Download bacteriology / mycology / parasitology

BACTERIOLOGY / MYCOLOGY
/ PARASITOLOGY
This sub-section covers the detection and isolation of bacteria, fungi and parasites. For
sexually-transmitted pathogens, see sub-section on Immunology / Serology / STD / Allergy;
for viruses, see sub-section on Virology.
CONTENTS
SPECIAL INSTRUCTIONS ON SAMPLE COLLECTION AND HANDLING
•
•
•
Introduction
Request form
Specimen collection
ALPHABETICAL TEST LISTING
•
Bacteria
– Culture
– Microscopy and other tests
•
•
Fungi
Parasites & other investigations
SPECIAL INSTRUCTIONS ON SPECIMEN COLLECTION AND HANDLING
INTRODUCTION
Accurate and relevant results in microbiology depend on both the client and the
laboratory. The many factors contributing to the successful isolation of potential
pathogens include specimen selection, collection and timely transport to the
laboratory. All diagnostic information from the microbiology laboratory is contingent
on the quality of specimen received. Consequences of a poorly collected or poorly
transported specimen include failure to isolate the causative microorganism and
recovery of contaminants or normal microbiota, which can lead to improper treatment
of the patient.
REQUEST FORM
Relevant clinical information is needed to help the laboratory in processing the
specimen optimally. The attending doctor’s name and contact number should be
clearly indicated, as he may need to be contacted for urgent or critical results.
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Recent, current or intended antimicrobial treatment should be indicated to help the
microbiologist interpret test results and to help in the selection of antimicrobials to
be tested. Previous culture or serological results should be given where possible. The
microbiologist should first be consulted if the attending clinician is unsure of which
appropriate test(s) to request for.
SAMPLE COLLECTION
GENERAL CONSIDERATIONS
SAFETY
1. Follow standard precaution guidelines. Treat all samples as potentially hazardous.
2. Do not contaminate the collection container or its accompanying paperwork.
Use plastic sealable bag with a separate pouch for the request form; the latter may
be stapled to a bag without a pouch.
COLLECTION
1. Collect sample before administering antimicrobial agents when possible.
2. Identify the sample source and specific site correctly, so that proper culture media
will be selected during processing in the laboratory.
3. Indicate when a particular organism is being specially sought for in the specimen.
4. If a sample is to be collected through intact skin, the skin should be prepared
first. For example, cleanse skin with 70% alcohol followed by disinfection with
chlorhexidine gluconate or iodine-containing preparations (1 to 2% tincture
of iodine or 10% solution of povidone-iodine). Both tincture of iodine and
chlorhexidine gluconate are considered superior to povidone-iodine preparations
for skin disinfection. Swab concentrically, starting at the centre and progressing
outwards. Sufficient standing time is needed for the disinfectant to work (30
seconds for tincture of iodine and chlorhexidine gluconate and 1.5 to 2 minutes
for povidone-iodine). Prevent burn by tincture of iodine by removing excess with
70% alcohol after specimen has been collected.
5. Use appropriate collection devices. Use sterile equipment and aseptic technique
to collect samples to prevent introduction of microorganisms during invasive
procedures.
6. Collect sample with as little contamination from indigenous microbiota as
possible, to ensure that the sample will be representative of the infected site.
7. Collect an adequate amount of sample. Inadequate amounts of sample may yield
false-negative results.
8. Collect samples in sturdy, sterile, screw-capped, leak-proof containers with lids
that do not create an aerosol when opened.
9. Clearly label the sample container with the patient’s name and identification
number, and with the date and time of collection.
10. Samples obtained using needle aspiration should be transferred to a sterile tube
or anaerobic transport vial before transport to the laboratory. If there is little
material in the syringe, the needle may be removed with a protective device to
prevent injury and the syringe capped prior to transporting to the laboratory.
TRANSPORT
1. Transport all samples to the laboratory promptly
(a) to ensure the survival and isolation of fastidious organisms and to prevent
overgrowth by more hardy bacteria;
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2.
3.
4.
5.
(b) to shorten the duration of specimen contact with some local anaesthetics
used during collection that may have antibacterial activity.
Specimens should reach the laboratory within two hours of collection.
When delay in transport of specimens for bacterial culture cannot be avoided,
refrigerate samples at 2 to 8°C, except for blood, CSF and anaerobic cultures
which should be held at room temperature or 35°C.
Pus, fluids, tissue, urine and sputum may be sent in a sterile container.
Special transport media are required for anaerobes, Bordetella pertussis, and
Leptospira. For Neisseria gonorrhoeae, Chlamydia, Mycoplasma and Ureaplasma,
see Immunology / Serology / STD / Allergy.
COLLECTION BY SPECIMEN TYPE
BLOOD CULTURE
1. Blood collection
(a) Put on a pair of sterile gloves.
(b) Wipe the diaphragm of the culture bottle with 70% alcohol (do not use
iodine). Cleanse and disinfect intact skin as detailed above in the section on
Sample Collection (Collection, point 4).
(c) Allow sufficient standing time for the disinfectant to dry. Do not palpate the
vein after disinfecting the skin prior to inserting needle. (Gowns and sterile
drapes are not needed if the above is strictly followed.)
(d) Draw blood through a needle and inoculate blood culture bottles. It is not
necessary to change the needle prior to inoculation of the bottles in order to
minimise the risk of a needlestick injury. If the blood drawn is to be also used for
other investigations, e.g. electrolytes, inoculate the blood culture bottles first.
(e) If iodine was used in skin preparation, wipe off residual iodine from patient’s
skin with 70% alcohol to prevent skin irritation.
(f ) Do not refrigerate the bottles. If delay in transport to the laboratory is
anticipated, you may leave the bottles at room temperature.
(g) The BACTEC bottles in use are: Aerobic Plus/F for aerobic bacterial blood
culture, Anaerobic Plus/F for anaerobic bacterial blood culture and Myco F/Lytic
for fungal blood culture. Do not paste labels over the bar codes of the bottles.
2. Volume, number and timing of blood cultures
(a) Each blood culture set may consist of an aerobic and an anaerobic bottle.
(b) Usually, two or three culture sets drawn from different sites should suffice.
Do not send only one culture set as intermittent bacteraemia may be missed
and it may be difficult to determine the significance of certain bacteria. Try
not to draw blood through indwelling intravascular catheters.
(c) Recommended volumes : Bacterial culture : 8 to 10 ml of blood from adult
patients should be inoculated in each bottle. Fungal culture : 1 to 5 ml of
blood should be inoculated into each bottle. Pediatric patients : 1 to 3 ml of
blood in each bottle, total volume of blood cultured should not exceed 1% of
estimated total blood volume.
