactericidal concentration (MBC) or the minimum fungicidal concentration
(MFC) of drugs in question. A precise aliquot of culture from the MIC wells or
tubes that exhibit no growth are sub-cultured onto a non-selective agar plate
and allowed to incubate for 24 hours. The number of colony-forming units per
milliliter (CFU/mL) is determined. The MBC is defined as the lowest
concentration of antibiotic that kills 99.9% of the final inoculum after a
24-hour incubation and in accordance with the standardized conditions stated
in document M26-A. The MFC is defined as the lowest concentration of an
antifungal drug that kills 98-99.9% when compared to the initial inoculum (the
sample in the clear wells or tubes).​6

9
Balouiri M, Sadiki M, Ibnsouda SK. Methods for ​in vitro​ evaluating antimicrobial activity: A review.
Journal of Pharmaceutical Analysis 2016;6:71-79.
10
CLSI, Methods for Determining Bactericidal Activity of Antimicrobial Agents. Approved Guideline,
CLSI document M26-A. Clinical and Laboratory Standards Institute, 950 West Valley Road, Suite
2500,Wayne, Pennsylvania 19087, USA, 1998.

Guide for Using LOINC Microbiology Terms ​• 36

 Method for MIC plates with dilutions of antimicrobials using 7H-9 broth are prepared or
slow-growing purchased. Standardized dilutions of the mycobacteria are prepared and .01
mycobacteria mL is pipetted into the wells. The microplate is then incubated at optimal
temperatures for 7, 10, 14 and 21 days. At each time interval the MICs are
determined by looking for the well with the lowest dilution of antimicrobial
11
that shows no growth of mycobacteria.

Phenotyping​* Phenotypic susceptibility assays directly measure whether a specific

antimicrobial drug inhibits microbial growth. Viral tropism is another type of
phenotyping that evaluates antiviral drug susceptibility. Some antiviral drugs
block the protein receptor where the virus would normally gain access to the
cell. If the virus requires that protein, then the drug is a good candidate for
12
treatment.
*​Note: Although phenotyping applies to viruses and bacteria, within LOINC, it
is only used in the context of viral phenotyping. Bacterial phenotyping uses
specific named ​Methods​ such as ​Agar diffusion​ and ​Gradient strip​.

KEY POINT

In LOINC, the ​Method​ ​Phenotyping​ is only used for viral susceptibility testing. For
microorganisms other than viruses, specific named ​Methods​ such as ​Agar diffusion​, ​MIC​,
and ​Gradient strip​ are used.

5.1.1 Bacterial or fungal phenotypic susceptibility testing

Assays that determine the antimicrobial susceptibility of a bacterium or fungus typically have either
quantitative (​Scale​ of Q
​ n​) or ordinal (​Scale​ of O
​ rd​) results. Some assays, such as M
​ IC​, can be
reported as either qualitative or quantitative. These assays represent a rare type of LOINC term that
has a ​Scale​ of O
​ rdQn​, enabling either ordinal results such as Sensitive, Intermediate, or Resistant or
numeric values for the minimum inhibitory concentration or minimum bactericidal concentration
to be reported using the same LOINC code. Often both the quantitative result and ordinal value are
reported in a single OBX segment, in fields OBX-5 and OBX-8, respectively.

LOINC terms for bacterial and fungal susceptibility tests are named with the following pattern:

Component {Generic name of drug}

Property Susc

Time Aspect {Time value}

11
Wallace RJ Jr, Nash DR, Steele LC, Steingrube V. Susceptibility testing of slowly growing mycobacteria by a
microdilution MIC method with 7H9 broth. J Clin Microbiol. 1986 Dec;24(6):976-81. [PMID: ​3097069​]
12
Jorgensen JH, Carroll KC, Funke G, Pfaller MA, Landry ML, Richter SS, Warnock DW (Eds.).
Manual of Clinical Microbiology, 11th edition 2015;1220-1221,1286.

Guide for Using LOINC Microbiology Terms ​• 37

 System {Specimen type}

Scale Qn

Ord

OrdQn

Method MIC

Gradient strip

Agar diffusion

MLC

Examples:
7009-4​ Erythromycin:Susc:Pt:Isolate:OrdQn:Gradient strip
LCN:​ Erythromycin [Susceptibility] by Gradient strip

6932-8​ Penicillin: Susc: Pt: Isolate: OrdQn: MIC

LCN: ​Penicillin [Susceptibility] by Minimum inhibitory concentration (MIC)

OBX|1|CE|​7009-4​^Erythromycin Islt Grad strip^LN|1|LA6676-6^Resistant^LN||...

As described above, the results for an MIC OrdQn assay can be reported either as quantitative in
OBX-5 with an interpretation in OBX-8 or ordinal in OBX-5 using the same LOINC, which is
illustrated in the following two OBX segment examples:

OBX|1|NM|​6932-8​^Penicillin [Susceptibility] by Minimum inhibitory concentration

(MIC)^LN||0.05|ug/mL||S|||F|...

OBX|1|CE|​6932-8​^Penicillin [Susceptibility] by Minimum inhibitory concentration

(MIC)^LN||LA6576-8^Susceptible^LN||||||F|...

5.1.2 Susceptibility testing for slow-growing bacteria

Susceptibility testing for known slow-growing mycobacteria, such as Mycobacterium tuberculosis,
use a special testing technique. In LOINC, this ​Method​ is named ​Method for slow-growing
mycobacteria​. The ​Component​ for such tests may contain either the name of the antibiotic or both
the name of the antibiotic and the concentration at which it is being tested.

Guide for Using LOINC Microbiology Terms ​• 38

The following table shows the naming pattern for such tests in LOINC:

Component {Generic name of drug}

{Generic name of drug + concentration}

Property Susc

Time Aspect {Time value}

System {Specimen type}

Scale OrdQn

Method Method for slow-growing mycobacteria

Example:
20373-7​ Amikacin:Susc:Pt:Isolate:OrdQn:Method for Slow-growing mycobacteria
LCN:​ Amikacin [Susceptibility] by Method for Slow-growing mycobacteria

OBX|1|CE|​20373-7​^Amikacin [Susceptibility] by Method for Slow-growing

mycobacteria^LN||LA24225-7^Susceptible^LN||...

5.1.3 Viral phenotypic susceptibility testing

Viral phenotypic susceptibility testing is similar to bacterial susceptibility testing in that viral growth
is measured in the presence of antiviral agents. However, the LOINC M ​ ethod​ for viral phenotypic
susceptibility testing is P
​ henotyping​, which does not differentiate between specific methodologies,
unlike bacterial testing, for which LOINC has specific phenotypic ​Methods​ such as M ​ IC​ and
Gradient strip​.

The following table contains the naming pattern for viral phenotypic susceptibility terms in LOINC:

Component {Generic name of drug}

Property Susc

Time Aspect {Time value}

System Isolate

Scale OrdQn

Guide for Using LOINC Microbiology Terms ​• 39

 Method Phenotyping

Example:
72861-8​ Ganciclovir: Susc: Pt: Isolate: OrdQn: Phenotyping
LCN:​ Ganciclovir [Susceptibility] by Phenotype method

OBX|1|CE|​72861-8​^Ganciclovir [Susceptibility] by Phenotype

method^LN||LA24225-7^Susceptible^LN||...

5.1.4 Susceptibility thresholds based on type of infection

(“Breakpoints”)
In most cases, susceptibility thresholds (the specific value at which an organism is predicted to be
susceptible to a particular antibiotic) are the same for a given organism and antibiotic combination
regardless of infection type or route of antibiotic administration. However, for some organism and
antibiotic combinations, the threshold (i.e. “breakpoint”) varies based on route of administration
and/or type of infection, such as meningitis, pneumonia, or urinary tract infection. These data are
published by the same agencies (FDA, CLSI, EUCAST) that publish the common susceptibility
thresholds.

Route of administration and type of infection are two independent parameters: there are cases where
one antibiotic could have multiple breakpoints depending on the combination of route and type of
infection, and others where one antibiotic will have a single breakpoint regardless of route and type
13
of infection. For example, there are two different breakpoints for parenteral penicillin: one for
meningitis and one for everything else. But, there is a single breakpoint for vancomycin. The
susceptibility test is carried out exactly the same way regardless of the breakpoint. It is only for the
final step of assigning a susceptibility result that the specific breakpoint becomes important.

LOINC terms for susceptibility testing based on different breakpoints for different infection types
contain the infection type in the ​System,​ for example, ​Isolate.meningitis​, ​Isolate.pneumonia​ and
Isolate.UTI​.

Note that I​ solate.meningitis​ (or “.pneumonia”, “.UTI”) indicates that the particular susceptibility
result being reported is for an antibiotic that has a meningitis breakpoint. It does not imply that the
patient has or is suspected to have meningitis. For the same patient, the result for the same antibiotic
based on the non-meningitis breakpoint may also be reported with a term that simply has I​ solate​ as
the S​ ystem,​ and the result for an antibiotic that only has a single published breakpoint will also be

13
In veterinary medicine susceptibility thresholds are critically dependent on host species. When
reporting susceptibility by threshold the host species must always be reported elsewhere in the
message.

Guide for Using LOINC Microbiology Terms ​• 40

reported with a term that has I​ solate​ as the ​System​.

The following table contains the naming pattern for these susceptibility threshold LOINC terms:

Component {Generic name of drug}

Property Susc

Time Aspect {Time value}

System Isolate.{infection type}

Scale OrdQn

Method MIC

Example:
31138-1​ Cefotaxime: Susc: Pt: Isolate.meningitis: OrdQn: MIC
LCN: ​Cefotaxime [Susceptibility] for meningitis by Minimum inhibitory concentration

OBX|1|CE|​31138-1​^Cefotaxime [Susceptibility] for meningitis by Minimum inhibitory

concentration^LN||LA6676-6^Resistant^LN||...

5.2 Phenotypic testing for resistance enzymes

At the current time, only one LOINC M ​ ethod​ exists for directly determining (i.e., phenotypic testing)
whether or not a microorganism has developed a specific resistance mechanism. Antimicrobial
resistance detection (ARD; LOINC ​Method​ ​Gradient strip ARD​), measures the growth of an
organism in the presence of an antimicrobial plus a specific resistance inhibitor to determine which
resistance mechanism(s), if any, the organism has acquired.

Gradient strip ARD​ is a reagent strip impregnated with a predefined concentration gradient of a
specific antibiotic or combination of antibiotics. The difference between this M ​ ethod​ and ​Gradient
strip​ in LOINC is that ​Gradient strip​ is used for susceptibility testing, while G
​ radient strip ARD
is used for antimicrobial resistance detection and is reported as the presence or absence of a specific
enzyme or other mechanism that confers resistance. ARD is determined by comparing the inhibitory
concentration (IC) of a specific antimicrobial with the IC of that antimicrobial plus a resistance
inhibitor.

LOINC terms for resistance mechanism testing follow this pattern:

Guide for Using LOINC Microbiology Terms ​• 41

 Component {Name of resistance enzyme} by {name of
antimicrobial} to {name of antimicrobial+name of
inhibitor} inhibitory concentration ratio

Property PrThr

Time Aspect {Time value}

System Isolate

Scale Ord

Method Gradient strip ARD

Example:
85046-1​ AmpC beta-lactamase by cefoTEtan to cefoTEtan+cloxacillin inhibitory
concentration ratio:PrThr:Pt:Isolate:Ord:Gradient strip ARD
LCN: ​AmpC beta-lactamase by cefoTEtan to cefoTEtan+cloxacillin inhibitory concentration ratio
[Presence] by ARD gradient strip

5.3 Genotypic resistance testing

The extensive use of antibiotics has pressured microorganisms to adapt with altered genes in a
number of ways. A type of testing that is closely related to phenotypic susceptibility testing and may
sometimes be categorized under the same umbrella is that done to look for such gene alterations or
the mechanisms of resistance encoded by these alterations. The subtle difference between
phenotypic susceptibility and genotypic resistance testing is that susceptibility testing is used to
determine whether or not a particular organism’s growth is a​ ctually inhibited​ in the presence of an
antimicrobial, while testing for resistance mechanisms or genes is used to determine whether the
organism has developed the c​ apability​ to evade the effects of a specific antimicrobial or class of
antimicrobials and the specific mechanism it uses to do so and to ​predict​ whether the organism will
be inhibited in the presence of a particular antimicrobial.

14
The table below describes some of the resistance mechanisms and their associated genes.

Resistance Mechanism Definition Example gene(s)

Inactivation of antibiotic Antibiotic itself is enzymatically blaOXA, blaIMP

inactivated

14
Jia et al. 2017. CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic
Resistance Database. Nucleic Acids Research, 45, D566-573. Available from:
https://card.mcmaster.ca/ontology/36006

Guide for Using LOINC Microbiology Terms ​• 42

 Antibiotic efflux Transport of antibiotic out of the tetK
cell

Alteration of antibiotic target Antibiotic target altered by rpoB, mcr-1, vanA, ermA
mutation or enzyme
modification

Replacement of antibiotic Exchange of antimicrobial target mecA, mecB, mecC, mecD

target protein for one that is not
recognized by the antibiotic

The resistance mechanisms above are all dependent on the ability of the organism to create or not to
create proteins that determine whether or not an antibiotic is lethal to the organism. The genes
responsible for the resistance proteins can be acquired either by genetic mutation or nucleic acid
transfer from another organism that carries the gene. As specified above, the genetic alterations can
change, replace, or cover up the protein to which the antibiotic attaches. Resistance genes can also
encode efflux pumps that move the antibiotic out of the microorganism. The antibiotic may be
inactivated, or the organism may become markedly less permeable to the drug, all due to genetic
15
changes in the microorganism.

Various M ​ ethods​ are available to test for the genetic information (e.g., specific resistance genes or
nucleotide alterations in native genes) that encodes resistance mechanisms, including
Probe.amp.tar​, N ​ on-probe.amp.tar​, and ​Sequencing​ (see Chapter 7 for definitions of these
Methods​). Until 2018, LOINC bacterial genotypic susceptibility testing terms used the specific
Methods​ named above; however, moving forward we are recommending using the ​Molgen​ ​Method
for all bacterial molecular resistance testing to obviate the need to create different terms for different
molecular M ​ ethods​ (​Probe.amp.tar​, S​ equencing​, etc.). Terms that were previously created with a
Method​ other than M ​ olgen​ are described below but their usage is not recommended.

Historically, susceptibility testing was always phenotypic and therefore was always performed on an
Isolate​, which is a microorganism from a patient specimen that is grown and isolated on culture
media. However, with new molecular techniques, genotypic testing can be performed directly on
patient specimens without isolating the organism. Rather than creating separate terms for every
possible patient specimen that can be tested, single terms for each resistance gene or
resistance-conferring mutation will be created with the S​ ystem​ ​Isolate/Specimen​, meaning that the
assay can be done using a traditional isolated colony or on a direct specimen. This does NOT imply
that every manufacturer’s genotypic assay is approved for testing on an isolate or any type of
specimen. Existing terms with I​ solate ​or other specific specimens as the S​ ystem​ may be updated over
time but are presented below in their present state.

15
Antibiotic Resistance [Internet]. Salt Lake City, Utah: University of Utah Genetic Science Learning
Center. Available from: ​http://learn.genetics.utah.edu/content/microbiome/resistance/

Guide for Using LOINC Microbiology Terms ​• 43

 EVOLVING MODEL

The specific ​Methods f​ or bacterial genotypic resistance testing such as ​Probe.amp.tar​ and
Sequencing ​are no longer recommended for use; the ​Method​ for existing bacterial molecular
resistance terms may be updated over time to ​Molgen.

EVOLVING MODEL

LOINC terms with specific ​Systems ​such as ​Bld​ or ​Isolate/Anorectal​ will no longer be created for
terms representing molecular resistance assays. Instead, the ​Isolate/Specimen​ ​System​ will be used
since newer molecular techniques can be used with a variety of specimens. Existing terms with more
specific ​Systems​ may be updated over time.

5.3.1 Bacterial molecular resistance testing

Note that there is a subtle difference between resistance genes that confer resistance simply by being
present, and resistance that is conferred due to one or more mutations in a native gene. For example,
the presence of the vanA gene means that the organism is predicted to be resistant to vancomycin. In
contrast, the presence of the rpoB gene by itself is not significant, however, the presence of specific
mutations in the rpoB gene suggest that the organism will be resistant to certain drugs. This
distinction is represented in LOINC by using two different C ​ omponent​ patterns as given below. Note
that the original LOINC terms for genotypic resistance may not have been modeled consistently
according to these patterns, but all of the existing terms will be reviewed and updated depending on
whether the gene specified in the​ Component​ is a native gene or a resistance gene.

5.3.1.1 Identifying the presence or absence of a resistance gene

LOINC terms that represent testing for resistance genes follow the pattern shown below. In the
Component​, the name of the drug or drug class and the word “resistance” precede the word “gene”,
since the gene by definition encodes resistance. And the ​Scale​ is O
​ rd​, because the presence or absence
of the gene is being reported.

Component Bacterial {name of antibiotic or antibiotic class}

resistance {name of resistance gene} gene

Property PrThr

Time Aspect {Time value}

System Isolate/Specimen

{Specimen type}*

Guide for Using LOINC Microbiology Terms ​• 44

 Isolate*
*Going forward terms with these ​Systems ​may be
updated to the Isolate/Specimen ​System ​(see
discussion above)

Scale Ord

Method Molgen

Probe.amp.tar*

Non-probe.amp.tar*
*Going forward terms with these ​Methods​ may
be updated to the Molgen ​Method​ (see
discussion above)

Examples:
72421-1​ ​Bacterial vancomycin resistance vanB
gene:PrThr:Pt:Isolate/Specimen:Ord:Molgen
LCN: ​Vancomycin resistance vanB gene [Presence] by Molecular method

85827-4​ Bacterial carbapenem resistance blaOXA-48-like

gene:PrThr:Pt:Isolate/Specimen:Ord:Molgen
LCN: ​Carbapenem resistance bla OXA-48-like gene [Presence] by Molecular method

OBX|1|CE|​72421-1​^Vancomycin resistance vanB gene [Presence] by NAA with probe

detection^LN||LA11882-0^Detected^LN||...

5.3.1.2 Identifying the presence or absence of a resistance-conferring

mutation
LOINC terms that represent testing for and reporting the presence or absence of
resistance-conferring mutations in native genes follow the pattern shown below. In the C ​ omponent,​
the gene name is followed by the name of the drug or drug class and the words “resistance mutation”,
since the gene itself does not encode resistance. The ​Scale​ is O
​ rd​, because the presence or absence of
the mutation is being reported.

Component Bacterial {name of gene} gene {name of antibiotic

or antibiotic class} resistance mutation

Property PrThr

Time Aspect {Time value}

Guide for Using LOINC Microbiology Terms ​• 45

 System Isolate/Specimen

{Specimen type}*

Isolate*
*Going forward terms with these ​Systems ​may
be updated to the Isolate/Specimen ​System (​ see
discussion above)

Scale Ord

Method Molgen

Probe*

Probe.amp.tar*

Non-probe.amp.tar*
*Going forward terms with these ​Methods​ may
be updated to the Molgen ​Method​ (see
discussion above)

Examples:
89372-7​ Mycobacterium tuberculosis complex rpoB gene rifAMPin resistance
mutation:PrThr:Pt:Isolate/Specimen:Ord:Molgen
LCN: ​Mycobacterium tuberculosis complex rpoB gene rifAMPin resistance mutation [Presence]
by Molecular method

5.3.1.3 Identifying the specific resistance-conferring mutation found

LOINC terms for reporting which resistance-conferring mutations were detected, rather than just
the presence or absence of such mutations, follow the pattern shown below. In the C
​ omponent​, the
gene name is followed by the name of the drug or drug class and the words “resistance mutation
detected”, and the S​ cale​ is N
​ om​.

Component Bacterial {name of gene} gene {name of antibiotic

or antibiotic class} resistance mutation detected

Property Prid

Time Aspect {Time value}

System Isolate/Specimen

Guide for Using LOINC Microbiology Terms ​• 46

 {Specimen type}*

Isolate*
*Going forward terms with these ​Systems ​may
be updated to the Isolate/Specimen ​System (​ see
discussion above)

Scale Nom

Method Molgen

Probe.amp.tar*

Non-probe.amp.tar*
*Going forward terms with these ​Methods​ may
be updated to the Molgen ​Method​ (see
discussion above)

5.3.2 Predicted susceptibility based on molecular testing

LOINC terms that represent the p​ redicted​ susceptibility of an organism to a particular antimicrobial
based on the presence or absence of resistance genes or resistance-conferring mutations in native
genes follow the pattern shown below:

Component {Generic name of drug}

Property Susc

Time Aspect {Time value}

System Isolate

Scale Ord

Method Genotyping

Examples:
89488-1​ Isoniazid:Susc:Pt:Isolate/Specimen:Ord:Genotyping
LCN: ​Isoniazid [Susceptibility] by Genotype method

72854-3​ Ganciclovir:Susc:Pt:Isolate:Ord:Genotyping
LCN: ​Ganciclovir [Susceptibility] by Genotype method

Guide for Using LOINC Microbiology Terms ​• 47

6 Antigen tests
Antigens are molecules that can elicit an immune response in a host organism based on host
recognition of the antigen as foreign. Antigens can be proteins or other types of molecules from
various parts of the microorganism, such as the cell surface or within the cell. When a
microorganism invades a host organism, its antigens stimulate the immune system to produce
antibodies and initiate a cascade of immune responses against it. The combination of the direct effect
of the microorganism on the host (e.g. via toxins) and the immune response to that microorganism
often results in a characteristic pattern of signs and symptoms that helps narrow down the potential
list of causative agents. Targeted antigen testing can be done for suspected organisms to identify the
single pathogen responsible.

6.1 LOINC ​Methods​ for antigen testing

The LOINC M ​ ethod​ is a key differentiator between many LOINC terms that represent assays that test
for the same antigen in a particular specimen type. The common ​Methods​ used to detect microbial
antigens are described in the following table:

LOINC ​Method Description

(null) No method specified. Laboratory tests often do not include the ​Method​ as part of the
name for common tests when different methods produce clinically equivalent
results, which is a common situation in antigen testing.

IA Immunoassay (​IA​) tests are ​assays where an immunological binding reaction

between a specific antibody and its target is used to detect the presence or amount
of the analyte being measured​. IAs can be used to detect either antibodies or
antigens. If binding between the antibody and target occur, the resulting signal or
enzymatic reaction can be measured either qualitatively or quantitatively to
16
indicate the presence or quantity of the organism.

IA.rapid LOINC defines rapid immunoassays as those producing results in 30 minutes or

less.

16
Darwish IA. Immunoassay Methods and their Applications in Pharmaceutical Analysis: Basic
Methodology and Recent Advances. Int J Biomed Sci. 2006 Sep;2(3):217-35. [PMID: ​23674985​]

Guide for Using LOINC Microbiology Terms ​• 48

 IF Immunofluorescence (​IF​) tests are immunoassays that use a fluorophore label
attached to the antibody. In LOINC, ​IF​ includes direct (DFA), indirect (IFA), and
anti-complement (ACIF) immunofluorescence methods, and is only used for assays
that provide information about the presence or amount of a target analyte AND its
location (or pattern) on a smear, tissue slice, or cell.

Immune stain An immune stain method is one where an antibody with an attached label reacts to
an antigen on cells within a tissue section. The labeled antibody produces a signal
when it binds to the antigen that can be detected by the assay instrument. In
LOINC, the ​Immune stain​ M​ ethod​ does not encompass Immunofluorescence, which
has its own ​Method​ type.

LA Latex agglutination is a method for detecting antigens using antibodies that are
attached to latex particles. When the antibody and antigen bind together, clumps
of latex particles are easily visible.

6.2 Identifying the presence or absence of a

suspected organism
The most common antigen tests in LOINC are those for determining whether or not a specific
organism is present. The C
​ omponent ​for these tests includes the name of the organism followed by
‘Ag’. The naming pattern for these terms reporting ordinal results is as follows:

Component {Name of microorganism} Ag

Property PrThr

Time Aspect {Time value}

System {Specimen type}

Scale Ord

Method {Method type} or method-less

Examples:
31754-5​ Brucella sp Ag: PrThr: Pt: Placenta: Ord:
LCN: ​Brucella sp Ag [Presence] in Placenta

43612-1​ Adenovirus Ag:PrThr:Pt:Nose:Ord:IF

LCN: ​Adenovirus Ag [Presence] in Nose by Immunofluorescence

48335-4​ Aspergillus sp Ag:PrThr:Pt:Tiss:Ord:Immune stain

LCN: ​Aspergillus sp Ag [Presence] in Tissue by Immune stain

Guide for Using LOINC Microbiology Terms ​• 49

 OBX|1|CE|​48335-4​^Aspergillus Ag Tiss Ql ImStn^LN|1|LA6577-6^Negative^LN||...

6.3 Identifying the specific subtype of a

suspected organism
LOINC also contains a small number of terms for assays that detect the presence and distinguish
between the subtypes within a class of microorganism, such as influenza A versus influenza B, or the
specific species of Plasmodium. Such tests are represented with the following naming pattern:

Component {Name of microorganism} Ag

Property Prid

Time Aspect {Time value}

System {Specimen type}

Scale Nom

Method {Method type}

Example:
72366-8​ Influenza virus A & B Ag: Prid: Pt: Nose: Nom: IA.rapid
LCN:​ Influenza virus A and B Ag [Identifier] in Nose by Rapid immunoassay

OBX|1|CE|​72366-8​^​ ​Influenza virus A and B Ag [Identifier] in Nose by Rapid

immunoassay^LN||LA6577-6^Negative^LN||...

6.4 Quantitative antigen tests

Some assays quantify the amount of antigen present in a sample. Most of these LOINC terms have
either T
​ itr ​or A
​ Cnc​ as the ​Property​. The ​ACnc​ ​Property​ represents the number of arbitrary units in
a volume (arbitrary concentration). Immunoassay results that are based on optical densities are
commonly represented in LOINC with this ​Property​. Because the units are truly arbitrary, they may
be represented in a variety of ways by different laboratories and also within LOINC. Please see
Chapter 10 “Choosing the right LOINC term (“mapping”)” or the LOINC Users’ Guide for more
information.

Guide for Using LOINC Microbiology Terms ​• 50

Such tests are represented with the following naming pattern:

Component {Name of microorganism} Ag

Property ACnc

Titr

Time Aspect {Time value}

System {Specimen type}

Scale Qn

Method {Method type}

Example:
9817-8​ Cryptococcus sp Ag: Titr: Pt: CSF: Qn: IA
LCN: ​Cryptococcus sp Ag [Titer] in Cerebral spinal fluid by Immunoassay

OBX|1|NM|​9817-8​^Cryptococcus sp Ag [Titer] in Cerebral spinal fluid by Immunoassay

^LN|1|1:32||...

Guide for Using LOINC Microbiology Terms ​• 51

7 Nucleic acid tests
Nucleic acid tests are used to detect and/or identify microorganisms based on their genetic material.
Some microorganisms contain DNA, and others contain RNA. The principle behind nucleic acid
tests is that they target genes or fragments of genetic material that are known to uniquely identify a
particular organism or group of organisms.

For example, ​Neisseria meningitidis​ is identified by the presence of the sodC gene. Different
serogroups of ​N. meningitidis​ can be identified based on the presence of additional genes: N.
meningitidis serogroup A contains the sacB gene, serogroup B contains synD, and serogroup Y
contains synF. By first testing for the sodC gene, the presence or absence of N. meningitidis can be
determined, and if it is found to be present, further testing for serogroup-specific genes can identify
the serogroup.

There are different types of nucleic acid tests, including individual tests that look for one specific
microorganism, and multiplex tests which simultaneously look for many different organisms based
on their individual genetic targets. Such multiplex tests are often represented in LOINC as panels,
such as 8​ 2159-5​ Respiratory pathogens DNA and RNA panel – Nasopharynx by NAA with non-probe
detection,​ where the panel code is used for the order and the individual children to report the result
for each specific pathogen.

When selecting the best LOINC term for the nucleic acid test you are mapping, it is important to
review the manufacturer’s package insert or test specification document mentioned in section 3.2 to
determine: 1) the specific target, such as the name of the gene, or an unnamed segment of DNA or
RNA; and 2) the M​ ethod​ being used. Be careful when choosing terms for PCR-based tests, because, as
described further in Section 10.2, two LOINC ​Methods​ include a PCR step: ​Probe.amp.tar​ and
Non-probe.amp.tar​.

7.1 Choosing LOINC terms with the correct

Component
PCR-based testing for the presence of microorganisms is becoming more common. Earlier in the
history of PCR-based testing, LOINC terms were created for generic DNA or RNA targets that did
not specify the specific gene. These tests have C
​ omponents​ such as A
​ cinetobacter baumannii DNA
or ​Influenza virus A RNA​. More recently, Regenstrief has received requests for tests that detect
bacteria, viruses, and other pathogens based on specific genetic targets. Thus, LOINC now contains

Guide for Using LOINC Microbiology Terms ​• 52

terms with more specific ​Components​ such as ​Clostridioides difficile toxin A+B tcdA+tcdB genes
and Z
​ ika virus 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, LOINC will continue to add new terms that specify the gene targets.

When mapping genetic tests, be sure to choose a LOINC term with the same specificity as the assay
you are mapping.

For tests that specify an individual genetic target, look for LOINC terms with a C
​ omponent
containing that specific target. For example:

● Bordetella holmesii fumC gene

● Escherichia coli stx1 gene
● Neisseria meningitidis serogroup A sacB gene
● Mycoplasma flocculare 16s rRNA gene

For tests that do not specify the specific gene target, look for LOINC terms with a ​Component​ that
contains the more generic DNA or RNA. For example:

● Adenovirus 3 DNA
● Bordetella pertussis DNA
● Chikungunya virus RNA

7.2 LOINC ​Methods​ for nucleic acid tests

Nucleic acid tests in LOINC are characterized by specific M
​ ethods,​ including ​Probe​, ​Probe.amp.tar​,
and N
​ on-probe.amp.tar​, which are briefly described in the table below. Before choosing a LOINC
term, carefully review the methodology for the assay you are mapping to decide which LOINC
Method​ would be most suitable. Pay particular attention to the technique used for the final step of
target identification.

LOINC ​Method Description

Probe A test that detects a specific nucleic acid sequence by using a segment of genetic
material (the probe) that is known to bind to that sequence. This ​Method​ does not
include nucleic acid amplification.

Probe.amp.sig A test that uses a probe (see description of ​Probe​ above) to detect a specific target,
followed by amplification of the signal attached to that probe, which makes the
signal easier to detect. This ​Method​ does not include nucleic acid amplification.

Guide for Using LOINC Microbiology Terms ​• 53

 Probe.amp.tar A test that first copies the genetic material in a specimen by using nucleic acid
amplification techniques such as polymerase chain reaction (PCR), then uses a
probe (see description of ​Probe​ above) to detect the presence of a specific nucleic
acid sequence. PCR significantly increases the amount of genetic material in the
sample, which makes it more likely to be detected by the probe. This ​Method
includes real-time PCR. In addition, for historical reasons it also includes traditional
techniques for identifying PCR target amplification products, such as gel
separation and staining to identify the fragments based on their expected sizes.

Non-probe.amp.tar This ​Method​ begins with PCR-based amplification of the genetic material in the
specimen, but instead of using probes to identify the targets of interest, other
techniques, such as melt curve analysis or turbidity, are used to detect and identify
the target.

7.3 Identifying the presence or absence of a

suspected organism
Nucleic acid tests are often used to detect the presence or absence of a suspected microorganism. Use
the information in the previous sections to determine the correct ​Component a​ nd M
​ ethod,​ and the
following table to determine the other relevant attributes.

Component {Name of microorganism} gene or DNA or RNA or

rRNA

Property PrThr

Time Aspect {Time value}

System {Specimen type}

Scale Ord

Method Probe

Probe.amp.sig

Probe.amp.tar

Non-probe.amp.tar

Examples:
87376-0​ Escherichia coli stx1 gene:PrThr:Pt:Isolate:Ord:Probe.amp.tar
LCN: ​Escherichia coli stx1 gene [Presence] in Isolate by NAA with probe detection

77959-5​ Yellow fever virus ns5 gene:PrThr:Pt:CSF:Ord:Non-probe.amp.tar

Guide for Using LOINC Microbiology Terms ​• 54

LCN: ​Yellow fever virus ns5 gene [Presence] in Cerebral spinal fluid by NAA with non-probe
detection

77369-7​ HIV 1 RNA:PrThr:Pt:Semen:Ord:Probe.amp.tar

LCN: ​HIV 1 RNA [Presence] in Semen by NAA with probe detection

OBX|1|CE|​87376-0​^Escherichia coli stx1 gene [Presence] in Isolate by NAA with probe

detection^LN|1|LA11882-0^Detected^LN||...

7.4 Identifying the subtype or species of a

suspected organism
Nucleic acid tests are also often used to determine the specific subtype or strain of a suspected
microorganism. The following table provides the representative P​ art​ values for LOINC terms
representing such tests.

KEY POINT

Remember the difference between ​Prid​ and ​Type​ is that ​Prid ​is used when the presence of the
organism is not certain, so either the absence (if it was not detected) or the specific subtype or strain
is reported, while ​Type ​is used when the organism is known to be present and the test is being done
to determine the specific subtype or strain.

Component {Name of microorganism} subtype or strain

Property Prid

Type

Time Aspect {Time value}

System {Specimen type}

Scale Nom

Method Probe.amp.tar

Non-probe.amp.tar

Examples:
72483-1​ BK virus subtype:Type:Pt:Ser/Plas:Nom:Probe.amp.tar
LCN: ​BK virus subtype in Serum or Plasma by NAA with probe detection

Guide for Using LOINC Microbiology Terms ​• 55

82354-2​ Human papilloma virus 16 & 18+45 E6+E7 mRNA:Prid:Pt:Cvx:Nom:Probe.amp.tar
LCN: ​Human papilloma virus 16 and 18+4
​ 5 E6+E
​ 7 mRNA [Identifier] in Cervix by NAA with probe
detection

OBX|1|CE|​72483-1​^BK virus subtype in Serum or Plasma by NAA with probe

detection^LN|1|LA19050-6^BK virus subtype II^LN|...

7.5 Multiplex assays

Multiplex assays are able to detect or identify multiple organisms in a single specimen and a single
test instance based on the individual genetic target of each organism. The results of multiplex assays
are typically available within several hours and are highly sensitive and specific for the organisms,
genes, or serotypes being investigated. The high negative predictive value of multiplex tests makes
them ideally suited as screening instruments during infectious outbreaks, as well as determining
when it is safe to remove isolation precautions from potentially infectious patients. There are two
classifications of multiplex panels:

1.​ S​ yndromic,​ which include the most common organisms known to be associated with a
particular condition that are likely to be tested together. One example is a multiplex panel of
bacteria, viruses, and parasites that are common etiologic agents of diarrhea, such as the
following:

Campylobacter jejuni, Salmonella, Shigella, ETEC/STEC, E. coli O157:H7, Vibrio cholerae,

Yersinia enterocolitica, and toxigenic Clostridioides difficile,Giardia lamblia,
Cryptosporidium, Entamoeba histolytica, Norovirus GI/GII, Adenovirus 40/41 and
Rotavirus A.

2. Pathogen class​, which also include groups of organisms associated with a specific
condition, but only those within a single class of either bacterial, viral, fungal, or parasite,
such as the following viral causes of diarrhea: Rotavirus, Norovirus, Sapovirus, Astrovirus,
and Adenovirus.

Such multiplex tests are often represented in LOINC as panels, where the panel contains individual
children for reporting the individual result for each specific pathogen. LOINC code​ 82159-5​, shown
below, is an example of a code that represents a multiplex panel.

Guide for Using LOINC Microbiology Terms ​• 56

 82159-5​ ​Respiratory pathogens DNA and RNA panel – Nasopharynx by NAA with non-probe detection
82160-3​ ​Adenovirus DNA [Presence] in Nasopharynx by NAA with non-probe detection
82161-1​ ​Human coronavirus HKU1 RNA [Presence] in Nasopharynx by NAA with non-probe detection
82162-9​ ​Human coronavirus NL63 RNA [Presence] in Nasopharynx by NAA with non-probe detection
82163-7​ ​Human coronavirus 229E RNA [Presence] in Nasopharynx by NAA with non-probe detection
82164-5​ ​Human coronavirus OC43 RNA [Presence] in Nasopharynx by NAA with non-probe detection
82165-2​ ​Human metapneumovirus RNA [Presence] in Nasopharynx by NAA with non-probe detection
82166-0​ ​ Influenza virus A RNA [Presence] in Nasopharynx by NAA with non-probe detection
82167-8​ ​Influenza virus A H1 RNA [Presence] in Nasopharynx by NAA with non-probe detection
82168-6​ ​Influenza virus A H1 2009 pandemic RNA [Presence] in Nasopharynx by NAA with non-probe
detection
82169-4 ​ ​Influenza virus A H3 RNA [Presence] in Nasopharynx by NAA with non-probe detection
82170-2​ ​Influenza virus B RNA [Presence] in Nasopharynx by NAA with non-probe detection
82171-0​ ​Parainfluenza virus 1 RNA [Presence] in Nasopharynx by NAA with non-probe detection
82172-8​ ​Parainfluenza virus 2 RNA [Presence] in Nasopharynx by NAA with non-probe detection
82173-6​ ​Parainfluenza virus 3 RNA [Presence] in Nasopharynx by NAA with non-probe detection
82174-4​ ​Parainfluenza virus 4 RNA [Presence] in Nasopharynx by NAA with non-probe detection
82175-1​ ​Rhinovirus+​Enterovirus RNA [Presence] in Nasopharynx by NAA with non-probe detection
82176-9​ ​Respiratory syncytial virus RNA [Presence] in Nasopharynx by NAA with non-probe detection
82177-7​ ​Mycoplasma pneumoniae DNA [Presence] in Nasopharynx by NAA with non-probe detection
82178-5​ ​Chlamydophila pneumoniae DNA [Presence] in Nasopharynx by NAA with non-probe detection
82179-3​ ​Bordetella pertussis toxin promoter region [Presence] in Nasopharynx by NAA with non-probe
detection

Historically, multiplex tests that produced two or three individual results but where the individual
results were reported together in one field were modeled in LOINC by a single term (not a panel),
where all of the analytes were named and separated by ampersands (&) in the ​Component​ and “and” in
the Long Common Name (see the “Part-specific mapping principles” section in Chapter 9 for the
usage of & versus + in the ​Component​). However, going forward, the panel model is recommended so
that each result can be reported in a separate field.

EVOLVING MODEL

Older LOINC terms for assays that produce individual results for two or three analytes were
sometimes modeled in LOINC as a single term with multiple analytes specified in the ​Component​ and
separated by “&”, and the ​Answer List a
​ ssociated with such terms would include combinatorial results.
Moving forward, only assays that truly produce a single result will be modeled this way; otherwise, a
panel will be created with individual children for each result.

Following is an example of an older LOINC term representing a multiplex assay that produces
individual results that are reported together as one:

51668-2​ Streptococcus pneumoniae DNA & Haemophilus influenza DNA & Pseudomonas
aeruginosa DNA:Prid:Pt:XXX:Nom:Probe.amp.tar
LCN: ​Streptococcus pneumoniae DNA and Haemophilus influenzae DNA and Pseudomonas aeruginosa
DNA [Identified] in unspecified specimen by NAA with probe detection

Guide for Using LOINC Microbiology Terms ​• 57

7.6 Quantitative assays
Quantitative nucleic acid assays determine the quantity of a particular organism present in a sample
using methods such as real-time PCR.

7.6.1 Real-time PCR

Real-time PCR is a ​Method​ during which PCR cycles are run continuously until the target genetic
material is detected. Once the target is detected, the cycles stop, and the number of cycles at which
the target was detected is reported (in contrast to reporting the total amount of organism present).
The ​Property f​ or these quantitative assays is T
​ hreshNum​, but this may be a misnomer because the
result does not represent the threshold of detection but rather the number of cycles that were run
before the analyte was detected. In the future, with the approval of the LOINC Laboratory
Committee, we may rename this P​ roperty​ to be more clear.

LOINC terms for real-time PCR assays use the following naming pattern:

Component {Name of microorganism} gene or DNA or RNA

Property ThreshNum

Time Aspect {Time value}

System {Specimen type}

Scale Qn

Method Probe.amp.tar

Examples:
74424-3​ Enterovirus RNA:ThreshNum:Pt:Stool:Qn:Probe.amp.tar
LCN: ​Enterovirus RNA [Cycle threshold #] in Stool by NAA with probe detection

85679-9​ Haemophilus influenzae bex gene:ThreshNum:Pt:XXX:Qn:Probe.amp.tar

LCN: ​Haemophilus influenzae bex gene [Cycle Threshold #] in Unspecified specimen by NAA with probe
detection

7.6.2 Viral loads

Viral loads are a specific type of nucleic acid detection test that determines the amount of virus
present. The amount of virus is characterized by how many copies or units are present per volume,
in either absolute or log scale. Viral loads are typically done for viruses such as HIV and hepatitis C.

Guide for Using LOINC Microbiology Terms ​• 58

Most viral load tests in LOINC have a ​Method​ of P
​ robe.amp.tar​; however, LOINC also contains
many terms in which the ​Method​ specifies a particular detection limit, e.g., P
​ robe.amp.tar
detection limit = 50 copies/mL​. LOINC terms that specify a detection limit are no longer
recommended, because the detection limit is not actually a ​Method​ but rather a measure of the
sensitivity of the test. Instead, we recommend reporting the viral load using the term with the
Probe.amp.tar​ ​Method​ and reporting the detection limit separately using LOINC 8​ 7706-8​ ​Laboratory
device Detection limit.

EVOLVING MODEL

Using LOINC terms with specific detection limit ​Methods​ is no longer recommended, and we
will likely not create any more terms that specify specific limits. Instead, we encourage
reporting viral load results using a term with ​Method​ ​Probe.amp.tar​ along with a second
LOINC term (​87706-8​ ​Laboratory device Detection limit)​ to report the detection limit as a
separate observation.

The following tables are a quick reference for determining the appropriate P​ roperty​ and ​Method​ for
viral load tests.

Matching units of measure to LOINC ​Property​ for viral loads:

Unit of measure LOINC ​Property

copies/mL; #/mL NCnc (number concentration)

Log copies/mL; LnCnc (log number concentration)

log #/mL

units/mL; IU/mL ACnc (arbitrary concentration)

Log units/mL; log LaCnc (log unit concentration)

IU/mL

Detection limit specification to LOINC ​Method​ match for viral loads:

Detection limit LOINC ​Method

specified

No Probe.amp.tar

Yes* Probe.amp.tar detection limit = {#} copies/mL

Probe.amp.tar detection limit = log {#} copies/mL
Probe.amp.tar detection limit = {#} units/mL
*See Evolving Model box above

Guide for Using LOINC Microbiology Terms ​• 59

7.6.2.1 Viral load reported as copies/volume
Viral loads reported as copies/volume may be determined using assays with or without defined
detection limits. LOINC terms for such viral load observations follow the naming pattern below:

Component {Name of microorganism} DNA or RNA

Property NCnc

LnCnc

Time Aspect {Time value}

System {Specimen type}

Scale Qn

Method Probe.amp.tar

Probe.amp.tar detection limit = {#} copies/mL*

Probe.amp.tar detection limit = {#} log copies/mL*

*Going forward terms with these ​Methods​ are not

recommended (see discussion above)

Examples:
20447-9​ HIV 1 RNA:NCnc:Pt:Ser/Plas:Qn:Probe.amp.tar
LCN: ​HIV 1 RNA [#/volume] (viral load) in Serum or Plasma by NAA with probe detection

41497-9​ HIV 1 RNA:LNCnc:Pt:CSF:Qn:Probe.amp.tar

LCN: ​HIV 1 RNA [Log #/volume] (viral load) in Cerebral spinal fluid by NAA with probe detection

48511-0​ HIV 1 RNA:NCnc:Pt:Ser/Plas:Qn:Probe.amp.tar detection limit = 50 copies/mL

LCN: ​HIV 1 RNA [#/volume] (viral load) in Serum or Plasma by NAA with probe detection limit = 50
copies/mL

7.6.2.2 Viral load reported as units/volume

Similar to viral loads reported as copies/volume, those reported as units/volume may also be
determined using assays with or without defined detection limits. LOINC terms for such viral load
observations use the following naming pattern:

Component {Name of microorganism} DNA or RNA

Guide for Using LOINC Microbiology Terms ​• 60

 Property ACnc

LaCnc

Time Aspect {Time value}

System {Specimen type}

Scale Qn

Method Probe.amp.tar

Probe.amp.tar detection limit = {#} IU/mL*

*Going forward terms with this type of ​Method

are not recommended (see discussion above)

Examples:
43730-1​ Epstein Barr virus DNA:ACnc:Pt:Ser/Plas:Qn:Probe.amp.tar
LCN: ​Epstein Barr virus DNA [Units/v​ olume] (viral load) in Serum or Plasma by Probe and target
amplification method

74419-3​ Parvovirus B19 DNA:LaCnc:Pt:Ser/Plas:Qn:Probe.amp.tar

LCN: ​Parvovirus B19 DNA [log units/v​ olume] (viral load) in Serum or Plasma by Probe and target
amplification method

49758-6​ Hepatitis C virus RNA:ACnc:Pt:Ser/Plas:Qn:Probe.amp.tar detection limit = 5 IU/mL

LCN: ​Hepatitis C virus RNA [Units/volume] (viral load) in Serum or Plasma by NAA with probe detection
limit = 5 IU/mL

OBX|1|CE|​49758-6​^Hepatitis C virus RNA [Units/volume] (viral load) in Serum or

Plasma by NAA with probe detection limit = 5 IU/mL^LN||325|IU/mL|<15|P...

8 Serology testing
When a microorganism invades a host organism, its antigen(s) stimulate the production of
antibodies in the host and initiate a cascade of immune responses against it. As described above in
the chapter about antigen testing, the combination of the direct effect of the microorganism on the
host (e.g., via toxins) and the immune response to that microorganism often results in a
characteristic pattern of signs and symptoms that helps narrow down the potential list of causative
agents. Targeted antibody testing can be done based on this list of suspected organisms to identify
the single pathogen responsible. Tests for antibodies against infectious agents are useful for

Guide for Using LOINC Microbiology Terms ​• 61

identifying acute, chronic, or prior infection. Antibody testing is also useful for determining
immunization status or response.

Several classes of antibodies are produced by the human immune system, including IgA, IgD, IgE,
IgG, and IgM, all of which have a specific function. The most common types related to infectious
diseases are IgG and IgM. IgM antibodies are the first ones produced in response to a foreign
antigen, and the presence of IgM antibodies usually indicates acute infection (either active or recent).
IgG antibodies provide long-term immunity, and indicate previous, convalescent, or chronic
infection. IgG antibodies are also indicative of an immune response to vaccination.

8.1 LOINC ​Components​ for antibody testing

LOINC terms for antibody testing include the name of the organism and Ab in the ​Component​. Some
terms also include one or more specific classes of antibody, and some include information about 1st
specimen and 2nd specimen, which is used to represent acute and convalescent titers or vaccine
efficacy. Both of these concepts are described in more detail below.

8.1.1 Specifying the antibody class in the ​Component

Components​ that include the word “Ab” without specifying IgG, IgM, etc. represent any type of
antibody. If a specific antibody class is being targeted, the ​Component​ will include that information,
e.g. ​Salmonella enteritidis Ab.IgG​. The following table provides a quick reference for the types of
antibodies contained in LOINC microbiology ​Components.​

Antibody class in Description

LOINC ​Component

Ab Antibody, which encompasses any of the specific antibodies and is used when the
assay does not specify which antibodies it is detecting

Ab.IgG IgG antibody

Ab.IgM IgM antibody

Ab.IgG+IgM Both IgG and IgM antibody can be detected, but not distinguished

Ab.IgG & IgM Both IgG and IgM can be detected and distinguished, and results are reported
separately for each

KEY POINT

Pay attention to the class(es) of antibody targeted by your test when choosing the
appropriate LOINC term. Often, the only distinguishing attribute of several LOINC terms is
that they differ in the specification of the antibody class.

Guide for Using LOINC Microbiology Terms ​• 62

8.1.2 Measuring acute and convalescent antibodies and
vaccine efficacy
Acute and convalescent antibody testing helps confirm a recent infection by comparing antibody
levels measured during the active phase of the infection with those measured 2-4 weeks later during
the recovery phase. Another example of a paired antibody test is pre- and post-immunization
testing, which is done in some clinical circumstances. LOINC creates paired terms that can be used
in both of these cases. One LOINC term includes ​1st specimen​ in the ​Component​ to represent the
acute or pre-immunization specimen, and the other term has 2​ nd specimen​, to represent the
convalescent or post-immunization specimen.

For example, the following term represents the test for Epstein-Barr virus in the acute phase of the
illness:

32843-5​ Epstein Barr virus capsid Ab.IgG^1st specimen: ACnc: Pt: Ser: Qn:
LCN:​ Epstein Barr virus capsid IgG Ab [Units/​volume] in Serum --1st specimen

And this term represents the test in the convalescent phase:

32844-3​ Epstein Barr virus capsid Ab.IgG^2nd specimen: ACnc: Pt: Ser: Qn:
LCN: ​Epstein Barr virus capsid IgG Ab [Units/​volume] in Serum --2nd specimen

8.2 LOINC ​Methods​ for antibody testing

The key differentiator between many LOINC terms for the same organism-antibody pair is the
Method​. A wide variety of ​Methods​ are used for antibody testing. The most common M
​ ethods​ for
LOINC antibody terms are given in the table below:

LOINC ​Method Description

(null) No method specified. Laboratory tests often do not include the Method as part of
the name for common tests when different methods produce clinically equivalent
results, which is a common situation in antibody and antigen testing. In these cases,
LOINC creates terms without a ​Method​ to allow laboratory professionals the
freedom to choose how the test is run.

Guide for Using LOINC Microbiology Terms ​• 63

 IA Immunoassay (​IA​) tests are ​assays where an immunological binding reaction
between a specific antibody and its target is used to detect the presence or amount
of the analyte being measured​. IAs can be used to detect either antibodies or
antigens. If binding between the antibody and target occur, the resulting signal (e.g.
fluorescence) or enzymatic reaction can be measured either qualitatively or
17
quantitatively to indicate the presence or quantity of the target analyte.

IA.rapid LOINC defines rapid immunoassays as those producing results within 30 minutes.

IF Immunofluorescence (​IF​) tests are immunoassays that use a fluorophore label

attached to the antibody. In LOINC, IF includes direct (DFA), indirect (IFA), and
anti-complement (ACIF) immunofluorescence methods, and is only used for assays
that provide information about the presence or amount of a target analyte AND its
location (or pattern) on a smear, tissue slice, or cell.

LA Latex agglutination is a method for detecting antibodies that react to specific

antigens which are attached to latex particles. When the antibody and antigen bind
together, clumps of latex particles are easily visible.

Aggl Agglutination tests detect antibodies to antigens. When antibodies and their
corresponding antigens are mixed together, clumps are easily visible, which
indicates the presence of antibodies to the specific antigen.

Comp fix The presence or absence of either antigens (or antibodies) is determined by
whether complement is fixed as a result of the formation of antigen-antibody
complexes. If no complexes are formed, the unfixed complement will attach to the
indicator red blood cells and lyse them. Lysis indicates that no antibody (or antigen)
is present in the patient’s serum. If no lysis occurs, the antigen-antibody complexes
have used up the available complement, so no lysis will occur. No lysis indicates the
presence of antigen (or antibody). 15​

HAI The hemagglutination-inhibition assay (​HAI​) can be used to identify subtypes of

hemagglutinin producing viruses, such as Influenza. ​HAI​ can also be used to
identify the subtype-specificity of antibodies against the virus. If antibodies specific
to the virus are present in the patient sample, they will bind to the virus, which
prevents the virus from binding to the red blood cells and therefore prevents
agglutination. To determine which subtype of virus is present, a viral isolate is
tested against a series of antibodies with known subtype specificities. Whichever
antibody inhibits red cell agglutination identifies the viral subtype. Similarly,
antibody specificity is identified by testing the patient sample against known virus
18
subtypes.

IB Immunoblotting identifies antibodies to specific infectious agents in serum by first

separating the proteins using electrophoresis. The separated bands of protein are
then pressed or ‘blotted’ onto a carrier membrane and then tested against the
specimen to determine whether antibodies to specific protein bands are present. In
LOINC, the ​IB​ ​Method​ is only used for assays that include the electrophoresis step.

17
Darwish IA. Immunoassay Methods and their Applications in Pharmaceutical Analysis: Basic
Methodology and Recent Advances. Int J Biomed Sci. 2006 Sep;2(3):217-35. [PMID: ​23674985​]
18
Pedersen JC. Hemagglutination-inhibition assay for influenza virus subtype identification and the
detection and quantitation of serum antibodies to influenza virus.Methods Mol Biol.
2014;1161:11-25. [PMID: 2​ 4899416​]

Guide for Using LOINC Microbiology Terms ​• 64

 Line blot Line blots are pre-manufactured immunoblot “strips”, in which membrane strips
are pre-coated with a specific set of antigens in parallel lines. Because the
electrophoresis step occurs during the manufacturing phase rather than in the
performing laboratory, these are not classified as ​IB​ in LOINC.

Neut Neutralization is used to detect antibody to a virus in patient serum. The virus and
serum are combined and allowed to incubate. Next, indicator cells are added
followed by a second incubation. After the second incubation, the indicator cells
are examined microscopically for evidence of visible cellular changes known as
viral cytopathic effect (CPE) or for immunofluorescent staining of the viral antigen.
If the virus was not neutralized by antibody in the serum, it will infect the indicator
cells that will then display CPE, or, if fluorescent stain was applied, will emit visible
fluorescence. If antibody is present, the virus will not invade the cells, and no CPE
19
will be observed or no fluorescence will be visible.

KEY POINT

If the test you are mapping is performed by one of these methods, be sure to choose a LOINC
term with a matching ​Method​ specification. If the precise method is not specified for your
test, choose the methodless LOINC term, unless the specific ​Method​ has a clinically
significant effect on the result. In this case, we recommend that you request a new,
method-specific LOINC code.

8.3 Testing for the presence or absence of

antibodies to a specific organism
Testing that determines the presence or absence of antibodies to a specific organism is commonly
done to confirm a suspected diagnosis. The ​Component​ for these tests includes the name of the
organism followed by ‘Ab’ and the antibody class, if applicable. LOINC terms for such ordinal results
are named with the following pattern:

Component {Name of organism} Ab.{antibody class}

Property PrThr

Time Aspect {Time value}

System {Specimen type}

Scale Ord

19
VNT (Virus Neutralisation Tests) [Internet]. Glasgow (Scotland): Biobest Laboratories Ltd. Available
from: h
​ ttp://www.biobest.co.uk/diagnostics/techniques/vnt-virus-neutralisation-tests.html

Guide for Using LOINC Microbiology Terms ​• 65

 Method {Method type}

Examples:
81097-8​ West Nile virus Kunjin strain Ab: PrThr: Pt: Ser: Ord:
LCN: ​West Nile virus Kunjin strain Ab [Presence] in Serum

83081-0​ Borrelia burgdorferi Ab.IgG+​IgM: PrThr: Pt: Ser: Ord: IA

LCN: ​Borrelia burgdorferi IgG+​IgM Ab [Presence] in Serum by Immunoassay

OBX|1|CE|​83081-0​^Borrelia burgdorferi IgG+​IgM Ab [Presence] in Serum by

Immunoassay^LN|1|LA6577-6^Negative^LN||...

8.4 Quantitative antibody testing

Assays that quantify the amount of antibody present can be useful in a number of clinical contexts.
For example, comparing antibody titers at two specific time intervals and finding a minimum
increase can help confirm a recent infection. Most quantitative LOINC terms have a P​ roperty​ of
either T
​ itr​ or ​ACnc​. Such tests are represented with the following naming pattern:

Component {Name of organism} Ab{.antibody class}

Property Acnc
Titer

Time Aspect {Time value}

System {Specimen type}

Scale Qn

Method {Method type}

Examples:
80618-2​ Zika virus Ab.IgM: ACnc: Pt: CSF: Qn: IA
LCN: ​Zika virus IgM Ab [Units/​volume] in Cerebral spinal fluid by Immunoassay

24176-0​ Adenovirus Ab^2nd specimen: Titr: Pt: Ser: Qn: Comp fix
LCN: ​Adenovirus Ab [Titer] in Serum by Complement fixation --2nd specimen

OBX|1|NM|​80618-2​^Zika virus IgM Ab [Units/​volume] in Cerebral spinal fluid by

Immunoassay^LN|1|25|U/L|...

Guide for Using LOINC Microbiology Terms ​• 66

8.5 Reporting the interpretation of a serologic
test panel
Results from multiple serologic tests are often evaluated as a whole set to determine the final clinical
interpretation. For example, testing for Lyme disease involves evaluating the presence of antibodies
to many different ​Borrelia burgdorferi​ protein bands. Even if antibodies to a handful of individual
bands are found, the overall result is only considered “positive” (i.e., B
​ . burgdorferi​ infection) if a
specific group of bands is positive. Such groups of bands are called band patterns and are reported
separately as an interpretation. Similarly, IgG and IgM antibody results are often taken together to
determine whether or not the patient had a recent infection or previous infection.

Interpretation terms in LOINC have the ​Property​ ​Imp​ and the ​Scale​ ​Nom ​or​ Nar​. Many ​Components
include a keyword such as “pattern”. In the case of impressions covering IgG and IgM, the LOINC
term name includes “&”, which indicates that different results that can be distinguished are being
compared.

Typical naming patterns for these terms in LOINC are as follows:

Component {Name of organism} Ab{.antibody class} band

pattern

{Name of organism} Ab.IgG & IgM

Property Imp

Time Aspect {Time value}

System {Specimen type}

Scale Nom

Nar

Method {Method type}

Examples:
23979-8​ Borrelia burgdorferi Ab.IgG band pattern: Imp: Pt: CSF: Nom: IB
LCN: ​Borrelia burgdorferi Ab.IgG band pattern [Interpretation] in Cerebral spinal fluid by Immunoblot

73560-5​ Mumps virus Ab.IgG & IgM: Imp: Pt: Ser: Nom:
LCN: ​Mumps virus IgG and IgM [Interpretation] in Serum

Guide for Using LOINC Microbiology Terms ​• 67

 OBX|1|CE|​23979-8​^Borrelia burgdorferi Ab.IgG band pattern [Interpretation] in
Cerebral spinal fluid by Immunoblot^LN|1|LA15256-3^Non-reactive ^LN||...

OBX|1|CE|​73560-5​^Mumps virus IgG and IgM [Interpretation] in Serum^LN|1|

LA19556-2^Results suggest prior exposure and immunity to mumps, or a convalescent
stage of infection^LN||...

Note that some laboratories use the same general term to report an interpretation across
organism-specific panels. In this case, the meaning of the result is understood in the context of the
panel. Examples of these general codes include 5​ 6850-1​ ​Interpretation and review of laboratory results​,
59464-8​ M
​ icrobiologist review of results,​ and ​69048-7​ ​Immunologist review of results​.

Guide for Using LOINC Microbiology Terms ​• 68

9 Mapping Qualitative Result
Values
In contrast to previous chapters, which describe how to choose the appropriate LOINC codes for
microbiology observations, this chapter addresses how to map observation r​ esult values​ for
qualitative results.

Qualitative result values are non-numeric and can be either ordinal or nominal. Ordinal result values
can be ranked, such as Detected/Not detected, Low/Medium/High,
Susceptible/Intermediate/Resistant, and Positive/Negative. Nominal result values cannot be ranked,
and include concepts such as the specific Streptococcus pneumoniae serotype that is detected, or the
species of bacteria identified in a blood culture. Nominal result values can be thought of as “short
answer” or those coming from a pick-list. Narrative result values, which consist of longer, free-text
entries, are not drawn from a formal vocabulary or terminology standard and are out of scope for
this chapter.

In the context of data exchange using HL7 v2, both the observation and the observation result
value(s) are reported in the OBX segment, with the observation in OBX-3 and the qualitative result
value(s) in OBX-5. More specifically, OBX-5.1 contains the code, 5.2 the text, and 5.3 the coding
system. Remember that in specific cases where the P​ roperty​ is O ​ rdQn​, such as antimicrobial
susceptibility testing, result values can be reported e​ ither as: 1) a quantitative value in OBX-5 with
an interpretation in OBX-8; or 2) as an ordinal result value in OBX-5 using the same LOINC. In this
chapter we are addressing the second reporting style; however, example OBX segments for both are
shown below for comparison. ​For more details, see the “OBX segments” section in Chapter 2 and/or
the “Phenotypic susceptibility testing” section in Chapter 5.

OBX|1|NM|​6932-8​^Penicillin [Susceptibility] by Minimum inhibitory concentration

(MIC)^LN||0.05|ug/mL||S|||F|...

OBX|1|CE|​6932-8​^Penicillin [Susceptibility] by Minimum inhibitory concentration

(MIC)^LN||LA6576-8^Susceptible^LN||||||F|...

As part of the LOINC distribution, we provide structured lists of possible result values for nearly
every ordinal qualitative LOINC observation term as well as many nominal terms. These LOINC
Answer Lists are sets that organize a collection of LOINC Answer strings and codes. LOINC Answer
Lists illustrate the ​possible​ result values associated with an observation, and LOINC Answer codes

Guide for Using LOINC Microbiology Terms ​• 69

provide unique identifiers for the strings representing them. A specific LOINC Answer List may be
associated with one or more individual LOINC terms.

KEY POINT

Local result values for qualitative tests can be mapped to LOINC Answer codes that
represent the equivalent string.

Different IVD manufacturers may recommend different result values, such as Detected/Not detected
versus Present/Absent, for similar assays. Users should always follow local reporting regulations, for
example, reporting qualitative results according to the IVD vendor’s package insert for the assay that
was used. There are ongoing efforts in the U.S. by the FDA’s Systemic Harmonization and
Interoperability Enhancement for Lab Data (SHIELD) initiative, the I​ VD Industry Connectivity
Consortium​ (IICC), and other collaborators to create constrained, publicly-available lists of answer
sets and/or equivalence mappings for result values that share the same meaning. Such constrained
answer sets, once approved by stakeholders, have the potential to make reporting across different
IVD assays more consistent, or at least comparable by way of equivalence mappings. When the
SHIELD initiative participants define such sets, this chapter will be updated to include information
about the appropriate use of manufacturer or public-health recommended coding sets and/or
equivalence mappings, their impact on LOINC Answer Lists, and how they will be made available.

9.1 Linking LOINC Answer Lists to LOINC terms

LOINC Answer Lists can be bound to LOINC observation terms as different types, including:
Example​, P ​ referred​, and ​Normative​. ​Example​ lists are meant to be illustrative of p​ ossible​ result
values. Users can also think of them as a starter set to which they may add or subtract depending on
their use case. P
​ referred​ lists contain a set of answers that users are strongly encouraged to use.
They represent a recommended set, however, in contrast to a N ​ ormative​ list, alternate result values
may be used if necessary. ​Normative​ lists are typically those that are defined by a validated survey
questionnaire (e.g., patient-reported outcomes (PRO) instruments), government form, or other
authoritative source. When using LOINC terms bound to N ​ ormative A ​ nswer Lists, only answers
in the specified set are allowed as result values.

In the microbiology domain, nearly all of the LOINC Answer Lists are ​Example​ type lists. They are
meant to give users an idea of the types of results associated with a particular LOINC observation.
For example, a list that contains result values such as “Detected” and “Not detected” is indicative of an
ordinal result representing the presence or absence of an analyte.

A LOINC term is typically bound to an Answer List based on information from the package insert
and sample report(s) for the original IVD test that term was created for. When new LOINC terms
are requested, we ask for supporting documentation in part to understand how the observation is

Guide for Using LOINC Microbiology Terms ​• 70

reported. If such documentation is not provided, we work with the submitter to determine the
appropriate set of result values for a particular assay.

KEY POINT

Example​ Answer Lists include Answer codes and strings that are meant to be illustrative of
possible​ result values. Answer Lists are typically bound to a particular LOINC term based on
the IVD test upon which that term was originally modeled. Depending on their reporting
needs, users may add or subtract result values from an ​Example​ LOINC Answer List if they
remain consistent with that term’s ​Scale (​ i.e., ordinal or nominal).

A handful (less than 20) of LOINC microbiology terms are bound to ​Preferred​ Answer Lists. These
are primarily observations with a finite set of result values, such as the type of Clostridium
botulinum toxin present. In such cases, the result values that were known to exist at the time the
term was created are all included in the associated LOINC Answer List. As of version 1.1 of this
guide, only a single LOINC microbiology term (LOINC: 5​ 5463-4​ I​ nfluenza virus A swine origin RNA
[Identifier] in Unspecified specimen by NAA with probe detection)​ is bound to a N
​ ormative​ list
(​LL745-1​), where the result values in that Answer List must be used as specified by the Centers for
Disease Control and Prevention (CDC).

The LOINC Answer List bound to a particular term is shown in the Answer List section of the
detailed display page for that term. Display pages are available in the online LOINC search
application (​https://search.loinc.org​) and the Regenstrief LOINC Mapping Assistant (RELMA).
The Answer List section will clearly indicate the linkage type, i.e. E​ xample​, ​Preferred​, or
Normative​. (For more information about the online search application and RELMA, see the
“Choosing the right LOINC term” chapter.) In addition, the linkages from LOINC terms to Answer
Lists are available in the LOINC Answer File that is available for d​ ownload from the LOINC
website​.

Guide for Using LOINC Microbiology Terms ​• 71

Guide for Using LOINC Microbiology Terms ​• 72
9.2 LOINC Answers and SNOMED CT concepts
SNOMED CT is an international terminology standard for clinical information, such as symptoms,
20
diagnoses, anatomy, and microorganism names. SNOMED CT provides codes that represent
nominal and ordinal values for the observations represented by LOINC terms and that are organized
by hierarchies, such as Clinical finding, Organism, and Qualifier value. If appropriate concepts exist
in SNOMED CT, the Regenstrief Institute recommends using SNOMED CT codes for reporting
qualitative laboratory result values if appropriate licensure is granted. In situations where the use of
SNOMED CT is not permitted, LOINC Answer codes or other terminologies could be used.

Some LOINC Answer Lists include a mapping between the LOINC Answer codes and
corresponding SNOMED CT codes, though this is a work in progress and a given list may only
contain mappings for a subset of the answers it contains. Note that due to licensing restrictions, this
guide does not yet include SNOMED CT codes, though the mappings are available in the LOINC
Answer File that is available for ​download from the LOINC website​. The mappings are also shown
on detailed display pages associated with each term.

9.3 Ordinal result values

LOINC contains a variety of Answer Lists that contain different sets of ordinal result values. The
three lists shown in the table below are the most common lists attached to LOINC microbiology
terms, accounting for over 75% of the terms that have ordinal lists. Remember, result value mapping
should be done at the level of the Answer code and Answer string, not at the level of the Answer
List.

LOINC LOINC Answer string LOINC Answer code

Answer
List ID

LL744-4 Detected LA11882-0

Not detected LA11883-8

LL360-9 Positive LA6576-8

Negative LA6577-6

LL1937-3 Present LA9633-4

Absent LA9634-2

20
SNOMED CT [Internet]. London (England): SNOMED International. Available from:
http://www.snomed.org/snomed-ct

Guide for Using LOINC Microbiology Terms ​• 73

Also, recall that the possible result values for a particular assay are defined by the product
information for that assay and not by the E ​ xample​ list associated with the corresponding LOINC
term.

KEY POINT

Result value mapping should be done at the level of the Answer code and Answer string, not
at the level of the Answer List.

For instance, suppose two different assays, “Assay A” and “Assay B”, produce ordinal result values for
whether or not IgM antibody to Legionella species is present in a serum specimen. The package
insert for Assay A recommends reporting result values as Detected/Not detected, whereas the
package insert for Assay B recommends reporting Present/Equivocal/Absent. Laboratories using
Assay A would use Answer codes LA11882-0 (Detected) and LA11883-8 (Not detected), and
laboratories using Assay B would use LA9633-4 (Present), LA11885-3 (Equivocal), and LA9634-2
(Absent). Both laboratories would map to the same LOINC term:

81118-2​ Legionella sp Ab.IgM:PrThr:Pt:Ser:Ord

LCN: ​Legionella sp IgM Ab [Presence] in Serum

The above LOINC term happens to be associated with ​Example​ LOINC Answer List L ​ L744-4​,
which contains LA11882-0 (Detected) and LA11883-8 (Not detected), but the same term can be used
with result values LA9633-4 (Present), LA11885-3 (Equivocal), and LA9634-2 (Absent), or any
other ordinal values that have the same meaning.

KEY POINT

The primary characteristics of an assay should determine which LOINC term to map to,
NOT the Answer List associated with that term. Result value mapping is an independent
process.

9.4 Nominal result values

Nominal results in microbiology include concepts such as the type of bacterium, specific species,
serotype, or toxin identified in a specimen. LOINC contains many more nominal LOINC Answer
Lists than ordinal lists due to the variety of possible nominal result values across LOINC terms.
However, the general principles of using LOINC Answer Lists are the same. ​Example​ Answer Lists
are representative of the types of results associated with a given observation. And, the primary
observation should be mapped to a LOINC term first, followed by mapping the allowable result
values.

Guide for Using LOINC Microbiology Terms ​• 74

One difference between nominal and ordinal results is that LOINC Answer strings and codes may
not exist for all reportable results given the breadth of result values that are possible. If no standard
code for a nominal microbiology result value is available (whether from LOINC or SNOMED CT), it
is possible to send a free text entry as the result value (e.g. in an HL7v2 OBX segment). However,
such unstandardized reporting makes it much more difficult for receiving systems to aggregate and
process the data.

9.5 Uncertain result values

For both ordinal and nominal types of results, there are instances in which a test may not produce a
definitive result value. (These are not the same as “flavors of null” described in the next section,
because a result value is still produced.) In many cases, IVD manufacturers specify the value that
should be used in various circumstances. LOINC contains a variety of Answer codes and strings that
represent these uncertain types of results as shown below.

LOINC Answer string LOINC Answer code

Equivocal LA11885-3

Indeterminate LA11884-6

Inconclusive LA9663-1

Invalid LA15841-2

Undetermined LA14100-4

Uncertain LA12719-3

Uncertain significance LA26333-7

9.6 Flavors of null

It is often necessary to indicate that a result value was not produced. In HL7 standards, these kinds of
response values are called null flavors (see h​ ttps://www.hl7.org/fhir/v3/NullFlavor​). There are two
techniques for communicating a null flavor. In version 3 messaging, there is a dedicated nullFlavor
attribute that is available for every observation, so these choices are not part of the actual answer list.
In version 2 messaging and FHIR, the convention includes the specific allowed null flavors within
the choices of the answer set.

Within LOINC, we do not want to make different Answer Lists that vary only by the inclusion or
exclusion of certain null flavors. Thus, our policy is to add specific null flavors as entries in the

Guide for Using LOINC Microbiology Terms ​• 75

Answer List only where we are aware of their specific relevance. However, LOINC Answer codes
exist for a variety of null flavor concepts. Users wishing to communicate such a null flavor concept
are free to do that regardless of whether it is present in the LOINC Answer List. Examples of LOINC
Answer strings and codes for null flavor result values are shown in the table below.

Answer string LOINC Answer code

Unknown LA4489-6

Not done LA6630-3

Test not done LA18373-3

Not performed LA7304-4

Equipment failure LA7497-6

Guide for Using LOINC Microbiology Terms ​• 76

10 Choosing the right LOINC term
(“mapping”)
Choosing the correct LOINC term for a given laboratory test can seem like a daunting task. But, by
approaching it systematically and taking advantage of available resources, mapping can be
straightforward for the majority of concepts. Keep in mind that mapping from the perspective of an
end-user is different from mapping as an IVD vendor, because a vendor should map to all of the
LOINC codes that support the range of specimens and reporting options approved for a single test
kit, while end-users should map to the set of LOINC codes that are appropriate for a particular
implementation. See Section 9.6 “Mapping an assay approved for multiple specimens and resulting
styles” for additional information about mapping from the vendor perspective and examples of the
differences between vendor and end-user mappings.

10.1 Minimum test information necessary to

map
This section describes the basic information you need in order to choose a LOINC term for a given
test. Even though it is not necessary to map all of your tests at the same time, it is more efficient to
start with all of the data that you need, and having the whole test catalog for reference as you are
mapping is helpful so that you can compare similar tests and figure out the appropriate mappings for
each one. The package inserts (PI) for commercially developed tests provide invaluable information
needed to map those tests to LOINC codes. The PI will include the specific analyte being measured,
the units of measure, how the results are reported, and what specimens can be used to measure the
analyte. For laboratory developed tests, the Standard Operating Procedure (SOP) can provide
similarly valuable information that is imperative when mapping those tests to LOINC codes.

KEY POINT

The vendor’s package insert and laboratory’s Standard Operating Procedure for commercial
and laboratory-developed tests, respectively, are the best starting point for mapping.

10.1.1 Analyte, Specimen, and Method

The key information necessary for choosing the correct LOINC term includes the name of the
analyte, the specimen type, and if relevant, the M
​ ethod​. T
​ his information may be found in the
vendor’s PI, the laboratory SOP, or, if working primarily from a laboratory catalog or LIS system,

Guide for Using LOINC Microbiology Terms ​• 77

the test name. ​If you are working with test names that do not include analyte or specimen
information, you must locate that information before you begin. The test ​Method​ may only be
specified for certain terms in which the particular ​Method​ is significant for interpreting the result.
However, if you are working with test names and none of them identify the M ​ ethod​, then it is likely
being recorded elsewhere and should be located before you begin mapping.

10.1.2 Sample results

Sample results and associated information such as average values and reference ranges are extremely
useful for differentiating between tests that may seem the same or similar based on the test name
alone. For example, sample results can help distinguish between tests that have qualitative results
that are ranked, such as 1+, 2+, 3+ (LOINC​ Scale​ ​Ord​) from those that cannot be ranked, such as
type of Adenovirus (LOINC S​ cale​ ​Nom​). If you do not have access to sample results, other
information that may be useful, if available, is the result type or data type, which indicates whether
the expected results are quantitative, based on an answer list, free text, etc. Keep in mind that a
single assay may be approved for multiple reporting options; these will be described in the package
insert.

10.1.3 Units of measure

The units of measure are critical for mapping to the correct LOINC term. For quantitative results,
LOINC has different terms for results reported in mass units versus molar units, for example, mass
concentration (mg/dL) and substance (molar) concentration (mol/L). Without unit of measure
information, you may not know which quantitative LOINC term is appropriate for your term.

KEY POINT

The analyte, specimen(s) that can be analyzed, qualitative sample results, units of measure for
quantitative results, and, if relevant, the ​Method​ of analysis, are essential for choosing a LOINC
term.

10.2 Additional useful data

10.2.1 List of abbreviations used by your laboratory in its
test names
Each organization tends to use its own conventions for abbreviations in local test names. Many
abbreviations are self-explanatory, but inevitably you’ll encounter a few ambiguous ones. If those
abbreviations are recorded in a central place, having that list available will save you time and
frustration during the mapping process.

Guide for Using LOINC Microbiology Terms ​• 78

10.2.2 Frequency data
If available, having usage frequency of your tests when mapping can be helpful for prioritizing your
work and giving some context about the LOINC terms you are looking for. For example, a test
associated with 50,000 results in a database of 3 million results is likely to match a commonly used
LOINC term. It should probably be given higher priority to get mapped. On the other hand, a test
that only appears 3 times is much less likely to match a commonly used LOINC term, and it probably
isn’t wise to spend very much of your mapping energy on that one test. You should also consider
prioritizing test results that are important for public health and safety and/or required to be reported
under local regulations.

10.3 Mapping tools

There are two tools you can use to find the LOINC terms that you need. Each has its benefits and
particular use cases that it is tailored for.

10.3.1 Regenstrief LOINC Mapping Assistant (RELMA)

RELMA​ is a desktop mapping program that was created specifically for LOINC mapping and is
maintained by the LOINC software development team. RELMA’s main purpose is to map your local
test codes to LOINC codes. It is a powerful tool with features to import your catalog of tests and map
each one to a specific LOINC term. RELMA stores those mappings and has multiple options for
exporting them to load back into your laboratory or other system.

RELMA is highly recommended for mapping anything more than just a handful of terms, because it
stores your data and provides features that will help you with the mapping process. RELMA’s main
limitation is that it only runs on the Microsoft Windows operating system, so Mac or Linux users
will have to configure a virtual machine with Windows in order to use RELMA. (Instructions for
how to do this are ​available on the LOINC website​). A new version of RELMA is released twice a
year in June and December, and must be downloaded after each release in order to stay current with
software updates.

10.3.2 Online search application

Our online search application (​https://search.loinc.org​) is fast, easy to use, and runs right from your
Internet browser without any installation necessary. It does not have all of the mapping features that
RELMA does, but it is useful for quickly running LOINC searches and is always updated to the latest
LOINC version.

Guide for Using LOINC Microbiology Terms ​• 79

10.4 General mapping principles
As a general rule, you should map to the most specific LOINC term possible based on the available
information. The key is to avoid assuming information that is not known and at the same time
preserving information that is known. For example, if you are mapping a test named “Rotavirus Ab
IgG Ser IA Titer” a search in RELMA for “Rotavirus Ab” will return these candidate terms:

Although this may seem like a lot of results, do not panic! Also, do not pick the first LOINC term
just because it’s at the top! Focusing on a few key details can make it easy to narrow down the list of
candidates. First of all, in this case, the test is specifically looking for IgG antibodies. So, you can
narrow your search results by including the search term “IgG”:

Guide for Using LOINC Microbiology Terms ​• 80

Five candidate terms are much more manageable to review than 19, but we can narrow this even
more by using the last two pieces of information in the test name – “IA” and “Titer”:

With that level of specificity, we now have a single, precise matching LOINC term for your test.

KEY POINT

Using combinations of multiple, specific search terms will return a smaller set of results to
review and will make your mapping more efficient and accurate.

Equally important, however, is not over-specifying your mapping by guessing about information
that you do not have. As you saw from the previous example, LOINC has a lot of seemingly similar
terms for the same analyte that vary by subtle distinctions. Mapping accurately requires attention to
those details and not making assumptions about the test you are trying to map.

For example, searching RELMA for the test name “Rotavirus Ab Ser IA Titer” will return:

Guide for Using LOINC Microbiology Terms ​• 81

Which LOINC term should you map to?

If all of the other microorganism antibody titer tests in the group you are mapping are for IgG (and
say so in the name), it may be tempting to map to the IgG term, but since IgG is NOT specified in
your Rotavirus test name, mapping to the IgG term would be over specifying based on the
information you have available.

You need to keep the constraints of your LIS or LIMS in mind. If the local system has a common
name of STAIN for all stains and CULT for all culture results, those two tests have to be mapped to
the most generic LOINC terms for those concepts: ​11546-9​ Microscopic observation [Identifier] in
Unspecified specimen by Other stain and 1​ 1475-1​ Microorganism identified in Unspecified
specimen by Culture, respectively. The specific LOINC mapping for urine culture, stool culture,
Giemsa stain, etc. will take place at the order level.

KEY POINT

Map to the most specific LOINC term possible based on the information you have available,
but do not over specify by making assumptions about test characteristics that you do not
have.

10.5 Part-specific mapping principles

10.5.1 ​Component
The ​Component​ is the most important axis for mapping because it describes the specific analyte that is
being measured. Be careful when mapping the C ​ omponent,​ as terms with seemingly similar
Components​ could potentially represent very different concepts. For example, the C
​ omponents
Rubella virus Ab​ and R ​ ubella virus Ag​ look very similar. However, the first represents
antibodies to the Rubella virus (an indicator of the patient’s immune response), and the second

Guide for Using LOINC Microbiology Terms ​• 82

represents a fragment of the actual virus particle itself. These two concepts are related in that
exposure to the virus leads to an immune response, but it is important to choose the correct
Component​ depending on whether the test detects the microorganism or the patient’s response to that
microorganism.

10.5.1.1 Types of antibodies

LOINC C ​ omponents​ that include the word “Ab” without specifying IgG, IgM, etc. represent any type
of antibody. However, if a particular assay is targeting a specific type of antibody, such as IgG, then
the C
​ omponent​ will include “Ab.IgG”. When the test is targeting IgG and IgM but does not
differentiate between the two when reporting the result, the C ​ omponent​ includes “Ab.IgG+IgM”;
when the result does differentiate between the two, the C ​ omponent u​ ses “Ab.IgG & IgM”.

10.5.1.2 Microorganism antigens versus genetic targets

In LOINC, antigens typically represent proteins or other fragments of the microorganism structure
that are detected by a given assay. For these, the LOINC ​Component​ contains the microorganism
name and the word “Ag”. For example, V ​ aricella zoster virus Ag​ or ​Streptococcus pneumoniae
Ag.

LOINC labels tests that detect a microorganism’s genetic material with “DNA”, “RNA” or “gene”,
depending on whether the assay has a specific, named target or is for an unnamed or undisclosed
portion of the DNA or RNA.

For example, the C ​ omponent​ ​Neisseria meningitidis DNA​ represents any fragment of DNA from
N. meningitidis,​ and N​ eisseria meningitidis serogroup w135 synG​ is used for assays that are
specifically looking for the serogroup w135 synG gene.

10.5.1.3 “&” versus “+”

Be careful when mapping to C ​ omponents​ that contain “+” or “&”. In LOINC, the “+” indicates that the
analytes on either side of the plus cannot be differentiated. The “&” indicates that the analytes can be
differentiated.

For example, ​HIV 1+2 Ab​ indicates a test that can detect both HIV 1 and HIV 2 antibodies but
cannot distinguish between them. In contrast, ​Chlamydia trachomatis & Neisseria gonorrhoeae
DNA​ indicates a test that can detect both C
​ hlamydia trachomatis​ and N
​ eisseria gonorrhoeae​ AND can
distinguish between the two. In these cases, the result distinguishes the different entities. For
example the answer values might be “Chlamydia trachomatis not detected” and/or “Neisseria
gonorrhoeae detected”.

KEY POINT

Analytes separated by & are distinguished in the result while those separated by + are not.

Guide for Using LOINC Microbiology Terms ​• 83

10.5.2 ​Property​ and ​Scale
As described, the LOINC ​Scale​ and P​ roperty​ are closely related. The S​ cale​ represents a high level
categorization of how the result is reported, such as quantitative (numeric) or qualitative. The
Property​ describes which aspect of the analyte is being measured, such as its mass concentration or
volume.

When reviewing a large list of candidate LOINC terms for mapping, it is often easier to narrow
down your choices by looking at the S​ cale​ first. Applying the coarser filter first will help focus in on
the fine grained distinctions in the P​ roperty.​

The following table illustrates how the P​ roperty​ and S​ cale​ differ for different types of results.

Type of result LOINC LOINC LOINC term examples

value Property Scale

Presence or PrThr Ord 8030-9​ Streptococcus pneumoniae Ab:

absence PrThr:Pt:Ser:Ord
Example results​: Present, Absent

86143-5​ Streptococcus pneumoniae Danish

serotype 8 Ab:PrThr:Pt:Ser:Ord
Example results​: Present, Absent

Absence or, if Prid Nom 85496-8​ Streptococcus pneumoniae

present, the serotype:Prid:Pt:XXX:Nom:Probe.amp.tar
specific type or Example results:​ Absent, S. pneumoniae Danish
identity of what serotype 19F, S. pneumoniae Danish serotype 3
is present
43389-6​ Streptococcus sp
identified:Prid:Pt:Isolate:Nom:Organism specific
culture
Example results:​ Absent, Streptococcus pneumoniae

Identification of Type Nom 72483-1​ BK virus subtype:Type:Pt:Ser/Plas:

the species or Nom:Probe.amp.tar
sub-species Example results​: BK virus subtype I, BK virus
when it is subtype II
known that a
microorganism
is present 86509-7​ Varicella zoster virus clad:Type:Pt:XXX:
Nom:Molgen
Example results:​ Varicella-zoster virus clade 1,
Varicella-zoster virus clade 2

Guide for Using LOINC Microbiology Terms ​• 84

 Quantitative ACnc Qn 22606-8​ Varicella zoster virus
LnCnc Ab.IgM:Titr:Pt:Ser:Qn
MCnc Example result:​ 1:4
NCnc
SCnc 8048-1​ Varicella zoster virus
ThreshNum Ab.IgM:ACnc:Pt:Ser:Qn
Titr Example result:​ 18.2 IU/mL

20447-9​ HIV 1
RNA:NCnc:Pt:Ser/Plas:Qn:Probe.amp.tar
Example result:​ 2,000 copies/mL

86701-0​ Rotavirus A
RNA:ThreshNum:Pt:XXX:Qn:Probe.amp.ta
r
Example result:​ 26 cycles

For quantitative tests, the reporting units of measure will determine the correct LOINC P​ roperty
and are essential for choosing the correct LOINC term. In the LOINC Users’ Guide, the “​ Property”
section of Chapter 2 contains a list of the LOINC ​Properties​ that are available, and Appendix E
“Examples for LOINC​ Property M ​ atching” includes detailed examples for matching units and
Properties.​

Before you start mapping, a useful exercise would be to determine which P​ roperty​ corresponds to the
units associated with each of your tests.

Adding a P​ roperty​ to your search query is an easy way to narrow down the list of candidate LOINC
terms. For example, if the test’s units of measure are mg/dL, searching for LOINC terms with the
​ Cnc​ (mass concentration) will significantly narrow the number of terms returned.
Property​ M

To illustrate further, consider the two searches in the images below. The first image shows the
search query “CSF Influenza virus Ab” and the second shows “CSF Influenza virus Ab MCnc”. The
second search returns less than half of the candidate LOINC terms than the first. Although you must
still choose between six candidate terms, the mapping will be straightforward if you know whether
the test measures Influenza virus A versus Influenza virus B and IgA, IgG and IgM.

Guide for Using LOINC Microbiology Terms ​• 85

10.5.3 ​Time Aspect
The ​Time Aspect​ axis of the LOINC term is usually straightforward for mapping. Most laboratory
tests are “point in time” measurements, meaning that they are measuring the amount of analyte
present in a given sample at the time the specimen was collected. This is represented by a value of P
​ t
in the T
​ ime Aspect​ axis of the LOINC term. In fact, a​ ll o​ f the current LOINC terms in the
microbiology class have a T ​ ime Aspect​ of P
​ t.

Guide for Using LOINC Microbiology Terms ​• 86

In other domains covered by LOINC, the ​Time Aspect​ is more distinctive. For example, timed
specimen collections, such as 24-hour urine measurements in chemistry, measure the amount of
analyte collected in the urine over 24 hours. The ​Time Aspect​ for such tests is ​24H​.

10.5.4 ​System
The LOINC S​ ystem​ represents the specimen, e.g. blood or urine. The most common laboratory
specimens in microbiology are blood (​Bld​), serum or plasma (​Ser/Plas​), urine, various respiratory
specimens, and cerebrospinal fluid (​CSF​). However, LOINC microbiology terms exist for many
other specimens as well, such as stool, tissue, pleural fluid, and urethral swab.

Note that some LOINC terms contain a S​ ystem​ with several specimen types separated by a slash (“/”).
The slash indicates that any of these specimen types are suitable for that test. It does NOT mean that
a specific manufacturer’s assay has to be approved for all of the specimens listed; it simply means that
the results are expected to be clinically equivalent regardless of which of the two (or three)
specimens are used, and the assay should be approved for at least one of the given specimens.

For example, the S​ er/Plas​ ​System​ in LOINC is used for assays where the analyte can be measured in
either serum or plasma. This is common, for example, in antibody tests. LOINC does not have
separate terms for tests on serum and plasma, unless there is a compelling reason to do so. One such
example is for ammonia assays, where the preferred specimen is plasma, and the results in serum
compared to plasma are significantly different. LOINC will never have a test with the S​ ystem
Ser/Plas​ as well as the exact same test but with the S​ ystem​ S​ er​ or the ​System​ ​Plas​. Over time as
testing methods have evolved, by policy, LOINC has added P ​ las​ to many LOINC terms that
originally had a ​System​ of ​Ser​. LOINC will continue to do so moving forward as new approaches are
developed and either specimen is approved by the laboratory or manufacturer.

KEY POINT

LOINC ​System​ ​Ser/Plas​ = “Serum OR Plasma”

Mapping a particular manufacturer’s assay to a ​Ser/Plas​ term does NOT imply that the
specific assay is approved for both specimens. Laboratories do not need to run the test on
both serum and plasma in order to use a LOINC code with a ​System​ of ​Ser/Plas​.

LOINC uses a S​ ystem​ of X

​ XX​ for terms where either the specimen is truly unknown (e.g. a solid or
liquid that is not otherwise identified) or is expected to be specified in a field other than the LOINC
name. The latter situation is common in the context of public health, where public health
laboratories may run the same test on a wide variety of specimens but only have a single order
and/or result code for that test. In these situations laboratories typically report the specimen by
another mechanism, such as the HL7 SPM segment. The ​XXX​ terms should only be used in these
two cases. They should NOT be used when the test you are mapping is always run on a specific
specimen, often as designated in the Intended Use section of the package insert for a particular assay.

Guide for Using LOINC Microbiology Terms ​• 87

In some cases, mapping to the more general “specimen agnostic” X ​ XX​ term may be useful, but this
practice is generally discouraged because it results in a loss of information and a failure to accurately
map across institutions (See the Section “Special issues related to XXX as a System” in the LOINC
Users’ Guide for more information).

10.5.5 ​Method
LOINC includes terms that specify a particular laboratory M ​ ethod​ as well as those that do not (i.e.,
methodless terms). In general, when the specific ​Method​ used has a clinically significant impact on
interpreting the results for a particular analyte, LOINC will specify the M ​ ethod​ in its term name. On
the other hand, if the result is the same clinically regardless of the methodology used, then the
LOINC name will generally be methodless.

Even when the ​Method​ is included in the term name, LOINC specifies the ​Method​ at a general level.
For example, Immunoassay (​IA​) includes enzyme immunoassay and chemiluminescence.

The same principle of mapping to the most specific term possible without over-specifying, applies to
choosing LOINC terms with the appropriate ​Method.​ If the assay you are mapping has a specific
methodology that is important for interpreting the result, then map to a LOINC term with that
specific ​Method​. If such a term does not exist, you may need to request a new one (see this guide’s
Appendix B “Requesting new LOINCs”).

10.6 Mapping an assay approved for multiple

specimens and resulting styles
Assays that are approved for use with multiple specimens and have multiple reporting options will
map to multiple LOINC codes. Therefore, mapping from an IVD vendor’s point of view is a little
different from the end-user laboratory’s point of view. When vendors provide a list of LOINC codes
to their clients, they should include a​ ll​ of the codes that are appropriate based on the information in
their package insert, and laboratories who are utilizing vendor mappings should pick the subset of
codes that are applicable to their local implementation of the assay as shown in the table below.

The same mapping principles described earlier apply for each approved specimen and reporting
format. For example, if an assay is approved for use with either serum or CSF, then the vendor
should provide two LOINC codes, one with ​System​ ​Ser​ or ​Ser/Plas​, and one with C
​ SF​. Similarly, if a
single assay can be configured to result an ordinal qualitative response or a numeric titer, then a
vendor should again provide two different LOINC codes, one for each type of result. It is up to each
downstream client to determine the best LOINC codes for their specific implementation of the test
and to select it from the options proposed. The lab may also decide to follow another mapping
strategy as shown for “Laboratory C” in the table below, but note the limitation presented in the
footnote for that strategy.

Guide for Using LOINC Microbiology Terms ​• 88

 KEY POINT

IVD vendors should map to ​all​ of the LOINC codes that support the range of specimens and
reporting options approved for a single test kit.

Laboratories should map to the ​subset​ of LOINC codes that are appropriate for the
specimens and reporting options they have implemented for that test kit.

The following table illustrates the sets of LOINC codes that IVD vendors could provide for various
hypothetical assays based on the information in the package insert along with the subset(s) of codes
that downstream laboratories would use depending on their individual LIS implementations.

Package insert assay IVD Vendor provided LOINC codes LOINC codes used by downstream
information clients for individual implementations

Adenovirus DNA PCR, 21055-9​ Adenovirus DNA: PrThr: Laboratory A​: only using the assay to
approved for serum, Pt: Ser/​Plas: Ord: Probe.amp.tar test CSF specimens
CSF, and urine, may 38375-2​ Adenovirus DNA: PrThr: 38375-2​ Adenovirus DNA: PrThr: Pt:
only be reported as a Pt: CSF: Ord: Probe.amp.tar CSF: Ord: Probe.amp.tar
qualitative ordinal 86512-1​ Adenovirus DNA: PrThr:
result Pt: Urine: Ord: Probe.amp.tar Laboratory B​: using the assay for all
three approved specimens, with three
individual test builds
21055-9​ Adenovirus DNA: PrThr: Pt:
Ser/​Plas: Ord: Probe.amp.tar
38375-2​ Adenovirus DNA: PrThr: Pt:
CSF: Ord: Probe.amp.tar
86512-1​ Adenovirus DNA: PrThr: Pt:
Urine: Ord: Probe.amp.tar

Laboratory C​: using the assay for all

three specimens, but with a single
build in the LIS that does not specify
21
the specimen
39528-5​ Adenovirus DNA: PrThr: Pt:
XXX: Ord: Probe.amp.tar

21
Using a single build for a generic specimen is not recommended as it results in a loss of information,
and the list of codes provided by the vendor should not include the generic LOINC code when more
specific ones are available (note that ​39528-5​ is not listed in the second column)

Guide for Using LOINC Microbiology Terms ​• 89

Adenovirus DNA PCR, 38375-2​ Adenovirus DNA: PrThr: Laboratory D​: result built in the LIS
approved for CSF only, Pt: CSF: Ord: Probe.amp.tar as an ordinal text string
may be reported as 49338-7​ Adenovirus DNA: NCnc: 38375-2​ Adenovirus DNA: PrThr: Pt:
qualitative ordinal or Pt: CSF: Qn: Probe.amp.tar CSF: Ord: Probe.amp.tar
quantitative viral load 66730-3​ Adenovirus DNA: LnCnc:
as copies/volume or log Pt: CSF: Qn: Probe.amp.tar Laboratory E​: numeric result
copies/volume expressed as # copies/mL
49338-7​ Adenovirus DNA: NCnc: Pt:
CSF: Qn: Probe.amp.tar

Laboratory F​: numeric result

expressed as log copies/mL
66730-3​ Adenovirus DNA: LnCnc:
Pt: CSF: Qn: Probe.amp.tar

Adenovirus DNA PCR, 21055-9​ Adenovirus DNA: PrThr: Laboratory G​: only using the assay to
approved for serum, Pt: Ser/​Plas: Ord: Probe.amp.tar test CSF specimens, reporting result
CSF, and urine, may be 38375-2​ Adenovirus DNA: PrThr: as a qualitative ordinal
reported as a Pt: CSF: Ord: Probe.amp.tar 38375-2​ Adenovirus DNA: PrThr: Pt:
qualitative ordinal 86512-1​ Adenovirus DNA: PrThr: CSF: Ord: Probe.amp.tar
result, quantitative viral Pt: Urine: Ord: Probe.amp.tar
load in copies/volume Laboratory H​: testing CSF and urine
or log copies/volume, or 49334-6​ Adenovirus DNA: NCnc: specimens, reporting results as
both an ordinal result Pt: Ser/Plas: Qn: Probe.amp.tar copies/mL
and if positive, a 49338-7​ Adenovirus DNA: NCnc: 49338-7​ Adenovirus DNA: NCnc: Pt:
quantitative viral load Pt: CSF: Qn: Probe.amp.tar CSF: Qn: Probe.amp.tar
48609-2​ Adenovirus DNA: NCnc: 48609-2​ Adenovirus DNA: NCnc: Pt:
Pt: Urine: Qn: Probe.amp.tar Urine: Qn: Probe.amp.tar

66723-8​ Adenovirus DNA: LnCnc: Laboratory I​: testing all three

Pt: Ser/Plas: Qn: Probe.amp.tar specimens specimens, reporting
66730-3​ Adenovirus DNA: LnCnc: initial results as ordinal, followed by
Pt: CSF: Qn: Probe.amp.tar viral load in log copies/mL if the
66719-6​ Adenovirus DNA: LnCnc: ordinal result is “Detected”
Pt: Urine: Qn: Probe.amp.tar 21055-9​ Adenovirus DNA: PrThr: Pt:
Ser/​Plas: Ord: Probe.amp.tar
38375-2​ Adenovirus DNA: PrThr: Pt:
CSF: Ord: Probe.amp.tar
86512-1​ Adenovirus DNA: PrThr: Pt:
Urine: Ord: Probe.amp.tar
66723-8​ Adenovirus DNA: LnCnc:
Pt: Ser/Plas: Qn: Probe.amp.tar
66730-3​ Adenovirus DNA: LnCnc:
Pt: CSF: Qn: Probe.amp.tar
66719-6​ Adenovirus DNA: LnCnc:
Pt: Urine: Qn: Probe.amp.tar

Guide for Using LOINC Microbiology Terms ​• 90

11 Putting it all together
The previous chapters provided detailed information on mapping individual tests to individual
LOINC codes. In clinical practice, however, tests are rarely performed one at a time, or even one
panel at a time, and a single test kit may allow for a variety of different results. In this chapter we
present a few clinical scenarios to help you synthesize the information in previous chapters and
understand how individual test mappings would come together in a workflow. Note that these
scenarios are meant to illustrate the use of LOINC codes for test results across microbiology domains
and are not guaranteed to be completely accurate in terms of clinical care.

KEY POINT

⚠
Note that these scenarios are meant to illustrate the use of LOINC codes for test results
across microbiology domains and are not guaranteed to be completely accurate in terms of
clinical care.

11.1 Scenario 1 - Sepsis evaluation for

two-week-old infant with fever
This scenario illustrates how the lab tests would be encoded for a young infant presenting with fever
and undergoing a sepsis evaluation. A typical sepsis evaluation includes a complete blood count,
urinalysis, CSF studies (glucose, protein, red and white blood cell count and differential), and blood,
CSF, and urine cultures. Depending on the clinical context, testing for organisms such as herpes
simplex virus (HSV) may also be performed. In this example, we will only focus on the microbiology
testing, i.e., cultures and HSV.

The following tables contain a variety of lab tests, the LOINC term(s) that correspond to those tests,
and sample results over a series of time points. The specific time intervals are less important than the
order in which the tests occur and results are reported. Each row also contains the specific chapter
and section in this guide that corresponds to the test in that row for easy reference.

Guide for Using LOINC Microbiology Terms ​• 91

Time period 1
Lab test Related LOINC term(s) Result(s) Result status
chapter and (LOINC Answer
section codes are
included where
available)

Blood culture with 4.1 600-7​ ​Bacteria identified in LA21123-7 No Preliminary

reflex to Gram Blood by Culture growth
stain, identification,
and susceptibility
testing

Urine culture with 4.1 630-4​ ​Bacteria identified in LA21123-7 No Preliminary

reflex to Gram Urine by Culture growth
stain, identification,
and susceptibility
testing

CSF culture with 4.1 606-4​ ​Bacteria identified in LA21123-7 No Preliminary

reflex to Gram Cerebral spinal fluid by growth
stain, identification, Culture
and susceptibility
testing

CSF HSV PCR 7.3 32141-4​ ​Herpes simplex virus LA11883-8 Final
1+2
​ DNA [Presence] in Not detected
Cerebral spinal fluid by Probe
and target amplification
method

Skin lesion HSV 4.2.2 5858-6​ ​Herpes simplex virus LA21123-7 No Preliminary
culture identified in Skin by Organism growth
specific culture

Time period 2
Lab test Related LOINC term(s) Result(s) Result status
chapter and (LOINC Answer
section codes are
included where
available)

Blood culture with 4.1 600-7​ ​Bacteria identified in Growth Preliminary

reflex to Gram Blood by Culture detected
stain,
identification, and 3.2.1 664-3 ​Microscopic Moderate Preliminary
susceptibility observation [Identifier] in Gram-negative
testing Unspecified specimen by rods
Gram stain

Guide for Using LOINC Microbiology Terms ​• 92

Urine culture with 4.1 630-4​ ​Bacteria identified in LA21123-7 No Final
reflex to Gram Urine by Culture growth
stain,
identification, and
susceptibility
testing

CSF culture with 4.1 606-4​ ​Bacteria identified in LA21123-7 No Preliminary

reflex to Gram Cerebral spinal fluid by growth
stain, Culture
identification, and
susceptibility
testing

Skin lesion HSV 4.2.2 5858-6​ ​Herpes simplex virus LA21123-7 No Preliminary
culture identified in Skin by growth
Organism specific culture

Time period 3
Lab test Related LOINC term(s) Result(s) Result status
chapter and (LOINC Answer
section codes are
included where
available)

Blood culture with 4.1 600-7​ ​Bacteria identified in LA21335-7 Final

reflex to Gram Blood by Culture Escherichia coli
stain,
identification, and
susceptibility
testing

Blood culture #2 4.1 600-7​ ​Bacteria identified in LA21123-7 No Preliminary

(ordered when Blood by Culture growth
blood culture #1
demonstrated
growth)

Skin lesion HSV 4.2.2 5858-6​ ​Herpes simplex virus LA21123-7 No Preliminary
culture identified in Skin by growth
Organism specific culture

Beta-lactam 5.3.1 85822-5​ ​Beta-lactam LA11882-0 Final

resistance testing resistance AmpC Detected
(ordered when the blaCMY+​blaMOX genes
organism in blood [Presence] by NAA with
culture #1 was probe detection
identified as E. coli)

Guide for Using LOINC Microbiology Terms ​• 93

Extended-spectru 5.3.1 85832-4 ​Beta-lactam LA11883-8 Not Final
m beta-lactam resistance ESBL blaCTX-M-1 detected
resistance testing Group gene [Presence] by
(ordered when the NAA with probe detection
organism in blood
culture #1 was 5.3.1 85844-9​ ​Beta-lactam LA11883-8 Not Final
identified as E. coli) resistance ESBL blaCTX-M-2 detected
Group gene [Presence] by
NAA with probe detection

5.3.1 85834-0​ ​Beta-lactam LA11883-8 Not Final

resistance ESBL blaCTX-M-9 detected
Group gene [Presence] by
NAA with probe detection

Time period 4
Lab test Related LOINC term(s) Result(s) Result status
chapter and (LOINC Answer
section codes are
included where
available)

Blood culture with 5.1 18864-9​ ​Ampicillin LA6676-6 Final

reflex to Gram [Susceptibility] Resistant
stain,
identification, and 18862-3 LA16550-8 Final
susceptibility Amoxicillin+C ​ lavulanate Intermediate
testing [Susceptibility]

18895-3​ ​cefTRIAXone LA16550-8 Final

[Susceptibility] Intermediate

18893-8​ ​cefTAZidime LA24225-7 Final

[Susceptibility] Susceptible

18928-2​ ​Gentamicin LA24225-7 Final

[Susceptibility] Susceptible

18868-0​ ​Aztreonam LA24225-7 Final

[Susceptibility] Susceptible

Blood culture #2 4.1 600-7​ ​Bacteria identified in LA21123-7 No Final

Blood by Culture growth

Skin lesion HSV 4.2.2 5858-6​ ​Herpes simplex virus LA21123-7 No Final
culture identified in Skin by growth
Organism specific culture

Guide for Using LOINC Microbiology Terms ​• 94

11.2 Scenario 2 - Determining the cause of likely
infectious diarrhea
This scenario illustrates lab test coding for a workup of diarrhea that is likely infectious in nature.
Such a workup would potentially include a complete blood count, stool studies such as leukocyte
differential, microscopic examination, antigen studies, nucleic acid studies, and stool culture. In this
example, we will only focus on the microbiology testing, i.e., microscopic examination, antigen and
nucleic acid tests, and culture. Note that all of these studies probably would not be ordered at the
same time for a single patient, but for the purpose of illustrating the use of LOINC codes we are
erring on the side of providing more examples and less on clinical accuracy in this scenario.

In this scenario, the tables are organized by test rather than time periods in order to illustrate specific
information about LOINC panels and multiplex testing.

Microscopic examination and stool culture

Lab test Related LOINC term(s) Result(s) Result status
chapter and (LOINC Answer
section codes are
included where
available)

Microscopic 3.2.2 14125-9​ Entamoeba LA11883-8 Not Final

examination of histolytica [Presence] in Stool detected
stool by Trichrome stain

3.1.2 10704-5​ ​Ova and parasites LA21402-5 No Final

identified in Stool by Light ova, cysts, or
microscopy parasites seen

Stool culture with 4.1 625-4​ ​Bacteria identified in LA21123-7 No Preliminary

reflex to Gram Stool by Culture growth (time
stain, period 1)
identification, and
susceptibility 625-4​ ​Bacteria identified in Growth Preliminary
testing Stool by Culture detected (time
period 2)

625-4​ ​Bacteria identified in Clostridioides Final

Stool by Culture difficile (time
period 3)

Guide for Using LOINC Microbiology Terms ​• 95

 3.2.1 649-4​ Microscopic Moderate Final
observation [Identifier] in Gram-positive
Stool by Gram stain rods and
polymorphonucl
ear leukocytes

Microorganism antigen testing

LOINC contains individual as well as panel terms for microorganism antigen testing, so that tests
may be ordered individually or as a battery. For example, the order codes for the Clostridioides
difficile and Escherichia coli Shiga-like toxins tests shown in the table below are the same as their
result codes, but the rotavirus, norovirus and adenovirus antigen tests can be ordered using a single
order code for the three as one package: 8​ 0374-2​ A​ denovirus and Norovirus and Rotavirus Ag panel -
Stool by Rapid immunoassay.​ On the other hand, if only the Rotavirus antigen test is being performed,
then that would be ordered by itself using ​5880-0​ Rotavirus Ag [Presence] in Stool by Immunoassay​.

Lab test Related LOINC term(s) Result(s) Result status

chapter and (LOINC Answer
section codes are
included where
available)

Clostridioides 6.2 6363-6​ ​Clostridioides LA11882-0 Final

difficile toxin A and difficile toxin A+​B Detected
B test [Units/v​ olume] in Stool by
Immunoassay

Escherichia coli 64013-6​ ​Escherichia coli LA11883-8 Not Final

shiga-like toxin 1 shiga-like toxin 1 and 2 detected
and 2 test [Identifier] in Stool by
Immunoassay

Rotavirus, 72174-6​ ​Rotavirus Ag LA11883-8 Not Final

Norovirus and [Presence] in Stool by Rapid detected
Adenovirus antigen Immunoassay
rapid immunoassay
profile 80375-9​ ​Norovirus Ag LA11883-8 Not Final
[Presence] in Stool by Rapid detected
immunoassay

78529-5​ ​Adenovirus Ag LA11883-8 Not Final

[Presence] in Stool by Rapid detected
immunoassay

Microorganism nucleic acid testing

Nucleic-acid based tests are often multiplex assays in which a single specimen can be tested for the
presence of several organisms simultaneously. As described in Chapter 7, these assays are
represented as LOINC panels. Although a full discussion regarding mapping to LOINC panel terms

Guide for Using LOINC Microbiology Terms ​• 96

is out of scope for this guide, it is helpful to understand two keys points: 1) if the battery you are
mapping contains the same or some subset of the analytes contained in a particular LOINC panel,
you may map to that panel provided that the remaining axes (​System,​ ​Method,​ etc.) match and that the
set of analytes that are not contained in your battery are not marked as required in the LOINC panel
definitions; and 2) if the battery you are mapping contains more required elements than the LOINC
panel you are considering, you may not map to that panel. However, we will consider a request for
terms to be added to a panel when appropriate.

In this scenario, the stool pathogen profile shown in the table below contains 10 elements out of the
22 in LOINC panel ​82195-9​ ​Gastrointestinal pathogens DNA and RNA panel - Stool by Target
amplification with non-probe based detection​. Since the 10 elements match the panel in terms of S​ ystem
and M​ ethod​, and none of the elements in the LOINC panel are required, this example stool pathogen
panel may be mapped to 8​ 2195-9​, and ​82195-9​ can be used as the order code. However, if the
example stool pathogen profile contained 15 elements, 3 of which were not contained in 8​ 2195-9​, or
if the M
​ ethod​ for the example profile was P​ robe.amp.tar​, then it could not be mapped to the existing
LOINC panel.

Lab test Related LOINC term(s) Result(s) Result

chapter (LOINC status
and Answer
section codes are
included
where
available)

Stool 7.3 82196-7​ ​Campylobacter coli+​jejuni+​upsaliensis DNA LA11883-8 Final

pathogen [Presence] in Stool by NAA with non-probe detection Not
profile detected

82197-5​ ​Clostridioides difficile toxin A+B (tcdA+tscB) LA11882-0 Final

genes [Presence] in Stool by NAA with non-probe Detected
detection

82199-1​ ​Salmonella enterica+bongori DNA [Presence] in LA11883-8 Final

Stool by NAA with non-probe detection Not
detected

80349-4​ ​Escherichia coli enteroaggregative pAA plasmid LA11883-8 Final

aggR+aatA genes [Presence] in Stool by NAA with Not
non-probe detection detected

82203-1​ ​Escherichia coli shiga-like toxin 1

​ +​2 LA11883-8 Final
(stx1+stx2) genes [Presence] in Stool by NAA with Not
non-probe detection detected

Guide for Using LOINC Microbiology Terms ​• 97

 80350-2​ ​Shigella species+EIEC invasion plasmid antigen LA11883-8 Final
H (ipaH) gene [Presence] in Stool by NAA with non-probe Not
detection detected

82213-0​ ​Sapovirus genogroups I+II+IV+V RNA LA11883-8 Final

[Presence] in Stool by NAA with non-probe detection Not
detected

82207-2​ ​Entamoeba histolytica DNA [Presence] in LA11883-8 Final

Stool by NAA with non-probe detection Not
detected

82208-0​ ​Giardia lamblia DNA [Presence] in Stool by LA11883-8 Final

NAA with non-probe detection Not
detected

82205-6​ ​Cryptosporidium sp DNA [Presence] in Stool LA11883-8 Final

by NAA with non-probe detection Not
detected

11.3 Scenarios 3, 4, and 5 - multiple reporting

options described in the package insert for a
single test kit
A manufacturer may offer several options for how a single test kit can be utilized. This provides
laboratories with the flexibility to use the same kit for different clinical situations or reporting
requirements, but can also cause confusion for mappers when trying to determine the correct
LOINC code(s) for that kit. This section contains hypothetical examples of how a single kit can
produce a variety of results and provides guidance for mapping these results to different LOINC
codes. LOINC Answer codes are not included for the example results in this section for brevity.

KEY POINT

⚠
Note that these examples do not represent any particular manufacturer or test kit, and we
recommend that you always follow the result reporting requirements as stated in the
manufacturer’s package insert or test specification document as well as local regulations.

Guide for Using LOINC Microbiology Terms ​• 98

11.3.1 Scenario 3 - Multiplex assay for HIV
This hypothetical assay is a multiplex HIV kit that includes individual tests for HIV-1 antibody,
HIV-2 antibody, and HIV-1 p24 antigen. The instrument reports the three individual qualitative
results as well as an overall qualitative result. Assuming that the package insert and local regulations
do not specify how the results should be reported, there are three potential strategies for LOINC
mapping and results reporting as shown in the table below. The first and third strategies provide
details about which specific analytes were identified, and the second only provides an overall result,
so there is no way of knowing which ​Components​ were detected. However, if this is a screening test
and a positive result will trigger further confirmatory testing, it may not be necessary to report each
individual result.

Order: ​85037-0​ ​HIV 1 and 2 Ab and HIV 1 p24 Ag panel

Option # LOINC term(s) Example results

1 - Report 18396-2​ ​HIV 1 p24 Ag [Presence] in Serum or Plasma by Detected/Not detected

the three Immunoassay
individual
results 29893-5​ ​HIV 1 Ab [Presence] in Serum or Plasma by Detected/Not detected
Immunoassay

30361-0​ ​HIV 2 Ab [Presence] in Serum or Plasma by Detected/Not detected

Immunoassay

2 - Report 56884-1​ ​HIV 1+2

​ Ab+H
​ IV1 p24 Ag [Presence] in Serum or Detected/Not detected
one Plasma by Immunoassay
overall
result

3 - Report 18396-2​ ​HIV 1 p24 Ag [Presence] in Serum or Plasma by Detected/Not detected

the three Immunoassay
individual
and 29893-5​ ​HIV 1 Ab [Presence] in Serum or Plasma by Detected/Not detected
overall Immunoassay
results
30361-0​ ​HIV 2 Ab [Presence] in Serum or Plasma by Detected/Not detected
Immunoassay

56884-1​ HIV 1+2

​ Ab+H
​ IV1 p24 Ag [Presence] in Serum or Detected/Not detected
Plasma by Immunoassay

Guide for Using LOINC Microbiology Terms ​• 99

11.3.2 Scenario 4 - Single kit that can be used for screening
and quantitative evaluation
Many test kits allow for initial screening of a specimen for a particular analyte, and if the analyte is
detected, then the amount is quantified. The hypothetical assay in this example is an
immunofluorescence test for varicella zoster IgG antibodies. If varicella IgG antibodies are detected
in the initial screening assay, then additional testing is done to determine the titer. In this case, the
two parts of the assay should be mapped to two different LOINC codes as shown in the table below.
Both codes are necessary, because if the initial result is “Not detected”, then the first code would be
used to report that result, and no further testing is performed. However, if the initial result is
“Detected”, then the second code becomes necessary to report the titer, and the first code is still used
to report the initial finding.

