Clinical Microbiology Laboratory Users Manual
February 2012 Review February 2014
Public Health Laboratory, Cherry Orchard Hospital, Dublin 10. Tel: +353-1-620 6175/6176 Fax: +353-1-623 1908 Email:
[email protected]
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Contents General Information .......................................................................................................................... 4 Location: ...................................................................................................................................... 4 Opening hours: ........................................................................................................................... 4 Out of hours service: .................................................................................................................. 4 Clinical Advice: ........................................................................................................................... 4 User satisfaction: ........................................................................................................................ 4 Staff Contact Numbers (01 6206715) ........................................................................................... 5 Collection of specimens and transport to the laboratory ................................................................... 6 Completion of Request Forms................................................................................................... 6 Specimen Identification.............................................................................................................. 8 Swabs/containers available in SJH ........................................................................................... 9 Transport of Specimens to the laboratory.............................................................................. 10 Sample retention in the Laboratory and further testing requests .................................................... 10 Recommended samples to be sent from patients with particular clinical syndromes ..................... 11 Suspected bacteraemia, Systemic Inflammatory Response Syndrome (SIRS), Sepsis, Septic Shock ................................................................................................................ 11 CNS infections........................................................................................................................... 11 Respiratory tract infection ....................................................................................................... 12 Gastrointestinal tract infection ................................................................................................ 13 Bone and joint infection. .......................................................................................................... 14 Urine specimens ....................................................................................................................... 15 Genital tract specimens............................................................................................................ 16 Skin and superficial wound swabs.......................................................................................... 17 Deep-seated wounds/abscesses/ post-operative wound infection...................................... 17 Mycobacterial Infection ............................................................................................................ 17 Fungal nail and skin infections................................................................................................ 18 Appendix 1 - List of available tests and organisms that require special investigations................... 21 Appendix 2 - Reference Laboratories currently used for specimen referral.................................... 27
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Foreword We hope that the production of this manual will help all users of the Microbiology Laboratory to get the best from the service. In particular, we hope that it will aid in selecting and obtaining the most appropriate specimen, submitting appropriate information for test selection and interpretation, transporting to the laboratory without delay and interpretation of results. The value of a particular bacteriology and virology test is still greatly dependant on this process. If you have any comments, corrections or suggestions on this manual we would like to hear from you.
Authors:
Dr. Eleanor McNamara Ms. Mary Linehan Dr. Brian O’Connell
February 2012
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General Information The Microbiology Laboratory is part of the Public Health Laboratory at Cherry Orchard Hospital and is located in the grounds of Cherry Orchard Hospital, Ballyfermot, Dublin 10. Opening hours: Routine service is provided from 9.30 a.m. to 5.00 p.m. Monday-Friday and a limited service on Saturday morning from 9.30 a.m. to 12.30 pm. Clerical staff are available for results or enquiries etc. from 9.30 a.m. to 5 p.m. Monday to Friday Out of hours service: An emergency ‘out of hours’ service is available between 5 p.m. and 9 a.m. Monday to Friday and between 12.30 p.m. on Saturday and 9.00 a.m. on Monday. Please contact the Microbiology Medical Scientist on-call who is available via the switchboard (01 6206400) Note that the Microbiology Medical Scientist must be bleeped for urgent specimens to be processed out of hours, users should not telephone the laboratory as telephones are not staffed out of routine hours.
Clinical Advice: Advice regarding diagnosis and treatment of infection is available at all times. Contact numbers are given overleaf. For out of hours advice including infection control advice, please contact the on-call consultant microbiologist via switchboard (01 6206400) or on-call medical scientist.
User satisfaction: The Clinical Microbiology Laboratory operates an on-going process of service evaluation and improvement to meet the needs and requirements of users. Laboratory management regularly assesses contributions and complaints received in the laboratory from users of the Microbiology service.
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Staff Contact Numbers (01 6206400) Name General secretarial office General enquiries/results
Ext.
E mail
Blee
6175 or 6176
Consultants Dr. Eleanor McNamara Dr. Brian O’Connell Chief Medical Scientist Ms. Mary Linehan Infection Control Clinical Nurse Specialist: Contact Dr. Eleanor McNamara
6214
[email protected]
6214
[email protected]
6263
[email protected]
6215 Laboratory Main clinical laboratory TB Laboratory Molecular laboratory
6174 6215 6172
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Collection of specimens and transport to the laboratory General Guidelines Collect specimens before commencement of antimicrobial therapy. This is usually possible for most mild infections. For more serious infections, antimicrobial therapy should not be withheld pending collection of a specific specimen. For example, antimicrobial therapy should not be withheld pending collection of CSF from an individual with suspected meningitis or collection of sputum from an individual with severe pneumonia. However, blood cultures can be obtained in nearly all cases prior to antimicrobial treatment of serious infection. If in any doubt as to the appropriate container, please contact the laboratory for advice. Please send an adequate amount of specimen. As a general rule – ‘the more specimen the better’. If pus is present, send pus rather than a swab and remember to send enough specimen if a whole series of tests are required. This applies to CSF and serology specimens in particular. Please ensure that relevant clinical details are included on the request form. All of the above may influence the type of test that the laboratory performs.
Completion of Request Forms Adequate identification of patient samples is essential for patient safety. The following details must be recorded on the request form:
Full Patient Name DOB Patients Address External laboratory number/MRN (where available) Gender Date of Collection Ward/Source Requesting Clinician Specimen Type Tests requested
Those highlighted in bold are essential patient identifiers. Specimens cannot be processed unless there is a minimum of two patient identifiers on the specimen container which match those on the request form, one of which must be the full patient name. Please ensure that relevant clinical details are included on the request form. For example, include details if the specimen is sent during an outbreak or there is a
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history of foreign travel or a specific diagnosis is being considered. All of the above may influence the type of test that the laboratory performs.
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Specimen Identification The following details should be recorded on all specimens:
Full Patient Name DOB MRN (where available) Date of collection
Those highlighted in bold are essential patient identifiers. Specimens cannot be processed unless there is a minimum of two patient identifiers on the specimen which match those on the request form, one of which must be the full patient name. It is laboratory policy NOT to process unlabelled or mislabeled specimens.
CJD: If a patient is at risk of developing a transmissible spongiform encephalopathy (TSE) or has a clinical syndrome compatible with a diagnosis of a TSE, tissue and CSF specimens must be labeled with the appropriate biohazard label. Other types of specimens may be sent without specified precautions. Please contact the medical staff in the laboratory prior to sample dispatch.
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Swabs/containers used in the PHL, Cherry Orchard 1. Universal container – two types with different apertures are used for collection of bodily fluids – pus, urine, pleural fluid, CSF etc.. 2. Amies Transport Swabs for routine collection of swab specimens of skin, wounds etc. 3. Pernasal swab – for Bordetella pertussis. If required please contact the Medical Staff in the Microbiology Department. 4. New York City Medium is available for culture of Neisseria gonorrhoeae (N.B. Store at 4ºC and return to room temperature before use.) 5. Blood culture bottles:
Oxoid SIGNAL blood culture BC100M Haemoline Perf. diphas blood culture bottles 52510
6. Viral transport medium and viral swabs: Please consult the Laboratory Diagnosis of Viral infections handbook for further details, or contact the Microbiology Medical Staff.
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Transport of Specimens to the laboratory Specimens should be transported to the laboratory without delay to ensure optimal results. All specimen containers must be tightly closed and placed in a transparent hazard bag for transport to the laboratory. It is the responsibility of the person dispatching the specimen to the laboratory to ensure that it is packaged correctly, and does not pose a risk to anyone coming in contact with it during transport or on receipt in the laboratory.
Sample retention in the Laboratory and further testing requests Samples are generally retained in the Microbiology Laboratory for 72 h. Requests for further testing on samples may be possible on a case-by-case basis. Please contact the Laboratory as soon as possible if the need for further testing is identified.
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Recommended samples to be sent from patients with particular clinical syndromes 1. Suspected bacteraemia, Systemic Inflammatory Response Syndrome (SIRS), Sepsis, Septic Shock Blood cultures - For optimum sensitivity, two sets of blood cultures should be collected from separate sites within a 24 h period. These should be taken at least 20 min apart. For patients with suspected endocarditis, three sets should be collected. Method: Observe standard precautions, wash hands, carefully disinfect the skin with alcohol, allow to dry, wear sterile gloves, insert vacutainer into vein, collect 10 ml of blood into Oxoid SIGNAL blood culture BC100M and 10 ml into Haemoline Perf. diphas blood culture bottles 52510. Yeasts and fungi may be detected in the normal blood culture system. Look for a focus of infection and culture those sites appropriate to a suspected focus.
