A case report of primary amebic meningoencephalitis in a Chinese adult male

Abstract

Primary amebic meningoencephalitis (PAM) is a rare neurological infectious disease with an extremely high mortality rate. This disease is caused by Naegleria fowleri invading the brain, and patient infections are usually linked to exposure to contaminated warm freshwater in summer. This case report describes a 56-year-old adult male, who presented with increased intracranial pressure, headache, blurred vision accompanied by dizziness, periorbital edema, fever (38.5 ℃), nausea, vomiting, and chills. The patient had bathed in a wild hot spring one week prior to symptom onset. In this case, we performed Wright-Giemsa staining on the sediment of the patient’s cerebrospinal fluid (CSF) and detected amoebic trophozoites. Through direct wet mount microscopy, we observed live amoebic trophozoites. We further conducted high-throughput pathogen sequencing on the patient’s CSF sediment. The results also confirmed that the infecting pathogen was Naegleria fowleri. Thus, the patient was diagnosed with PAM, and administered combined anti-infection treatment with amphotericin B (1.5 mg/kg·d) and rifampicin (10 mg/kg·d). The patient’s condition remained in critical condition and ultimately died of terminal cerebral hernia. PAM is a rare and difficult to diagnose infectious disease. We achieved rapid diagnosis of PAM through a combination of traditional microbiological microscopic examination and high-throughput sequencing of pathogenic microorganisms. The case report provides valuable experience for the diagnosis and treatment of PAM.

Introduction

Primary amebic meningoencephalitis (PAM) is a neurological infectious disease caused by Naegleria fowleri. PAM is more common in children and adolescents exposured to contaminated water (Hall et al. 2024). After invading the nasal mucosa, Naegleria fowleri migrates along the olfactory nerve, traverses the cribriform plate, and ultimately infiltrates brain tissue. This leads to inflammation of the olfactory bulb and subsequent destruction of both the olfactory bulb and surrounding brain tissue (Jahangeer et al. 2020). Early symptoms of PAM are similar to those of upper respiratory tract infections, but frontal headache is more severe. Subsequently, the patient presents with meningeal irritation signs such as neck rigidity, as well as taste, smell and vision disorders. The disease progresses rapidly, and patients often die within one week due to severe cerebral edema, which causes respiratory and circulatory center failure (Haston and Cope 2023). PAM is an extremely rare case, with only a few hundred cumulative cases worldwide and a mortality rate as high as 95% (Siddiqui and Khan 2014). This case report systematically details the patient’s medical history, comprehensive clinical manifestations, imaging and laboratory findings, and treatment regimens during the disease course. Its purpose is to enhance understanding of PAM, prevent misdiagnosis, and provide evidence for the clinical management and prognosis of PAM.

Case description

A 56-year-old male patient presented to the Emergency Department of Yan’an Hospital Affiliated to Kunming Medical University at 6:41 p.m. on May 27, 2025, presenting with generalized intracranial pressure and pain, blurred vision with dizziness, periorbital edema, fever (38.5 ℃), nausea, vomiting and chills. The patient denied a history of hypertension, coronary artery disease, diabetes mellitus, infectious diseases, or previous surgical procedures. It is worth noting that the patient had been exposed to a wild natural hot spring one week prior. The wild hot spring is in Sanjiangkou, Luquan County, Kunming City.

Emergency physicians performed a physical examination and found no abnormalities. Cranial computed tomography (CT) showed no hemorrhage, and magnetic resonance imaging (MRI) plain scan and diffusion-weighted imaging (DWI) revealed no definite abnormalities. Laboratory test results showed that the proportion of neutrophils in peripheral blood was abnormally elevated (89.3%), while the proportion of lymphocytes were abnormally decreased (8.0%). Meanwhile, C-reactive protein (CRP) was significantly elevated (74.51 mg/L). Cerebrospinal fluid (CSF) cytological examination showed a nucleated cell count of 810 × 10⁶/L (with neutrophils accounting for 85%), and the red blood cell count was 736 × 10⁶/L. The patient was initially diagnosed with intracranial infection and transferred to the Department of neurology for anti-infection treatment.

On May 28, 2025, the patient’s condition was remained critical, with a high fever of 39 ℃ and comatose consciousness. Both pupils were equal in size and round, with presented light reflexes. The patient was transferred from the Department of neurology to the Intensive Care Unit (ICU), and we further expanded microbiological testing. The 1,3-β-d-Glucan test and galactomannan test were negative. Cryptococcus species were not detected by India ink staining. Nucleic acid tests for Epstein-Barr (EB) virus, influenza A and B viruses, and COVID-19 virus were all negative. Aerobic and anaerobic cultures of whole blood and CSF yielded no growth of fungi or bacteria. Wright-Giemsa staining of CSF sediment revealed numerous neutrophils and amoebic trophozoites on microscopic examination (Fig. 1A). Wet mount microscopic examination of the CSF sediment identified motile amoebic trophozoites (Fig. 1B). In addition, high-throughput sequencing of pathogenic microorganisms in CSF was conducted for the identification of infectious agent.