(d) Timing of blood cultures (regular intervals or in relation to fever) is not as
important as the total blood volume cultured.
(e) Preferably, obtain cultures before the use of systemic antimicrobials.
(f ) Acute sepsis, meningitis, osteomyelitis, arthritis, pneumonia: obtain two or
three sets of blood cultures.
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(g) Fever of unknown origin (such as that caused by an occult abscess): obtain
two sets initially, then another two sets 24 - 36 hours later.
(h) Suspected early typhoid fever or brucellosis: obtain four sets over 24 - 36 hours.
(i) Infective endocarditis:
(i) Acute, no antibiotics given within the past two weeks : Blood cultures
should be drawn immediately to avoid unnecessary delays in treatment.
Obtain three blood culture sets within a 30-minute period before
administration of empiric antimicrobial agents.
(ii) Subacute, or antibiotics given within past two weeks, or prosthetic valve:
Obtain three blood culture sets, spaced 30 minutes to 1 hour apart.
This may help document a continuous bacteremia. If initial cultures are
negative at 24 hours, obtain two more sets, for a total of five sets overall.
CENTRAL NERVOUS SYSTEM SPECIMENS
1. CSF
Suggested volumes are 1 and 2 mL for bacterial and fungal direct smears, cultures
and antigen testing respectively.
(a) Lumbar puncture
(i) Clean the puncture site with 70% alcohol and 10% povidone-iodine or 1
– 2% tincture of iodine before needle insertion.
(ii) Insert the needle with stylet at the L3-L4, L4-L5 or L5-S1 interspace.
When the subarachnoid space is reached, remove the stylet and spinal
fluid will appear in the needle hub.
(iii) Slowly drain the CSF into the sterile leak-proof tubes. Three tubes are
generally required for microbiology, haematology and biochemistry testing.
Send the second tube for microbiology and the third tube for haematology.
In any case, always send the most turbid tube to microbiology.
(b) Ommaya reservoir fluid
(i) Clean the Ommaya reservoir with antiseptic solution and alcohol.
(ii) Remove Ommaya fluid via the Ommaya reservoir unit, and place it in a
sterile tube.
2. Other CNS samples
(a) Brain abscess
(i) Aspirate material from the lesion and send it immediately to the laboratory
in an anaerobic transport medium, or the syringe, or a sterile container.
(ii) Request for Gram stain and culture (aerobic and anaerobic).
(b) CNS biopsy
Send sample obtained at surgery in a sterile container or in an anaerobic
transport medium. Do not add formalin.
GASTROINTESTINAL TRACT SPECIMENS
1. Stool and Rectal Swabs
Submitted primarily for the detection of Salmonella, Shigella, Campylobacter and
Vibrio and in certain cases, Yersinia, enteropathogenic E. coli and Clostridium
difficile. For enteric pathogens other than C. difficile, do not send more than 3
stool specimens and not after the third hospital day.
(a) Do not use toilet paper to collect stool. Toilet paper may be impregnated with
barium salts which are inhibitory for some faecal pathogens.
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2.
3.
4.
5.
(b) Transport stool to the laboratory within two hours.
(c) Obtain stool by having the patient pass stool into a clean, dry bedpan and
transfer stool into the container.
(d) Rectal swab
In general, rectal swab specimens have lower sensitivity than stool specimens
for fecal pathogens. Their major utility is in screening for Vancomycin
Resistant Enterococcus (VRE).
To perform a rectal swab, pass the tip of a sterile swab approximately 2.5 cm
beyond the anal sphincter. Carefully rotate the swab to sample the anal crypts
and withdraw the swab. The swab must be heavily loaded with faeces. For
detection of N. gonorrhoeae, plate immediately on Thayer-Martin medium
(see sub-section in Immunology / Serology / STD / Allergy).
Gastric lavage
Submitted primarily for the detection of lower respiratory tract pathogens in
patients (most frequently children) unable to produce quality sputum. Should
be performed after the patient wakes in the morning, so that sputum swallowed
during sleep is still in the stomach.
Pass a well-lubricated tube orally or nasally through to the stomach of the patient,
and perform the lavage. Before removing the tube, release the suction and clamp to
prevent mucosal trauma or aspiration (see sub-section in Mycobacteriology).
Duodenal aspirate
Submitted primarily for the detection of Giardia and larvae of Strongyloides
stercoralis and Ascaris lumbricoides. Pass a tube orally through to the duodenum
of the patient. To aspirate a sample for giardiasis, the end of the tube should be at
least in the third portion of the duodenum.
Endoscopic biopsy of stomach and duodenum
This is for detection of Helicobacter pylori in the stomach and duodenum, and
Strongyloides stercoralis and Giardia lamblia in the duodenum. Keep the sample
moist in a small amount of sterile saline in a sterile bottle, and despatch to the
laboratory without delay.
Small bowel biopsy should also be sent for histopathological examination if you
are looking for Giardia, Cryptosporidium, Microsporidium and Helicobacter
pylori.
Perianal sample for pinworm (Enterobius vermicularis)
Swab perianal area when patient gets up in the morning before patient bathes
or defaecates. You may use a commercial collection kit consisting of sticky
cellophane tape.
GENITAL TRACT SPECIMENS
1. Female
For the detection of Neisseria gonorrhoea and Haemophilus ducreyi, see subsection on Immunology / Serology / STD / Allergy.
For the detection of Herpes simplex virus, see sub-section on Virology.
(a) Amniotic fluid
Aspirate fluid by catheter, at Caesarean section or at amniocentesis.
(b) Bartholin gland
Decontaminate the skin with antiseptic and aspirate material from the duct(s).
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(c) Cervix
Do not use lubricant during procedure as certain lubricants may have an inhibitory
effect on microorganisms. Wipe the cervix clean of the vaginal secretion and
mucus. Insert a sterile swab stick into the endocervical canal and rotate the swab.
Allow the swab to remain in place for a few seconds and remove it.
(d) Endometrium
Collect endometrium samples by transcervical aspiration through a
telescoping catheter.
(e) Fallopian tubes
Obtain aspirates (preferably) or swab samples during surgery. Bronchoscopy
cytology brushes may be used if exudate is not expressed.
(f ) Urethra
Collect specimens one hour or more after patient has urinated. Stimulate
discharge by gently massaging the urethra against the pubic symphysis
through the vagina. Collect the discharge with a sterile swab.
If discharge cannot be obtained, wash external urethra with soap and rinse
with water. Insert a urethrogenital swab 2 to 4 cm into the endourethra, gently
rotate the swab, and leave it in place for 1 to 2 seconds. Withdraw the swab and
submit it for culture using the appropriate transport media for N. gonorrhoea.
(g) Vagina
Use a speculum without lubricant in collecting vaginal specimens.
