Victorian Infectious Diseases Reference Laboratory

Test Handbook Third Edition 2004

Address for Specimens & Deliveries: VIDRL Jane Bell House 10 Wreckyn St North Melbourne Victoria, 3051 Australia. Postal Address: Victorian Infectious Diseases Reference Laboratory (VIDRL) Private Bag 815 Carlton South Victoria, 3053 Australia A receptacle for specimen deliveries after hours is available at this address. VIDRL Contact numbers:

Area Codes: within Australia (03) International (613) General Enquiries (24 hours) Phone 9342 2600 Fax 9342 2660 9342 2666 Pathologist on call (Australia only) Phone 0438 599 437 Laboratories: Phone Biochemistry 9342 2640 Electron Microscopy 9342 2678 Haematology 9342 2642 HIV Characterisation 9342 2623 Infectious Diseases Serology 9342 2647 Microbiology 9342 2668 Molecular Microbiology 9342 2615 Mycobacterium Reference 9342 2674 National Polio Reference 9342 2607 Specimen Reception 9342 2644 Virus Identification 9342 2628 Internet: VIDRL Website http://www.vidrl.org.au

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VIDRL Hours of Operation: 0800 - 2000 Monday to Friday 1000 - 1200 Saturday (urgent specimens only)

An on-call service is provided at other times and a pathologist is available for emergency after hours consultations (including information on the availability of the National High Security Quarantine Laboratory). For both these services call 0438 599 437 or 0438 599 439.

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1. Patient and Specimen Identification The following information should be included with test requests: Patient Information Surname and given name(s) (or name code) Gender Date of birth Address Clinical Details Presenting signs and symptoms Date of onset of illness Any recent travel history Recent immunisation history Specimen Information Type of specimen Date of specimen Tests Requested VIDRL requires that each specimen and its accompanying request card are labelled with at least two identifiers which together are capable of distinguishing one individual from another. Some requests may be coded to protect patient confidentiality. A four-letter code consisting of the first two initials of the surname and given name is the accepted convention. The full name (or name code) and date of birth should be written on both the specimen and the request card. Failure to comply with this procedure may delay specimen processing and reporting. 2. Specimens for Virus Detection Some knowledge of the pathogenesis of the suspected viral infection is necessary for optimal choice of specimens. For example: the duration and site of viral shedding, or the presence and timing of viraemia. When possible, specimens for virus detection should be obtained from the suspected site of infection (for example, CSF in enteroviral meningitis, vesicular material in herpes simplex infection). Viruses are often shed via the respiratory or gastrointestinal tracts, and occasionally in urine, all of which are readily accessible. When specimens are difficult to obtain from the affected organ system, these peripheral sites of viral shedding may provide the only source of specimens for virus detection. For instance, enteroviruses potentially may be detected in both faeces and respiratory secretions in a case of meningitis should CSF not be available. Demonstration of peripheral shedding only provides indirect evidence of end organ involvement however. Polymerase Chain Reaction (PCR) is the method of choice at VIDRL for detection of most viruses. PCR provides high levels of sensitivity, and the ability to detect viral

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nucleic acid irrespective of viral particle viability. However specimen quality still has a profound effect on rates of detection. Swabs should be rubbed firmly on the affected site, generally a lesion base or mucosal surface, to dislodge infected cells and to soak them thoroughly in potentially infected secretions. Vesicular lesions will require careful “de-roofing” with a small gauge needle or scalpel blade to provide access to virus-rich vesicular fluid, and the lesion base. By the time vesicular lesions crust quantities of virus are minimal and sampling is not generally recommended. Sampling of several lesions and pooling swabs or vesicle fluid may improve detection rates. Detection rates from the respiratory tract can potentially be improved by pooling a throat swab and a swab from one or both nostrils. Swabs should be broken off into viral transport medium and transported to the laboratory as rapidly as possible. For detection of viraemias anticoagulated blood is the preferred specimen. This allows either plasma or the cellular fraction to be tested depending on which is the most appropriate. Acid Citrate Dextrose (ACD) or EDTA are the preferred anticoagulants. Heparin should never be used as it potentially inhibits PCR assays. Body fluids such as CSF or urine are best transported undiluted in a sterile leak-proof container. Tissue samples should be transported unfixed in a sterile leak-proof container. A pea-sized sample of tissue is generally ample. Addition of a small volume of sterile saline to very small specimens may alleviate the risk of drying in transport. In general, specimens should be kept cool (4°C - 8°C) when being transported. The exception is blood for detection or quantitation of HIV nucleic acids, which should be sent at room temperature. 3. Specimens for Infectious Diseases Serology. Serum is the specimen of choice for serological testing. A minimum of 10 ml of blood should be collected into a plain tube (no anti-coagulant) and transported to the laboratory at 2-8°C as soon as possible. Unseparated blood may be stored at 2-8°C for up to 24 hrs if immediate transport cannot be arranged. Lysed blood will produce a less satisfactory serum for testing. If longer delays in transporting are anticipated, the serum should be separated into a suitable screw-cap vial and stored at 2-8°C. Plasma can also be used for serological testing and should be transported to the laboratory at 2-8°C within 24 hrs of collection. If long transport delays are anticipated, separate the plasma from the red cells to avoid haemolysis. The usefulness of serological results for diagnosis is highly dependent on the timing of the specimens submitted. The appearance of measurable antibody responses may vary between pathogens and between tests and some knowledge of those factors is necessary to optimally time serum collection. For example specific IgM to hepatitis A virus is usually present at symptom onset while measles IgM usually appears

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between 3-7 days after rash. When attempting to demonstrate a rising titre of total or IgG antibody it is important to obtain an acute serum specimen early in the course of an illness and an appropriately timed convalescent serum. Two weeks after symptom onset is a general rule of thumb for timing of convalescent bleed collection, but timing of IgG appearance varies. For example C. psittaci complement fixing antibody may take over 3 weeks to appear, while measles IgG may generally be detected by enzyme immunoassay from 1 week after rash. 4. Specimens for Haematology All blood samples should be securely capped, then mixed by gentle inversion. Blood tubes should be stored at 4oC. If no refrigerator is available, keep the samples in a cool place. Please ensure that the samples are not exposed to direct sunlight. 5. Bacteriology Parasitology Specimen jars are now supplied in kit form (Para-Pak) for the transport of faecal samples for both culture and parasite preservation. Directions to patients are included with each kit. For parasite studies, two specimens should be sent, each collected two days apart to exploit the intermittent excretion of some parasites. Transport at room temperature in SAF preservative supplied Notes: Some substances may depress numbers of eggs or destroy protozoan parasites - eg. urine, kaolin, magnesia, bismuth, barium, antibiotics, anti-protozoan or anti-helminthic agents. Faecal Specimens for Vibrio If infection with Vibrio species is suspected (eg Cholera or enteric infections following consumption of seafood), please send a fresh faecal specimen in a preservative-free container, in addition to any samples submitted in preservative. Legionella Legionella from respiratory specimens. Suitable specimens include expectorated sputum, induced sputum, nasopharyngeal aspirate, endobronchial secretions, pleural fluid, lung biopsy or post-mortem tissue. Legionella antigen detection. Legionella pneumophila serogroup 1 can be diagnosed by detection of antigen in urine. Transport at room temperature. Transport medium is not required. 6. Mycobacterium Reference Laboratory

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MRL Specimen Collection Data It is essential that the following information be supplied for all Mycobacteriology requests, as the MRL data provides part of Victoria’s TB and Mycobacteria surveillance data. The standard MRL request form is preferred. In addition to the usual information required (see section 1) the following information is requested where possible: • A succinct summary of the patient's history and findings. This may be important

for the assessment of significance of non-tuberculous mycobacterial isolates. • Laboratories referring mycobacterial isolates should also note their smear result

(on ZN or AR staining) on the request slip. • Further patient information on prior disease, contacts and treatment, country of

birth or extended residence, immunosuppression and other details will be sought on new positive TB and Leprosy cases.