2. CNS infections 1. Blood cultures Blood cultures should be collected from all patients with suspected meningitis.
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3. Respiratory tract infection Tonsillopharyngitis Send a throat swab. Please contact the laboratory if diphtheria or pertussis is suspected. Sinusitis: Using a syringe aspiration technique, a specially trained physician or an ENT surgeon can obtain material from maxillary, frontal, or other sinuses. Place the contents of the syringe into a sterile universal container. Otitis media: Usually no specimens are forwarded to the laboratory. Diagnosis of Whooping cough: Please discuss with laboratory medical staff. Bronchitis: A good quality purulent or mucopurulent sputum specimen should be obtained, preferably before antimicrobial therapy. Pneumonia: It is not necessary to perform a full range of microbiological investigations on all patients with community-acquired pneumonia. The extent of investigation should be determined by the severity and clinical course. Specimens that should/may be sent include:
Blood cultures should be obtained from all patients. Sputum: A good quality purulent or mucopurulent sputum specimen should be obtained, preferably before antimicrobial therapy although antimicrobial therapy should not be delayed unnecessarily while awaiting a sputum specimen. The specimen should be transported to the laboratory within 2 h. Salivary or mucosalivary specimens are unsuitable and as such are not processed.
.
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4. Gastrointestinal tract infection Gastroenteritis Please note that this laboratory employs a cost-effective approach to the diagnosis of infectious diarrhoea. Not all specimens are examined for every pathogen. It is therefore important that clinical details or suspected diagnoses are included on the request form or OCM. Information that is of use when processing specimens includes: travel history, relationship to a particular food, prolonged diarrhoea, antibiotic use, suspected outbreak. The laboratory examines all stool samples routinely for: Salmonella Shigella E. coli O157 Campylobacter. Clostridium difficile toxin detection and culture is performed on all specimens from patients over 2 years of age. Other pathogens e.g. Cryptosporidium, Yersinia, Vibrio, Aeromonas, ova and parasites etc. are only examined if the clinical details suggest that possibility. Rotavirus/Adenovirus detection is performed on patients under 5 years of age. Please note the possibility of Norovirus infection and state whether vomiting is a feature or whether an outbreak is suspected. Please send a blood culture if typhoid fever is suspected.
When to send a stool specimen: Send a stool specimen to the laboratory when there are ≥3 liquid or very loose stools per day. There may be other symptoms suggestive of infectious diarrhoea e.g. abdominal pain or discomfort, nausea, faecal urgency, tenesmus, fever, blood or mucus in stools. Within the hospital specimens must be sent to the laboratory immediately. In General Practice, please refrigerate if there is to be a delay in transporting the specimen.
How many samples to send: One stool specimen is normally all that is required for culture. As microscopy for parasites is less sensitive, please send 3 specimens (but no more than 3) on different days as some parasites are excreted intermittently. If a worm is excreted, please send the worm and faeces sample.
How much to send: Please fill the specimen container to between ¼ and ½ full. Please do not fill to the brim.
Detection of Verocytoxin-producing E. coli …..
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5. Bone and joint infection. Osteomyelitis
Blood culture Blood cultures should be performed an all patients with suspected osteomyelitis, preferably before antibiotics are started.
Blood cultures Blood cultures should be performed an all patients with septic arthritis, preferably before antibiotics are started.
Joint aspirate A joint aspirate obtained using an aseptic technique should be submitted in a sterile universal container from all patients with septic arthritis.
Reactive arthritis
Faeces culture may be requested for Salmonella, Shigella, Campylobacter and Yersinia.
If a sexually transmitted aetiology is suspected then urethral, cervical or rectal swabs may be taken for gonococcal detection.
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7. Urine specimens When should you send a sample of urine: It is probably reasonable to treat a young sexually active female with symptoms of simple cystitis empirically but a urine specimen should be sent for microbiological examination from all other cases. In severe or complicated UTI, a follow-up specimen should be taken 5 days post completion of antibiotic therapy. Persistence of bacteriuria implies a structural abnormality. A specimen should be sent from patients with symptoms as asymptomatic bacteriuria is generally not a cause for concern except in pregnant women and patients undergoing surgery on the g-u tract. The role of asymptomatic bacteriuria in children is controversial. The same applies to patients with in-dwelling urinary catheters. Bacteriuria occurs in the vast majority of patients who are catheterised for more than 5 days, a urine specimen should only be sent if there are symptoms or signs suggestive of a urinary or a systemic infection.
What type of specimen should you send? Send a mid-stream specimen of urine (MSU) where possible. Patients should be instructed to pass a little urine into the toilet first, then pass enough urine into the specimen container to half fill it and finish urinating into the toilet. Never obtain urine from a bedpan or commode. Obtain about 10 ml of urine in a sterile universal container tighten the lid and transport to the laboratory without delay. Specimens should be processed within 4 h. In General Practice if transport to the laboratory has to be delayed, the specimen can be stored at 4 C for up to 48 h. A clean catch urine may also be obtained if the patient cannot co-operate. A catheter specimen of urine (CSU) may also be sent to the laboratory. Urine should be obtained from an already catheterised patient by a syringe and needle from the catheter before it enters the collection bag. Clean the access point with a swab saturated with 70% isopropyl alcohol and allow time to dry. Using a sterile syringe and needle (if necessary), aspirate the required amount of urine from the access point. Re-clean access point with a swab saturated with 70% isopropyl alcohol.