High vaginal swab: Collect secretions from the mucosal wall high in the
vaginal canal (near the cervical area) with sterile pipette or swab. In general, a
high vaginal swab is not useful for investigating the cause of a pelvic infection,
although it is useful for vaginal infection. Vaginitis is most commonly due to
Trichomoniasis, Candidiasis or Bacterial Vaginosis.
Low vaginal swab : Insert sterile swab 1 to 2 cm into the lower entrance of the
vagina and collect secretions. For determining Group B Streptococcal (GBS)
carriage, a low vaginal swab should be taken and sent in suitable transport
medium (e.g. using Transwab® with semisolid modified Amies medium).
Screening for GBS carriage is best accomplished by a combination of low
vaginal and rectal/perianal swabs.
2. Male
(a) Anal swab for gonococcal infection and HSV – see sub-sections on
Immunology / Serology / STD / Allergy and Virology respectively.
(b) Epididymis
Use a needle and syringe to aspirate material from the epididymis after skin
disinfection.
(c) Penile lesion
Clean the surface of the lesion with 0.85% NaCl. Remove any crust if necessary.
Scrape the lesion until serous fluid emerges. For HSV, see instructions given
in sub-section on Virology. For Haemophilus ducreyi (chancroid), see subsection in Immunology / Serology / STD / Allergy.
(d) Prostatic specimens
For prostatic massage urine specimens, see “Prostatic massage” under “Urine”
later. A prostatic abscess detected by ultrasound may be aspirated. Prostatic
chips may be sent in a sterile container.
(e) Urethra
For N. gonorrhoeae, see sub-section in Immunology / Serology / STD / Allergy.
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OCULAR SPECIMENS
1. Conjunctival scrapings
(a) 1 or 2 drops of topical anaesthetic are generally instilled.
(b) Scrape the lower tarsal conjunctiva with a sterilised Kimura spatula.
(c) Inoculate the appropriate media directly (blood plate for bacteria, GC plate
for Neisseria gonorrhoeae).
(d) Prepare smears by applying the scraping in a circular manner to a clean glass
slide or by compressing material between two glass slides.
2. Corneal scrapings
(a) 1 or 2 drops of topical anaesthetic are generally instilled.
(b) Using short, firm strokes in one direction, scrape multiple areas of ulceration
and suppuration with a sterilised Kimura spatula.
(c) Inoculate each scraping directly onto appropriate media.
(d) Prepare smears by applying the scrapings in a gentle circular motion over a
clean glass slide or by compressing material between two glass slides.
3. Intraocular fluid
(a) Samples are obtained by needle aspiration or vitrectomy.
(b) Inoculate appropriate solid or liquid culture media directly (do not try
plating more than 0.5 mL of fluid on agar plate) or transport the sample in
a capped sterile syringe or place larger volumes of vitreous material into a
sterile container. Transport to the laboratory immediately.
RESPIRATORY SPECIMENS
1. General considerations
(a) 24-hour sputum collections are not recommended for culture.
(b) Sputum cultures for usual bacterial culture are less likely to be meaningful if
the patient has been on antibiotics, or if there is a dry non-productive cough.
(c) If Corynebacterium diphtheriae is suspected, inform the laboratory
beforehand, so that the appropriate media may be prepared. For N.
gonorrhoeae, Chlamydia and Mycoplasma, contact the “Serology” laboratory.
(d) For microscopy for Pneumocystis jirovecii (formerly P. carinii), bronchoalveolar
lavage (BAL) should be sent. Induced sputum with 3% hypertonic saline may
be obtained but the procedure should be done by skilled personnel trained in
the technique (see below).
2. Lower respiratory tract
(a) Expectorated sputum
(i) If possible, have the patient rinse mouth and gargle with water prior to
sputum collection.
(ii) Instruct the patient not to expectorate saliva or post-nasal discharge
into the container.
(iii) Collect sample resulting from deep cough in sterile screw-capped container.
(b) Induced sputum
(i) Using a wet toothbrush, brush the buccal mucosa, tongue and gums
before the procedure.
(ii) Rinse the patient’s mouth thoroughly with water.
(iii) Using an ultrasonic nebulizer, have the patient inhale approximately 20
to 30 mL of 3 to 10% NaCl.
(iv) Collect the induced sputum in a sterile screw-capped container.
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(c) Tracheostomy aspiration
Aspirate the specimen into a sterile sputum trap. Tracheostomy is followed
by colonisation within 24 hours of insertion of the tube. Results must be
correlated with clinical and X-ray findings.
(d) Endotracheal aspirate
Suction the excess secretions in the mouth around the tube. Using a new
suction catheter, place it within the tube and aspirate into a sterile sputum trap.
Endotracheal tubes (ETT) are often colonised with bacteria and results should be
correlated with clinical and X-ray findings. ETT tips are not acceptable samples.
(e) Bronchoscopy samples
These include bronchoalveolar lavage (BAL), bronchial washing, bronchial
brushing and transbronchial biopsy samples. For bacterial culture, BAL or
bronchial brushing using a protected bronchial brush is preferred.
(i) Pass the bronchoscope transnasally or transorally in non-intubated
patients or via the endotracheal tube in intubated patients.
(ii) Wedge the tip of the bronchoscope in a segmental (for bronchial wash)
or subsegmental (for BAL) bronchus.
(iii) To obtain specimens for bronchial wash or BAL, inject sterile nonbacteriostatic 0.85% NaCl (generally 5 to 20 mL aliquots) from a syringe
through a biopsy channel of the bronchoscope. Gently suction the 0.85%
NaCl into a sterile container before administering the next aliquot. (In
general, 50 – 75% of the 0.85% NaCl instilled is recovered in the lavage
effluent). Keep aliquots separate during collection. Combine aliquots
from the same site for microbiology cultures and smears
(iv) Bronchial brush specimens
Insert a telescoping double catheter plugged with polyethylene glycol
at the distal end (to prevent contamination of the bronchial brush)
through the biopsy channel of the bronchoscope.
(v) Transbronchial biopsy
Obtain the biopsy sample through the biopsy channel of the
bronchoscope, and transport it in a sterile container with a small
amount of sterile non-bacteriostatic 0.85% NaCl.
(f ) Lung aspiration
Using CT Scan guidance, obtain lung aspirate by inserting a needle through
the chest wall into a pulmonary infiltrate. Aspirate material from the lesion.
If the lesion is large or if there are multiple lesions, collect multiple specimens
from representative sites. Send the aspirate in a sterile container and/or
anaerobic transport medium.
(g) Lung biopsy
Obtain a 1 to 3 cm square piece of tissue if possible. If the lesion is large or
if there are multiple lesions, collect multiple specimens from representative
sites. Submit in a sterile container(s) without formalin.
(h) Pleural fluid
(i) Clean the puncture site with 70% alcohol and iodine solution (1% tincture
of iodine or 10% povidone-iodine). Aspirate and send as much pleural fluid
as possible in a sterile container and/or in anaerobic transport medium.
Taking samples from drains is not encouraged as any growth may represent
colonization. Please indicate in the form if this has been done.
(ii) Request for Gram stain and culture (aerobic and anaerobic).
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3. Upper Respiratory Tract
(a) Throat swab
Submitted primarily for detection of group A streptococcus. For pharyngeal
infection with N. gonorrhoeae, plate on Thayer-Martin medium, see subsection in Immunology / Serology / STD / Allergy).
(i) Depress tongue gently with tongue depressor.
(ii) Extend sterile swab between the tonsillar pillars and behind the uvula.
Avoid touching the cheeks, tongue, uvula or lips.
(iii) Sweep the swab back and forth across the posterior pharynx, tonsillar
areas and any inflamed or ulcerated area to obtain sample.
(b) Nasal swab
Submitted primarily for the detection of MRSA carriers.
(i) Insert a sterile swab into the nose. Rotate the swab against the anterior nares.
(ii) Repeat the process on the other side with the same swab.
(c) Nasopharyngeal suction
Submitted for the detection of carriers of group A Streptococcus, N.
meningitidis, C. diphtheriae and B. pertussis.
Suction material from the nasopharynx and collect it in a sterile container.
(d) Sinus aspirates
(i) Using a syringe aspiration technique, obtain material from the maxillary,
frontal or other sinuses.
(ii) Send the sample in the syringe or a sterile container.
(e) Tympanocentesis fluid
Submitted primarily to diagnose middle ear infections only if previous
therapy has failed.
(i) Clean the external canal with mild detergent.
(ii) Using a syringe aspiration technique, obtain fluid through the ear drum.
Send the sample in the syringe or in a sterile container.
(iii) If the ear drum is ruptured, collect exudate by inserting a sterile swab
through an auditory speculum.
4. Other considerations
For fungal infections of the lung, lung biopsy or aspirates are the best specimens.
Otherwise, collect three early-morning fresh specimens of 3 – 5 mL each from
deep cough or sputum induction.
Anaerobes should only be sought from sinus aspirates, tympanocentesis fluid,
lung aspirates, protected BAL, protected specimen brushings and biopsy
specimens. Sputum and bronchial washings are not acceptable as they are usually
contaminated with oral anaerobes.
STERILE BODY FLUIDS (OTHER THAN CSF AND BLOOD)
1. Clean the needle puncture site with alcohol and disinfect it with an iodine solution
(1 to 2% tincture of iodine or 10% povidone-iodine).
2. Aseptically perform percutaneous aspiration to obtain pleural, pericardial,
peritoneal or joint fluid.
3. Expel air bubbles from the syringe, and send the specimen immediately in a sterile
container and/or in anaerobic transport medium.
4. Send 1 – 5 mL for aerobic bacterial isolation, 1 – 5 mL for anaerobic bacterial
isolation, >10 mL for fungal isolation, and >10 mL for mycobacterial isolation.
Inform the laboratory if gonococcal arthritis is suspected so that the appropriate
plates will be set up.
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SUBCUTANEOUS TISSUE AND SKIN SPECIMENS
1. Burns
Surface swabs may reflect colonising organisms rather than invasive species. If
necessary, try to obtain tissue from an infected area at the margins where bacteria
are invading healthy tissue.
2. Superficial wound, bacterial
(a) Syringe aspiration is preferable to swab collection.
(b) Disinfect the surface of the wound with 70% alcohol and then with an iodine
solution (1 to 2% tincture of iodine or 10% povidone-iodine). Allow the
disinfectant to dry prior to collecting the specimen.
(c) Using a 3 to 5 mL syringe with a 22 to 23 gauge needle, aspirate the deepest
portion of the lesion. If a vesicle is present, collect both fluid and cells from
the base of the lesion.
(d) If the initial aspiration fails to obtain material, inject sterile, non-bacteriostatic
0.85% NaCl subcutaneously.
(e) Repeat the aspiration attempt.
3. Superficial lesions, fungal
(a) Clean the surface with sterile water.
(b) Using a scalpel blade, scrape the periphery of the lesion. Samples
from scalp lesions should include hair that is selectively collected for
examination. If there is nail involvement, obtain scrapings of debris or
material beneath the nail plate. Transport in a sterile container. Skin
scrapings can be wrapped in a piece of clean, smooth-surfaced paper or
sandwiched between 2 slides (precleaned with 70% alcohol) and taped
together.
4. Ulcers and nodules
(a) Clean the area with 70% alcohol and then with an iodine solution (1 to 2%
tincture of iodine or 10% solution of povidone-iodine).
(b) Remove overlying debris.
(c) Curette the base of the ulcer or nodule.
(d) If exudate is present from ulcer or nodule, collect it with a syringe or sterile swab.
DEEP WOUNDS, ASPIRATES AND TISSUE SPECIMENS
1. Bite wounds and Traumatic wounds
Aspirate pus from the wound, or obtain it at the time of incision, drainage or
debridement of infected wound. Do not culture fresh bite or trauma wounds as
relevant infectious agents will likely not be recovered. Indicate clearly on the
request form if this is a bite wound and the animal involved if relevant, so that the
laboratory can look for specific pathogens.
2. Bone
(a) Obtain bone specimen at surgery.
(b) Submit in sterile container without formalin. Sample may be kept moist with
sterile 0.85% NaCl.
3. Deep wounds or abscesses
(a) Disinfect the surface with 70% alcohol and then with an iodine solution (1 to
2% tincture of iodine or 10% povidone-iodine).
(b) Aspirate the deepest portion of the lesion, avoiding wound surface
contamination. If collection is done at surgery, a portion of the abscess wall
should also be sent for culture.
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(c) For abdominal and other deep abscesses where anaerobic infection is likely,
send for Gram stain and culture (aerobic and anaerobic).
4. Soft tissue aspirate
(a) Disinfect the surface with 70% alcohol and then with an iodine solution (1 to
2% tincture of iodine or 10% povidone-iodine).
(b) Aspirate the deepest portion of the lesion or sinus tract. Be careful to avoid
wound surface contamination.
5. Further considerations
(a) Biopsy specimens or aspirates are better than swab specimens.
(b) For actinomycosis, send pus immediately in syringe, sterile container or
anaerobic transport medium.
URINE SPECIMENS
1. General considerations
Do not force fluids to make the patient void urine. Excessive fluid intake will
dilute and may decrease the organism count.
(a) Never collect urine from a bedpan or urinal.