Blood Cultures for Mycobacteria These specimens are especially useful for recovery of Mycobacterium avium complex. Special mycobacteria blood culture bottles (Bactec Myco/F lytic) are available from VIDRL. Specimens for PCR and related tests to detect Mycobacteria General Notes: The cell wall of Mycobacteria is resistant to chemical attack, and current DNA and RNA extraction methods for Mycobacteria are less efficient than for other organisms. False-negative results occur in specimens with low numbers of Mycobacteria present. Culture is still the most sensitive method for detection of viable MTB at the time of writing. In addition culture provides an isolate for further study, namely antimycobacterial drug susceptibility testing, or RFLP fingerprinting for epidemiological purposes. A number of biological substances, including blood and faecal material, may interfere with the assays leading to false negative results. PCR may detect DNA from non-viable organisms, and is not suitable for monitoring of therapy at this stage. For CSF examination by PCR for the presence of MTB, we recommend that at least 1 mL of un-centrifuged CSF be submitted to achieve adequate assay sensitivity. Please note that PCR type assays for the diagnosis of tuberculosis are not yet included on the Australian Medicare Benefits schedule, and a charge for the test will be made in most cases.

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The Mycobacterium genus PCR, which can identify Mycobacteria to species complex level is not intended as a routine diagnostic test, and will only be performed if specifically requested and adequate clinical notes are provided. Requests for “Mycobacterial PCR” that do not provide adequate information will initially be tested using the TB PCR. Requests for the Mycobacterium genus PCR on fixed tissues (unsuitable for culture) will only be performed if AFB have been seen in the specimen, or there is other clinical or pathological evidence supporting a mycobacterial infection. From paraffin embedded fixed tissue specimens, we require at least 6 sections, each 10-20 µm thick. We strongly recommend discussing the case with VIDRL before submitting such specimens. Specimen Types for Mycobacterial Culture Gastric Lavage. This is appropriate when the patient cannot produce expectorated sputum. These specimens must be neutralised to pH 7 within four hours of collection to ensure the viability of any mycobacteria present. Laryngeal Swab. These are taken as an alternative to the examination of gastric juice from patients who cough but can produce no sputum. Serous Fluids. These include inter-alia, cerebrospinal, pleural, pericardial, ascitic and joint fluids. Note that tissues from these sites are often superior to fluids in terms of recovery of mycobacteria. Skin and Wound Swabs. Skin biopsies (obtained by excision or punch biopsies) should be collected in sterile screw capped containers. In the case of wounds it is advisable to send an aspirate of the exudate in preference to a swab. Sputum. Three single, early morning samples of expectorated sputa collected on different days are appropriate. A volume of 5-10 ml is adequate for each sample. Once a diagnosis of tuberculosis has been established, specimens need to be sent only every two to three months. (See section below on specimens for monitoring of treatment). Urine. Three single mid-stream specimens voided in the early morning should be submitted. If delay is unavoidable, specimens should be refrigerated. Note that microscopy is not routinely performed on urine specimens submitted for examination for mycobacteria, due to the presence of commensal mycobacteria. Tissue. Any tissue to be processed must be collected aseptically and transported to the laboratory at once. If delay occurs, specimens should be transported to the laboratory in a small volume of saline and kept at 4° C (not frozen). Specimens in formal saline are not suitable for mycobacterial investigation by culture.

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MRL recommendations for specimen collection for the monitoring of anti-tuberculous chemotherapy. For further information, please visit the VIDRL website (http://www.vidrl.org.au) under the MRL section. Examinations for Leprosy (Hansen's Disease) For further information on specimen collection and result interpretation, please visit the VIDRL website (http://www.vidrl.org.au). QuantiFERON ® -TB Gold assay notes The QuantiFERON ® -TB Gold assay detects CMI responses in-vitro to tuberculosis infection by measuring interferon-gamma (IFN- γ) harvested in plasma from whole blood incubated with the M. tuberculosis-specific antigens, ESAT-6 & CFP-10. An IFN- γ response to either ESAT-6 or CFP-10 above the test cut-off is considered indicative of M. tuberculosis infection This test should be considered as an alternative to the Mantoux test, but has the advantages that it can be used to detect latent TB infection in patients who have been vaccinated with BCG and therefore have a positive Mantoux test. It can also be used when a Mantoux test is contraindicated. Please note this test is primarily intended to detect latent infection with M. tuberculosis, and not for the diagnosis and management of active tuberculosis. Should active TB be suspected, culture (and/or PCR testing) of appropriate clinical specimens is still necessary for a definitive diagnosis. This assay will not detect infection with M. bovis BCG strains used for vaccination or immunotherapy. For further information on this test and its interpretation, please visit the VIDRL website (http://vidrl.org.au) under the MRL section. 7. Collection and Transport of Specimens from a Patient with

Suspected Risk Group 4 Virus Infection. When a patient with suspected quarantinable viral haemorrhagic fever (VHF) (associated with Ebola, Marburg, Lassa, Rift Valley Fever or Crimean Congo virus infection) is suspected, direct contact with the pathologist on-call at VIDRL is essential to arrange receipt of specimens and for advice regarding specimen collection, packaging and transport to the laboratory. Specimens most useful for detection of the above viruses include venous blood (clotted and unclotted (EDTA), urine and a combined nose/throat swab. Collection of specimens should be undertaken with extreme care and using personal protective equipment including gloves, gown, mask and eye protection. Glass

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containers should not be used. Disposable sharp objects such as scalpel blades should not be handled unnecessarily after use and should be autoclaved or incinerated. Needles used to collect blood should not be recapped, bent, broken, removed from disposable syringes or otherwise handled. Blood-taking equipment should be placed in a rigid plastic container filled with disinfectant solution and autoclaved or incinerated. Prior to transport, the outside of each specimen container should be swabbed with disinfectant (sodium hypochlorite, 5000 ppm available chlorine is recommended) and a label should be attached bearing the patient's name, hospital identification, the date of collection and the nature of the suspected infection. Specimens should be double-bagged in secure, airtight and watertight bags which have been similarly labelled. Bags containing specimens should be swabbed with disinfectant before they are removed from the patient's room. Specimens thought to contain Risk Group 4 viruses, or isolates of these viruses, must be transported under highly regulated conditions, irrespective of whether the shipment is by air, road, rail or sea. In general, the International Air Transportation Association (IATA) Dangerous Goods Regulations are the most comprehensive and cover the requirements of other non-airline organizations. Senders should be aware of their obligation to satisfy current shipping requirements when they first make contact with the Pathologist on-call or other senior staff regarding the transport of possible Risk Group 4 viruses to VIDRL. Senders should notify VIDRL of shipping details when they become available. These include the airline, flight departure and arrival times, air waybill number and contact details of the courier assigned the job of transporting the package between airports. The packaging required for transport to and from VIDRL of Risk Group 4 viruses is stringent, and must comply with NZ/CAA 38281-1. Such packaging is available commercially (eg. LabPak-1, LabServ). A diagnostic specimen or virus isolate reasonably expected to fall within the category of a Risk Group 4 pathogen must be identified as UN No. 2814 (infectious substance affecting humans) and should comply with Packaging Instruction No. 602. The maximum allowable shipment quantity under these regulations is 50 ml (passenger aircraft) or 4 litres (cargo plane). A completed Shipper’s Declaration for Dangerous Goods form should be attached to the outside of all packages shipped to VIDRL. In most instances, biological material contained in packages shipped to VIDRL will be transported cold or in the frozen state. This requires the use of freezer bricks or dry ice, respectively, held within an outer polystyrene container. Regulations applying to the use of these substances should be followed and couriers should be made aware of their presence and of the need to keep the package cool during transport.

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Test List Test Activated Partial Thromboplastin Time

(APTT) Specimen Required Blood (sodium citrate 3.8%) When Tested Daily Normal Ranges Manual: 30-45 sec

Automated: 20-35 sec Therapeutic Range: Manual 50-100 sec Automated: 40-75 sec

Contact 9342 2644 Test Adenovirus PCR Specimen Required Eye swab, respiratory specimens, faeces,

urine, biopsy When Tested M,W,F See also: Respiratory Virus PCR Notes Eye swabs are best tested in this PCR.

Respiratory specimens are tested in the Respiratory virus PCR.