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8. Genital tract specimens
Vaginal specimens Obtain a high vaginal swab by use of a speculum and a trans swab and submit to the laboratory. Cervical / endocervical swabs Use a speculum without lubricant. Wipe the cervix clean of vaginal secretions and mucus. Gently insert a swab into the endocervical canal and rotate to obtain any exudate. Chlamydia trachomatis Please contact the laboratory if this test is required. This service is not offered by the Microbiology Laboratory at Cherry Orchard Hospital. Urethral swabs In both the male and female, this is usually taken for the detection of N. gonorrhoeae . Rectal swabs Used to detect rectal carriage and infection due to N. gonorrhoeae .Pass the tip of a sterile swab approximately 2.5 cm beyond the anal sphincter. Rotate the swab gently and withdraw it into the appropriate transport medium. NB. If Urethral / rectal specimens for the detection of Neisseria gonorrhoeae are inoculated directly onto New York City medium, ensure the medium is within the marked expiry date. The plates should be stored at 4º C and returned to room temperature before inoculating. Transport the inoculated plates to the Laboratory as soon as possible. Recovery of organisms may be affected by inappropriate storage of New York City medium
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9. Skin and superficial wound swabs Note that routine sampling of skin lesions that do not appear clinically infected should generally not be performed. If there is a clinically infected lesion, please send a sample of pus in a universal container wherever possible. Pus is always preferable to a swab. If there is insufficient specimen, then use Amies Transport swab, sample the infected area and send to the laboratory.
10. Deep-seated wounds/abscesses/ post-operative wound infection Please send a sample of pus in a universal container wherever possible. Pus is always preferable to a swab. If there is insufficient specimen, then use an Amies Transport Swab, sample the infected area and send to the laboratory. Clean the surface of the wound with sterile saline or water before taking the swab.
11. Mycobacterial Infection The diagnosis of mycobacterial infection requires special staining and culture techniques. Please ensure that you request TB culture on the request form if the diagnosis is suspected. Suitable specimens: The following is a list of suitable specimens to submit:
Good quality early morning Sputum Specimens obtained at Bronchoscopy Pus CSF, Pleural, Peritoneal, Joint and other Sterile Fluids Tissue Lymph node biopsy Pus aspirated from lymph nodes Pleural biopsy Surgical sample for routine culture Radiological sample for routine culture Histology sample where non-respiratory TB is a possibility Aspiration sample where non-respiratoryTB is a possibility Bone Gastric aspiration Blood Bone marrow Urine in certain circumstances
Unsuitable specimens: The following is a list of unsuitable specimens that will usually be rejected by the laboratory:
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1. 2. 3.
Poor quality sputum specimens e.g. salivary specimens or specimens of minute quantities Faeces Urine, except when: A diagnosis of renal tuberculosis is suspected or The patient is immunocompromised or following prior discussion with a laboratory doctor.
An early morning MSU or CSU sample, taken into a sterile plastic container, should be procured and immediately submitted on each of three consecutive days.
Sputum specimens: Three consecutive early morning specimens should be submitted before the commencement of therapy. The specimen should be coughed from deep within the lungs.
Specimens obtained at bronchoscopy Specimens should be placed in a sterile universal container and transported to the laboratory without delay. Tissue Tissue is preferable to necrotic material. Do not place any fixatives in the sterile universal container. If there is a possibility that the specimen may dry out before it reaches the laboratory, then sterile saline may be added to the container Blood Please contact the laboratory if blood culture for TB is required. Bone marrow The volume of bone marrow obtained determines how the specimen should be collected. Specimens of less than 0.5 ml should be taken into a plastic sterile universal container. Specimens of greater than 0.5 ml should be inoculated directly into a Bactec MYCO/F LYTIC blood culture bottle. Please contact the laboratory to obtain a Bactec MYCO/F LYTIC bottle.
CSF/sterile bodily fluids The yield from examination of CSF specimens is dependant on the volume obtained. Ideally 10 ml should be obtained. Similarly, about 10 ml should be submitted for mycobacterial culture from other normally sterile bodily fluids e.g. pleural, ascitic, joint.