(b) Thoroughly clean the urethral opening (and vaginal vestibule in females)
prior to collection procedures to ensure that the specimen obtained is not
contaminated with colonizing micro-organisms in this area.
(c) Soap rather than disinfectants, is recommended for cleaning the urethral
area. If disinfectants are introduced into the urine during collection, they
may be inhibitory to the growth of the microorganisms.
(d) Transport specimen to the laboratory within two hours of collection. If a delay is
expected, urine can be stored in the refrigerator at 4°C for a maximum of 24 hours.
(e) Use sterile containers to transport urine. Alternatively, use a dip-slide for urine
culture if urine is collected after office hours, on weekends or public holidays.
(f ) Any urine collection involving catheterisation should be done with
scrupulous aseptic technique to avoid introducing microorganisms into the
bladder. Catheterisation solely for the purpose of obtaining a urine specimen
for culture is not usually recommended.
(g) Send the first morning voided urine.
(h) Do not submit 24-hour urine collections for culture.
(i) Foley catheter tips are also not suitable samples.
2. Collection techniques
(a) Clean-catch urine samples (female)
(i) The person collecting the urine should wash hands with soap and water,
rinse and dry. If the patient is collecting the sample, she should be given
detailed instructions.
(ii) Cleanse the urethral opening and vaginal vestibular area with soapy
water or clean gauze pads soaked with liquid soap, from front-to-back.
(iii) Rinse the area well with water or wet gauze wipes, with the same frontto-back motion. Use each pad/wipe only once.
(iv) Hold labia apart during voiding.
(v) Allow a few mL of urine to pass. Do not stop the flow of urine.
(vi) Collect the midstream portion of urine in a sterile container.
(b) Clean-catch urine specimens (male)
(i) The person collecting the urine should wash hands with soap and water,
rinse and dry. If the patient is collecting the sample, he should be given
detailed instructions.
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SECTION 4: SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS & LAB TESTS
(ii)
(c)
(d)
(e)
(f )
(g)
Cleanse the penis, retract the foreskin (if not circumcised), and wash
with soapy water.
(iii) Rinse the area well with sterile water.
(iv) Keeping the foreskin retracted, allow a few mL of urine to pass. Do not
stop the flow of urine.
(v) Collect the midstream portion of urine in a sterile container.
Dip-slide collection
(i) Check dip-slide to make sure media has not fallen off, been contaminated
or dried up.
(ii) Collect mid-stream urine in another sterile container. Do not use the
dip-slide container to collect the mid-stream urine.
(iii) Dip the slide into the urine for 2 seconds. There must be sufficient urine
to cover all the media on the slide.
(iv) Drain off the excess urine from the slide.
(v) Replace the dip-slide in its own sterile container and screw the cap into place.
Ileal conduit urine
(i) Remove the external urinary appliance and discard the urine within
the appliance.
(ii) Gently swab and clean the stomal opening with a 70% alcohol pad and then
with an iodine solution (1 to 2% tincture of iodine or 10% povidone-iodine).
Using sterile technique, insert a double catheter into the stoma. (A double
catheter helps to minimise contamination of the sample with skin flora).
(iii) Catheterise the ileal conduit to a depth beyond the fascial level.
(iv) Collect the urine drained into a sterile container.
Straight catheter urine (in/out catheter)
Insertion of a catheter solely for the purpose of collecting a urine specimen
is generally discouraged. It may be considered when clean-catch urine is
unobtainable and a diagnosis is critical. Indicate on the request form that the
specimen was obtained by in/out catheterisation.
(i) Clean the patient’s urethral opening (and, in females, the vaginal
vestibule) with soap, and carefully rinse the area with water.
(ii) Using aseptic technique, pass a catheter into the bladder.
(iii) Discard the initial 15 – 30 mL of urine.
(iv) Collect a sample from the mid- or later flow of urine in a sterile container.
(v) Remove catheter upon completion of the procedure.
Indwelling catheter urine
Indicate on the request form that this is a catheterised specimen.
(i) Clean the catheter collection port with a 70% alcohol wipe.
(ii) Using aseptic technique, puncture the collection port with a needle
attached to a syringe. (Do not collect urine from collection bag).
(iii) Aspirate the urine, and place it in a sterile container.
Suprapubic aspiration (SPA) of the urinary bladder
SPA is useful in determining urinary infection in adults in whom infection
is suspected, and for whom results from routine procedures have been
equivocal and diagnosis is critical. SPA is also useful in paediatric patients
when clean-catch urine samples are difficult to obtain.
(i) Shave if necessary, and disinfect the suprapubic skin overlying the
urinary bladder.
(ii) Make a lance wound through the epidermis at the midline just above
the symphysis pubis.
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BACTERIOLOGY / MYCOLOGY / PARASITOLOGY
(iii) Introduce the needle and aspirate urine from the bladder and place
specimen in a sterile container.
(h) Bladder washout test (Fairly Method)
The bladder washout test is useful in determining the site of infection in the
urinary tract. Results are equivocal in about 10 to 20% of patients.
(i) Clean the urethral area with soapy water and rinse the area well with water.
(ii) Insert an indwelling catheter into the bladder through the urethra.
(iii) Collect an initial urine sample into a sterile container and refrigerate it.
(iv) Empty the bladder through the urethral catheter and then irrigate it
using sterile non-bacteriostatic 0.85% NaCl.
(v) Collect three additional samples (5 – 10 mL each) at 10 minutes interval
into separately labelled containers after irrigation of the bladder is
performed.
(vi) Submit the initial and timed collection samples to the laboratory, clearly
labelled with the time of each specimen collection.
(i) Cystoscopy: bilateral ureteral catheterisation
This is useful for determining the site of infection in the urinary tract.
(i) The patient is to have a full bladder before performing cystoscopy.
(ii) Clean the urethral area with soapy water and rinse the area well with water.
(iii) Insert a cystoscope (obturator in place) into the bladder.
(iv) With aseptic technique, collect 5 – 10 mL of urine from open stopcock
into a sterile container.
(v) Label this sample CB (catheterised bladder urine) and refrigerate it.
Then irrigate the bladder using sterile non-bacteriostatic 0.85% NaCl.
(vi) After irrigation of the bladder and insertion of the ureteral catheters, collect
irrigating fluid passing from the bladder through the ureteral catheters by
holding the ends of both catheters over an opened sterile container.
(vii) Label this WB (washed bladder urine) and refrigerate it.
(viii) Pass the ureteral catheters to each midureter or renal pelvis without
introducing additional irrigating fluid. Open both stopcocks of the
cystoscope to empty the bladder.
(ix) Discard the first 5 – 10 mL of urine from each ureteral catheter.
