PROPERTIES AND UNITS IN THE CLINICAL LABORATORY SCIENCES

VIII. PROPERTIES AND UNITS IN CLINICAL MICROBIOLOGY

(Technical report - IUPAC—IFCC 1999)

Prepared  for publication by

Urban Forsum¹, Henrik Olesen² , Wilhelm Frederiksen³ , Birgitta Persson¹

¹Division Clin. Microbiol., Faculty of Health Sciences, Linköping, Sweden
²Office of Laboratory Informatics, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
³Dept. of Microbiology, Statens Seruminstitut, Copenhagen, Denmark

*^#The combined Memberships of the Commission and the Committee during the preparation of this report (1994 to 1996) were as follows:

Chairman: 1989-1995 H. Olesen (Denmark); 1996 - D Kenny (Ireland). Members:  X. Fuentes-Arderiu (Spain; 1991-1997); J.G. Hill (Canada; 1987-1997); D. Kenny (Ireland; 1994-1997); H. Olesen (Denmark; 1985-1995);  PL Storring (United Kingdom; 1989-1995); P Soares de Araujo (Brazil; 1994-1997); Clem McDonald (USA; 1996-1997).

Please forward comments to:
H. Olesen, Office of Laboratory Informatics, Copenhagen University Hospital (Rigshospitalet), 9 Blegdamsvej, DK-2100 Copenhagen, Denmark. E-mail: [email protected]

Synopsis

The document describes the use of the concept property and the presentation of results in clinical microbiology. Systematic names in clinical microbiology require the use of a nominal scale kind of property to describe taxonomy. For this purpose the kind of property ”taxon” is introduced. The document further lists properties commonly used in clinical microbiology. The document follows the IUPAC-IFCC systematic syntax and this creates a basis for integration of the format of clinical microbiology laboratory reports in the general clinical laboratory sciences laboratory reports format.

Preface

The present document is part eight (VIII) of a series on properties determined in the clinical laboratory sciences, initiated in 1987.

     The series will comprise the five general parts (I-IV and XI) and a series of special parts:

I        Syntax and semantic rules [1]
II       Kinds-of-property [2]
III      Elements (of properties) and their and code values
IV      Properties and their code values 
V       Properties and units in Thrombosis and Haemostasis
VI      Properties and units in IOC defined Drugs of Abuse
VII     Properties and units in Inborn Errors of Metabolism
VIII    Properties and units in Clinical Microbiology (this report)
IX       Properties and units for Trace Elements
X        Properties and units in General Clinical Chemistry
XI       Coding systems - structure and guidelines [3]
XII     Properties and units in Clinical Pharmacology and Toxicology
XIII    Properties and units in Reproduction and Fertility
XVI    Properties and units in Clinical Allergology

     The size of part III and IV is such that their lists will be presented in electronic format. This is for ease of handling and to facilitate expression of concepts in different languages. The content of the documents is in agreement with the comprehensive monograph [4] and the standards [5; 6].

Foreword and  Scope

Clinical Laboratory Sciences are characterised by the exacting nature of the work performed and the demand for a precise presentation of the outcome.
     In clinical microbiology the microorganisms and/or host response is usually named in a report although specific traits of microorganisms or a component of the immune response are often the components studied by the laboratory.
     The adherent informatics system therefore needs to identify the findings accurately and to present them with the degree of detail required. At the same time it has to facilitate the transfer over linguistic and cultural barriers without distortion or loss of clarity, in order to promote clear, unambiguous, meaningful  and fully informative communication in different terminologies.
     The degree to which a message (such as a laboratory report) needs to be expressed in a formal, systematic language depends on the geographical, linguistic, social or professional distance between the communicating parties. The greater the distance, the greater the risk of misunderstanding.
     Within one laboratory, local jargon terms may be used which are usually well understood between colleagues, but which would not be sufficiently widely known for communication with the outside world. Likewise, a laboratory and its local community of users, such as hospital or community physicians, may use a "local dialect" of the language of clinical laboratory sciences which is well understood by all concerned; but when the communication possibilities are wider, even transnational, risks of serious misunderstanding arise.
     The purpose of this document is to apply the IFCC–IUPAC recommended syntax structures [4] for request and report and to create a systematic terminology which can be used as the basis for coding laboratory messages in the domain of clinical microbiology. This is  to facilitate communication of messages about such properties in publications and through computing and telecommunication between databases, messages that contain sufficient information to allow translation from and to the required "local dialect" at each end.
     The systematic names recommended here are primarily for the purpose of unambiguous data exchange. Their use in routine language by clinicians or laboratory practitioners is optional but encouraged.

Definitions

coding scheme: collection of rules that maps the elements of one set on to the elements of a second set  [ISO7826-1:1994; 7]

component: definable part of a system [ENV 1614:1995; 5]

EXAMPLES:

international coding scheme identifier, ICSI: identifier assigned to uniquely identify a registered coding scheme for use in information interchange [ISO7826-1:1994; 7]

kind-of-property; property (in a general sense): attribute of a phenomenon, body or substance that may be distinguished qualitatively [ENV 1614:1995; 5]

EXAMPLES: Colour; transparency; length; amount of substance

subject field: section of human knowledge, the border lines of which are defined from a purpose-related point of view [ISO1087:1990; 9]

NOTE: In terminology science and its practical applications the subject field is determined through the establishment of systems of concepts.

superordinate concept: concept that in a hierarchical relation is ranked on a higher level [ISO1087:1990; 9]

EXAMPLES: kind-of-property; component; unit; specification to system.

system: demarcated arrangement of a set of elements and a set of relationships between these elements [ENV 1614:1995; 5]

EXAMPLES:

Systematic Report

By convention,  properties and results of observation or measurement are represented by the equation:

Equation 1

Property =  Result

       The parts comprised in the concept of ‘property’ and in the concept of ‘result’ are presented in table 1.
     A full report on a request to a clinical laboratory comprises all four sections presented in table 1. Section 1 is not dealt with further as it follows local usage, for example EDIFACT or HL7. Section 2 indicates parts of a request. In a report also section 3 and, if needed, section 4 is included. To each part of a property may be added a specification as a parenthetic suffix for clarification. Thus the equation in its extended form is:

Equation 2

System(specification to system)¾Component(specification to component); kind-of-property(specification to property) = result (value × unit)

For details on rules and conventions see part I and XI of this series [1; 3].

Coding Scheme for Elements

Equation 2 comprises 7 (8) superordinate concepts. In order to define uniquely the elements of these superordinate concepts, each element is identified by an international coding scheme identifier and a code value. This is for ease of expression in different idioms and to assure uniform spelling throughout the coding scheme for properties evolving.
     Code values are from a series of ICSI, the major part for this document being from ATCC [10] and UMLS [11].
     One might assume that latin names for bacteria could be used as such; however, in some countries these are transcribed and also their latin designation in some cases are changed, while retaining the concept identifier (for example the ATCC code value).

EXAMPLE

ATCC00186 Micrococcus roseus becomes Kocuria rosea

ATCC33236 Bacteriodes gracilis becomes Campylobacter gracilis

     In clinical microbiology variability is extensive, in particular for the superordinate concepts “system” and “result”, in that a sample may originate from any part of a human or its surroundings, and the outcome of examination may be any of a plethora of bacteria and their subtypes.

System and Specification to system

Some examples and their ICSI + code values are given in table 2. Specifications to system are numerous and comprise any anatomical localisation of  e.g. an abscess and other information (“midstream”; “puncture of urinary bladder”). 

EXAMPLE

Abscess(Hand; right)—

Biopsy(Kidney)—

Secretion(Contact lens; Eye; left )—

Secretion(Nasopharynx)—

Component and Specification to component

These are numerous but some of them are of a more general nature and are used systematically (table 3). Specifications are frequently the name of a particular bacterium.

 Kinds-of-property and Scale

Well over 150 of this type of superordinate concepts  are defined in the Silver Book [4], but only about 7 relate to clinical microbiology (table 4).
     The most extensively used are “taxon” and “susceptibility”. In clinical microbiology the term “taxon” relates to all of the hierarchical classification. It is from Greek “tassein” (to arrange). It is well defined and represents only one particular concept. For this reason it has been adopted in this series of documents also for other subject fields to replace terms such as “found”, “present”, “class” and other. 

The term “arbitrary” in princible cannot be related to a volume. In clinical chemistry however a less well defined “inhouse” or a regional calibrator is often referred to and is expressed in “arbitrary unit per litre” in order to enable comparison of patient data over time and regionally. In each of these instances further information should be given in the parenthesis “procedure”. This could be information on the calibrator used, f.ex. “BCR/CRM148/149R“  or it could refer to the inlaboratory document “procedure xx”. which is available on request.

In the examples given, a question mark, “?”, has been used to represent the value of a result for properties including quantities.

EXAMPLES

1        Urine—
     Bacterium; 
          taxon(procedure)
          [NPU06073]
          U—Bacterium; taxon(proc.57) = Escherichia coli; Proteus vulgaris

2        Urine—
     Bacterium(specification); 
          arbitrary concentration(procedure)
          [NPU06673]
          U—Bacterium(Escherichia coli);arb.c.(0 1 2 3; proc.58) = 2

3        Secretion(Urethra)—
     Bacterium;
          taxon(procedure)
          [NPU06085]
          Secr(Urethra)—Bacterium; taxon(proc.57) = ATCC19424 (= Neisseria gonorrhoeae)

4        Secretion(Urethra)—
     Bacterium(specification);
          susceptibility(list; ordinal scale; procedure)
          [NPU13745]
          Secr(Urethra)—Bacterium(Neiss. gon.); suscept.(list; ord. sc.; R I S)
          [NPU12866]    Syst—Ansamycin; suscept. = R
          [NPU06008]    Syst—Benzylpenicillin; suscept. = S
          [NPU13588]    Syst—Ceftriaxone; suscept. = I
          [NPU06049]    Syst—Ciprofloxacin; suscept. = S
          Note: R: Resistant; I: Intermediate; S: Susceptible

5        Secretion(Urethra)—
     Bacterium(specification);
          susceptibility(list; ratio scale; procedure)
          [NPU07285]
          Secr(Urethra)—Bacterium(Neiss. gon.); suscept.(list; rat. sc.; MBC)
          [NPU13506]    Syst—Ansamycin; threshold subst.c. = 2,2 µmol/l
          [NPU13574]    Syst—Benzylpenicillin; threshold subst.c. = 2,2 µmol/l
          [NPU13577]    Syst—Ceftriaxone; threshold subst.c. > 200 µmol/l
          [NPU06052]    Syst—Ciprofloxacin; threshold subst.c. > 200 µmol/l
          Note: MBC: Minimal bacteriocidal concentration

6         Plasma—
Borrelia burgdorferi antibody; 
    arbitrary substance concentration(procedure)
    arbitrary unit/litre
    [NPU08002]
    P—Borrelia burgdorferi antibody; arb.subst.c.(proc. 62) = 7 arb. unit/l

 7        Urine—
     Bacterium(specification); 
          number concentration(procedure)
          10⁶/litre
          [NPU07420]
          U—Bacterium(Escherichia coli); num.c.(proc. 60) = 6,5 × 10⁶/l

8        Cerebrospinal fluid—
     Treponema pallidum flagel antibody(Immunoglobulin G);
          relative substance concentration(Cerebrospinal fluid/Plasma)
          [NPU09319]
          Csf—Treponema pallidum flagel antibody(IgG); rel.subst.c.(Csf/P) = ?
 

Operator and Value

The more commonly used operators [12] are in table 5.

Table 5
Operator	Operator meaning
»	Approximately equal to
=	Equal to
>	Greater than
³	Greater than or equal to
<	Less than
£	Less than or equal to

 The “equal to” operator is often omitted, for example in cumulative laboratory reports.

 EXAMPLE 

	Date 1	Date 2	Date 3	Date 4	Unit
U¾Escherichia coli; num.c.	500	100	10	< 1	106/l

 If no bacteria are present (or detected) the choice for presentation of the result varies: “0”, “negative”, “not detected” or “< 10⁶/l”. Of these the latter is more informative, while the first may be more convenient.

