Exploring the extrachromosomal plasmid rDNA of Naegleria fowleri AY27 genotype II: A human brain-eating amoeba via high-throughput sequencing.

Naegleria fowleri, also known as brain-earing amoeba, causes severe and rapidly fatal CNS infection in humans called primary amebic meningoencephalitis (PAM). The DNA from the N. fowleri clinical isolate was sequenced for circular extrachromosomal ribosomal DNA (CERE - rDNA). The CERE contains 18 S, 5.8 S, and 28 S ribosomal subunits separated by internal transcribed spacers, 5 open reading frames (ORFs), and mostly repeat elements comprising 7268 bp out of 15,786 bp (46%). A wide variety of variations and recombination events were observed. Finally, the ORFs that comprised only 4 hypothetical proteins were modeled and screened against Zinc drug-like compounds. Two compounds [ZINC77564275 (ethyl 2-(((4-isopropyl-4 H-1,2,4-triazol-3-yl) methyl) (methyl)amino) oxazole-4-carboxylate) and ZINC15022129 (5-(2-methoxyphenoxy)-[2,2'-bipyrimidine]-4,6(1 H,5 H)-dione)] were finalized as potential druggable compounds based on ADME toxicity analysis. We propose that the compounds showing the least toxicity would be potential drug candidates after laboratory experimental validation is performed.

A giant virus infecting the amoeboflagellate Naegleria.

Giant viruses (Nucleocytoviricota) are significant lethality agents of various eukaryotic hosts. Although metagenomics indicates their ubiquitous distribution, available giant virus isolates are restricted to a very small number of protist and algal hosts. Here we report on the first viral isolate that replicates in the amoeboflagellate Naegleria. This genus comprises the notorious human pathogen Naegleria fowleri, the causative agent of the rare but fatal primary amoebic meningoencephalitis. We have elucidated the structure and infection cycle of this giant virus, Catovirus naegleriensis (a.k.a. Naegleriavirus, NiV), and show its unique adaptations to its Naegleria host using fluorescence in situ hybridization, electron microscopy, genomics, and proteomics. Naegleriavirus is only the fourth isolate of the highly diverse subfamily Klosneuvirinae, and like its relatives the NiV genome contains a large number of translation genes, but lacks transfer RNAs (tRNAs). NiV has acquired genes from its Naegleria host, which code for heat shock proteins and apoptosis inhibiting factors, presumably for host interactions. Notably, NiV infection was lethal to all Naegleria species tested, including the human pathogen N. fowleri. This study expands our experimental framework for investigating giant viruses and may help to better understand the basic biology of the human pathogen N. fowleri.

Development and immunological evaluation of an mRNA-based vaccine targeting Naegleria fowleri for the treatment of primary amoebic meningoencephalitis.

More than 95% of patients fall victim to primary amoebic meningoencephalitis (PAM), a fatal disease attacking the central nervous system. Naegleria fowleri, a brain-eating microorganism, is PAM's most well-known pathogenic ameboflagellate. Despite the use of antibiotics, the fatality rate continues to rise as no clinical trials have been conducted against this disease. To address this, we mined the UniProt database for pathogenic proteins and selected assumed epitopes to create an mRNA-based vaccine. We identified thirty B-cell and T-cell epitopes for the vaccine candidate. These epitopes, secretion boosters, subcellular trafficking structures, and linkers were used to construct the vaccine candidate. Through predictive modeling and confirmation via the Ramachandran plot (with a quality factor of 92.22), we assessed secondary and 3D structures. The adjuvant RpfE was incorporated to enhance the vaccine construct's immunogenicity (GRAVY index: 0.394, instability index: 38.99, antigenicity: 0.8). The theoretical model of immunological simulations indicated favorable responses from both innate and adaptive immune cells, with memory cells expected to remain active for up to 350 days post-vaccination, while the antigen was eliminated from the body within 24 h. Notably, strong interactions were observed between the vaccine construct and TLR-4 (- 11.9 kcal/mol) and TLR-3 (- 18.2 kcal/mol).

A primary amoebic meningoencephalitis case associated with swimming in seawater.