Contact 9342 2628 Test Adenovirus Serology Assay IgG Specimen Required: Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650 Test Alanine aminotransferase (ALT) Specimen Required Serum (clotted blood) When Tested Daily See also: Liver Function Tests Reference Ranges <50 Units U/L Contact 9342 2640 Test Albumin Specimen Required Serum (clotted blood) When Tested Daily See also: Liver Function Tests References Ranges 35-52 Units gm/L Contact 9342 2640

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Test Alkaline phosphatase (ALP) Specimen Required Serum (clotted blood) When Tested Daily See also: Liver Function Tests Reference Ranges Male 0-2y: 25-95

2-24y: 25-250 >24y: 25-95 Female 0-2y: 25-95 2-19y: 25-250 >19y: 25-95

Units U/L Contact 9342 2640 Test Amylase (Total & Pancreatic) Specimen Required Serum (clotted blood) When Tested Daily Reference Ranges Total: 30-125

Pancreatic: 5-90 Units U/L Contact 9342 2640 Test Anti-gastric parietal cell antibodies Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2644 Test Anti-mitochondrial antibodies Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2644 Test Anti-nuclear (ANA) antibodies Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2644 Test Anti-smooth muscle antibodies Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2644 Test Aspartate aminotransferase (AST) Specimen Required Serum (clotted blood) When Tested Daily See also: Liver Function Tests Reference Ranges <40 Units U/L Contact 9342 2640

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Test Astrovirus by Electron Microscopy Specimen Required Faeces (not frozen) Contact 9342 2678 Test Australian encephalitis virus PCR (see

Flavivirus PCR for MVE) Test Australian encephalitis Serology (see

Murray Valley encephalitis virus Serology) Test Barmah Forest virus Serology (BFV) Assay or Procedure IgG

IgM Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650 Test Bicarbonate (Total CO2) Specimen Required Serum (clotted blood) or heparinised blood When Tested Daily See also: U&E Reference Ranges 24.0 – 31.0 Units mmol/L Contact 9342 2640 Test Billirubin (Total) Specimen Required Serum (clotted blood) When Tested Daily See also: Liver Function Tests Total Ranges <17.0 Units mmol/L Contact 9342 2640 Test BK virus PCR (See Polyomavirus PCR)

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Test Blood Culture (Bacterial) Specimen Required 8-10 ml/’Bactec plus’ aerobic & anaerobic

bottles When Tested Daily Notes Please provide clinical details. Extended

incubation is required for query endocarditis, brucellosis or fungal infection.

Contact 9342 2670 Test Blood Culture (Mycobacterial)

(see Mycobacterial blood culture) Test Blood film (without FBE) Specimen Required Blood (EDTA) When Tested Daily Contact 9342 2644 Test Blood group (ABO, RhD) Specimen Required Blood (EDTA) When Tested Daily Contact 9342 2644 Test Blood group screen and hold Specimen Required Serum (clotted blood)

Blood (EDTA) When Tested Daily Contact 9342 2644 Test Bordetella pertussis Culture Specimen Required Nasopharyngeal swab or aspirate.

(Transport medium available for swabs) When Tested On request Contact 9342 2670 Test Bordetella pertussis PCR Specimen Required Any respiratory sample When Tested On request Contact 9342 2628 Test Brucella Culture Specimen Required 8-10 ml blood in blood culture bottle Notes Contact Laboratory before sending Contact 9342 2670

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Test Brucella spp Serology Assay Rose Bengal (RB) agglutination (total)

Standard agglutination Test (SAT) Anti-human globulin (Coombs) (IgG)

Specimen Required Serum (clotted blood) When Tested Weekly Notes A negative RB test generally excludes a

diagnosis of Brucellosis. The SAT detects IgM and complete IgG in acute disease. The Coombs test detects ‘incomplete’ IgG in chronic disease.

Contact 9342 2649/9342 2650 Test Calcium Specimen Required Serum (clotted blood) When Tested Daily Reference Ranges Serum: 2.00 – 2.63 Units mmol/L Contact 9342 2640 Test Calicivirus by Electron Microscopy (see

Norovirus) Test Campylobacter jejuni Serology Assay IgA, IgG and IgM Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650 Test Carbamazepine Specimen Required Serum (clotted blood) When Tested On request Reference Ranges 17 – 42 Units µmol/L Contact 9342 2640 Notes The reference range applies to a trough

specimen collected just prior to the morning dose. Serum peak level is reached 6-12 hours after oral dose administration.

Test Cardiac Enzymes:

(creatine kinase (CK), CK-MB subunit, lactate dehydrogenase (LD))

Specimen Required Serum (clotted blood) When Tested On request See also: Individual tests Reference Ranges CK: 15 – 140

CK-MB: <10 LD: 185 – 505

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Units U/L Contact 9342 2640 Test Chlamydia Group Antigen Assay or Procedure IgG Specimen Required Serum (clotted blood) When Tested Daily Notes Primary screening test for chlamydia Contact 9342 2628 Test Chlamydia pneumoniae PCR Specimen Required Any respiratory sample – data eg. sputum When Tested On request Contact 9342 2628 Test Chlamydia pneumoniae Serology Assay or Procedure IgG Specimen Required Serum (clotted blood) When Tested x2-3 weekly Notes Only performed on samples positive by the

Group Antigen screening test. Contact 9342 2628 Test Chlamydia psittaci PCR Specimen Required Any respiratory sample – data eg. sputum When Tested On request Contact 9342 2628 Test Chlamydia psittaci Serology Assay or Procedure IgG Specimen Required Serum (clotted blood) When Tested x2 or x3 weekly Notes Only performed on samples positive by the

Group Antigen screening test. Contact 9342 2649/9342 2650 Test Chlamydia trachomatis PCR Specimen Required Urine, endocervical, urethral, pharyngeal,

eye or rectal swabs. When Tested Daily Notes Use swabs collected in Amies/charcoal

transport medium. Transport at room temperature.

Contact 9342 2670 Test Chlamydia trachomatis Serology Assay or Procedure IgG & IgA Specimen Required Serum (clotted blood) When Tested x2 Weekly Contact 9342 2649/9342 2650

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Test Chloride Specimen Required Serum (clotted blood) or blood

heparinised) When Tested Daily Reference Ranges 101 – 111 mmol/L Contact 9342 2640 Test Cholesterol Specimen Required Serum (clotted blood) When Tested Daily See also: Lipids Normal Ranges <5.5 Units mmol/L Contact 9342 2640 Notes For accurate lipid determinations, the

patient should fast for 12 hours prior to specimen collection.

Test Clostridium difficile cytotoxin Assay Cell culture neutralisation assay Specimen Required Faeces (no preservative) When Tested On request Contact 9342 2670 Test CMV testing (see under Cytomegalovirus

for all procedures) Test Coagulation profile Specimen Required Blood, (sodium citrate, 3.8%) When Tested Daily See also: APTT and PTT Contact 9342 2644 Test Cold agglutinins Specimen Required Serum (clotted blood) When Tested Daily Normal Ranges <20 Contact 9342 2640 Test Coombs (direct antiglobulin) test Specimen Required Blood (EDTA) When Tested Daily Contact 9342 2644

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Test Coronavirus PCR Specimen Required Any respiratory specimen. Sputum. When Tested On request Notes Tests available for common cold associated

coronaviruses OC43 and 229E and the SARS-related coronavirus. Ring laboratory before requesting SARS PCR.

Contact 9342 2628 Test Coxsackie virus PCR (see Enterovirus PCR) Test Creatinine Specimen Required Serum (clotted blood) or blood

(heparinised) When Tested Daily See also: U & E Reference Ranges 0.02 – 0.12 Units mmol/L Contact 9342 2640 Test Creatine Kinase (CK) Specimen Required Serum (clotted blood) When Tested Daily See also: Cardiac enzymes Reference Ranges 15 – 140 Units U/L Contact 9342 2640 Test Creatinine Kinase – MB subunit Specimen Required Serum (clotted blood) When Tested Request See also: Cardiac enzymes Reference Ranges <10 Units U/L Contact 9342 2640 Test Crimean-Congo haemorrhagic fever virus

PCR Specimen Required Blood (ACD or EDTA), respiratory swabs When Tested On request Notes This is a PC4 level pathogen. Requests for

testing must be discussed with the laboratory in advance.

Contact 9342 2628

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Test Crimean-Congo haemorrhagic fever virus

Serology Specimen Required Serum (clotted blood) When Tested On request Notes This is a PC4 level pathogen. Requests for

testing must be discussed with the laboratory in advance.

Contact 9342 2628 Test Cryptosporidium detection Specimen Required Faeces When Tested Daily Contact 9342 2670 Test Cryptococcal antigen detection Specimen Required CSF, Serum (clotted blood) When Tested On request Contact 9342 2670 Test Cysticercosis (Taenia solium) Serology Assay IgG Specimen Required Serum (clotted blood) When Tested On request Contact 9342 2649/9342 2650 Test Cytomegalovirus (CMV) Genotyping for

drug resistance Specimen Required Blood (ACD or EDTA) When Tested On request Notes UL54 (pol) and UL97 (TK) sequenced Contact 9342 2628 Test Cytomegalovirus (CMV) PCR Specimen Required Saliva, CSF, urine, blood (ACD or EDTA),

BAL, faeces, tissue When Tested Daily Notes Qualitative assay, part of herpesvirus

multiplex PCR assay Contact 9342 2628 Test Cytomegalovirus (CMV) Quantitation Specimen Required Blood (ACD or EDTA as anticoagulant) When Tested On request When Tested Testing only performed on plasma/serum

positive by cytomegalovirus PCR (above) Contact 9342 2628

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Test Cytomegalovirus (CMV) Serology Assay or Procedure IgG and IgM

IgG Avidity Index Latex agglutination (total antibodies)

Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650 Test Dengue virus PCR (see Flavivirus PCR) Test Dengue virus Serology (see Flavivirus

Serology) Test Differential Leucocyte Count (adult) Normal Range Neutrophilis 2.0 – 7.5 x 109/L

Lymphocytes 1.5 – 4.0 x 109/L Monocytes 0.2 – 0.8 x 109/L Eosinophilis 0.04 – 0.4 x 109/L Basophilis 0.01 – 0.1 x 109/L

Specimen Required Blood (EDTA) When Tested Daily See also: FBE Contact 9342 2644 Test Digoxin Specimen Required Serum (clotted blood) When Tested Request Normal Ranges 1.0 – 2.8 Units nmol/L Notes Preferred sampling time is at the end of a

24 hr dosing interval. Contact 9342 2640 Test Ebola virus PCR Specimen Required Blood (ACD or EDTA), respiratory swab When Tested On request Notes This is a PC4 level pathogen. Requests for

PCR must be discussed with the laboratory in advance.

Contact 9342 2628 Test Echinococcus granulosis (hydatid) Serology Assay Total antibodies (IHA) Specimen Required Serum (clotted blood) When Tested x2 weekly See also: Hydatid Contact 9342 2649/9342 2650

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Test Echovirus PCR (see Enterovirus PCR) Test Entamoeba histolytica Serology Assay or Procedure Total antibodies (IHA)

EIA IgG - confirmation only Specimen Required Serum (clotted blood) When Tested x2 weekly Contact 9342 2649/9342 2650 Test Enterovirus PCR Specimen Required CSF, NTS, swab, faeces, blood

(ACD or EDTA) When Tested Daily Notes Detects enterovirus, coxsackie virus and

poliovirus genera. Contact 9342 2628 Test Epstein-Barr virus PCR Specimen Required CSF, blood, saliva, respiratory swabs When Tested On request Contact 9342 2628 Test Epstein-Barr virus Serology (EBV) Assay early antigen IgG, (IF)

early antigen IgM, (IF) nuclear antigen IgG (EBNA) viral capsid antigen IgG (VCA) viral capsid antigen IgM (VCA)

Specimen Required Serum (clotted blood) When Tested x2 weekly (Immunofluorescence testing on

request) Contact 9342 2649/9342 2650 Test Equine morbillivirus (EMV) PCR Specimen Required Respiratory specimens, CSF When Tested On request Contact 9342 2628 Test Equine morbillivirus (EMV) Serology Assay or Procedure EIA for IgG Specimen Required Serum (clotted blood) When Tested On request Contact 9342 2649/9342 2650

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Test Erythrocyte sedimentation rate (ESR) Specimen Required Blood (EDTA) or vacu-tec tube When Tested Daily Normal Ranges Male: <10 mm

Female: 20 mm in first hour Contact 9342 2644 Test Estradiol Specimen Required Serum (clotted blood) When Tested Tue (am)

Fri (am) Reference Ranges Male: <200

Female: foll: <420 Mid-Cy: 300 – 1500 Lut: 200 – 1000 Post m/pausal: <175

Contact 9342 2640 Test Eye, ear, nose or throat Culture Specimen Required Swab. Provide smears for Gram stain of

eye and ear sites. When Tested Daily Notes Use swabs collected in Amies/Charcoal

transport medium. Transport at room temperature.

Contact 9342 2670 Test Faecal Culture and Microscopy (wet prep

only) (FMCS) Specimen Required Faeces C&S supplied by VIDRL When Tested Daily Notes Microscopy of unconcentrated specimen

only. Maximum of 1 specimen tested per 7-day period.

Contact 9342 2670 Test Faecal Microscopy (only) Specimen Required Faeces collected in SAF (supplied by

VIDRL) When Tested Daily Notes Includes microscopy for ova, cysts

trophozoites, cryptosporidia. Contact 9342 2670 Test Faecal occult blood Specimen Required Freshly collected faecal specimen (no

transport medium) When Tested On request Notes Chemical and immunological assays used. Contact 9342 2670

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Test Faecal parasites (see parasite detection

(enteric)) Test FBE (full blood examination) Specimen Required Blood (EDTA) When Tested Daily See also: Leucocyte count, Red Cell count,

Haemoglobin, PCV, MCV, MCH, MCHC Contact 9342 2644 Test Ferritin Specimen Required Serum (clotted blood) When Tested x2 weekly See also: Iron studies Reference Ranges Male: 30 – 284

Female: 10 – 186 Units ng/mL Contact 9342 2640 Test Fertility hormones (estradiol, follicle

stimulating hormone (FSH, Lutenizing hormone, progesterone, prolactin, testosterone) See individual tests.

Test Filariasis (Microfilaria detection in blood) Specimen Required Blood (EDTA) When Tested On request Notes Includes immunochromatography test

(ICT) Contact 9342 2644 Test Flavivirus PCR Specimen Required CSF, serum (clotted blood) When Tested On request Notes This PCR will detect members of the

flavivirus genus including dengue, MVE, West Nile, kunjin, yellow fever and Japanese B viruses. Contact with the laboratory is recommended before requesting this test.

Contact 9342 2628

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Test Flavivirus Serology Assay or Procedures Total antibodies and IgM (IF) Specimen Required Serum (clotted blood) When Tested x2 weekly Notes Procedure detects antibodies to flaviviruses

including Murray Valley encephalitis, dengue and Kunjin viruses. An assay specific for antibodies to Murray Valley encephalitis virus is also available.

Contact 9342 2649/9342 2650 Test Folate: serum and red blood cell Specimen Required Serum (clotted blood) for detection of

serum folate. Blood (EDTA) for detection of red cell associated folate.

When Tested x2 weekly Reference Ranges S: 4.5 – 23.0

RC: >355 Units nmol/L Contact 9342 2640 Test Follicle Stimulating Hormone (FSH) Specimen Required Serum (clotted blood) When Tested x2 weekly Normal Ranges Male: 1 – 19

Female: foll: 4 – 9 Mid-Cy: 5 – 23 Lut: 2 – 5 Post m/pausal: 17 – 114

Units MIU/mL Contact 9342 2640 Test Fungal Microscopy & Culture Specimen Required Skin scrapings, nail clippings When Tested On request Notes Collect skin scrapings from margin of

lesion. 20-30 flakes. Place in sterile urine container.

Contact 9342 2670 Test Fungal Susceptibility Testing Specimen Required Yeast isolates When Tested On request Contact 9342 2670

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Test Gamma-glutamyl transferase (GGT) Specimen Required Serum (clotted blood) When Tested Daily See also: Liver Function Tests Reference Ranges Male: <50

Female: <40 Units U/L Contact 9342 2640 Test G6PD (Glucose 6 Phosphate

Dehydrogenase (Red Cell)) Specimen Required Blood (EDTA) When Tested Daily Normal Ranges <50 min Contact 9342 2644 Test Glucose Specimen Required Blood (NaF) When Tested Daily Reference Ranges Fasting: 3.3 – 6.0

Random: 3.3 – 7.8 Units mmol/L Notes The specimen should be identified as a

fasting or random collection. Contact 9342 2640 Test Glucose Tolerance Test Specimen Required Blood (NaF) When Tested Daily Reference Ranges Fasting: 3.3 – 6.0

One hour: 5.3 – 11.1 2 hour: 3.3 – 7.8

Units mmol/L Notes Fasting protocol available from the

Laboratory Contact 9342 2640 Test Gonorrhoea Culture Specimen Required Endocervical, urethral pharyngeal or rectal

swabs. Provide smears for Gram Stain of urethral or endocervical sites.

When Tested Daily Notes Use swabs collected in Amies/charcoal

transport medium. Transport at room temperature.

Contact 9342 2670

Page 24

Test Gonorrhoea PCR Specimen Required Urine, endocervical, urethral, pharyngeal or

rectal swabs When Tested Daily Notes Transport at room temperature. Culture is

preferred for pharyngeal specimens. Contact 9342 2670 Test Haemoglobin (single estimation) Specimen Required Blood (EDTA) When Tested Daily Normal Ranges Adult Male 130 – 180 g/L

Adult Female 115 – 165 g/L Contact 9342 2644 Test Hantavirus PCR Specimen Required Blood (ACD or EDTA), respiratory

specimens, CSF When Tested On request Notes This PCR will detect members of the

Hantavirus genus including Hantaan and Sin Nombre (4 corners) viruses. Contact with the laboratory is recommended before requesting this test.

Contact 9342 2628 Test Hantavirus Serology Assay P.Aggl Total Ab Specimen Required Serum (clotted blood) When Tested On request Contact 9342 2649/9342 2650 Test HDL Cholesterol Specimen Required Serum (clotted blood) When Tested Daily Reference Ranges Male: 0.7 – 1.9

Female: 0.9 – 2.4 Units mmol/L Notes For accurate lipid level determination, the

patient should fast for 12 hours prior to specimen collection.

Contact 9342 2640 Test Helicobacter pylori Serology Assay or Procedure IgG Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650

Page 25

Test Hendra virus PCR (see Equine morbillivirus (EMV) PCR)

Test Hendra virus Serology (see Equine

morbillivirus (EMV) Serology) Assay or Procedure EIA for IgG Specimen Required Serum (clotted blood) When Tested On request Contact 9342 2649/9342 2650 Test Hepatitis A virus PCR Specimen Required Serum (clotted blood),

Blood (ACD or EDTA) When Tested On request Cut Off (lower limit of detection)

2,000 copies/ml

Notes * Do not send heparinised blood Contact 9342 2615 Test Hepatitis A virus Serology Assay or Procedure Total Ab

IgM Specimen Required Serum (clotted blood) When Tested Total Ab - daily

IgM - x3 weekly Contact 9342 2649/9342 2650 Test Hepatitis B virus DNA Assay or Procedure Hybrid capture Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650 Test Hepatitis B virus PCR Specimen Required Serum (clotted blood)

Blood (ACD or EDTA) When Tested x2 weekly Cut Off (lower limit of detection

1,000 copies/ml

Notes * Do not send heparinised blood Contact 9342 2649/9342 2650 Test Hepatitis B virus Sequencing Specimen Required Serum (clotted blood)

Blood (ACD or EDTA) When Tested On request Notes * Do not send heparinised blood Contact 9342 2615

Page 26

Test Hepatitis B virus Serology Assay or Procedure core antibody total

core antibody IgM e antibody e antigen surface antibody surface antigen

Specimen Required Serum (clotted blood) When Tested x2 or x3 weekly Contact 9342 2649/9342 2650 Test Hepatitis C virus Genotyping Specimen Required Serum (clotted blood)

Blood (ACD or EDTA) When Tested x2 weekly Notes * Do not send heparinised blood Contact 9342 2615 Test Hepatitis C virus PCR Specimen Required Serum (clotted blood)

Blood (ACD or EDTA) When Tested x3 weekly Cut Off (lower limit of detection)

50 1µ/ml

Notes * Do not send heparinised blood Contact 9342 2615 Test Hepatitis C virus Quantitation Specimen Required Serum (clotted blood)

Blood (ACD or EDTA) When Tested 1x fortnight Cut Off (lower limit of detection)

25,000 copies/ml

Normal Ranges <5,000 to 7,000,000 1µ/ml Notes * Do not send heparinised blood Contact 9342 2615 Test Hepatitis C virus Serology Assay or Procedure IgG Specimen Required Serum (clotted blood) When Tested x3 weekly Contact 9342 2649/9342 2650 Test Hepatitis D virus PCR Specimen Required Serum (clotted blood)

Blood (ACD or EDTA) When Tested As requested Cut Off (lower limit of detection)

2,000 copies/ml

Notes Do not send heparinised blood Contact 9342 2615

Page 27

Test Hepatitis D virus Serology Assay or Procedures Antigen

Antibody Serum (clotted blood) Weekly 9342 2649/9342 2650

Specimen Required When Tested Contact

Test Hepatitis E virus PCR Specimen Required

Blood (ACD or EDTA) As requested 2,000 copies/ml

Notes Contact

Serum (clotted blood)

When Tested Cut Off (lower limit of detection)

Do not send heparinised blood 9342 2615

Test Hepatitis E virus Serology Assay or Procedure Specimen Required When Tested

IgG Serum (clotted blood) Weekly

Contact 9342 2649 Test Hepatitis G virus PCR Specimen Required Serum (clotted blood)

Blood (ACD or EDTA) When Tested As requested Cut Off (lower limit of detection)

10,000 copies/ml

Notes Do not send heparinised blood Contact 9342 2615 Test Herpes simplex virus (HSV) Phenotyping

for drug resistance Specimen Required HSV isolate or specimen for HSV isolation When Tested On request Notes Testing for acyclovir and foscarnet

susceptibility requires a virus isolate. Specimen sent must be HSV PCR positive before virus isolation is attempted.

Contact 9342 2628 Test Herpes simplex virus PCR Specimen Required Swabs, tissue, CSF, saliva, urine, BAL,

blood (ACD or EDTA) When Tested Daily Notes Part of a multiplex herpesvirus assay. Test

distinguishes between HSV-1 and HSV-2 Contact 9342 2628

Page 28

Test Herpes simplex virus Serology (HSV) Assay IgG

IgM Specimen Required Serum (clotted blood) When Tested x2 weekly Contact 9342 2649/9342 2650 Test HIV (see under Human Immunodeficiency

Virus for all tests offered) Test HTLV Serology (see under Human T

lymphotropic viruses) Test Human herpesvirus 6 PCR Specimen Required Blood (ACD or EDTA), CSF, swab, tissue When Tested Weekly Contact 9342 2628 Test Human herpesvirus 6 Serology Assay or Procedure Total Ab

IgM Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650 Test Human herpesvirus 8 PCR Assay or Procedure Total Ab

IgM Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2615 Test Human immunodeficiency virus Serology

Screening Specimen Required Serum (clotted blood) When Tested Daily Notes Negative results are reported within 24

hours of specimen receipt. Contact 9342 2649/9342 2650

Page 29

Test Human immunodeficiency virus Serology Confirmation

Assay Procedure Western Blot Specimen Required Serum (clotted blood) When Tested x2 weekly Notes Performed on repeatedly reactive samples

detected in the screening test and specimens found to be reactive by other laboratories.

Contact 9342 2649/9342 2650 Test Human immunodeficiency virus p24

antigen Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650 Test Human immunodeficiency virus Genotyping

for drug resistance Specimen Required Blood (ACD or EDTA) When Tested On request Notes Protease, RT and GP41 sequenced Contact 9342 2623 Test Human immunodeficiency virus RNA

Quantitation (Virus Load, HIV-1)) Specimen Required Blood (ACD or EDTA) When Tested On request Units RNA copies per ml of plasma Notes Assay can also be performed on CSF.

An assay is also available for HIV-2. Quantifiable range of this assay is 400 – 750,000 RNA copies/ml. The ultrasensition quantitation assay (50-100,000 copies per ml) is also available on blood specimens.

Contact 9342 2623 Test Human T lymphotropic viruses I and II

Serology Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2647 Test Hydatid (Echinococcus granulosus)

Serology Assay or Procedure Total Ab (IHA) Specimen Required Serum (clotted blood) When Tested x2 weekly Contact 9342 2649/9342 2650

Page 30

Test Infectious mononucleosis (see Paul Bunnell assay and Epstein-Barr virus testing procedures)

Test Influenza virus PCR Specimen Required Any respiratory sample, CSF When Tested Daily Notes Assay is part of Respiratory virus PCR.