12. Fungal nail and skin infections Affected areas should be scraped with a blunt scalpel to harvest affected hairs, broken-off hair stubs and scalp scale. This is preferable to plucking, which may remove uninvolved hairs. Scrapings should be transported in a folded square of paper preferably fastened with a paper clip, but commercial
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packs are also available (e.g. ‘Mycotrans’). It is easier to see affected hairs on white paper rather than black.
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Appendix 1 - List of available tests and organisms that require special investigations TEST SPECIMEN When performed Estimated Turnaround time Abscess - pus Pus in sterile universal Daily Microscopy: Same day container Aerobic culture: 48 – 72h. Anaerobic culture: 4 days. Adenovirus culture NPA, tissue, faeces, eye swab 1 week Adenovirus DNA 5ml blood EDTA Antibiotic assay 5-10 ml clotted blood Not available at PHL. Anti-streptolysin O titre 5-10 ml clotted blood Twice weekly 1 - 4 days. (ASOT) Ascitic fluid 5 ml in sterile universal Daily Microscopy: Same day container. Culture: 48 – 72 h. Bartonella 5-10 ml clotted blood 10 –14 d. Biopsy Place in sterile universal Daily. Microscopy: Same day container. Immerse in sterile saline if likely to dry. Culture: 48 – 72 h. Blood culture 7-10 ml in Oxoid SIGNAL Daily. Negative report in 8 days. Positive blood culture bottle and report telephoned as soon as detected. anaerobic blood culture bottle. Bone Marrow Bordetella pertussis Borrellia burgdorferi (Lyme disease) Bronchial washing/ Bronchoalveolar lavage Brucella Campylobacter spp.
Place aspirate in sterile Daily universal container. Please discuss with Laboratory medical staff 5-10 ml clotted blood Place in container.
sterile
5-10 ml clotted blood Faeces specimen.
universal Daily
Daily
Comments Prolonged incubation for anaerobes Sent to Reference Lab. Sent to Reference Lab. Please contact laboratory.
Sent to Reference Lab.
Culture: 48 – 72 h
5 days.
Sent to Paediatric Hospital Laboratory Sent to Reference laboratory.
Microscopy – Same day Culture - 48 – 72 h. 10 – 14 days 48-72 h.
Sent to Reference laboratory.
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TEST
SPECIMEN
When performed
Estimated Turnaround time
Serology - 5-10 ml clotted blood.
Allow 10 –14 days.
Cerebrospinal fluid
Send in 3 sterile universal Daily containers.
Microscopy: Same day
Chlamydia trachomatis detection. Clostridium difficle – toxin detection CMV DNA
See detailed advice on page Not available at 22 PHL. Send a stool specimen. Daily
Coxiella burnetti (Q fever) Cryptococcal antigen
5-10 ml clotted blood
Comments Available for patients with reactive arthritis or Guillainbarré syndrome – sent to reference laboratory. Result routinely telephoned to ward/doctor.
Culture: 48 – 72 h.
5ml blood EDTA
Cryptosporidium detection Dengue Fever EBV DNA
5-10 ml clotted blood CSF Send stool specimen. 5-10 ml clotted blood 5ml blood EDTA
Epstein Barr (EBV) Echinocococcus Ehrlichia
Please contact laboratory. 1 day
Not available at PHL.
Please contact laboratory 10-14 days
Not available at PHL. Daily
Sent to reference laboratory. Please contact laboratory.
Same day 10 – 14 days
Request cryptosporidium. Sent to Reference laboratory. Please contact laboratory.
CSF
1 Week
Sent to reference laboratory.
5-10 ml clotted blood Bloodfilm (haematology)
Allow 10 –14 days.
Sent to reference laboratory.
Allow 10 –14 days.
Please discuss with Microbiology medical staff.
Serology available – 5-10 ml clotted blood
Not available at PHL.
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TEST Eye swab Faeces
SPECIMEN When performed Collect sample as skin swab. Daily. Send faeces in sterile Daily. universal container. 5-10 ml clotted blood
Filaria Fluid – see individual site e.g. pleural fluid etc Galactomannan 5-10 ml clotted blood
Not available at PHL.
Gastric biopsy
Send antral and corpus biopsy in sterile universal container.
Hair for fungal infection.
Send hair follicles
Twice weekly
H. pylori serology Hepatitis B: Anti-HBs
5-10ml clotted Blood.
Weekly
HbsAg
Estimated Turnaround time Culture: 48- 72 h. Microscopy: not routinely performed Culture: 4 days. Allow 10 –14 days.
Comments
Sent to reference laboratory. Please discuss with Microbiology medical staff. Please discuss with Microbiology medical staff prior to sending.