Fig. 1.

The patient’s cerebrospinal fluid was stained with Wright-Giemsa and examined under a microscope with a wet mount. A Wright-Giemsa staining revealed numerous neutrophils and amoebic trophozoites on microscopic examination. The position indicated by the arrow is the trophozoite of Amoeba. B Amoeba trophozoites under wet mount microscopy. The position indicated by the arrow is the trophozoite of Amoeba

On May 29, 2025, the patient’s condition remained critical with intermittent respiratory distress. High-throughput pathogen sequencing results confirmed the pathogen as Naegleria fowleri. The specific experimental details are as follows: Total nucleic acid was extracted from 300 µL of CSF supernatant following mechanical disruption with 0.5 mm glass beads and centrifugation (12,000 × g, 1 min) using the MataPure™ DNA/RNA Extraction Kit (Cat. 20250501, King Create Biotechnology Inc., China). Libraries were constructed via end repair, adapter ligation, and PCR amplification, followed by targeted enrichment using the MetaCAP Pathogen Capture Metagenomic Assay Kit (Cat. 20250801, King Create Biotechnology Inc., China). After filtering low-quality reads and depleting host sequences via alignment to the human reference genome (hg38) using Burrows-Wheeler Aligner (BWA), non-human reads were mapped against a comprehensive microbial database comprising 13,214 bacteria, 9,811 viruses, 3,180 fungi, and 405 parasites. Analysis identified 2,112,053 non-human reads. Of these, specific mapping to the Naegleria fowleri genome yielded a coverage of 4.53% and a high average sequencing depth of 147.53×, confirming species identification (Fig. 2). Based on the above results, the patient was diagnosed with PAM after a multidisciplinary consultation. The patient was administered combined anti-infection treatment with amphotericin B (1.5 mg/kg·d) and rifampicin (10 mg/kg·d). At 0:00 on May 30, 2025, the patient’s condition deteriorated to extremely critical. The patient presented with a deep coma, characterized by bilaterally dilated and fixed pupils (7 mm diameter) and absent light reflexes. The patient’s family requested to discontinue treatment and be discharged. They were informed of the risks associated with discharge and signed a confirmation form. Follow-up on May 31, 2025, revealed that the patient had ultimately died of terminal cerebral hernia.

Fig. 2.

Genomic specificity of Naegleria fowleri identification. A Taxonomic distribution of microbial reads. Sankey diagram illustrates the flow of taxonomic classification for all non-human sequencing reads. The dataset is overwhelmingly dominated by the Eukaryota lineage leading to N. fowleri (94.1% of total non-human reads), with only negligible fractions attributed to environmental background bacteria (e.g., Candidatus Pelagibacter) and viruses. B Species-specificity analysis. Comparison of total mapped reads (dark blue) versus unique species-specific reads (light blue) across Naegleria species (log10 scale). While sequence homology results in non-specific mapping to N. lovaniensis, the overwhelming abundance of N. fowleri-unique reads unambiguously confirms species identity.

Discussion

The incubation period of PAM is relatively short, usually only 3 to 5 days, and at most 7 to 12 days (Gharpure et al. 2021). Early symptoms include abnormal taste and smell, which are reactions to pathogen invasion. The disease typically presents with severe headache, high fever and projectile vomiting, followed by generalized or localized seizures and obvious meningeal irritation signs (Güémez and García 2021; Berger 2022). Most patients progress to delirium, paralysis and coma within a few days and often die within one week due to respiratory and circulatory central failure caused by severe brain edema (Capewell et al. 2015). Among the presently characterised members of the genus Naegleria only Naegleria fowleri is known to infect the human central nervous system and to cause PAM. Naegleria fowleri is an obligate thermophile that can grow at temperatures as high as 46 °C (Leal Dos Santos et al. 2022). Warm freshwater rich in bacteria as a food source provides an ideal habitat for Naegleria fowleri. Many sites of Naegleria fowleri infections are contaminated water sources (Joseph et al. 2021). The patient in this case had been exposed to a wild natural hot spring one week prior, which is likely the main cause of Naegleria fowleri infection. This case highlights that avoiding activities in unfiltered, high-temperature water is an important measure to prevent Naegleria fowleri infection.

