Parasitology Specimen Collection Guidelines

Specimen TypeCollectionaReplica limitsTransport Time and Temp to labComment(s)
GuidelinesDevicePreservativeMinimum Vol.

Arthropod (Tick) for ID

Place in leakproof container with 70% alcohol

Leakproof container

70% alcohol

Entire Arthropod


Indefinite at RTa

See separate collection procedure for scabies.

   Direct smear

1.  Warm the patient’s hands by covering them with a hot moist towel, by immersing them in warm water, or by rubbing them together briskly. 
2. Disinfect the palmar surface of the tip of the middle or “ring” finger with gauze soaked with 70% alcohol (do not use cotton as it may introduce artifacts). 
3. Allow alcohol to dry completely, as residual alcohol does not permit a drop of blood to “round up” and may also fix the red cells, rendering the thick smear unsuitable for staining.
4. Puncture the palmar area with a sterile disposable lancet, resulting in free-flowing blood.

Wear gloves when preparing thin or thick films.
Thin-smear preparation:
1. Place one drop of blood near one end of a slide.
2. Hold another slide at 45o angle and draw it into the drop of blood.
3. Allow the blood to spread the width of the slide and then rapidly push the spreader slide to the opposite end, producing a feathered smear.
4. Label slide, dry at RT, and stain as soon as visibly dry.
Thick-smear preparation:
1.  Touch a slide to a drop of blood (rounded up on the finger).
2.  Rotate the slide to form a circular film about the size of a nickel. (For blood without anticoagulant, stir blood 20-30 seconds to prevent formation of a fibrin clot.)


Malaria: STAT
Other: 2 h or less, RTa

Optimal time to obtain smear
Babesia spp: any time
Brugia malayib:
≈ midnight
Leishmania donovanivb: any time
Loa loab: ≈ noon
Mansonella ozzardib: day or night
Mansonella perstansb: night better than day
Plasmodium spp.c: between chills
Trypanosoma cruzib: acute stage
Trypanosoma brucei gambienseb,d: acute stage
Trypanosoma brucei rhodesienseb,d: acute stage
Wuchereria bancroftib: ≈ midnightc; additional smears obtained 6, 12, or 24 h after admission may be necessary.


1. For buffy coat concentration if filariasis, trypanosomiasis, and to a lesser extent leishmaniasis, collect 10 ml. of whole blood with heparin or EDTA (0.002 g/10 ml of blood).
2. Submit directly ( 15 min or less) to the laboratory at RTa.
3.  Thick or thin smears should be obtained via finger puncture; see above.


Heparin: filariasis, Trypanosoma spp.
EDTA: malaria; see comments

10 ml. or more

1 day

30 min or less, RTa

Common parasites: L.donovani, Trypanosoma spp., microfilariae
Venipuncture for malaria is common but not recommended because smears must be made within 1 h to detect stippling. However, this approach is common, and personnel learn to identify with or without stippling.


See “Specimen Type: CSF” (Table 1) for specific guidelines for obtaining a CSF specimen.

Sterile tube


1 ml or more


30 min or less, RTa

Common parasites:
Acanthamoeba spp, Balamuthia mandrillaris, Echinococcus spp., larval cestodes, microsporidia, Naegleria fowleri, Taenia solium, Toxoplasma gondii, Trypansoma spp.

Duodenal aspirate

Place aspirate in a sterile centrifuge tube and transport it directly (15 min or less) to the laboratory since specimens must be examined within 1 h of collection.

Sterile centrifuge tube


2 ml or more


15 min or less, RTa

Common parasites:
Clonorchis sinensis (eggs), Cryptosporidium parvum (oocyst),
Giardia lamblia (trophozoite), Isospora belli (oocyst), Strongyloides spp. (larvae)

Eye: corneal scraping for Acanthamoeba spp.

1. Instill two drops of local anesthetic into the conjunctival sac and/or onto the corneal epithelium.
2. Using a sterile spatula, scrape ulcers or lesions and either inoculate a non-nutrient agar plate directly or place scraping in PBS and transport to the laboratory.
3.  Apply remaining material to two clean glass slides for staining and fix immediately with 95% ethanol (cysts may become airborne when allowed to air-dry).

Direct inoculation of non-nutrient agar coated with bacterial overlay of PBS.




24 h or less, RTa

Common parasites:
Acanthamoeba spp., Naegleria spp.
Also contact lenses, lens cases, and all opened solutions.