Unit and Note

Units are dealt with in detail in [4]. Often a prefix is useful for indication of magnitude, for example nano (10^-9). The combination of a prefix and a unit such as mole/litre forms a new unit nanomole/litre (nmol/l). Nominal and ordinal scale values carry no unit.
     While specifications may be added to the parts of a property this is not so for results. If needed, they are given as a note to the report.

References

1.       IUPAC–IFCC (International Union of Pure and Applied Chemistry– International Federation of Clinical Chemistry), Commission/Committee on Quantities and Units(in Clinical Chemistry), 1995. Properties and units in the clinical laboratory sciences. I. Syntax and semantic rules. Prepared for publication by H Olesen. Pure and Appl Chem 1995; 67: 1563-74; Eur J Clin Chem Clin Biochem 1995; 33: 627-36.

2.       IUPAC–IFCC (International Union of Pure and Applied Chemistry– International Federation of Clinical Chemistry), Commission-Committee on Nomenclature, Properties and Units. Properties and units in the clinical laboratory sciences. II. Kinds-of-property (Recommendations 1996). Prepared for publication by H Olesen, D Kenny. Eur J Clin Chem Clin Biochem 1997; 35: 317-44.

3.       IUPAC–IFCC (International Union of Pure and Applied Chemistry– International Federation of Clinical Chemistry), Commission-Committee on Nomenclature, Properties and Units. Properties and units in the clinical laboratory sciences. XI. Coding systems - structure and guidelines. (Technical report 1997). Prepared for publication by H Olesen, D Kenny, R Dybkær, I Ibsen, I Bruunshuus, X Fuentes-Arderiu, G Hill, P Soares de Araujo, C McDonald. Pure and Appl Chem 1997; 35: 317-44.

4.       IUPAC–IFCC (International Union of Pure and Applied Chemistry–International Federation of Clinical Chemistry), Commission/Committee on Quantities and Units(in Clinical Chemistry), 1995. Compendium of terminology and nomenclature of properties in clinical laboratory sciences. The Silver Book. JC Rigg, SS Brown, R Dybkaer, H Olesen. Oxford: Blackwell Science, 290 pp.

5.       CEN/TC 251, 1995. European Prestandard ENV 1614:1995. Medical Informatics. Structure for nomenclature, classification and coding of properties in clinical laboratory sciences.

6.       CEN/TC 251, 1996. European Prestandard ENV 12435:1996. Medical Informatics. Expression of the results of measurement in health sciences.

7.       International Standards Organization. International Standard ISO/IEC7826-1,1994. Information technology - General structure for the interchange of code values. Part I. Identification of coding schemes.

8.       CEN/TC 251, 1996. European Prestandard ENV 12264:1996. Medical Informatics. Categorial structures of concepts. Model for representation of semantics.

9.       International Standards Organization. International Standard ISO1087,1990. Terminology - Vocabulary.

10.     American Type Culture Collection (ATCC), Rocksville, USA.

11.     UMLS^â (Unified Medical Language System) Knowledge Sources, 1999. U.S. Department of Health and Human Services. Bethesda: National Institutes of Health, National Library of Medicine.

12.     ISO 31-11:1992. Quantities and Units - Part 11. Mathematical signs and symbols for use in physical sciences and technology.

Index of Abbreviations

ATCC       American Type Culture Collection
EDIFACT Electronic Data/Document Interchange for Administration, Commerce and Transport
ENV         Europäische Normung Vorschlag
HL7          Health Level 7
ICSI          International Coding Scheme Idenfitier
IFCC         International Federation of Clinical Chemistry
IUPAC      International Union of Pure and Applied Chemistry
ISO           International Standardization Organization
MSH         Medical Subject Headings, Bethesda: National Library of Medicine
UMD        Universal Medical Device Nomenclature Systemä. Product Categories Thesaurus 1996. Copyright 1995 by ECRI
UMLS       Unified Medical Language Source. Bethesda: National Library of  Medicine. National Institute of Health