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Test ID: FLARP Free-Living Amebae, Molecular Detection, PCR, Varies

Useful For

Aids in the diagnosis of primary amebic meningoencephalitis and granulomatous amebic encephalitis in spinal fluid and tissue in conjunction with clinical findings


This test should not be used to screen asymptomatic patients.

Method Name

Real-Time Polymerase Chain Reaction (PCR)/TaqMan DNA Probe Hybridization

Reporting Name

Free-living Amebae Detection, PCR

Specimen Type


Necessary Information

Specimen source is required.

Specimen Required

Submit only 1 of the following specimens:


Specimen Type: Cerebrospinal fluid

Container/Tube: Sterile container

Specimen Volume: 0.5 mL

Collection Instructions: Send vial #2.


Specimen Type: Tissue: Fresh

Sources: Brain, skin, lung

Container/Tube: Sterile container

Specimen Volume: 5-10 mm

Collection Instructions: Submit tissue in a sterile container with 1 mL of sterile saline or minimal essential media (MEM).


Preferred Paraffin-embedded tissue block:

Supplies: Tissue Block Container (T553)

Specimen Type: Formalin-fixed, paraffin-embedded tissue block (FFPE)

Sources: Brain, skin, lung

Container/Tube: Tissue block

Collection Instructions: Submit a FFPE tissue block to be cut and returned.


Acceptable Paraffin-embedded tissue block:

Specimen Type: Formalin-fixed, paraffin-embedded tissue block (FFPE)

Sources: Brain, skin, lung

Container/Tube: Sterile container for each individual cut section (scroll).

Collection Instructions: Perform microtomy and prepare five separate 10-micron sections. Each section (scroll) must be placed in a separate sterile container for submission.

Specimen Minimum Volume

CSF: 0.3 mL; Tissue: 5 mm biopsy

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Refrigerated (preferred) 7 days
  Frozen  7 days

Clinical Information

Several free-living amebae can infect the central nervous system (CNS) and cause devastating, usually fatal, disease. The route of entry and clinical course of infection varies with the type of ameba involved. Naegleria fowleri typically causes rapidly progressive primary amebic meningoencephalitis (PAM) in previously healthy children or adults. Infection is acquired during contact with contaminated water, including swimming and diving in warm stagnant freshwater lakes and by nasal irrigation with nonsterile water. During contact, the amebae enter the nasal sinuses and travel along the olfactory nerve through the cribriform plate of the skull and into the CNS. PAM is almost uniformly fatal within several days of exposure. Because of the rarity of the infection and difficulty in initial detection, about 75% of diagnoses are made after the death of the patient. In contrast, Acanthamoeba species and Balamuthia mandrillaris usually cause a subacute CNS illness, usually in adults who are immunocompromised, called granulomatous amebic encephalitis (GAE). The presentation of GAE can mimic a brain abscess, aseptic or chronic meningitis, or CNS malignancy. The amebae may enter the nasal sinuses like N fowleri or can disseminate to the CNS from the lungs or a primary skin lesion.


These amebae are usually identified by microscopic examination of cerebrospinal fluid or brain tissue and agar culture. Culture is more sensitive than microscopy alone but takes up to 7 days to produce a positive result. Also, B mandrillaris will not grow in routine culture. Real-time polymerase chain reaction assays offers a rapid and sensitive alternative to microscopy and culture.

Reference Values



A positive result indicates the presence of free-living amoeba DNA and is consistent with active or recent infection. While positive results are highly specific indicators of disease, they should be correlated with symptoms and clinical findings of primary amebic meningoencephalitis and granulomatous amebic encephalitis.

Clinical Reference

1. Trabelsi H, Dendana A, Sellami A, et al: Pathogenic free-living amoebae: epidemiology and clinical review. Pathol Biol (Paris). 2012;60:399-405

2. Thompson PP, Kowalski RP, Shanks RM, Gordon YJ: Validation of real-time PCR for laboratory diagnosis of Acanthamoeba keratitis. J Clin Microbiol. 2008;46:3232-3236

Day(s) Performed

Monday through Sunday

Report Available

2 to 3 days

Test Classification

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information

87798 x 3

87798 (if appropriate for government payers)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
FLARP Free-living Amebae Detection, PCR 96910-5


Result ID Test Result Name Result LOINC Value
SSFLA Specimen Source 31208-2
38061 Acanthamoeba species PCR 41429-2
38062 Naegleria fowleri PCR 87758-9
38063 Balamuthia mandrillaris PCR 41432-6


If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.

Testing Algorithm

See Meningitis/Encephalitis Panel Algorithm in Special Instructions.

Mayo Clinic Laboratories | Microbiology and Infectious Disease Catalog Additional Information: