Naegleria Infection and Primary Amebic Meningoencephalitis (PAM) Workup

Updated: May 22, 2019
  • Author: Subhash Chandra Parija, MD, MBBS, PhD, DSc, FRCPath; Chief Editor: Mark R Wallace, MD, FACP, FIDSA  more...
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Laboratory Studies

The diagnosis of primary amebic meningoencephalitis (PAM) is always parasitic and is based on detection and identification of N fowleri trophozoites in the CSF or brain biopsy samples.


The CSF is the specimen of choice for demonstration of the amebae. Brain tissue biopsy can also be used for detection of antigen. [30]

Direct wet-mount microscopy

The CSF is centrifuged at 150 xg for 5 minutes. The supernatant is aspirated, and the sediment is suspended in the remaining fluid. A drop of sediment suspension is kept on a slide and mounted with a coverslip and is examined with compound light microscopy using 10X and 40X objectives. The specimen is best examined with phase contrast microscopy. This may show trophozoites with lobopodia extension and retraction.

The amebae are detected based on their active directional movements. Close observation is important because PAM can be diagnosed based on the observation of trophozoites; however, these have been confused with WBCs in reported cases. Cyst and flagellated stages are not found in CSF samples; if both cysts and trophozoites are found in CSF, it is highly suggestive of Acanthamoeba infection, ruling out Naegleria PAM.

A few drops of CSF are mixed with 1 mL of distilled water and examined after 1 hour for flagellated forms typical of N fowleri. Trophozoites of N fowleri measure around 10-25 μm, with typical limacine/eruptive amoeboid movement, indicating a positive enflagellation test result. [31]

Examination of stained CSF smear

CSF Gram stain findings are usually negative. RBCs are present. CSF stained with Wright-Giemsa or modified trichrome stain may show trophozoites with large karyosome and a contractile vacuole. [1] Direct fluorescent antibody staining of CSF smears is useful for demonstrating N fowleri in the CSF.


Naegleria species can be readily cultivated on either nonnutrient agar or agar media containing low concentrations of nutrients (eg, peptone 0.05%, yeast extract 0.05%, glucose 0.1%) in the presence of living or killed bacteria or in defined axenic media, as proposed by Chang et al and Nerad et al, among others. The culture plate can be incubated at 42°C, which facilitates the growth of only the thermophilic amoebae while killing the other free-living amoebae. [1] A nonnutrient/low-nutrient agar is chosen to prevent overgrowth of bacteria. [32] In general, the bacteria of choice include nonmucoid strains of Klebsiella pneumoniae, Enterobacter species (Enterobacter aerogenes and Enterobacter cloacae), and Escherichia coli. After several days, the plate is microscopically inspected; Naegleria cysts are identified by trails left by migrating amebae in the lawn of the bacteria. Various molecular methods can be used for final confirmation of the identity of the species.

In 2017, a liquid encystment medium modified from Page’s amoeba saline was reported to be useful for obtaining pure N fowleri cysts. [33]


Serologic testing has no role in the diagnosis of acute PAM, since little time is available from onset to death to mount an antibody response. In one survivor, detectable antibody persisted for more than 4 years.

Molecular diagnosis

PCR is available at some research sites using numerous primers. Molecular characterization of strains is also useful in tracking infections to a source and in recognizing potential risks for swimmers or bathers in particular locales. A species-specific DNA probe is available to identify N fowleri in environmental samples, followed by restriction fragment length polymorphism (RFLP) analyses of whole-cell DNA for confirmation. Epidemiologic typing of N fowleri was used in an analysis of the 5.8S rRNA gene and the internal transcribed spacer (ITS) of clinical isolates. In a study performed in the United States, a rapid, sensitive, and specific assay for the detection of N fowleri was developed using Mp2C15 probe in a nested PCR assay format. [34] A nested PCR assay has also been applied to detect the presence of the parasite in domestic water sources. [35]

Recently, flow cytometry has been used for the diagnosis of N fowleri infection. [36] Flores et al evaluated flow cytometry and monoclonal antibodies in differentiating Naegleria fowleri from Acanthamoeba species. [37]

Lately, a real-time PCR using hybridization fluorescent-labelled probes, targeting the N fowleri Mp2Cl5 gene sequence, has been developed. The reaction detection limit in their study was 1 copy of the Mp2Cl5 DNA sequence. [38]

Visvesvara has reported the development of a multiplex real-time PCR that could simultaneously look for Naegleria, Acanthamoeba, and Balamuthia species in a single specimen, thus reducing the time for diagnosis. This is especially useful as infection with any of the 3 amoebae could have clinical presentations indistinguishable from each other. [39] Similarly, Qvarnstrom et al described a TaqMan-based multiplex real-time PCR that targets the 18S rRNA gene in the detection of N fowleri, Acanthamoeba species, and Balamuthia mandrillaris. [40]


Both immunofluorescence and immunoperoxidase methods are useful for demonstrating N fowleri trophozoites in the histologic sections of the brain biopsy samples. [30]


Imaging Studies

Head CT scanning yields nonspecific findings, showing a loss of the subarachnoid space and diffuse gray material enhancement.


Other Tests

CSF studies show the following:

  • Sanguinopurulent or bloody CSF, showing a nonspecific polymorphonuclear (PMN) neutrophil – predominant neutrophilia

  • Increased opening pressure

  • PMN pleocytosis

  • Elevated RBC count or frank hemorrhagic CSF

  • Normal-to-low CSF glucose level

  • Elevated protein level



Lumbar puncture: Wet-mount examination of CSF is the main diagnostic tool in PAM.


Histologic Findings

N fowleri infection produces lesions mainly in the base of the brain, brain stem, and cerebellum. The olfactory mucosa and bulbs are the most commonly affected areas. The lesions consist of an acute necrotizing meningoencephalitis associated with moderately purulent exudates. Only trophozoites are found in the CNS lesions, not cysts