Detects influenza types A and B Contact 9342 2628 Test Influenza virus Serology Assay or Procedure CFT Specimen Required Serum (clotted blood) When Tested Weekly Notes Detects antibodies to influenza types

A and B Contact 9342 2649/9342 2650 Test Iron Specimen Required Serum (clotted blood) When Tested Iron studies: daily Reference Ranges Male: 10.0 – 30.0

Female: 9.0 – 27.0 mmol/L

Contact 9342 2640 Test Iron studies Specimen Required Serum (clotted blood) When Tested Iron, transferrin: daily

Ferritin: x2 weekly See also: Individual tests Reference Ranges Iron:

Male: 10.0 – 30.0 Female: 9.0 – 27.0 Transferrin: 1.7 – 3.4

Units Iron: µmol/L: Trans: g/L; Ferritin: ng/mL

Contact 9342 2640 Test Japanese B encephalitis virus PCR (see

Flavivirus PCR) Test Japanese B encephalitis virus Serology Assay or Procedure IF Total

IF IgM Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650

Page 31

Test JC virus PCR (see Polyomavirus PCR) Test Kunjin virus Serology (see Flavivirus

Serology) Test Kunjin virus PCR (see Flavivirus PCR) Test Lactate dehydrogenase (LD) Specimen Required Serum (clotted blood) When Tested Daily See also: Cardiac enzymes Reference Ranges 185 – 505 Units U/L Contact 9342 2640 Test Lactic acid (lactate) Specimen Required Blood (NaF) When Tested Daily See also: Lipids Reference Ranges 0.4 – 2.2 Units mmol/L Contact 9342 2640 Test LDL cholesterol Specimen Required Not required When Tested Calculated daily See also: Lipids Reference Ranges <3.5 Units mmol/L Notes For accurate lipid determinations, the

patient should fast for 12 hours prior to specimen collection. LDL cholesterol is determined using the Friedewald equation, which is only reliable if the triglyceride concentration is less than 4.6 mmol/L.

Contact 9342 2640 Test Legionella Culture Specimen Required Respiratory specimen When Tested On request Notes Preferably collected prior to antibiotic

therapy. Contact 9342 2670

Page 32

Test Legionella PCR Specimen Required Sputum, bronchial washings, aspirates and

lavages, pleural and other sterile-site body fluids, and fresh biopsy specimens.

When Tested Weekly Notes Duplex LightCycler real-time PCR to directly

detect L pneumophila and other Legionella species by 16s rRNA gene sequence.

Contact 9342 2670 Test Legionella Serology (screen) Assay or Procedure IF Total Specimen Required Serum (clotted blood) When Tested Daily. A supplementary test to enable

strain differentiation is done twice weekly. Notes Testing detects response to L.longbeachae

and L.micdadei and pneumophila Contact 9342 2649/9342 2650 Test Legionella urinary antigen detection Specimen Required Urine When Tested Daily Notes Only detects L.pneumophila serogoup 1

antigen Transport at room temperature

Contact 9342 2670 Test Leishmania spp (donovani) Serology Specimen Required Total Ab (IHA) When Tested x2 weekly Contact 9342 2649/9342 2650 Test Leprosy (Microscopy of ZN stained smears) Specimen Required Skin snips, nasal secretions. When tested On request Notes See text (MRL section) for further details Contact MRL Reference Lab: 9342 2674 Test Leptospira culture Specimen Required Urine, blood (heparin or sodium oxalate

treated), CSF. Transport at room temperature, avoid refrigeration.

When Tested On request Contact 9342 2670 Test Leucocyte Count Specimen Required Blood (EDTA) When Tested Daily Normal Ranges Adult 4.0 – 11.0 x 10 9/L Contact 9342 2644

Page 33

Test Lipids: (cholesterol, triglycerides, HDL, LDL)

Specimen Required Serum (clotted blood) When Tested Daily See also: Individual tests Normal Ranges HDL:

LDL: <3.5 C: <5.5 T: 0.4 – 1.9

Units mmol/L Contact 9342 2640 Test Liver Function Tests (LFTs): AST, albumin,

ALP, bilirubin, GGT, total protein, ALT Specimen Required Serum (clotted blood) When Tested Daily See also: Individual tests Reference Ranges See Individual tests Units See Individual tests Contact 9342 2640 Test Lutenizing hormone Specimen Required Serum (clotted blood) When Tested x2 weekly Reference Ranges Male: 1.9

Female: fol.: 2-11 Mid-Cy: 19-103 Lut: 1-13 Post m/pausal: 11-59

Units miu/mL Contact 9342 2640 Test Magnesium Specimen Required Serum (clotted blood) When Tested Daily Reference Ranges 0.62 – 1.03 Units mmol/L Contact 9342 2640 Test Malarial examination Specimen Required Blood (EDTA) and/or thick & thin blood

films When Tested Daily Notes Test includes confirmation and typing Contact 9342 2644 Test Malarial immuno-chromatography test

(ICT) Specimen Required Blood (EDTA) When Tested Daily Contact 9342 2644

Page 34

Test Marburg haemorrhagic fever virus PCR Specimen Required Blood, respiratory swabs When Tested On request Notes This is a PC4 level pathogen. Requests for

PCR must be discussed with the laboratory in advance.

Contact 9342 2628 Test Marburg haemorrhagic fever virus Serology Specimen Required Serum (Clotted blood) When Tested On request Notes This is a PC4 level pathogen. Requests for

PCR must be discussed with the laboratory in advance.

Contact 9342 2628 Test Mean Corpuscular Haemoglobin

Concentration (MCHC) Specimen Required Blood (EDTA) When Tested Daily Normal Ranges Adult 310 – 360 g/L Contact 9342 2644 Test Mean Corpuscular Volume (MCV) Specimen Required Blood (EDTA) When Tested Daily Normal Ranges Adult 76 – 96 fL. Contact 9342 2644 Test Mean Corpuscular Haemoglobin (MCH) Specimen Required Blood (EDTA) When Tested Daily Normal Ranges Adult 27 – 32 pg. Contact 9342 2644 Test Mean Platelet Volume (MPV) Specimen Required Blood (EDTA) When Tested Daily Normal Ranges 7.4 – 10.4µm3 Contact 9342 2644 Test Measles virus Genotyping Specimen Required Blood (ACD or EDTA), NTS, urine, CSF When Tested On request Notes For epidemiological purposes only.

Serology is the preferred method for diagnosis.

Contact 9342 2628

Page 35

Test Measles virus PCR Specimen Required Blood, NTS, urine, CSF When Tested On request Notes Request when measles diagnosis is

required. Contact 9342 2628 Test Measles virus Serology Assay or Procedure IgG, IgM Specimen Required Serum (clotted blood) When Tested Daily Contact 9342 2649/9342 2650 Test Microsporidium detection Specimen Required Faeces, urine, sputum, tissue sections, eye

swabs When Tested On request Contact 9342 2670 Test Molluscum contagiosum by Electron

Microscopy Specimen Required Vesicle fluid When Tested On request Contact 9342 2678 Test Mumps virus Serology Assay IgG

Igm Specimen Required Serum (clotted blood) When Tested x2 weekly Contact 9342 2649/9342 2650 Test Murray Valley encephalitis virus (MVE) PCR

(see Flavivirus PCR) Notes MVE specific PCR can be performed but

only if Flavivirus PCR positive. Test Murray Valley encephalitis virus Serology Assay Total Ab

IgM Specimen Required Serum (clotted blood) When Tested Weekly Notes See also, Flavivirus Serology Contact 9342 2647

Page 36

Test Mycobacterial blood Culture Specimen Required 1-5 mL of blood collected into a Myco/F

lytic blood culture bottle available from MRL.

When Tested Daily Notes See text (MRL section) for further details Contact 9342 2674 Test Mycobacterial identification and sensitivity

testing on a referred pure isolate Specimen Required Slope or broth culture. Please provide ZN

or AR result from the original specimen. When Tested Weekly Notes See text (MRL section) for further details Contact 9342 2674 Test Mycobacterial Culture Specimen Required Sputum, bronchial washings, gastric

lavage, CSF and other fluids, stain and wound swabs, urine, faeces.

When Tested Daily Notes See text (MRL section) for further details Contact 9342 2674 Test M tuberculosis complex PCR Specimen Required Respiratory specimens, biopsies, whole CSF

(>1ml) and other fluids. Paraffin embedded tissue sections (at least 6 sections, each 10-20 µm thick).

When Tested Weekly Notes See text (MRL section) for further details.

Contact laboratory for suitability of specimens. Current method: TaqMan real-time PCR (IS6110 – based target).

Contact 9342 2674 Test Mycobacterium ulcerans PCR Specimen Required Fresh tissue biopsy, dry swabs and

paraffin-embedded fixed tissue sections (at least 6 sections, each 10-20 µm thick).

When Tested Weekly Notes All specimens should be collected

aseptically and submitted to the laboratory in sterile containers. Current method: TaqMan real-time PCR.

Contact 9342 2674

Page 37

Test Mycobacterium genus PCR Specimen Required Tissue biopsies, dry swabs, AFB positive

paraffin-embedded fixed tissue sections, smear positive respiratory specimens which are negative for M.tuberculosis

When Tested On request Notes See text (MRL section) for further

information. It is advisable to contact the laboratory to check suitability prior to submitting a specimen. Method; Nested ITS region PCR and sequencing.

Contact 9342 2674 Test Mycoplasma pneumoniae PCR Specimen Required Any respiratory sample When Tested On request Contact 9342 2628 Test Mycoplasma pneumoniae Serology Assay or Procedure Total Ab

IgM CFT – Total Ab

Specimen Required Serum (clotted blood) When Tested Daily (Total)

x2 weekly (IgM) Contact 9342 2644 Test Neisseria gonorrhoeae PCR (see

Gonorrhoea PCR) Test Neonatal Serology (post natal Serology, Rh

negative mothers) Specimen Required Serum (clotted blood) for mother; blood

(EDTA) or serum (clotted blood) for neonate

When Tested Daily Contact 9342 2649/9342 2650 Test Norovirus PCR Specimen Required Faeces (not frozen) When Tested Contact Laboratory Notes Detects genogroups 1 and 2 Contact 9342 2678 Test Norovirus by Electron Microscopy Specimen Required Faeces (not frozen) When Tested Contact Laboratory Contact 9342 2678

Page 38

Test Norwalk virus – (see Norovirus) Test Occult blood Specimen Required Faeces (no transport medium) When Tested On request Contact 9342 2644 Test Orf virus – see Poxvirus by Electron

Microscopy Test Packed Cell Volume (PCV) Haematocrit Specimen Required Blood (EDTA) When Tested Daily Normal Ranges Adult Male 0.4 – 0.54

Adult Female 0.37 – 0.47 Contact 9342 2644 Test Parainfluenza virus detection (see

Respiratory viruses by PCR and Immunofluoresence)

Test Parasite detection (see Faecal Microscopy) Contact 9342 2670 Test Parasite detection (enteric) Specimen Required Faeces in SAF transport medium

(Para-Pak supplied by VIDRL) When Tested Daily Note Faecal microscopy with concentration &

fixed stains for ova, cysts, trophozoites, Cryptosporidium and Microsporidium. Maximum 2 specimens tested per 7-day period.

Contact 9342 2670 Test Parasite detection (urinary) (see

Schistosoma haematobium microscopy) Test Parasite Identification (ecto- or endo-

parasites) Specimen Required Parasite – fresh or in 60% ethanol

Avoid crushing When Tested On request Note Please provide source information Contact 9342 2670

Page 39

Test Parvovirus B19 PCR Specimen Required Blood (ACD or EDTA), amniotic fluid When Tested Weekly, Friday Contact 9342 2628 Test Parvovirus B19 Serology Assay or Procedure IgG

IgM Specimen Required Serum (clotted blood) When Tested x3 weekly Contact 9342 2649/9342 2650 Test Paul Bunnell test Specimen Required Serum (clotted blood) When Tested Daily Normal Ranges <1:20 Contact 9342 2644 Test Phenytoin Specimen Required Serum (clotted blood) When Tested Request Reference Ranges 33 – 67 Units µmol/L Notes Preferred sampling time is immediately

before the first morning dose Contact 9342 2640 Test Phosphate Specimen Required Serum (clotted blood) When Tested Daily Reference Ranges Serum: 0.80 – 1.50 Units mmol/L Contact 9342 2640 Test Picornavirus (see Enterovirus PCR and

Respiratory virus PCR) Contact 9342 2628 Test Platelet Count Specimen Required Blood (EDTA) When Tested Daily Normal Ranges 150 – 400 x 10 9/L Contact 9342 2644

Page 40

Test Pneumocystis carinii detection Specimen Required Induced sputum, bronchial washing, BAL

(cytospin preparation – contact lab first) When Tested On request Notes Methods: Toluidine Blue O Stain, Direct

Immunofluorescence Contact 9342 2670 Test Polyomavirus PCR (BK and JC viruses) Specimen Required Urine, CSF, serum When Tested Weekly Contact 9342 2615 Test Poliovirus Detection Test method Cell culture

Identification using neutralising antibodies EIA Nucleic acid probe RT-PCR

Specimen Required Two faecal specimens collected 24-48 hours apart within 14 days of onset of symptoms

When Tested Daily Contact 9342 2607 Test organism Poliovirus 1, 2, 3 Serology Specimen Required Serum (clotted blood) or blood (ACD or

EDTA) When Tested On request Notes Poliovirus serology is only performed if

there is a clinical indication of acute infection in a susceptible person. Discuss with laboratory staff before specimens are sent.

Contact 9342 2607 Test Potassium Specimen Required Serum (clotted blood) or blood

(heparinised) When Tested Daily See also: U&E Normal Ranges Serum 3.5 – 4.8 Units mmol/L Notes The specimen must not be haemolysed

and there should be minimal statis before and during blood collection.

Contact 9342 2640

Page 41

Test Poxvirus PCR Specimen Required Vesicle fluid/swab When Tested On request Notes Assay detects ‘old world’ pox viruses

including variola (smallpox), vaccinia, monkey pox, cowpox, buffalo pox and camel pox. Requests for PCR must be discussed in advance with the laboratory.

Contact 9342 2628 Test Poxvirus by Electron Microscopy Specimen Required Vesicle fluid, skin scraping When Tested On request Notes Requests must be discussed in advance

with the laboratory. Contact 9342 2678 Test Pregnancy test (qualitative) Specimen Required Serum (clotted blood) When Tested Daily Contact 9342 2644 Test Progesterone Specimen Required Serum (clotted blood) When Tested x2 weekly Reference Ranges Male: 0.5 – 3.0

Female: foll: 1.0 – 4.9 Lut: 16.5 – 60.0 Post m/pausal: 0.0 – 2.5 Pregnant (1st Tri) 150 – 162.0

Units mmol/l Contact 9342 2640 Test Prolactin Specimen Required Serum (clotted blood) When Tested x2 weekly Reference Ranges Male: 40 – 275

Female: 40 – 420 Units mlU/L Contact 9342 2640 Test Prostate Specific antigen Specimen Required Serum (clotted blood) When Tested x2 weekly Reference Ranges 0.0 – 4.0 Units ng/mL Contact 9342 2640

Page 42

Test Prothrombin time/ratio (PTT, PR, INR) Specimen Required Blood (sodium citrate 3.8%) When Tested Daily Normal Ranges Ratio: <1.2 INR:

Therapeutic range INR: 2.0 – 4.0

Contact 9342 2644 Test Q Fever (Coxiella burneti) Phase 1 SerologyAssay CFT Total Ab Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650 Test Q Fever (Coxiella burneti) Phase 2 SerologyAssay Total Ab, IgM Specimen Required Serum (clotted blood) When Tested Total Daily, IgM x2 weekly Contact 9342 2649/9342 2650 Test Q Fever (Coxiella burneti) Phase 2

Serology, (pre-vaccination screen) Assay CFT Total Ab Specimen Required Serum (clotted blood) When Tested X2 Weekly Contact 9342 2649/9342 2650 Test QuantiFERON ® -TB Gold assay

(Gamma-IFN response to MTB antigens) Specimen Required Heparinised blood, minimum 5 mL When Tested Weekly Notes See text (MRL section) for further

information. The specimen must be processed within 10 hours of collection. Do not centrifuge, refrigerate or freeze the specimen

Contact 9342 2670 Test Random Distribution Width (RDW) Specimen Required Blood (EDTA) When Tested Daily Normal Ranges 11.5 – 14.5% Contact 9342 2644 Test Red Cell Count Specimen Required Blood (EDTA) When Tested Daily Normal Ranges Adult Male: 4.0 – 6.0 x 10 12/L

Adult Female: 3.5 – 5.5 x 1012/L Contact 9342 2644

Page 43

Test Respiratory Syncytial virus PCR (see Respiratory virus PCR)

Test Respiratory Syncytial virus Serology Assay or Procedure CFT Total Ab Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650 Test Respiratory virus antigens by

Immunofluorescence Specimen Required NPA, BAL When Tested Daily Notes Specimen required at laboratory by midday

for same day results. Antigens detected are influenza A, influenza B, parainfluenza 1, 2 and 3, RSV and adenovirus.

Contact 9342 2628 Test Respiratory virus PCR Specimen Required Any respiratory specimen When Tested Daily Units Specimen must be in the laboratory by

9:00 am for same day result. Notes Test detects influenza A & B, parainfluenza

1,2,3, picornavirus, (enterovirus and rhinovirus) RSV and adenovirus.