This case report describes a 62-year-old male fisherman who presented with persistent vomiting, headache, and behavior changes. Despite initial antibiotic and corticosteroid treatment, his condition worsened, leading to coma and subsequent death. Macro-genome sequencing of cerebrospinal fluid (CSF) revealed the presence of Naegleria fowleri infection, which had been missed during initial laboratory tests. The patient's exposure history included sea-swimming near Zhoushan Island.

Molecular identification of Acanthamoeba spp., Balamuthia mandrillaris and Naegleria fowleri in soil samples using quantitative real-time PCR assay in Turkey; Hidden danger in the soil!

Acanthamoeba spp., Balamuthia mandrillaris, and Naegleria fowleri are pathogenic free-living amoeba (FLA) and are commonly found in the environment, particularly soil. This pathogenic FLA causes central nervous system-affecting granulomatous amebic encephalitis (GAE) or primary amebic meningoencephalitis (PAM) and can also cause keratitis and skin infections. In the present study, we aimed to determine the quantitative concentration of Acanthamoeba spp., B. mandrillaris, and N. fowleri in soil samples collected from places where human contact is high by using a qPCR assay in Izmir, Turkey. A total of 45.71% (n = 16) of Acanthamoeba spp., 20% (n = 7) of B. mandrillaris, and 17.4% (n = 6) of N. fowleri were detected in five different soil sources by the qPCR assay. The quantitative concentration of Acanthamoeba spp., B. mandrillaris, and N. fowleri in various soil sources was calculated at 10 × 105 - 6 × 102, 47 × 104 to 39 × 103, and 9 × 103 - 8 × 102 plasmid copies/gr, respectively. While the highest quantitative concentration of Acanthamoeba spp. and B. mandrillaris was determined in garden soil samples, N. fowleri was detected in potting soil samples. Three different genotypes T2 (18.75%), T4 (56.25%), and T5 (25%) were identified from Acanthamoeba-positive soil samples. Acanthamoeba T4 genotype was the most frequently detected genotype from soil samples and is also the most common genotype to cause infection in humans and animals. To the best of our knowledge, the present study is the first study to identify genotype T5 in soil samples from Turkey. In conclusion, people and especially children should be aware of the hidden danger in the garden and potting soil samples that come into contact most frequently. Public health awareness should be raised about human infections that may be encountered due to contact with the soil. Public health specialists should raise awareness about this hidden danger in soil.

Occurrence and molecular characterization of Acanthamoeba, Naegleria fowleri and Blastocystis in water samples from various sources in Egypt.

PCR-testing coupled to isolate sequencing was conducted to detect prevalence and various genotypes/subtypes of 3 neglected waterborne protists (Acanthamoeba, Naegleria fowleri and Blastocystis) in water samples from various sources in Dakahlia governorate, Egypt. Out of 62 protozoan-suspected samples by microscopy, Acanthamoeba was molecularly confirmed in 24 (38.7%) samples from various sources including tap water. Twenty Acanthamoeba isolates were successfully-sequenced; 18 were designated as the genotype T3 and 2 as T4. Naegleria spp. were detected in 6 (9.6%) samples from the Nile, of them 2 (3.2%) were identified as N. fowleri. Blastocystis spp. were found in 4 (6.4%) samples from waste water and ground water. Blastocystis subtype 2 was found in a sample from waste water, which may reflect human infection with this subtype and constitutes a public health hazard because waste water is occasionally discharged in the Nile with minimal treatments. Findings of the present study were analyzed in combination with those of earlier surveys from the other Egyptian governorates to evaluate the whole situation of the 3 protists in water from Egypt. Results of this analysis showed that Acanthamoeba had a high mean prevalence (43.03%) throughout Egypt, with insignificant variations among various water sources. Various Acanthamoeba genotypes were detected, and the highly pathogenic T4 was the most significantly identified type. A common T4 haplotype circulated in water from Egypt and 3 other countries (Tanzania, Rwanda, Uganda) located on the Nile basin, and included isolates from keratitis-infected patients, which confirms the potential role of water in the epidemiology of Acanthamoeba keratitis infecting humans in these countries. The estimated mean prevalence for Naegleria spp. was 23.79%, being the highest in the Nile water. In the present study, occurrence of 3 potentially pathogenic protists has been confirmed in water from Egypt, which should alert the authorities to revise the procedures for controlling these pathogens in water.

