AUSTRALIAN PATHOLOGY UNITS AND TERMINOLOGY (APUTS) Reporting Terminology and Codes Microbiology (v2.1) ISBN: Pending 1 State Health Publication Number (SHPN): Pending Online copyright © RCPA 2014 This work (Standards and Guidelines) is copyright. You may download, display, print and reproduce the Standards and Guidelines for your personal, non- commercial use or use within your organisation subject to the following terms and conditions: 1. The Standards and Guidelines may not be copied, reproduced, communicated or displayed, in whole or in part, for profit or commercial gain. 2. Any copy, reproduction or communication must include this RCPA copyright notice in full. 3. No changes may be made to the wording of the Standards and Guidelines including commentary, tables or diagrams. Excerpts from the Standards and Guidelines may be used. References and acknowledgments must be maintained in any reproduction or copy in full or part of the Standards and Guidelines. Apart from any use as permitted under the Copyright Act 1968 or as set out above, all other rights are reserved. Requests and inquiries concerning reproduction and rights should be addressed to RCPA, 207 Albion St, Surry Hills, NSW 2010, Australia. This material contains content from LOINC® (http://loinc.org). The LOINC table, LOINC codes and LOINC panels and forms file are copyright © 1995-2012, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and available at no cost under the license athttp://loinc.org/terms-of-use. This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO®). All rights reserved. SNOMED CT was originally created by The College of American Pathologists. IHTSDO®, SNOMED® and SNOMED CT® are registered trademarks of the IHTSDO First published: February, 2013, 1st Edition (version 1.0) 2 Terminology for Reporting Pathology: Microbiology TRIM Document #: D156352 Document History: Version Reason for Change Author Date Initial Terminology for Microbiology: Organisms mapped to SNOMED CT, published by Michael Legg / Dr 1.0 12-Feb-13 the RCPA Pathology Units and Terminology Standardisation Project. Christiaan Swanepoel 2.0 Donna Moore 06-Jun-14 Changed the name of this spreadsheet from "PUTS Microbiology Urine Microbiology LOINC subset " to "APUTS Microbiology terminology reference set ". Added Document Revision History worksheet. The following are the updates to the 'Terminology for Urine MCS' worksheet: Corrected "15 Flucytosine" should have been "5 Flucytosine" on the Terminology for Urine MCS worksheet. Updated 'Yeast' to now say 'Yeasts'. Removed "RCPA Pathology Units and Terminology Standardisation Project - Terminology for Reporting Pathology: Microbiology : Urine Microbiology Report v1" title from Urine MCS LOINC subset. Removed columns that were used during reviewing the SNOMED codes. Added Terminlogy for Salmonella worksheet, compiled by PITUS-14 WG5. Urine Microbiology Report LOINC Component Property Timing System Scale Method Specimen Collection Method 19159-3 Urinalysis specimen collection method Prid Pt Urine Nom Dipstick/Chemistry Glucose 25428-4 Glucose ACnc Pt Urine Ord Test strip Bilirubin 5770-3 Bilirubin