LOINC term Example results

41512-5​ Varicella zoster virus IgG Ab [Presence] in Serum by Detected/Not detected

Immunofluorescence

6569-8​ Varicella zoster virus IgG Ab [Titer] in Serum by 1:4, 1:32

Immunofluorescence

11.3.3 Scenario 5 - Immunoblot assay that produces multiple

related results that have to be interpreted together
Some assays produce multiple results where each individual result has little meaning, but taken as a
group, they can be interpreted in a meaningful way. One example of such an assay is an immunoblot
study for B
​ orrelia burgdorferi​ infection. In this case, the immunoblot analysis produces separate
results for the presence of antibodies to different ​B. burgdorferi​ proteins (also called “bands”). The
presence of antibodies to a certain number of specific key bands is necessary for the diagnosis of
Lyme disease, and the criteria are different for IgM and IgG antibodies. Therefore, the clinician must
know how many as well as which bands were positive for the different antibodies. Different
laboratories may choose to report this information in different ways as shown in the following table:

Option # LOINC term(s) Example results

1 - Report 9598-4​ ​Borrelia burgdorferi 23kD IgM Ab [Presence] in Serum by Detected/Not

all of the Immunoblot detected
bands
separately 9599-2​ ​Borrelia burgdorferi 39kD IgM Ab [Presence] in Serum by Detected/Not
Immunoblot detected

Guide for Using LOINC Microbiology Terms ​• 100

 9587-7​ ​Borrelia burgdorferi 41kD IgM Ab [Presence] in Serum by Detected/Not
Immunoblot detected

9588-5​ ​Borrelia burgdorferi 18kD IgG Ab [Presence] in Serum by Detected/Not

Immunoblot detected

9589-3​ ​Borrelia burgdorferi 23kD IgG Ab [Presence] in Serum by Detected/Not

Immunoblot detected

9590-1​ ​Borrelia burgdorferi 28kD IgG Ab [Presence] in Serum by Detected/Not

Immunoblot detected

9591-9​ ​Borrelia burgdorferi 30kD IgG Ab [Presence] in Serum by Detected/Not

Immunoblot detected

9592-7​ ​Borrelia burgdorferi 39kD IgG Ab [Presence] in Serum by Detected/Not

Immunoblot detected

9593-5​ ​Borrelia burgdorferi 41kD IgG Ab [Presence] in Serum by Detected/Not

Immunoblot detected

9594-3​ ​Borrelia burgdorferi 45kD IgG Ab [Presence] in Serum by Detected/Not

Immunoblot detected

9595-0​ ​Borrelia burgdorferi 58kD IgG Ab [Presence] in Serum by Detected/Not

Immunoblot detected

9596-8​ ​Borrelia burgdorferi 66kD IgG Ab [Presence] in Serum by Detected/Not

Immunoblot detected

9597-6​ ​Borrelia burgdorferi 93kD IgG Ab [Presence] in Serum by Detected/Not

Immunoblot detected

2 - Report 13503-8​ ​Borrelia burgdorferi Ab.IgM band pattern [Interpretation] in IgM to the
the band Serum by Immunoblot following two
pattern bands detected,
supporting a
diagnosis of Lyme
disease: 39, 41

13502-0​ ​Borrelia burgdorferi Ab.IgG band pattern [Interpretation] in IgG to the

Serum by Immunoblot following seven
bands detected,
which supports a
diagnosis of Lyme
disease: 18, 28,
30, 41, 45, 58, 93

Guide for Using LOINC Microbiology Terms ​• 101

3 - Report See above See above
all of the
results
shown in
options 1
and 2

Guide for Using LOINC Microbiology Terms ​• 102

12 Mapping validation,
maintenance, and publication
After the initial mapping of your test codes to LOINC is complete, you should celebrate (Woohoo!).
But unfortunately, the job is not yet done. You must consider how you will validate and maintain
those mappings over time as both your local testing and the LOINC standard continue to evolve.
Lastly, you’ll want to plan for how you will make your mappings available to the people and systems
that need them. Different use cases for mapping have different requirements, so one approach won’t
satisfy all. In this section we discuss some recommendations for addressing these issues.

12.1 Validating your mappings

Mapping validation is an important step. Even when highly qualified professionals perform the
22
mapping, errors and inconsistencies are probable. Be sure to take advantage of any mappings
provided by reference laboratories and IVD vendors and confirm them for use in your context,
keeping in mind that those mappings are informative and not prescriptive.

For higher confidence in the accuracy and consistency of your mappings, multiple experts should be
involved. To minimize the potential for bias, each expert could independently map each test,
followed by a comparison and reconciliation of discrepancies. Resources may not support this level
of mapping redundancy, in which case we still recommend having at least one other reviewer
confirm the LOINC choices. This review could be performed across all mappings, or even for a
subset of tests with different analytes, methods, and units of measure.

Of special note is that the Regenstrief Institute offers a service called the Mapping Validity Checker,
which is a semi-automated algorithm that checks the LOINC mappings for each test in a test catalog.
The algorithm looks for inconsistencies and probable errors in the mappings and returns a detailed
report highlighting areas that need further review. Where possible, the report provides suggestions
for choosing the correct LOINC code. The Mapping Validity Checker is available for a small fee as
part of the L
​ OINC Premium Membership program​. The detailed feedback and consistency checking
represents an exceptional value, even for expert mappers. (Regenstrief hasn’t yet seen a mapping file
completely free of issues).

22
Lin MC, Vreeman DJ, McDonald CJ, Huff SM. Correctness of Voluntary LOINC Mapping for
Laboratory Tests in Three Large Institutions. AMIA Annu Symp Proc. 2010 Nov 13;2010:447-51.
[PMID: ​21347018​]

Guide for Using LOINC Microbiology Terms ​• 103

Lastly, for the highest degree of confidence in your mappings you might consider working directly
with Regenstrief’s LOINC staff on a special project basis. Such an arrangement has been used
successfully by IVD vendors, professional associations, government agencies, and other
organizations. With dedicated resources from Regenstrief, this approach is especially helpful where
there is likely to be new LOINC content needed (e.g. for new tests) and a high degree of confidence
in the mappings is desired.

12.2 Maintaining your mappings

The mappings of local tests to LOINC terms must be maintained, because both your testing and
LOINC continue to evolve. Over time you may replace or add new tests to your catalog. In addition,
LOINC publishes new releases (at least) twice a year, in June and December. Each LOINC release
includes new LOINC terms and all previously released terms, some of which may have been updated
since the previous release. Regenstrief Institute and the LOINC Committee recommend that users
update to the current version of LOINC within 90 days of its publication.

LOINC terms may be edited for a variety of reasons, but Regenstrief’s policy is to not modify any
term in a way that would change its fundamental meaning. Terms can be updated for a variety of
reasons without changing the meaning, including modeling changes, nomenclature updates,
corrections, and changes in status.

A LOINC term can have one of four different statuses as described in the following table. If a LOINC
term is discovered to be erroneous or ambiguous, its status is set to “Deprecated”, but it is not
removed from the database.

LOINC status Description

Active Concept is active. Use at will.

Trial Concept is experimental in nature. Use with caution as the concept and associated
attributes may change.

Discouraged Concept is not recommended for current use. New mappings to this concept are
discouraged; existing mappings may continue to be valid in context.

Deprecated Concept is deprecated. Concept should not be used, but it is retained in LOINC for
historical purposes.

For more details regarding statuses and other editorial policies, see the “Editorial policies and
procedures” chapter in the LOINC Users’ Guide.

Users should review each release for changes in status for all LOINC terms they are using. If a
previously active LOINC term you mapped to has now become discouraged or deprecated, users
should review the documented rationale for that change and update the mapping to an appropriate

Guide for Using LOINC Microbiology Terms ​• 104

LOINC when possible. For deprecated and discouraged terms, LOINC contains pointers to
superseding concepts where appropriate. Replacement terms are identified in the MAP_TO table
that is distributed with the primary LOINC Table.

Users should also review edits to any terms they are using. For example, updates to the LOINC Long
Common Name are quite common in subsequent LOINC versions as we refine our naming
conventions. If you are using this attribute in your system, it should be updated with each release.

In addition, many users would benefit from reviewing the new LOINC terms published in each
release to see if new terms are available for tests previously unmapped or if there are now more
suitable matches for underspecified mappings.

The two main ways to find newly edited LOINC terms are:

1. Filter on the current version number in the VersionLastChanged field in the LOINC Table
(either the .csv or .mdb version), which can be downloaded from the L ​ OINC download page
of the LOINC website​. Once you have filtered on this field, the value in the CHNG_TYPE
field will indicate whether the term is new, discouraged, deprecated, or updated (see
“Appendix A LOINC Database Structure” in the LOINC Users’ Guide for descriptions of the
CHNG_TYPE values).
2. Download the L ​ OINC Table Changes File​, which is available as an independent download
from the LOINC website.

KEY POINT

We recommend updating your local system with the latest version of LOINC within 90
days of each release, which occurs twice a year in June and December.

From the local database maintenance standpoint, consider the following recommendations:

1. Anytime there is a change in the display name, specimen type, reporting format, units of
measure, workstation assignment or interpretive data, there is a potential for a LOINC
attribute change, so the existing mapping should be reviewed any time such a change is
implemented;
2. If instrument downtime or a kit change occurs, the LOINC mappings for the tests run by
the substitute bench or referral lab performing the temporary downtime runs should be
reviewed. If the LOINC is “stamped” on an open result field and a different LOINC is going
to be used, the pre-determined override procedure (which varies from LIS to LIS) will need
to be invoked;
3. If any local tests are mapped to a LOINC term with ​System​ ​XXX ​or no ​Method (​ i.e.,
methodless), consider looking for new codes with a more accurate S​ ystem ​or M
​ ethod w ​ ith
each new LOINC release.

Guide for Using LOINC Microbiology Terms ​• 105

12.3 Mapping publication
12.3.1 Publishing your mappings
After completing your mapping validation, you’ll be ready to share the output with the people and
systems who will put them into action. Consideration should be given ahead of time to the full
lifecycle of these mappings. Different situations will require different processes, so here we describe
some general approaches.

First, recognize that you will almost inevitably have to inactivate some mappings and update to
superseding codes. Consider where the history logs of those mappings should be stored. (In the
source systems that use them? Offline in your mapping environment?) Next, consider what the
optimal communication and approval process should be when the mappings are finalized and ready
for publication to downstream recipients. You’ll also want to determine what the format should be
of the mapping file, including its structure and contents (e.g. which data fields). RELMA has a highly
configurable set of features for exporting mappings (See the “Exporting Local Terms and their
LOINC Mappings” section in the RELMA Manual).

If you are an IVD vendor, we strongly recommend that you publish the mappings of your test codes
to LOINC codes for your customers using the newly developed LIVD specification (described
below).

12.3.2 LIVD specification for vendor to LOINC mappings

LIVD​ specifies a standard digital format for IVD vendors to publish the LOINC terms associated
with each of their test results. The LIVD specification was published by the I​ VD Industry
Connectivity Consortium​ (IICC), a global, non-profit organization whose members include multiple
major IVD device vendors in partnership with the Clinical and Laboratory Standards Institute
(CLSI), HL7, and Integrating the Healthcare Enterprise (IHE).

The LIVD specification was created for publishing and exchanging mappings of LOINC terms for
IVD test results as a resource for downstream users such as clinical laboratories. IVD vendors are
well positioned to identify the appropriate LOINC terms for their test results because they possess all
of the relevant information about the test. When paired with expert LOINC knowledge and review,
IVD vendors have the opportunity to create high quality mappings that can then be used by their
customers to achieve more consistent coding choices across the industry. As IVD vendors make
these mappings available in the LIVD format, the reduced effort and expense of choosing the correct
LOINC term will dramatically boost the ability of labs to implement standard terminology.

For more information regarding the LIVD project, see the L

​ IVD page​ on the IICC website.

Guide for Using LOINC Microbiology Terms ​• 106

 KEY POINT

If you are an IVD vendor mapping your tests to LOINC, we recommend that you publish
your mappings using the LIVD format.

12.3.3 Future considerations for centralized LIVD mapping

publication
Initially, we expect that IVD vendors will publish the mappings of vendor test codes to LOINC on
their own websites and customer portals. This is an excellent first step and it should be encouraged.

For several reasons, it could be advantageous if a trusted, neutral third party such as the Regenstrief
Institute or IICC, would serve as an expert curator and central repository of mappings between IVD
assays and LOINC. In addition to its role as the developer of LOINC, Regenstrief could help provide
a single point of contact for all vendor-mapped codes in a common format (e.g. LIVD) and make
them broadly available from a central location for downstream users such as laboratories, EHR
systems, public health departments, and health information exchanges (HIEs). In general, by
minimizing the number of times each test has to be mapped, the risk of incorrect mappings will be
reduced. However, it is also important to keep in mind that ultimately, it is the laboratory
professionals’ responsibility to determine which LOINC terms are most appropriate for the tests
they perform.

Such an approach is not without issues, including synchronization between the many IVD vendors
and the source; business, legal, and IP issues with publication outside of the organization’s control;
and the resources it would take to maintain such a service. Nevertheless, Regenstrief would welcome
feedback (pros, cons, suggestions) about such an approach at ​https://loinc.org/contact/​.

Guide for Using LOINC Microbiology Terms ​• 107

Appendix A - Resources
About LOINC
LOINC Users’ Guide
The LOINC® Users' Guide is the definitive document about LOINC®. It explains the structure of the
table, its rationale, and the rules LOINC® uses for naming test results.
https://loinc.org/download/loinc-users-guide/

LOINC website
The LOINC® website has multiple resources available for new and experienced LOINCers. From the
home page, you can click “Get Started” for a quick tour. Dig a little deeper and you will find domain
specific information, videos, details on available downloads, events and community activities, and
information on submitting new LOINC terms.
https://loinc.org

Videos to learn more about LOINC

There are three videos available for no cost and several more available through our Premium
Membership program (see below). The three freely available presentations include A ​ n Introduction to
LOINC, LOINC Overview, ​and​ Understanding the Nature of LOINC Names.​ The videos range from 22-65
minutes in duration and are a great way to learn more about LOINC quickly.
https://loinc.org/videos/

Through the Premium Membership program, you can gain access to real-time and archived
LOINCinars (webinars). Past topics have included a tour of the new LOINC artifacts, tips for
searching in LOINC, and the lifecycle of a submission.
https://loinc.org/members/webinar/

Journal publications
Forrey AW, McDonald CJ, DeMoor G, Huff SM, Leavelle D, Leland D, Fiers T, Charles L, Griffin B,
Stalling F, et al. Logical observation identifier names and codes (LOINC) database: a public use set of
codes and names for electronic reporting of clinical laboratory test results. Clin Chem. 1996 Jan;
42(1):81-90. [PMID: ​8565239​]

Guide for Using LOINC Microbiology Terms ​• 108

McDonald CJ, Huff SM, Suico JG, Hill G, Leavelle D, Aller R, Forrey A, Mercer K, DeMoor G, Hook
J, Williams W, Case J, Maloney P. Clin Chem. LOINC, a universal standard for identifying
laboratory observations: a 5-year update. 2003 Apr;49(4):624-33. [PMID: 1​ 2651816​]

Mapping and Validation

Introduction to Mapping
There are a variety of slideshows available on the LOINC website, with three focused specifically on
mapping in LOINC. You’ll find Using RELMA Tutorial, Advanced LOINC Mapping Topics, and
Top 10 Tips for Mapping to LOINC. Look for these great resources under the header Laboratory
LOINC Mapping with RELMA - Tutorials and Boot Camps.
https://loinc.org/slideshows/

RELMA Users’ Manual

This document contains all the ins and outs of the RELMA program, from basics to advanced
mapping topics.
https://loinc.org/download/relma-manual/

LOINC Essentials
A thorough, detailed step-by-step guide for getting your local terms mapped to LOINC written by
LOINC Director Dr. Daniel Vreeman. Available for $39, this eBook will help you learn LOINC fast.
https://danielvreeman.com/loinc-essentials/

LOINC Premium Membership program

In addition to showing their support for LOINC, premium members receive special benefits
including access to LOINCinars, technical support, access to the archive of past releases, a discount
on LOINC Essentials eBook, and automatic delivery of the change file with each release.
Additionally, premium members can purchase the mapping validity check for a small fee.
https://loinc.org/members/

Journal Publications
Abhyankar S, Demner-Fushman D, McDonald CJ. Standardizing clinical laboratory data for
secondary use. ​Journal of biomedical informatics​. 2012;45(4):642-650. doi:10.1016/j.jbi.2012.04.012.
[PMID: 2​ 2561944​]

Guide for Using LOINC Microbiology Terms ​• 109

Vreeman DJ, Hook J, Dixon BE. Learning from the crowd while mapping to LOINC. J Am Med
Inform Assoc. 2015;22(6):1205-11. doi: 10.1093/jamia/ocv098. [PMID: 2​ 6224334​]

Kim H, El-Kareh R, Goel A, Vineet F, Chapman WW. An Approach to Improve LOINC Mapping
through Augmentation of Local Test Names. Journal of biomedical informatics. 2012;45(4):651-657.
doi:10.1016/j.jbi.2011.12.004. [PMID: 2​ 2210167​]

Related standards
UCUM
The Unified Code for Units of Measure (UCUM) is a code system intended to include all units of
measures being contemporarily used in international science, engineering, and business. The
purpose is to facilitate unambiguous electronic communication of quantities together with their
units.

http://unitsofmeasure.org

HL7 v2
http://www.hl7.org/implement/standards/product_brief.cfm?product_id=185

HL7 CDA
http://www.hl7.org/implement/standards/product_brief.cfm?product_id=7

HL7 FHIR
http://www.hl7.org/implement/standards/product_brief.cfm?product_id=449

Guide for Using LOINC Microbiology Terms ​• 110

Appendix B - Requesting new
LOINCs
LOINC codes are primarily created based on community (user) requests. If you cannot find an
appropriate LOINC term for your test, you are welcome to submit a request for a new LOINC term
to Regenstrief Institute. You can submit either through RELMA or via e-mail using one of our
submission templates. However, we ask that you please check the L ​ OINC website pre-release page,
to see if there is a similar new term prior to submitting your request. Likewise, we welcome
suggestions for changes to existing terms or other enhancements like additional synonyms or term
descriptions.

Regenstrief balances the desire to respond quickly to new term submissions with the review
processes necessary for a high quality standard. We can only be quick if the requesters provide clear
and comprehensive information about the terms they are submitting. A list of information required
for a submission is provided below.

How to submit
The information you provide about your local test/measurement and how it is used is more
important than the proposed LOINC name you come up with. Having complete information about
your local test makes the review process much smoother and helps us create clear term definitions as
well as verifying and enhancing other accessory content, which benefits everyone.

Required information
The set of information required for a particular submission depends on the content of the request. In
order for us to process your request, we need:

● Local test/observation name

● Local order (panel) name
● Name of send out lab (if applicable)
● Name of healthcare organization that stimulated the request for this term (if you are
submitting on behalf of someone else)
● Description of the test, which indicates what is measured, how it is performed, and how it is
used clinically (e.g. what conditions does it diagnose, monitor, screen for, etc.)
● Units of measure (for quantitative observations)
● Answer lists (for qualitative observations) (both normal and abnormal answers

Guide for Using LOINC Microbiology Terms ​• 111

 ● Sample results, reports (if applicable)
● If the request is for a panel, the request should include the tests that comprise the panel.
○ Whether or not each test already has a LOINC code should be included, and for any
tests that do not already have a code, all of the above information for each
individual test should be provided.
● Commercial test Package inserts, internal test kit specification documentation if applicable,
e.g., for lab-developed tests
● Vendor, instrument, and/or reagent kit used to perform this test (if applicable)
● Any other documentation that may assist us in creating the requested codes

Reminders about common issues in lab term requests

Here are a few reminders about common issues that come up in LOINC term submissions. Note that
our policy is to allow both methodless (no method) as well as method-specific measures in serology
(measures of Ab and Ag), and in antibiotic susceptibility testing. Please pay special attention to
submissions that include the ​System​ of serum or plasma alone. For most microbiology assays there is
no important clinical difference between the values obtained from serum and those obtained from
plasma, and we would like to represent them in the database as S​ er/Plas​ to indicate our indifference
to the distinction. Unfortunately, many requesters of new terms define their request in terms of the
one that they happen to use (e.g. serum or plasma) without telling us that the measure can really be
done on either serum or plasma. Most such requests should be for S​ er/Plas​ as the S​ ystem​ (sample). If
the measurement MUST be done on either serum or plasma, please scientifically justify your request
and send documentation.

Format for submissions

There are three possible ways to make your request, including: the​ ​online request form​, RELMA's
built in functions, or one of the​ s​ preadsheet templates​ available on the LOINC web site.

Regardless of format, we ask that users submit no more than 50 proposed terms at a time.

See the sections below for more details about each of the three submission formats.

Online request form

New LOINC terms can be requested directly from the LOINC website using the​ online request form​.
The request form can build a set of requested terms by entering the required information for each
term and/or by uploading a spreadsheet file with the required fields. Requested terms and
supporting information are sent to Regenstrief, and users can review the status of their submissions
from the​ My Submissions​ section of the LOINC website.

Guide for Using LOINC Microbiology Terms ​• 112

RELMA submission
The RELMA program can aid you in creating submissions by allowing you to create, manage and
store term submissions in a way that is similar to how the program creates, manages and stores local
working sets. With RELMA, you can work on term proposals for submission over time and submit
them in batches. The program will track when the term was created and the date when you
submitted the term. The program will help you organize the terms that you create and it will
automate the process of creating the submission files.

For detailed instructions on how to use RELMA to propose a term, please see Appendix A of the
RELMA manual. You can download the RELMA Manual here:

http://loinc.org/downloads/files/RELMAManual.pdf​.

Excel file submission

If you are not using RELMA for a submission, please use one of the templates provided on our
website:

http://loinc.org/submissions/new-terms

Other formats (e.g. distributed database fields, exported internal/local formats) will not be accepted.

Sending submission files to Regenstrief Institute

Regardless of the file type, please email your submission and related documents to
[email protected]​. Within a day or two of receipt of your file, you will receive a confirmation
email and the submission process will be underway. You may receive additional communication
from Regenstrief with requests for further information if necessary. Once the submission process
has been completed, you will receive files containing your requested codes.

Guide for Using LOINC Microbiology Terms ​• 113

Appendix C - LOINC Primer
Six major Parts of a LOINC concept
LOINC terms are not intended to transmit all possible information about a test or observation.
Rather, they are intended to provide enough information to identify and distinguish a result from
other, similar ones. To that end, each LOINC concept is defined by a name containing six major
Parts:​

● Component
● Property
● Time Aspect
● System
● Scale
● And where relevant, the M
​ ethod.​

No single attribute (​Part​) alone can completely describe a given measurement; only when they are
taken together do six attribute names define a single LOINC concept. Each type of ​Part​ is briefly
described in Table 1 and in more detail in later chapters when relevant. In addition, you can find a
thorough description of each P​ art​ in the LOINC Users’ Guide “Major Parts of a test or observation
name” chapter.

LOINC does not include information about certain parameters that either are not relevant for
interpreting the result or are expected to be reported elsewhere in the context of the test result. Such
attributes include the specific manufacturer or instrument used for testing, the specific anatomic site
of blood collection, such as “right antecubital fossa”, testing priority, such as “stat”, information about
who collected the specimen or verified the result, and the place of testing.

Part name Description Examples

Component The analyte being measured ● HIV-1 p24 antigen

● Bordetella pertussis IgM

antibody

Property The dimension of the analyte that is being ● Mass concentration (​MCnc​)
measured
● Presence or Threshold (​PrThr​)

Guide for Using LOINC Microbiology Terms ​• 114

 ● Presence or identity (​Prid​)

● Type

● Titer (​Titr​)

Time aspect Whether the measurement is an observation ● Point in time (​Pt​)

at a moment in time, or an observation
integrated over an extended duration of ● 24 hours (​24H​)
time

System The type of sample, substance, or, in some ● Blood (​Bld​)

cases, such as samples collected using swabs,
23
the anatomic location from which the sample ● Serum or Plasma (​Ser/Plas​)
was taken.
● Stool (​Stl​)

● Aspirate (​Asp​)

● Nasopharynx (​Nph​)

● Cervix (​Cvx​)

● Unspecified specimen
(​XXX​)

Scale A general classification of the type of result ● Quantitative (​Qn​)

that is reported, whether quantitative,
qualitative (ordinal or nominal), narrative, ● Ordinal - results can be ranked
etc. (​Ord​)

● Nominal - results cannot be

ranked (​Nom​)

Method How the analyte was measured. The ​Method ● No method specified (no value
is the only major axis that does not have to for the ​Method​)
be populated for every LOINC term.
● Immunoassay (​IA​)

● Agglutination (​Aggl​)

23
Note that a slash (/) in the​ System​ means “or”, indicating that any of the specimen types included are
suitable for that test. It does NOT mean that a specific manufacturer’s assay is approved for both
specimens; it simply means that results are expected to be clinically equivalent regardless of which of
the two (or three) specimens are used.

Guide for Using LOINC Microbiology Terms ​• 115

Orders, Observations, and Results
In LOINC, an “order” is a request for a specific test to be performed, an “observation” is the test itself,
and a “result” is the value produced by the observation. In the laboratory community, observations
are sometimes referred to as “test results” and results as “test result values.” In this guide, we use the
words order, observation, and result as defined in this section.

KEY POINT

Definitions
An order (“battery” or “profile”) is a request for a single test or group of tests to be
performed
An observation (“test result”) is a single resultable test
A result (“test result value”) is a quantitative or qualitative value produced by the test

Orders versus Observations

LOINC terms can represent orders, observations, and in many cases, the same term represents both
an order and an observation. LOINC does not create different terms when a concept is being used as
an order or an observation. Rather, the designation of whether a term can be used as an order,
observation, or both is carried in the OrderObs field within the LOINC database.

For example, ​Borrelia burgdorferi IgG+IgM with reflex to immunoblot panel - Serum​ is an order, but it is
not an observation because it does not represent a single test that can be resulted. The OrderObs
value for such a term is O​ rder​. On the other hand, ​Borrelia burgdorferi IgG Ab [Presence] in Serum by
Immunoblot​ is a single test that could be ordered and resulted individually, so in LOINC, its OrderObs
value is B
​ oth​ (meaning that the same term can function as both the order and observation). Finally,
some observations are such that they would never be ordered by themselves, and these have an
OrderObs value of O ​ bservation​. Examples include the presence or absence of IgG antibodies to
various Borrelia protein bands (e.g., 23 kDa), which would not be ordered in isolation.

The concepts of orders and observations are closely related to the panel and panel children
constructs in LOINC. LOINC “panels” are always order-only terms that contain a discrete set of
enumerated child elements (children), corresponding to what is typically called a “Battery” or
“Profile” in the laboratory setting. A given panel term does not represent a single resultable test;
rather, it represents an order for a set of tests. Panel terms often have a dash (​-)​ for the ​Property​ and
Scale​ since the child terms may not all have the same values for these attributes. In addition, although
in almost all cases the child elements within a LOINC panel are enumerated, they are not necessarily
all required; rather, some may be optional or conditional, and the same LOINC panel term may be

Guide for Using LOINC Microbiology Terms ​• 116

used by different laboratories or manufacturers whose specific batteries may not be exactly the same.
For more information regarding panels and business rules for mapping local batteries to LOINC
panels, see the LOINC Users’ Guide “Panels (Batteries)” chapter and “Business rules for users
mapping their local panels to LOINC panels” section.

LOINC terms that are observations only are, by definition, children or resultable tests within an
orderable panel and cannot be ordered by themselves. In contrast, those classified as both an order
and an observation may be included in a panel but also have to be orderable (and resultable) on their
own.

KEY POINT

OrderObs​ values
LOINC panel terms = ​Order
LOINC terms that ​only exist within panels​ = ​Observation
LOINC terms that ​can be ordered singly or as part of a panel​ = ​Both

Following is an example of a LOINC Borrelia burgdorferi panel showing the order-only panel term
and its children:

Guide for Using LOINC Microbiology Terms ​• 117

The fact that 6​ 2341-3​ is a panel term is evident by its P​ roperty​ being a dash (​-)​ , being in a Class that
starts with “PANEL.”, and having a Panel Type value of ​Panel​. In addition, it is designated as an
Order​ in the OrderObs field display.

Guide for Using LOINC Microbiology Terms ​• 118

On the other hand, the following IgG+IgM term has a ​Property​ that is not ​-,​ a Class that does not
start with “PANEL.”, and its OrderObs value is B
​ oth​.

Observations versus Results

It is important to understand the difference between observations and results. In LOINC, as
described above, an observation is the test itself (what is being measured), and a result is the value
produced by the observation; in the laboratory community, these concepts may be known as “test

Guide for Using LOINC Microbiology Terms ​• 119

results” and “test result values,” respectively. For example, ​718-7​ ​Hemoglobin [Mass/volume] in Blood​ is
a LOINC term for an observation, and the result of that observation is a quantitative value, such as
14 mg/dL. A different way to think about it is that observations are the “questions” and results are
the “answers.” For observations that are reported as quantitative values, the result is simply
represented as a number, along with the unit of measure (e.g. 14 mg/dL). However, when the
observation result is qualitative, then there are different ways to represent the result, including as
free text or coded entries like LOINC Answer codes or codes from SNOMED CT. As described
above, in HL7 v2 messages, both the observation and result are reported in the OBX segment, with
the observation in OBX-3 and the result in OBX-5.

SNOMED CT is an international terminology standard for clinical information, such as symptoms,

24
diagnoses, anatomy, and microorganism names. SNOMED CT provides codes that may represent
nominal and ordinal values (e.g. answers) for the observations (questions) represented by LOINC
terms. The Regenstrief Institute recommends using SNOMED CT codes for reporting qualitative
laboratory result values in SNOMED CT member countries or affiliates where appropriate licensure
is granted. In situations where the use of SNOMED CT is not permitted, LOINC Answer codes or
other terminologies could be used.

As part of the LOINC distribution, we provide lists of LOINC Answer codes for nearly every
qualitative LOINC observation term. Where possible, we also publish a mapping between LOINC
answer codes and corresponding SNOMED CT codes, though this is a work in progress. Note that
due to licensing restrictions, this guide does not yet include SNOMED CT codes.

In the laboratory domain, nearly all of the LOINC Answer lists are EXAMPLE type lists that are
meant to give users an idea of the types of results associated with a particular LOINC. Users should
always follow local reporting regulations, for example, reporting qualitative results according to the
vendor’s package insert.

LOINC ​Components​ and ​Properties​ for

microbiology assays
This section describes how different kinds of microbiology tests are typically represented in LOINC,
based on patterns in their P​ art ​names.

Component
The ​Component​ part of a LOINC term describes what is being measured. For assays such as cultures
or stains when the purpose is to identify whether or not a microorganism is present and if yes,
which type, the ​Component​ name is usually general, such as ​Bacteria identified​ (for cultures) or

24
SNOMED CT [Internet]. London (England): SNOMED International. Available from:
http://www.snomed.org/snomed-ct

Guide for Using LOINC Microbiology Terms ​• 120

Microscopic observation​ (for stains). For terms looking for specific organisms, genes, or
antibodies, the ​Component​ includes the organism name, which antigen or gene is the target of the
study, or the type of antibody (e.g. IgG or IgM). Different terms have different levels of granularity
for each of these dimensions. The table below shows how the different dimensions together create a
unique ​Component.​

Organism Antigen, nucleic LOINC ​Component

acid, or antibody

Streptococcus pneumoniae Ag Streptococcus pneumoniae Ag

Streptococcus pneumoniae Ab.IgG Streptococcus pneumoniae Ab.IgG

Streptococcus pneumoniae Ab Streptococcus pneumoniae Danish

Danish serotype 12F serotype 12F Ab

Varicella zoster virus DNA Varicella zoster virus DNA

Varicella zoster virus Ab.IgM Varicella zoster virus Ab.IgM

Varicella zoster virus clade - Varicella zoster virus clade

Hepatitis B virus core Ab Hepatitis B virus core Ab

Hepatitis B virus core Ag Hepatitis B virus core Ag

Property​ and ​Scale

The ​Property​ and S​ cale​ are closely related and describe what characteristic of the C
​ omponent​ is being
measured. The S​ cale​ represents a higher-level concept, such as quantitative (numeric) or qualitative,
and the ​Property​ describes the kind of quantity or aspect of the analyte that is being measured in
more detail, such as its mass concentration or volume. For example, qualitative tests may detect the
presence, absence or identity of an analyte, and quantitative tests may report how much of a given
analyte is present.

Qualitative results
LOINC Microbiology terms include two types of qualitative results: those that represent the
presence or absence of an analyte (​Scale​ ​Ord​), and those that represent the identity of an analyte
(Scale N
​ om​). LOINC terms with an ordinal ​Scale​ are used for categorical results that can placed in an
order, such as Detected/Not detected, Low/Medium/High, and Positive/Negative. All tests that are
reported in this manner are labeled as ordinal because the result categories can be ranked. The
Property​ for ordinal terms is typically ​PrThr​, which stands for “Presence or Threshold”, meaning
either the actual presence or absence of an analyte or that the amount of analyte detected is over
some predetermined threshold.

Guide for Using LOINC Microbiology Terms ​• 121

LOINC terms with a ​Scale​ of N​ om​ (for nominal) are used to represent categorical results that cannot
be ranked, such as the specific Streptococcus pneumoniae serotype that is detected, or the species of
bacteria identified in a blood culture. Such terms usually have a P​ roperty​ of ​Prid​, which stands for
“Presence or identity”, or ​Type​. Terms with the P ​ rid​ P​ roperty​ are used to report whether or not an
analyte of a particular kind is present, and if it is, to report which one. For example, when a bacterial
culture is performed, it is not known in advance whether or not any bacteria will be present.
Therefore, one possible result for a bacterial culture is “No growth”, but if one or more types of
bacteria are determined to be present, then the specific identity (e.g. Staphylococcus aureus) is
determined and reported. Bacterial culture terms in LOINC have a ​Property​ ​Prid​ and ​Scale​ ​Nom​.

Terms with the ​Property​ of ​Type​ are used for assays that identify the specific analyte in cases when
the baseline presence of the analyte is known. For example, if an isolate known to contain
Streptococcus pneumoniae is further analyzed to determine the specific serotype, the serotype assay
would have a ​Property​ of ​Type​, not P
​ rid​, because the presence of the Streptococcus is already
known.

KEY POINT

Property​ ​PrThr​ + ​Scale​ ​Ord​ = presence or absence of an analyte

Example results: Detected, Not detected

Property​ ​Prid​ + ​Scale​ ​Nom​ = absence of an analyte, or, if present, the type of analyte found;
the result is often selected from a list of organisms
Example results: Not detected, Leptospira biflexa, Leptospira interrogans, Leptospira
kirschneri

Property​ ​Type​ + ​Scale​ ​Nom​ = type of analyte found, when the presence is already known;
the result is often selected from a list of organisms
Example results: Leptospira biflexa, Leptospira interrogans, Leptospira kirschneri

Note that the example answers for a Type/Nom term are the same as the Prid/Nom term,
except the Prid/Nom term includes another choice for “Not detected”

Quantitative results
Assays that measure the amount of analyte present have a S​ cale​ of Q ​ n​. These terms can vary in the
specification of their P​ roperty​, depending on the specific characteristic that is being measured, such
as titer, mass concentration, or number per area. The LOINC P​ roperty​ is closely related to the units
of measure; the ​Property​ determines the kind of units that are reportable with that term. LOINC has
different ​Properties​ for analytes measured in mass units versus substance units (e.g. milligrams versus
millimoles), but does not have different P​ roperties​ to represent different orders of magnitude, such as
milligram versus gram. Thus, when mapping, users must choose a LOINC term with a P​ roperty​ that

Guide for Using LOINC Microbiology Terms ​• 122

is consistent with the reporting units. The table below provides some examples of common
microbiology units of measure and the corresponding LOINC P​ roperty​ and S​ cale.​

The ​ACnc​ P​ roperty​ represents the number of arbitrary units in a volume (arbitrary concentration).
Immunoassay results that are based on optical densities are commonly represented in LOINC with
this ​Property​. Because the units are truly arbitrary, they may be represented in a variety of ways by
different laboratories and also within LOINC, as shown in the table below.

Units of measure Property Scale

mg/dL; ng/mL MCnc Qn

mmol/L; nmol/dL SCnc Qn

copies/mL; #/mL NCnc Qn

log copies/mL; log #/mL LnCnc Qn

#/area Naric Qn

IU/L; IU/mL; index ACnc Qn

value; EIA units;
units/mL

Qualitative results versus the interpretation of quantitative results

It is important to distinguish qualitative results from an ordinal interpretation of a quantitative
result. For example, a rapid test for Streptococcus pyogenes antigen that is routinely done in a
physician’s office yields a true qualitative result, either the antigen is present or it is not, and there is
no quantitative result that can be reported. There may be a particular concentration at which the test
reads positive, but that information is not part of the reported result. On the other hand, an assay for
which the concentration of a particular analyte is its primary reportable result is fundamentally a
quantitative assay. The quantitative result may be interpreted as positive or negative based on a
particular threshold, but the interpretation of the quantitative result, which would be reported in
OBX-8 of an HL7 version 2 message, is different from a primary qualitative result, which would be
reported in OBX-5.

The package insert will tell you whether a particular assay is approved for quantitative and/or
qualitative reporting; some assays are approved for both and may map to two LOINC codes. For
assays that map to two LOINC codes, the code that is appropriate for the result being reported in a
particular instance should be used.

KEY POINT

Guide for Using LOINC Microbiology Terms ​• 123

Result: “Positive” or “Negative” → LOINC Scale = Ord
Result: 3 mg/dL → LOINC Scale = Qn; may be interpreted as “Positive” or “Negative”, but
the interpretation is not the primary result

Guide for Using LOINC Microbiology Terms ​• 124