Microscopy: 24 h Culture: 3-4 weeks Same day
Sent to reference laboratory.
5-10ml Clotted blood 5-10ml Clotted blood
Sent to NVRL Sent to reference lab.
Other Hep. B markers Hepatitis B DNA
5-10ml Clotted blood 5ml blood EDTA
Hepatitis C
Serology: 5-10ml Clotted blood PCR: 5-10ml Clotted blood
Sent to NVRL Sent to reference lab. Sent to reference lab.
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TEST Histoplasma capsulatum HIV Ag/Ab
SPECIMEN 5-10 ml clotted blood 5-10 ml clotted blood
Legionella pneumophila
Send urine for legionella urinary antigen. 5-10 ml clotted blood Urine for dark ground microscopy.
Leishmaniasis Leptospirosis
When performed
Estimated Turnaround time Allow 10 –14 days.
Allow 10 –14 days.
Comments Sent to reference lab. Sent to NVRL Sent to reference lab. Contact Microbiology medical staff. Sent to reference lab. Please contact the laboratory Sent to reference lab.
Line tips
Lyme disease (see Borrelia bugdorferi) Microsporidiosis MRSA screen Mycobacteria (TB)
Serology: 5-10 ml clotted blood Cut the distal 3 cm of the line Daily with a sterile scissors and transport to the laboratory in a sterile universal container.
Culture: 48 – 72 h.
Send faeces.
Allow 10 –14 days.
Send swabs of nose, throat Daily and perineum/groin. Specimen depends on clinical Daily presentation. The following may be submitted: Sputum, Specimens obtained at Bronchoscopy, Pus, CSF, Pleural, Peritoneal, Joint and other Sterile Fluids, Tissue, Bone, Gastric aspiration, Blood, Bone marrow, Urine in
48 –72 h.
Request microsporidium. Sent to reference laboratory.
Please see full details in Microscopy: 24 h. Mycobacteriology section Culture: 7 weeks for negative report. Positive results telephoned as soon as page 29. available.
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TEST Nail for fungal culture Nose swab Ova and parasites Pericardial fluid/aspirate Peritoneal fluid/aspirate Pleural fluid/aspirate Rickettsia Schistosomiasis
SPECIMEN When performed certain circumstances. Send nail clippings in sterile Twice weekly. universal container or use a ‘Mycotrans’ container Send swab. Daily Send faeces or send sellotape Daily slide. Send 5-10 ml in sterile universal container Send 5-10 ml in sterile universal container
Daily.
Send 5-10 ml in sterile universal container 5-10 ml clotted blood 5-10 ml clotted blood
Daily.
Daily.
Urine On request. Skin scrapings for suspected Scrape lesion with back of meningococcal disease needle until blood is seen. Gently depress sterile glass slide. Send to laboratory in slide container. Sputum Send specimen in sterile Daily universal container. Strongyloides 5-10 ml clotted blood Syphilis Dark ground Microscopy
Estimated Turnaround time
Comments
Microscopy: 24 h Culture: 3-4 weeks 48-72 h. 24 h.
Sellotape slide for diagnosis of Enterobius vermicularis infection.
Microscopy: Same day Culture: 48-72 h Microscopy: Same day Culture: 48-72 h Microscopy: Same day Culture: 48-72 h Allow 10 –14 days. Allow 10 –14 days. 24 h. Microscopy: 1 h
Microscopy: 8 h. Culture: 48 – 72 h. Allow 10 –14 days.
Sent to reference laboratory. Sent to reference laboratory. Available on request. Available on request. Please contact laboratory.
Store at 4°C if delay of > 4 h. Sent to reference laboratory. Please contact laboratory.
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TEST
SPECIMEN
When performed
Serology Throat swab
5-10 ml clotted blood Throat swab
Trypanosomiasis Tuberculosis (see Mycobacteria) Urine
5-10 ml clotted blood Send MSU or CSU.
Daily
Vaginal swab
Send high vaginal swab.
Daily
Wound swab
Send pus in sterile universal container if possible. If insufficient material, send swab. Faeces
Daily
Yersinia spp.
Daily
Estimated Turnaround time Culture: 48 – 72 h Allow 10 –14 days.
Daily
Comments Result telephoned if BHS group A isolated. Sent to reference laboratory.
Microscopy: same day Please refrigerate pending Culture: 24-48 h delivery. Microscopy for Bacterial vaginosis: 24 h. Culture: 48 h. Microscopy: Same day Culture: 48-72 h. 48-72 h.