ACnc Pt Urine Ord Test strip Ketones 2514-8 Ketones ACnc Pt Urine Ord Test strip Specific Gravity 5811-5 Specific gravity Rden Pt Urine Qn Test strip pH 5803-2 pH LsCnc Pt Urine Qn Test strip Protein 20454-5 Protein ACnc Pt Urine Ord Test strip Urobilinogen 5818-0 Urobilinogen ACnc Pt Urine Ord Test strip Nitrites 5802-4 Nitrite ACnc Pt Urine Ord Test strip Haemoglobin 5794-3 Hemoglobin ACnc Pt Urine Ord Test strip Leucocyte Esterase 5799-2 Leukocyte esterase ACnc Pt Urine Ord Test strip Microscopy Cells White blood cell count 30405-5 Leukocytes NCnc Pt Urine Qn Red blood cell count 30391-7 Erythrocytes NCnc Pt Urine Qn Red blood cell morphology 53974-2 Erythrocyte morphology Imp Pt Urine sed Nar Microscopy.light Epithelial cells 30383-4 Epithelial cells NCnc Pt Urine Qn Microorganisms Bacteria 50221-1 Bacteria ACnc Pt Urine Ord Automated Parasites 33017-5 Parasites Naric Pt Urine sed Qn Microscopy.light.LPF Yeasts 32356-8 Yeast ACnc Pt Urine sed Ord Microscopy.light Fungi 20457-8 Fungi.filamentous ACnc Pt Urine sed Ord Microscopy.light Casts Casts present 24124-0 Casts ACnc Pt Urine sed Ord Microscopy.light Casts number 9842-6 Casts Naric Pt Urine sed Qn Microscopy.light.LPF Casts type 58436-7 Casts Type Pt Urine sed Nom Microscopy.light Crystals Crystals present 49755-2 Crystals ACnc Pt Urine sed Ord Microscopy.light Crystals number 38459-4 Crystals Naric Pt Urine sed Qn Microscopy.light.HPF Crystals type 5782-8 Crystals Prid Pt Urine sed Nom Microscopy.light Other 58442-5 Prid Pt Urine sed Nom Microscopy.light Spermatozoa 8248-7 Spermatozoa ACnc Pt Urine sed Ord Microscopy.light Antibacterial activity Antibacterial activity 30910-4 Antimicrobials ACnc Pt Urine Ord Culture The same LOINC should be used if multiple organisms are cultured. The HL7 Sub ID (OBX-4) field can be used to distiguish organisms from each other and group relevant colony counts and susceptiblity testing. Culture result/Organism 630-4 Bacteria identified Prid Pt Urine Nom Culture Colony count 19090-0 Colony count NCnc Pt Urine Qn Page 2 of 7 Urine Microbiology Report Antimicrobial Susceptibility The LOINC terms listed below are an extract from a large selection of antimicrobial substances available. All are methodless and have the scale property of OrdQn. The OrdQn scale property allows results to be reported as as resistant, intermediate, susceptible or as the mm diameter of the inhibition zone/ MIC numeric value. In addition to the methodless LOINC terms there are versions with the following methods: Agar diffusion, MIC, MLC (Minimum lethal concentration), SBT (Serum bactericidal titre)and Gradient strip (E-Test or gradient strip) Antibacterials Amikacin 18860-7 Amikacin Susc Pt Isolate OrdQn Amoxycillin 18861-5 Amoxicillin Susc Pt Isolate OrdQn Ampicillin 18864-9 Ampicillin Susc Pt Isolate OrdQn Augmentin 18862-3 Amoxicillin+Clavulanate Susc Pt Isolate OrdQn Azithromycin 18866-4 Azithromycin Susc Pt Isolate OrdQn Aztreonam 18868-0 Aztreonam Susc Pt Isolate OrdQn Cefepime 18879-7 Cefepime Susc Pt Isolate OrdQn Cefotaxime 18886-2 Cefotaxime Susc Pt Isolate OrdQn Cefpirome 18889-6 Cefpirome Susc Pt Isolate OrdQn