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APUTS) Reporting Terminology and Codes Microbiology (V1.0 AUSTRALIAN PATHOLOGY UNITS AND TERMINOLOGY (APUTS) Reporting Terminology and Codes Microbiology (v1.0) 1 12/02/2013 APUTS Report Information Model - Urine Microbiology Page 1 of 1 Specimen Type Specimen Macro Time Glucose Bilirubin Ketones Specific Gravity pH Chemistry Protein Urobilinogen Nitrites Haemoglobin Leucocyte Esterases White blood cell count Red blood cells Cells Epithelial cells Bacteria Microscopy Parasites Microorganisms Yeasts Casts Crystals Other elements Antibacterial Activity No growth Mixed growth Urine MCS No significant growth Klebsiella sp. Bacteria ESBL Klebsiella pneumoniae Identification Virus Fungi Growth of >10^8 org/L 10^7 to 10^8 organism/L of mixed Range or number Colony Count growth of 3 organisms 19090-0 Culture Organism 1 630-4 LOINC >10^8 organisms/L LOINC Significant growth e.g. Ampicillin 18864-9 LOINC Antibiotics Susceptibility Method Released/suppressed None Organism 2 Organism 3 Organism 4 None Consistent with UTI Probable contamination Growth unlikely to be significant Comment Please submit a repeat specimen for testing if clinically indicated Catheter comments Sterile pyuria Notification to infection control and public health departments PUTS Urine Microbiology Information Model v1.mmap - 12/02/2013 - Mindjet 12/02/2013 APUTS Report Terminology and Codes - Microbiology - Urine Page 1 of 3 RCPA Pathology Units and Terminology Standardisation Project - Terminology for Reporting Pathology: Microbiology : Urine Microbiology Report v1 LOINC LOINC LOINC LOINC LOINC LOINC LOINC Urine Microbiology Report 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 Yeast 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 Page 1 of 3 12/02/2013 APUTS Report Terminology and Codes - Microbiology - Urine Page 2 of 3 RCPA Pathology Units and Terminology Standardisation Project - Terminology for Reporting Pathology: Microbiology : Urine Microbiology Report v1 LOINC LOINC LOINC LOINC LOINC LOINC LOINC Urine Microbiology Report Component Property Timing System Scale Method 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 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 allow 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 Page 2 of 3 12/02/2013 APUTS Report Terminology and Codes - Microbiology - Urine Page 3 of 3 RCPA Pathology Units and Terminology Standardisation Project - Terminology for Reporting Pathology: Microbiology : Urine Microbiology Report v1 LOINC LOINC LOINC LOINC LOINC LOINC LOINC Urine Microbiology Report Component Property Timing System Scale Method Meropenem 18943-1 Meropenem Susc Pt Isolate OrdQn Methicillin 18945-6 Methicillin Susc Pt Isolate OrdQn Metronidazole 18946-4 Metronidazole Susc Pt Isolate OrdQn 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 Antifungals Amphotericin B 18863-1 Amphotericin B Susc Pt Isolate OrdQn 15 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 Others ESBL 6984-9 Beta lactamase.extended spectrum Susc Pt Isolate OrdQn Metallo Beta lactamase No LOINC Notifying Infection / Public Health departments 54217-5 Public health notifiable condition Prid Pt XXX Nom 11323-3 General health Find Pt ^Patient Nom Reported Page 3 of 3 12/02/2013 APUTS Report Terminology and Codes - Microbiology - Serology and Molecular Page 1 of 6 RCPA Pathology Units and Terminology Standardisation Project - Terminology for Reporting Pathology: Microbiology Serology and Molecular v1 Preferred term Synonym Usage guidance Specimen PUTS Unit LOINC term LOINC Component LOINC Property LOINC Timing LOINC System LOINC Scale LOINC Method Alphavirus group Any No Unit 51663-3 Alphavirus RNA ACnc Pt XXX Ord Probe.amp.tar Bacillus anthracis DNA Any No Unit 41623-0 Bacillus anthracis DNA ACnc Pt XXX Ord Probe.amp.tar Bacterial 16S rRNA Any No Unit 66885-5 Bacterial 16S rRNA sequencing Prid Pt XXX Nom Barmah Forest virus IgG Ab Blood/Serum No Unit 31247-0 Barmah forest virus Ab.IgG ACnc Pt Ser Ord Barmah Forest virus IgM Ab Blood/Serum No Unit 31248-8 Barmah forest virus Ab.IgM ACnc Pt Ser Ord Bartonella henselae DNA Any No Unit 33986-1 Bartonella henselae DNA ACnc Pt XXX Ord Probe.amp.tar Bartonella quintana DNA Any No Unit 57910-2 Bartonella quintana DNA ACnc Pt XXX Ord Probe.amp.tar BK virus DNA For qualitative reporting Any No Unit 47251-4 BK virus DNA ACnc Pt XXX Ord
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