PAM has an extremely high fatality rate. In addition to its sudden onset, the difficulty in making a definitive diagnosis is another key reason for the high mortality rate. The patient’s initial clinical symptoms are similar to conventional meningitis (Chen et al. 2019). The patient in this case initially presented with generalized headache and distension, accompanied by fever, nausea and vomiting, which was similar to those of the clinical symptoms of meningitis and other common infectious diseases. Hematological laboratory tests showed a sharp increase in neutrophils and CRP, but fungal and bacterial tests and cultures were negative. The culture of Naegleria fowleri is highly challenging and requires special non-nutritive agar covered with bacteria such as Escherichia coli as food. Such culture media are not commonly available in ordinary laboratories, and the optimal growth temperature is 37 °C (Zaongo et al. 2018). In the early stages of infection, the number of Naegleria fowleri in patients’ CSF is extremely low. Moreover, these amoebas lose viability rapidly once isolated, which renders wet mount microscopy and culture techniques highly challenging. In this case, we performed Wright-Giemsa staining on the sediment of the patient’s cerebrospinal fluid and found amoebic trophozoites. Through direct wet mount microscopy, we observed live amoebic trophozoites. With the development of sequencing technology, high-throughput sequencing technology for pathogens has played a key role in the diagnosis of difficult pathogen infections. In this case, we performed high-throughput sequencing of the pathogen on the patient’s CSF sediment. To definitively characterize the pathogen and assess the background microbial composition, we performed comprehensive bioinformatic analysis of the metagenomic data. The assay generated 2,112,053 quality-filtered non-human reads. Taxonomic classification, visualized via a Sankey diagram, revealed that 94.1% (1,987,728 reads) of the microbial load aligned to the Naegleria genus. The remaining non-target sequences represented trace environmental and aquatic background microorganisms (e.g., Candidatus Pelagibacter, Synechococcus), consistent with the patient’s exposure history, but exhibited negligible abundance compared to the pathogen. To further validate species specificity and rule out cross-hybridization with other Free-Living Amoebae (FLA), we performed a competitive genomic alignment against phylogenetically related species. Of the reads mapping to N. fowleri, 1,627,651 (81.9%) were identified as unique, species-specific markers with no cross-alignment to other genomes. In contrast, while the closely related N. lovaniensis recruited 63,237 reads due to conserved sequence homology, only 466 reads were unique to its genome. The dramatic enrichment of N. fowleri-specific sequences (> 3,000-fold higher than N. lovaniensis) conclusively distinguishes the pathogen from other amoebic species and confirms the diagnosis of PAM. In addition, the typing system, which is based on the internal transcribed spacers (ITS) and 5.8 S rDNA sequences, also makes the identification of other Naegleria spp. a much easier task (De Jonckheere 2011). For medical structures that do not have high-throughput sequencing technology, multiplex qPCR can be used to quickly detect Acanthamoeba spp.(Córdoba-Lanús et al. 2024).

The Centers for Disease Control and Prevention (CDC) recommends a combined anti-amebic regimen (conventional amphotericin B, azithromycin, fluconazole, miltefosine, rifampin and dexamethasone) alongside neuroprotective management, based on expert consensus (Strickler 2024; Gharpure et al. 2021; Burqi et al. 2024). In this case, the patient was given combined anti-infection treatment with amphotericin B (1.5 mg/kg·d) and rifampicin (10 mg/kg·d). As the patient was in the advanced stage of the disease, there was no obvious improvement. It is thus evident that early diagnosis and treatment of PAM are of critical importance. Laboratory technicians must be capable of promptly identifying amoebas in CSF samples and immediately initiating a treatment regimen that includes conventional amphotericin, fluconazole, azithromycin, and rifampicin. Only in this way can there be a glimmer of hope for the patient.

In conclusion, PAM is a rare and difficult to diagnose infectious disease. We conducted rapid diagnosis of PAM through the combination of traditional microbiological microscopic examination and high-throughput sequencing of pathogenic microorganisms. Regrettably, despite our prompt treatment of the patient with amphotericin B (1.5 mg/kg·d) and rifampicin (10 mg/kg·d), we were unable to save the patient’s life. The case report provides some experience for the diagnosis and treatment of PAM.

Author contributions

Y.K. and Q.Y.L. contributed equally to the review and collection of data, writing and revision of the manuscript. HML contributed to record of the disease course and the diagnosis of the disease. Y.F.G. conducted high-throughput sequencing and analysis of pathogens. J.W., C.M.P., P.H. and S.L.C. conducted laboratory tests and microbiological cultures. S.Y.N. and L.F. performed the data analysis and review of the manuscript. All authors approved the final manuscript.

Funding

This work was supported by the National Natural Science Foundation of China (82160402 and 82360030); Central guidance for local scientific and technological development special funds (202407AD110004); High-level Talent Cultivation and Attraction Support Plan for Yunnan Province (YNQR-QNRC-2020-091).

Data availability

No datasets were generated or analysed during the current study.

Declarations

Ethics and consent to participate

This study protocol complies with the guidelines of the Declaration of Helsinki and was approved by the Ethics Committee of the Yan’an Hospital Affiliated to Kunming Medical University (trial registration number: 2025-214-01).

Consent for publication

All authors and patients have approved the manuscript for publication and that it has not been published elsewhere.

Disclosure

The author reports no conflicts of interest in this work.

Competing interests

The authors declare no competing interests.