Contact 9342 2628 Test Reticulocytes Specimen Required Blood (EDTA) When Tested Daily Normal Ranges 0.5 – 2.5% Contact 9342 2644 Test Rheumatoid Factor (qualitative &

quantitative) Specimen Required Serum (clotted blood) When Tested Daily Contact 9342 2644 Test Rhinovirus PCR (see Respiratory viruses by

PCR)

Page 44

Test Rickettsia spp screen Serology Assay or Procedure Total Ab

IgM Specimen Required Serum (clotted blood) When Tested Weekly Notes Testing detects response to Spotted Fever,

Typhus and Scrub Typhus groups. Contact 9342 2649/9342 2650 Test Rift Valley fever virus PCR Specimen Required Blood (ACD or EDTA), NTS, Swab When Tested On request Notes Rift Valley fever virus is a PC4 level

pathogen. Requests for PCR must be discussed with the laboratory in advance.

Contact 9342 2628 Test Rift Valley fever virus Serology Specimen Required Serum (clotted blood) When Tested On request Notes Rift Valley fever is a PC4 level pathogen.

Requests for PCR must be discussed with the laboratory in advance.

Contact 9342 2628 Test Ross River virus Serology Assay or Procedure IgG

IgM Specimen Required Serum (clotted blood) When Tested x2 weekly Contact 9342 2649/9342 2650 Test Rotavirus by electron microscopy Specimen Required Faeces (not frozen) When Tested Contact laboratory Contact 9342 2678 Test RSV PCR (See: Respiratory viruses by PCR) Test Rubella virus PCR Specimen Required Blood (ACD or EDTA), swab, NTS, amniotic

fluid When Tested On request Contact 9342 2628

Page 45

Test Rubella virus Serology Assay IgG

IgM HI Total Ab HI IgM

Specimen Required Serum (clotted blood) When Tested Daily

Daily X1 weekly Request (confirmatory)

Contact 9342 2649/9342 2650 Test SARS-associated Coronavirus PCR (see

Coronavirus PCR) Test SARS - Coronavirus Serology Specimen Required Serum (clotted blood) When Tested On request Notes Test only available for SARS-associated

coronavirus. Patient must satisfy WHO case definition for testing to proceed.

Contact 9342 264728 Test Schistosoma haematobium Microscopy Specimen Required Terminal urine or semen sample (collected

between 10am – 2pm) When Tested On request Contact 9342 2670 Test Schistosoma spp (mansoni) Serology Assay or Procedure IHA Total Ab Specimen Required Serum (clotted blood) When Tested x2 weekly Contact 9342 2649/9342 2650 Test Simian B virus (herpes simiae) PCR Specimen Required Lesion swab, CSF When Tested On request Notes Contact laboratory before sending

specimen. Contact 9342 2628 Test Smallpox virus PCR (see poxvirus PCR)

Page 46

Test Sodium Specimen Required Serum (clotted blood) or Blood heparinised When Tested Daily See also: U&E Reference Ranges Serum: 130 – 145 Units mmol/L Contact 9342 2640 Test Sputum Culture and Microscopy Specimen Required Sputum When Tested Daily Notes Optimum specimen collected early

morning. Check quality. Avoid presence of saliva.

Contact 9342 2670 Test Strongyloides Stercoralis Serology Assay IgG Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650 Test Syphilis Serology Assay or Procedure RPR

TPPA EIA – Total Ab FTA EIA IgM

Specimen Required Serum (clotted blood), CSF (0.5 ml) When Tested Daily

Daily Daily x2 weekly Weekly

Contact 9342 2649/9342 2650 Test Synovial Fluid Culture, Microscopy and

Polarised Light Microscopy Specimen Required Fluid collected into a plain tube; also small

volume in heparinised (non sterile) tube for cell count.

When Tested On request Contact 9342 2670

Page 47

Test T cells counts (reference range) Reference Range CD3 (Total T Cells) 760-2480/µl

CD4 (Helper T Cells) 400-1630/µl CD8 (Suppressor T Cells) 175-900/µl CD19 (B Cells) 80-560/µl CD56/16 (NK Cells) 90-500/µl CD4:CD8 Ratio 0.8-5.3 (no units)

Specimen Required Blood (EDTA or heparin) When Tested Daily Contact 9342 2644 Test Testosterone Specimen Required Serum (clotted blood) When Tested x2 weekly Reference Ranges Male: 6.0 – 27.0

Female: 0.6 – 3.0 Units nmol/L Contact 9342 2640 Test Thyroid Function Tests:

(free thyroxine, FT4), Thyroid Stimulating Hormone (TSH)

Specimen Required Serum (clotted blood) When Tested x2 weekly Reference Ranges FT4: 7 – 19

TSH: 0.3 – 4.1 Units FT4: pmol/L

TSH: mIU/µL Contact 9342 2640 Test Thyroid Stimulating Hormone (TSH) (see

Thyroid Function Tests Test Thyroxine (see thyroid function tests) Test Toxoplasma PCR Specimen Required CSF, tissue, vitreous fluid When Tested On request Contact 9342 2628

Page 48

Test Toxoplasma Serology Assay or Procedure IgG

IgM IF Total Ab IF IgM

Specimen Required Serum (clotted blood) When Tested x2 weekly

x2 weekly (Confirmatory) (Confirmatory)

Contact 9342 2649/9342 2650 Test Transferrin Specimen Required Serum (clotted blood) When Tested Daily See also: Iron studies Reference Ranges 1.7 – 3.4 Units G/L Contact 9342 2640 Test Trichomonas detection Specimen Required Vaginal swab When Tested Daily Notes Use swabs collected in Amies/Charcoal

transport medium. Alternatively contact laboratory for broth medium for direct inoculation. Transport at room temperature.

Contact 9342 2670 Test Triglycerides Specimen Required Serum (clotted blood) When Tested Daily See also: Lipids Reference Ranges 0.4 – 1.9 Units mmol/L Contact 9342 2640 Test Trypanosoma cruzi (American

Trypanosomiasis) Serology Assay or Procedure IF Total Ab Specimen Required Serum (clotted blood) When Tested On request Contact 9342 2649/9342 2650 Test Trypanosoma gambiense (African

Trypanosomiasis) Serology Assay or Procedure IHA Total Ab Specimen Required Serum (clotted blood) When Tested x2 weekly Contact 9342 2649/9342 2650

Page 49

Test Urate/Uric acid Specimen Required Serum (clotted blood) When Tested Daily Normal Ranges Male: 0.21 – 0.45

Female: 0.15 – 0.40 Units mmol/L Contact 9342 2640 Test Urea and Electrolytes (U&E): Sodium,

Potassium, Chloride, Bicarbonates, Urea and Creatinine

Specimen Required Serum (clotted blood) or Blood (heparinised)

When Tested Daily See also: Individual tests Normal Ranges See individual tests Units mmol/L Contact 9342 2640 Test Urea Specimen Required Serum (clotted blood) When Tested Daily See also: U & E Normal Ranges 2.0 – 7.8 Units mmol/L Contact 9342 2640 Test Urine Culture Specimen Required Mid stream urine When Tested Daily Notes Refrigerate specimen if delay in transport

(> 2 hr) is expected Contact 9342 2670 Test Vaginal Culture and Microscopy Specimen Required Vaginal swab. Provide smear for Gram

Stain. When Tested Daily Notes Use swabs collected in Amies/Charcoal

transport medium. Transport at room temperature. Includes diagnosis of Trichomonas, Gardnerella and Candidiasis

Contact 9342 2670

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Test Valproate Specimen Required Serum (clotted blood) When Tested On request Normal Ranges 277 – 346 (trough)

300 – 600 (peak) Units µmol/L Notes Both trough and peak levels are

recommended. Contact 9342 2640 Test Varicella zoster virus PCR Specimen Required Swabs, CSF, urine, blood, saliva When Tested Daily Contact 9342 2628 Test Varicella zoster virus Serology Assay or Procedure EIA IgG

EIA IgM Latex Total Ab

Specimen Required Serum (clotted blood) When Tested x2 weekly

x2 weekly Request

Contact 9342 2649/9342 2650 Test Vitamin B12 Specimen Required Serum (clotted blood) When Tested x2 weekly Normal Ranges 130 – 675 Units pmol/L Contact 9342 2640 Test Wound culture Specimen Required Use swabs with Amies/charcoal transport

medium. Provide smear for Gram stain. When Tested Daily Contact 9342 2670 Test Yellow fever virus Serology Assay or Procedure Total Ab & IgM (IF) Specimen Required Serum (clotted blood) When Tested Weekly Contact 9342 2649/9342 2650 Test Yellow fever virus PCR (see Flavivirus PCR)