1. Pass directly into a clean, dry container.
2. Specimens that cannot be examined within the recommended time must be transferred to an appropriate preservative (SAF).  Carefully remove the cap and attached spoon to pick several spoonfuls of the stool, especially from areas that are slimy, bloody, or watery.  Place the stool into the vial to the fill line. Mix well and allow to stand at RT for 30 min for adequate fixation.
3. For unpreserved specimens, the transport times must correspond to the recommendations provided below.
4. Submit three specimens over 7-10 days because shedding may be intermittent.

Sterile, leakproof, wide-mouth container.

SAF one vial system. Hold at RTa for 30 min for fixation.

1 part feces to 3 parts fixative


Indefinite, RTa

Common parasites: helminths, protozoa
Unacceptable stool specimen: (1) Contaminated with urine or water (e.g., from diapers); (2) nonpuncturable or dried specimen; (3) specimens containing bismuth, barium, magnesia, mineral oil, gallbladder dye.

The general waiting period necessary to allow substances to clear is 7 days, except for gallbladder dye which may require 21 days.


Parasite and cyclical peak:
Ascaris lumbricoides,
Dientamoeba fragilis, irregular
Diphyllobothrium latum, irregular
E. histolytica, 7-10 days
Giardia lamblia, 3-7 days
Hookworm, constant
Trichuris trichiura constant;
Schistosoma spp., irregular

Sterile, leakproof, wide-mouth container




Liquid: 30 min or less, RTa
Semisolid: 1 h or less, RTa
Formed: less than 24 h, 4oC


Pinworm paddle

1. Gently press the paddle’s stick side against several areas of the perianal region which spreads open the perianal folds.
2. Place the paddle in the transport container and tighten the cap.
3.  Daily consecutive specimens (6 or more) should be obtained before patient is considered infection-free.

Pinworm paddle kit




24 h or less, RTa

Common parasites:
Enterobius vermicularis, Taenia spp.
Specimens are best obtained at 10-11 p.m. or upon waking and before a bowel movement or both.
Wash hands after collection.

Skin snip

1.  A sharp razor blade can be used to obtain a sample of skin which may be so superficial that no bleeding occurs.
2.  Alternatively, a needle can be used to raise the skin and with a scalpel remove the skin below the needle.
3.  Any body location is satisfactory but the middorsal region just to one side of the midline is frequently selected.
4. Place the skin snip in a tube containing 0.2-0.4 ml. of saline.

Sterile tube

Sterile saline



30 min or less, RTa

Common parasites:

Onchocerca volvulus

Skin ulcer

1. Obtain scrapings or biopsies of the active margin of cutaneous or mucocutaneous ulcers. A punch biopsy is recommended.
2. Place sample in a sterile tube containing enough sterile saline to keep it moist.

Sterile tube

Sterile saline



30 min or less, RTa

Common parasites:
Acanthamoeba spp.; Entamoeba histolytica;
Leishmania spp.

  Schistosoma spp.

Peak egg excretion occurs between 12 and 3 p.m.
1. Collect a midday urine specimen in a sterile container.
2. In patients with hematuria, eggs are associated with the terminal (last-voided) portion of the specimen containing mucus and blood.

Sterile leakproof container


Entire midday urine


2 hr or less, RTa

Parasites: Schistosoma haematobium; Strongyloides stercoralis; Trichomonas vaginalis; W. bancrofti


Trophozoites can be found in the urine of both sexes.
1.  For males, prostatic massage may be useful.
2. Collect first voided urine in a sterile container.
3. Transport it to the laboratory within 1 h or less at RTa. If transportation will be delayed,  centrifuge urine at 500 x g for 5 min, remove supernatant, swab sediment and transport at RTa.
4. The sediment can also be smeared on a microscope slide, air dried, and stained
(Papanicolaou or Gram Stain).

a. Sterile, leakproof container




b. Alternatively, the centrifuged pellet may be adsorbed onto a dacron swab and transported in Amies medium, in which the organisms remain viable for ≈ 24 h. Do not use calcium alginate swabs

a. None





b. Liquid Amies culture device

a.Entire void





b. Sediment

a. 1/day





b. 1/day

a. < 1 h, RTa
Do not refrigerate



b. 24 h or less, RTa Do not refrigerate

a. Specimens must be held at RTa and processed within 1 h of collection.


b. Specimens must be held at RTa and processed within 24 h of collection.

a RT=room temperature; CSF=cerebrospinal fluid; CNS=central nervous system; SAF=sodium acetate-formalin.

b Collect 10 ml of heparinized blood for buffy coat concentration.

c Additional smears obtained 6, 12, or 24 h after admission may be necessary.

d CSF is specimen of choice for patients infected more than 6 months.

No Appointment Necessary
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