(x) Collect four consecutive paired urine specimens (5 – 10 mL) directly
into opened sterile containers.
(xi) Label these samples LK-1, RK-1, LK-2, RK-2 (LK for left kidney and RK
for right kidney). Submit all samples to the laboratory for culture.
(j) Prostatic massage
Indicated in the diagnosis of chronic prostatitis, but contraindicated in the
setting of acute prostatitis (as there is a risk of bacteraemia).
(i) Patient should have a full bladder before performing the procedure.
(ii) Retract foreskin (if necessary) and cleanse penis as described in Clean
Catch Urine Collection (male).
(iii) Collect pre-massage midstream Urine Specimen into a sterile container.
(iv) Once patient stops voiding, insert gloved finger per rectum with lubrication.
(v) Massage prostate from periphery to midline.
(vi) Collect a few drops of secretion from urethra into a second sterile container.
(vii) Collect 10 mL of urine for post-massage Urine Culture into a third
sterile container.
(viii) Label these samples appropriately and submit them to the laboratory
for culture.
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SECTION 4: SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS & LAB TESTS
ALPHABETICAL TEST LISTING – BACTERIA
CULTURE – PLEASE SEE GUIDELINES ON SPECIMEN COLLECTION
BACTERIAL IDENTIFICATION (REFERRED ISOLATES FROM OTHER LABORATORIES)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Pure culture of bacterial isolate on blood or nutrient agar
slant/plate, sealed and transported in a leak-proof bag
with accompanying request form stating name of referring
laboratory and contact number of pathologist, source of
isolate, patient particulars, salient clinical information and
clinician-in-charge. Isolate should not be more than 24
hours old.
: Culture, biochemical and serological tests
: Identification reported
: 2 – 3 days, depending on the nature of the organism.
Fastidious strains may require longer workup.
: Monday – Saturday
BACTERIAL CULTURE, AEROBIC (CLINICAL SAMPLE)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: For further details, see special instructions on collecting
specimens. It is important to indicate the source and type
of sample sent. Majority of samples are: blood, body fluids
and aspirates, cerebrospinal fluid, respiratory specimens
(sputum, throat swab, BAL, ETT aspirate), urine, swabs
from infected skin and other sites. Unacceptable specimens:
ETT tip, urinary Foley catheter
: Culture
: Organisms reported; no bacterial growth; no growth of
pathogens; normal oropharyngeal flora; no significant
bacterial growth; mixed flora; mixed enteric flora
: Negative
: 1 – 3 days
Positive
: 2 – 4 days depending on the number and
type of organisms and source of sample.
Urine
Negative
: 1 – 2 days
Positive
: 2 – 4 days
Blood
Negative
: 2 – 3 days
Positive
: 2 – 7 days
Sputum
Negative
: 1 – 3 days
Positive
: 2 – 5 days
Wounds
Negative
: 1 – 3 days
Positive
: 2 – 7 days
CSF and sterile fluids
Negative
: 3 – 4 days
Positive
: 2 – 7 days
: Monday – Saturday
(Monday – Sunday for Blood and CSF/sterile fluid cultures)
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BACTERIOLOGY / MYCOLOGY / PARASITOLOGY
BACTERIAL CULTURE, ANAEROBIC (CLINICAL SAMPLE)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
:
: For further details, see guidelines on collecting samples. It
is important to indicate the source and type of sample sent.
Suitable samples include anaerobic blood culture bottles, pus
sent in a syringe, tissue or swab sent in anaerobic transport
media, protected BALs, protected brush specimens
and sterile fluids sent to the laboratory within one hour.
Unacceptable samples include dry swabs and samples from
sites normally colonised by anaerobic bacteria, e.g. sputum,
ETT aspirate, bronchial washings, stool (except for C. difficile
culture), voided urine, vaginal swab, superficial material
collected from skin surface. If both aerobic and anaerobic
culture is desired, separate swabs must be sent.
: Culture
: Organisms reported; no growth of anaerobes; mixed
growth of aerobes and anaerobes
Negative : 4 – 8 days
Positive
: 4 – 8 days
Blood culture
Negative
: 4 – 5 days
Positive
: 4 – 7 days
Actinomyces
Negative
: 14 days
Positive
: 16 days
: Monday – Saturday
(Monday to Sunday for Blood cultures)
BORDETELLA PERTUSSIS CULTURE
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Nasopharyngeal aspirate or pernasal swab in casamino acid
transport medium. Request for the transport medium one
day beforehand. Specimen should also be sent for antigen
detection by immunofluorescence.
: Culture
: Bordetella pertussis isolated;
No Bordetella pertussis isolated
: Negative
: 7 days
Positive
: 4 – 14 days
: Monday – Saturday
CHANCROID CULTURE
(See sub-section on Immunology / Serology / STD / Allergy.)
CORYNEBACTERIUM DIPHTHERIAE CULTURE
Specimen required
: Sputum, pseudomembrane, nasal and throat swabs,
swab from skin lesions. Request for detection of this
organism must be specifically stated on the form. Inform
the laboratory beforehand so that the appropriate culture
media may be prepared, particularly if several people are
being screened for carriage.
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SECTION 4: SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS & LAB TESTS
Method
Test results
Turnaround time
Day(s) test set up
: Culture
: Corynebacterium diphtheriae isolated;
No Corynebacterium diphtheriae isolated
: Negative
: 2 days
Positive
: 3 – 5 days
The ward will be informed earlier of any presumptive
positive result pending further tests.
: Monday – Saturday
ENVIRONMENT CULTURE
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: e.g. air sampling by agar strips or other methods. As environmental
cultures are useful only in very specific circumstances,
consult the microbiologist for guidance if necessary.
: Culture
: Total bacterial count; no growth
Total bacterial count < 3 cfu/m3
Total fungal count < 3 cfu/m3
: Air and biological samples: preliminary report on Day 3
and final report on Day 8
: Monday – Saturday
LEGIONELLA CULTURE (CLINICAL SPECIMEN)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Sputum, BAL, lung tissue. Send also for antigen detection by
immunofluorescence and send blood for legionella serology.
: Culture
: Legionella pneumophila reported; No Legionella
pneumophila isolated
: Negative
: 10 days
Positive
: 6 – 14 days
: Monday – Saturday
MYCOPLASMA CULTURE
(See sub-section on Immunology / Serology / STD / Allergy.)
NEISSERIA GONORRHOEAE CULTURE
(See sub-section on Immunology / Serology / STD / Allergy.)
STOOL CULTURE (AEROMONAS/YERSINIA)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Stool in screw-capped container sent within two hours to
the laboratory. Specimens taken more than 72 hours after
hospitalisation may not be appropriate.
: Culture
: Organism reported; Negative for (organism requested)
: Negative
: 2 – 3 days
Positive
: 3 – 4 days
: Monday – Saturday
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BACTERIOLOGY / MYCOLOGY / PARASITOLOGY
STOOL CULTURE (CLOSTRIDIUM DIFFICILE)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Stool in screw-capped container sent within two hours to
the laboratory
: Culture
: C. difficile reported; No C. difficile isolated
: Negative
: 2 – 4 days
Positive
: 6 – 10 days
: Monday – Saturday
STOOL CULTURE (SALMONELLA, SHIGELLA, VIBRIO, CAMPYLOBACTER)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Stool in screw-capped container sent within two hours to
the laboratory. Specimens taken more than 72 hours after
hospitalisation may not be appropriate.
: Culture
: Organism reported; No Salmonella, Shigella, Vibrio,
Campylobacter species isolated
: Negative: 2 days
Positive: 3 – 4 days
: Monday – Saturday
STOOL SCREEN FOR VANCOMYCIN-RESISTANT ENTEROCOCCI (VRE)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Stool in screw-capped container (preferred) or rectal swab
: Culture on selective agar
: Enterococcus faecium (VRE), Enterococcus faecalis (VRE),
No Vancomycin-resistant
Enterococcus species isolated
: 3 – 6 days
: Monday – Saturday (Office hours)
UREAPLASMA CULTURE
(See sub-section on Immunology / Serology / STD / Allergy.)
BACTERIAL CULTURE (OTHER UNUSUAL ORGANISMS)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Consult microbiologist. Not all organisms can be cultured,
and some require special conditions to survive and grow.
: Culture
: Organism reported; No (organism) isolated
: Depends on the type of organism
: Monday – Saturday
STERILITY TESTING
Specimen required
: Commercial spore strip in a paper envelope for testing of hot
air oven (using Bacillus atrophaeus) or ethylene oxide (using
B. atrophaeus) or steam sterilization (using Geobacillus
stearothermophilus). Testing of other patient-use products
is not recommended; consult microbiologist before sending.
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SECTION 4: SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS & LAB TESTS
Method
Test results
Turnaround time
Day(s) test set up
:
:
:
:
For testing of pharmaceutical products, refer to sub-section
on Pharmaceutical Microbiology.
Culture
Growth reported; No bacterial growth
7 days (preliminary result issued in 2 days)
Monday – Saturday
MICROSCOPY AND OTHER TESTS
BACTERIAL ANTIGEN DETECTION (CSF)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: 1 mL CSF
: Latex Agglutination for Neisseria meningitidis serogroups
A, C, Y, W135, E. coli K1/N. meningitidis B, Haemophilus
influenzae type b, Streptococcus pneumoniae, group B
Streptococci
: Positive test reported
Negative (for organism requested)
: 4 – 18 hours
: Monday – Saturday
BORDETELLA PERTUSSIS IF (IMMUNOFLUORESCENCE) ANTIGEN DETECTION
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Nasopharyngeal aspirate
: Immunofluorescence
: Positive for B. pertussis by immunofluorescence;
Negative for B. pertussis by immunofluorescence
: 1 day
: Monday – Saturday
CHLAMYDIA, ANTIGEN DETECTION
(See sub-section on Immunology / Serology / STD / Allergy.)
CLOSTRIDIUM DIFFICILE TOXINS A AND B
(See sub-section on Immunology / Serology / STD / Allergy.)
GRAM STAIN
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Swab or pus from wound, abscess, eye, sputum and other
sites. Bacterial culture should usually be requested together
with the Gram stain. Please send separate swabs for gram
stain and culture. Please note that Gram Stain is routinely
done and reported for all sputum and CSF culture requests.
: Gram Stain
: Gram-positive/negative cocci/coccobacilli/bacilli
No organism seen; polymorphs and epithelial cells reported
where applicable (usually for sputum)
: 2 – 4 hours
: Monday – Saturday
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BACTERIOLOGY / MYCOLOGY / PARASITOLOGY
LEGIONELLA PNEUMOPHILA IF (IMMUNOFLUORESCENCE) ANTIGEN DETECTION
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Expectorated sputum, BAL, lung tissue
: Pooled monoclonal antibodies to L. pneumophila types 1 – 6
: Positive for L. pneumophila by immunofluorescence;
Negative for L. pneumophila by immunofluorescence
: 1 day
: Monday – Saturday
MRSA SCREENING (CLINICAL SPECIMEN)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Swab from anterior nares, swab from groin and axilla,
wounds, skin lesions (e.g. eczema), sputum. For screening
of carriers without lesions, only nasal swabs should be sent.
: Culture
: Positive for MRSA; No methicillin resistant Staphylococcus
aureus isolated
: 2 – 3 days
: Monday – Saturday
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SECTION 4: SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS & LAB TESTS
ALPHABETICAL TEST LISTING – FUNGI
CRYPTOCOCCUS MICROSCOPY
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: 1 mL CSF Cryptococcal antigen detection should be
requested too, as the latter is more sensitive.
: India Ink Stain
: Encapsulated blastoconidia seen, suggestive of C.
neoformans
No Cryptococcus species seen
: 2 – 4 hours
: Monday – Saturday
CRYPTOCOCCUS NEOFORMANS ANTIGEN (QUALITATIVE)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: 1 mL CSF; 5 mL blood in plain tube
: Latex Agglutination
: Positive for C. neoformans antigen;
Cryptococcus antigen: negative
: 2 – 24 hours
: Monday – Saturday
CRYPTOCOCCUS NEOFORMANS ANTIGEN (QUANTITATIVE)
Specimen required
Method
Test results
Method
Turnaround time
Day(s) test set up
: 1 mL CSF; 5 mL blood in plain tube. For following
progress of patient with cryptococcal meningitis, CSF is
preferred; blood may be useful for monitoring some HIV
patients.
: Latex Agglutination with serial dilution of CSF or sera
: Titre reported
: Blood : Cryptococcus neoformans antigen – negative (< 1:2)
CSF : Cryptococcus neoformans antigen – negative (undiluted)
: 24 hours
: Monday – Saturday
FLUCONAZOLE SUSCEPTIBILITY TEST FOR CANDIDA SPECIES
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Isolate from culture
: Minimum Inhibitory Concentration by (MIC) E-Test
: MIC value:
≤ 8 µg/mL
: susceptible (S)
16 – 32 µg/mL : susceptible-dose dependent (S-DD)
≥ 64 µg/ mL
: resistant (R)
: 1 week
: Monday – Saturday
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BACTERIOLOGY / MYCOLOGY / PARASITOLOGY
FUNGUS/CRYPTOCOCCUS/CANDIDA CULTURE
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Swab, pus, tissue, blood, CSF, skin scraping, nail clipping,
hair. Blood should be sent in fungal blood culture medium
which will be supplied on request. No special transport
medium is needed for the others. Skin scraping for
dermatophyte isolation may be sent wrapped in a piece of
clean, smooth black paper and enclosed in an envelope, or
sandwiched between two glass slides. For skin scraping,
scrape the active border with the blunt edge of a scalpel;
for nail clippings, scrape the infected tissue underneath the
nail; for hair, get representative abnormal hair, removed
with forceps, and including some scalp scales obtained
by scraping. Please indicate if a specific pathogen is being
sought e.g. Cryptococcus, Candida, Histoplasma.