5-10 ml clotted blood Allow 10 –14 days. Sent to reference laboratory. 1.Tests performed daily are performed on working days only. 2.This is not a comprehensive list. If any test required is not on this list please contact the Medical Staff in the Microbiology Laboratory.
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Appendix 2 - Reference Laboratories currently used for specimen referral Test Specimen Required Reference laboratory Actinomycosis antibodies Serum Mycology Reference Laboratory Bristol Adenovirus Culture Nasopharyngeal asp, Virology Dept, Manchester Medical Micro Partnership PCR tissue, Blood Faeces, Eye swab Amoebiesis Serum UCL Hospitals Dept of Clinical Parasitology Arbovirus Serum Special Pathogens Porton Down Aspergillus Precipitins Serum Mycology Reference Laboratory Bristol Atypical Pneumoniae Sreen Serum National Virus Reference Laboratory UCD Dublin 4 Avian antibodies Serum Mycology Reference Laboratory Bristol Babesia Serum UCL Hospitals Dept of Clinical Parasitology Bartonella (CatScratch) Serum Lab of Respiratory & Systemic Infection, Colindale BK PCR Urine/EDTA Virology Dept, Manchester Medical Micro Partnership Blastomycosis antibodies Serum PHLS Mycology Reference Laboratory Leeds Bordetella pertussis ID Isolate Lab of Respiratory & Systemic Infection, Colindale Swab Our Lady’s Hospital for Sick Children Dublin 12 Bordetella pertussis culture Borrelia burdorferi (Lyme) Serum National Virus Reference Laboratory UCD Dublin 4 Serum PHLS Lyme Disease Ref. Unit Southampton Borrelia burgdorferi Brucella IgM Serum Liverpool Public Health Laboratory Candida anti-fungal MIC Isolate Mycology Reference Laboratory Bristol Test Specimen Required Reference laboratory Chages Disease Chlamydia Serology Non STI CMV Culture
Serum Serum Throat swab/washings, urine, BAL
UCL Hospitals Dept of Clinical Parasitology National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4
CMV PCR CSF CMV Serology
CSF Serum
Virology Dept, Manchester Medical Micro Partnership National Virus Reference Laboratory UCD Dublin 4
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Coccidiodes antibodies Coryne diph. Toxin testing Cryptosporidia genotyping CSF for CJD Cycloserine levels Cysticercosis Dengue E.coli 0157 antibodies E.coli 0157 Typing EBV PCR Echinococcal Test Entamoeba Enterococcus Typing Test Enteroviral PCR Enterovirus/ECHO/Coxackie Epstein Barr Virus EBV Epstein Barr Virus EBV PCR Extrinsic Allergic Alveolitis Screen Faeces Rotavirus/SRSV Farmers Lung Filaria Flucytosine levels Fungal ID Haemorrhagic fever Hantavirus antibodies Hepatitis A Virus Hepatitis B core Antibody Hepatitis B Markers
Serum Isolate CSF Serum Serum Serum Serum Isolate EDTA/CSF Serum Serum Isolate Specimen Required CSF Faeces, tissue, CSF, pleural fluid Serum Plasma CSF Serum Faeces Serum Serum Serum Isolate Serum Serum Serum Serum Serum
PHLS Mycology Reference Laboratory Leeds Lab of Respiratory & Systemic Infection, Colindale Lab. Of Enteric Pathogens. Colindale Neuropathology Laboratory Beaumont Hospital Antimicrobial Reference Laboratory UCL Hospitals Dept of Clinical Parasitology Special Pathogens Porten Down Lab. Of Enteric Pathogens. Colindale Public Health Laboratory COH Virology Dept, Manchester Medical Micro Partnership UCL Hospitals Dept of Clinical Parasitology UCL Hospitals Dept of Clinical Parasitology Lab of Hospital Infections Colindale Reference laboratory Virology Dept, Manchester Medical Micro Partnership National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4 Virology Dept, Manchester Medical Micro Partnership Mycology Reference Laboratory Bristol National Virus Reference Laboratory UCD Dublin 4 Mycology Reference Laboratory Bristol UCL Hospitals Dept of Clinical Parasitology Antimicrobial Reference Laboratory Mycology Reference Laboratory Bristol Special Pathogens Porten Down Special Pathogens Porten Down National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4
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Hepatitis C Genotyping Hepatitis C Viral Load Hepatitis C Virus PCR Hepatitis D Virus Test Herpes simplex Virus 1,2 HSV Herpes simplex Virus 1,2 HSV Herpes simplex Virus Type Specific HHV6 PCR HHV8 PCR Histoplasma Urinary Antigen HIV Confirmation Test HIV Genotyping HIV Viral Load HSV PCR HTLV I and II Hydatid Influenza