Ceftazidime 18893-8 Ceftazidime Susc Pt Isolate OrdQn Ceftriaxone 18895-3 Ceftriaxone Susc Pt Isolate OrdQn Cephalexin 18897-9 Cephalexin Susc Pt Isolate OrdQn Cephalothin 18900-1 Cephalothin Susc Pt Isolate OrdQn Cephazolin 18878-9 Cefazolin Susc Pt Isolate OrdQn Chloramphenicol 18903-5 Chloramphenicol Susc Pt Isolate OrdQn Ciprofloxacin 18906-8 Ciprofloxacin Susc Pt Isolate OrdQn Clarithromycin 18907-6 Clarithromycin Susc Pt Isolate OrdQn Daptomycin 35789-7 Daptomycin Susc Pt Isolate OrdQn Doripenem 60535-2 Doripenem Susc Pt Isolate OrdQn Ertapenem 35802-8 Ertapenem Susc Pt Isolate OrdQn Erythromycin 18919-1 Erythromycin Susc Pt Isolate OrdQn Flucloxacillin/ 18923-3 Floxacillin Susc Pt Isolate OrdQn Flucloxacillin/Dicloxacillin 18916-7 Dicloxacillin Susc Pt Isolate OrdQn Fosfomycin 25596-8 Fosfomycin Susc Pt Isolate OrdQn Fusidic acid 18927-4 Fusidate Susc Pt Isolate OrdQn Gentamicin 18928-2 Gentamicin Susc Pt Isolate OrdQn Gentamicin (high level) 18929-0 Gentamicin.high potency Susc Pt Isolate OrdQn Linezolid 29258-1 Linezolid Susc Pt Isolate OrdQn lmipenem 18932-4 Imipenem Susc Pt Isolate OrdQn Meropenem 18943-1 Meropenem Susc Pt Isolate OrdQn Methicillin 18945-6 Methicillin Susc Pt Isolate OrdQn Metronidazole 18946-4 Metronidazole Susc Pt Isolate OrdQn Page 3 of 7 Urine Microbiology Report Moxifloxacin 31039-1 Moxifloxacin Susc Pt Isolate OrdQn Mupirocin 20389-3 Mupirocin Susc Pt Isolate OrdQn Nitrofurantoin 18955-5 Nitrofurantoin Susc Pt Isolate OrdQn Norfloxacin 18956-3 Norfloxacin Susc Pt Isolate OrdQn Penicillin 18964-7 Penicillin Susc Pt Isolate OrdQn Piperacillin 18969-6 Piperacillin Susc Pt Isolate OrdQn Polymyxin B (Colistin) 18972-0 Polymyxin B Susc Pt Isolate OrdQn Quinupristin/Dalfopristin (Synercid) 23640-6 Quinupristin+Dalfopristin Susc Pt Isolate OrdQn Rifampicin 18974-6 Rifampin Susc Pt Isolate OrdQn Streptomycin (high level) 18983-7 Streptomycin.high potency Susc Pt Isolate OrdQn Tazocin 18970-4 Piperacillin+Tazobactam Susc Pt Isolate OrdQn Teicoplanin 18989-4 Teicoplanin Susc Pt Isolate OrdQn Tetracycline 18993-6 Tetracycline Susc Pt Isolate OrdQn Tigecycline 42357-4 Tigecycline Susc Pt Isolate OrdQn Timentin 18995-1 Ticarcillin+Clavulanate Susc Pt Isolate OrdQn Tobramycin 18996-9 Tobramycin Susc Pt Isolate OrdQn Trimethoprim 18997-7 Trimethoprim Susc Pt Isolate OrdQn Vancomycin 19000-9 Vancomycin Susc Pt Isolate OrdQn Amphotericin B 18863-1 Amphotericin B Susc Pt Isolate OrdQn 5 Flucytosine 18855-7 5-Fluorocytosine Susc Pt Isolate OrdQn Fluconazole 18924-1 Fluconazole Susc Pt Isolate OrdQn Itraconazole 32603-3 Itraconazole Susc Pt Isolate OrdQn ESBL 6984-9 Beta lactamase.extended spectrum Susc Pt Isolate OrdQn Metallo Beta lactamase XXXXX-X Other 54217-5 Public health notifiable condition Prid Pt XXX Nom 11323-3 General health Find Pt ^Patient Nom Reported Page 4 of 7 Salmonella Infection Report LOINC Component Property Timing System Scale Method Long Name Request Information Clinical information 55752-0 Clinical information Find Pt ^Patient Nar Clinical information Specimen Information Laboratory Accession number 57723-9 Unique bar code number ID Pt Current sample Nom