: Culture
: Organism reported; No fungal growth
: 1 – 6 weeks
: Monday – Saturday
FUNGUS MICROSCOPY
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Scraping from skin, pus. For diagnosis of invasive fungal
infection, tissue should be sent for histopathological
examination.
: 20% Potassium hydroxide Wet Mount, Gram Stain,
Calcofluor White
: Blastoconidia seen;
Blastoconidia and pseudohyphae seen;
Hyphae seen; Hyphae and conidia seen;
No fungus seen
: 2 – 4 hours; longer for skin and nail
: Monday – Saturday
HISTOPLASMA CAPSULATUM ANTIBODY TEST
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: 3 mL blood in plain tube / 0.5 mL cerebrospinal fluid
: Micro-immunodiffusion
: Positive for Histoplasma Ab M and H band;
Positive for Histoplasma Ab M band;
Negative for Histoplasma Ab M and H bands
: 24 hours
: Once a week
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SECTION 4: SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS & LAB TESTS
ALPHABETICAL TEST LISTING – PARASITES & OTHER INVESTIGATIONS
ACANTHAMOEBA/NAEGLERIA CULTURE
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Corneal scraping, cerebospinal fluid, brain biopsy tissue
: Culture on non-nutrient agar containing Escherichia coli
: Positive for Acanthamoeba/Naegleria fowleri;
No Acanthamoeba/Naegleria fowleri isolated
: 10 days
: Monday – Saturday
CRYPTOSPORIDIUM/ISOSPORA/CYCLOSPORA MICROSCOPY
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Fresh stool, transported in screw-capped container to the
laboratory within 24 hours
: Modified Kinyoun Stain; Immunofluorescence in selected cases
: Organism reported; No Cryptosporidium parvum/ Isospora
belli or Cyclospora cayetanensis oocysts seen
: 2 – 4 hours
: Monday – Saturday
LEPTOSPIRA CULTURE
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Heparinised bood and cerebrospinal fluid in the first week of
illness. Urine after the first week of illness. Inoculate one drop
of fluid into each of two tubes of Fletcher’s medium (obtain
from Parasite Laboratory/Diagnostic Bacteriology). Send a
second sample 24 hours later. If there is a delay, keep the tubes
at room temperature in a dark place. Send for Leptospira
serology as well (see sub-section on Serology & Immunology).
: Wet Mount dark-ground microscopy (Direct microscopy
on clinical specimen is not recommended)
: Leptospira species seen; No Leptospira species seen
Leptospira species grown; No Leptospira species isolated
: 2 – 4 hours (microscopy), 14 days (culture)
: Monday – Saturday
LEUCOCYTE MICROSCOPY
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
:
:
:
:
:
Stool in screw-capped container
Wet Mount
Leucocytes seen/No Leucocytes seen
2 – 4 hours
Monday – Saturday
MICROSPORIDIA MICROSCOPY
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
:
:
:
:
:
Stool; eye scraping
Trichrome Blue Stain
Microsporidia seen; No Microsporidia species seen
4 – 6 hours
Monday – Saturday
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BACTERIOLOGY / MYCOLOGY / PARASITOLOGY
OCCULT BLOOD, STOOL
Specimen required
Patient preparation and
special precautions
Method
Test results
Turnaround time
Day(s) test set up
: Stool in screw-capped container delivered to the laboratory
within 24 hours. Because of the non-homogeneity of stool,
three consecutive samples may be sent (as three separate
tests; i.e. do not pool stools over several days).
: Aspirin, non-steroidal anti-inflammatory drugs,
corticosteroids, phenylbutazone, reserpine and alcohol can
cause irritation of the gastric mucosa and occult bleeding in
some patients. These agents should be avoided for a minimum
of two days prior to testing. No specific dietary restrictions
are necessary as this test is specific for human haemoglobin.
Patients with bleeding conditions (haemorrhoids and
menstrual bleeding) are not considered appropriate for testing.
: Immunochromatographic reaction using antibodies specific
to human Hb
: Positive; Negative
: 2 – 4 hours
: Monday – Saturday
OVA & PARASITE MICROSCOPY (BY TRICHROME STAIN)
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Fresh stool, transported in screw-capped container to the
laboratory within two hours. Specimens taken more than
72 hours after hospitalisation may not be appropriate.
: Trichrome Stain and Concentration
: Trophozoites/Cyst/Ova/Larva reported; No Ova, cyst,
trophozoites seen
: 8 – 24 hours
: Monday – Saturday
PNEUMOCYSTIS JIROVECII (FORMERLY P. CARINII) MICROSCOPY
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: Bronchoalveolar lavage. Induced sputum is acceptable,
provided it is correctly done by well-trained staff using 3%
hypertonic saline; it is nevertheless less sensitive than BAL.
: Silver Stain; Immunofluorescence using Monoclonal
Antibodies
: Pneumocystis jirovecii seen;
No Pneumocystis jirovecii seen
: 4 – 24 hours
: Monday – Saturday
SARCOPTES SCABIEI IN SKIN SCRAPING
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
:
:
:
:
:
Skin scraping from affected area
Wet Mount
Sarcoptes scabiei seen/No Sarcoptes scabiei seen
2 – 4 hours
Monday – Saturday
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SECTION 4: SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS & LAB TESTS
SCHISTOSOMA OVA IN URINE
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
:
:
:
:
:
Urine
Wet Mount
Schistosoma species seen/No Schistosoma species seen
2 – 4 hours
Monday – Saturday
STRONGYLOIDES IN RESPIRATORY SPECIMEN
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
:
:
:
:
:
Sputum, endotracheal aspirate
Wet Mount
Strongyloides stercoralis seen/No Strongyloides species seen
2 – 4 hours
Monday – Saturday
TRICHOMONAS MICROSCOPY
Specimen required
Method
Test results
Turnaround time
Day(s) test set up
: High vaginal swab; vaginal secretions
: Wet Mount
: Trichomonas species seen;
No Trichomonas species seen
No ova, cyst, trophozoites seen
: 2 – 4 hours
: Monday – Saturday
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