Serum Serum Serum Serum Specimen Required Serum Skin, vesicle fluid Serum EDTA EDTA Urine Serum Blood in EDTA Blood in EDTA CSF Serum Serum Throat swab/washings, Nasal swab
National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4 Reference laboratory National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4 Virology Dept, Manchester Med. Micro Partnership Enteric Respiratory/ Neurological Virus lab.Colindale Royal Free Hospital London National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4 Virology Dept, Manchester Medical Micro Partnership National Virus Reference Laboratory UCD Dublin 4 UCL Hospitals Dept of Clinical Parasitology National Virus Reference Laboratory UCD Dublin 4
Itraconazole levels Japanese Encephalitis JC Virus Lassa Fever Test Leishmanii Leptospirosis Lyme PCR Measles Virus
Serum
Mycology Reference Laboratory Bristol Special Pathogens Porton Down Virology Dept, Manchester Medical Micro Partnership Special Pathogens Porton Down Reference laboratory UCL Hospitals Dept of Clinical Parasitology National Virus Reference Laboratory UCD Dublin 4 PHLS Lyme Disease Ref. Unit Southampton National Virus Reference Laboratory UCD Dublin 4
CSF Serum Specimen Required Serum Serum Serum Serum
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Measles Virus Test
Nasopharyngeal asp, Throat swab, CSF Specimen Required
Reference laboratory
Meningococcal PCR Microsporidia Mumps Virus Mumps Virus
CSF/Blood Faeces Serum Throat swab, CSF, Urine
IMMRL Childrens Hospital Temple Street Dublin 1 UCL Hospitals Dept of Clinical Parasitology National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4
Mushroom Pickers Disease Mycobacteria ID Susc Mycobacteria Specimens PCR Mycoplasma pneumoniae Nocardia ID P.aeruginosa Typing Parainfluenza virus
Serum Isolate Specimens Serum Isolate Isolate NP asp, mouth washings
Mycology Reference Laboratory Bristol Scottish Mycobacteria Reference Lab HPA Mycobacteria Reference Unit, Clinical Recearch National Virus Reference Laboratory UCD Dublin 4 Enteric Respiratory/ Neurological Virus lab.Colindale Lab of Hospital Infections Colindale National Virus Reference Laboratory UCD Dublin 4
Test
Specimen Required
Reference laboratory
Parvovirus PCR Pneumococcal PCR Polio Q Fever (Coxiella burnetti) Respiratory Flu Screen Respiratory Syncytial Virus RSV
Serum Serum Serum Serum Nasopharyngeal asp, Nasopharyngeal asp, sputum Serum Serum Serum Isolate Serum Faeces
Enteric Respiratory/ Neurological Virus lab Colindale Molecular/PCR PHL Newcastle Polio Enterovirus Ref. Lab. Colindale National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4
Rickettsia Rocky mountain Spotted Fever Rubella Salmonella ID Shistosoma SRSV (Norovirus)
National Virus Reference Laboratory UCD Dublin 4
Special Pathogens Porton Down Special Pathogens Porton Down National Virus Reference Laboratory UCD Dublin 4 National Salmonella Reference Lab. UCL Hospitals Dept of Clinical Parasitology National Virus Reference Laboratory UCD Dublin 4
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Strongloides Toxacara antibodies Toxaplasma Dye/PCR Toxocara Toxoplasma gondii Trichinella Trypanosomes Test Typhoid Varicella zoster Virus VZV Varicella zoster Virus VZV VRE ID VZV PCR West Nile Virus Whipples Disease PCR Whipples Disease PCR Yellow Fever
Serum Serum CSF/ EDTA Serum Serum Serum Serum Specimen Required Isolate Serum Skin, vesicle fluid Isolate CSF Serum/CSF EDTA/ CSF Gastric Biopsy Serum
UCL Hospitals Dept of Clinical Parasitology UCL Hospitals Dept of Clinical Parasitology Toxaplasma Reference Unit UCL Hospitals Dept of Clinical Parasitology National Virus Reference Laboratory UCD Dublin 4 UCL Hospitals Dept of Clinical Parasitology UCL Hospitals Dept of Clinical Parasitology Reference laboratory Enteric Respiratory/ Neurological Virus lab Colindale National Virus Reference Laboratory UCD Dublin 4 National Virus Reference Laboratory UCD Dublin 4 Lab of Hospital Infections Colindale Virology Dept, Manchester Medical Micro Partnership Special Pathogens Porton Down PHLS Mycology Reference Laboratory Leeds PHLS Mycology Reference Laboratory Leeds Special Pathogens Porton Down
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