Role of cathepsin B of Naegleria fowleri during primary amebic meningoencephalitis.

Naegleria fowleri causes primary amoebic meningoencephalitis in humans and experimental animals. It has been suggested that cysteine proteases of parasites play key roles in metabolism, nutrient uptake, host tissue invasion, and immune evasion. The aim of this work was to evaluate the presence, expression, and role of cathepsin B from N. fowleri in vitro and during PAM. Rabbit-specific polyclonal antibodies against cathepsin B were obtained from rabbit immunization with a synthetic peptide obtained by bioinformatic design. In addition, a probe was designed from mRNA for N. fowleri cathepsin B. Both protein and messenger were detected in fixed trophozoites, trophozoites interacted with polymorphonuclear and histological sections of infected mice. The main cathepsin B distribution was observed in cytoplasm or membrane mainly pseudopods and food-cups while messenger was in nucleus and cytoplasm. Surprisingly, both the messenger and enzyme were observed in extracellular medium. To determine cathepsin B release, we used trophozoites supernatant recovered from nasal passages or brain of infected mice. We observed the highest release in supernatant from recovered brain amoebae, and when we analyzed molecular weight of secreted proteins by immunoblot, we found 30 and 37 kDa bands which were highly immunogenic. Finally, role of cathepsin B during N. fowleri infection was determined; we preincubated trophozoites with E-64, pHMB or antibodies with which we obtained 60%, 100%, and 60% of survival, respectively, in infected mice. These results suggest that cathepsin B plays a role during pathogenesis caused by N. fowleri mainly in adhesion and contributes to nervous tissue damage.

The First Molecular Genotyping of Naegleria fowleri Causing Primary Amebic Meningoencephalitis in Thailand With Epidemiology and Clinical Case Reviews.

Primary amebic meningoencephalitis (PAM) is a rare and fatal central nervous system infection caused by Naegleria fowleri, a free-living amoeba found in the environment. To date, eight pathogenic N. fowleri genotypes have been reported worldwide. We aimed to explore the genotypes of N. fowleri that cause primary amebic meningoencephalitis in Thailand. In 2021, the 17th PAM case was reported, and a retrospective literature search of PAM cases in Thailand from 1982 through April 2021 was performed. Phylogenetic and genotyping analyses of the two mitochondrial (12S rRNA and 16S rRNA) and nuclear (ITS1 and 5.8s rRNA) genes of N. fowleri were performed on four available clinical isolates. Based on the mitochondrial and nuclear genes, N. fowleri genotype T3 was found to cause PAM in three out of four cases. However, disagreement between the genotype based on the mitochondrial and nuclear genes was found in one of the PAM cases, in which the 12S rRNA locus suggested the causative genotype as T1, while the ITS1 implied genotype T4. The discrepancy between the mitochondrial and nuclear genome was previously observed, which suggests the possible horizontal gene transfer among N. fowleri species. Based on the ITS1 gene, two N. fowleri genotypes, T3 and T4, were found to be the genotypes causing PAM in this study. In addition, N. fowleri genotype T2 was previously reported in a traveler who was infected in Thailand. Thus, at least three genotypes (T2, T3, and T4) of N. fowleri are found to be associated with PAM in Thailand.

Insights into genome evolution, pan-genome, and phylogenetic implication through mitochondrial genome sequence of Naegleria fowleri species.

In the current study, we have systematically analysed the mitochondrial DNA (mtDNA) sequence of Naegleria fowleri (N. fowleri) isolate AY27, isolated from Karachi, Pakistan. The N. fowleri isolate AY27 has a circular mtDNA (49,541 bp), which harbours 69 genes (46 protein-coding genes, 21 tRNAs and 2 rRNAs). The pan-genome analysis of N. fowleri species showed a Bpan value of 0.137048, which implies that the pan-genome is open. KEGG classified core, accessory and unique gene clusters for human disease, metabolism, environmental information processing, genetic information processing and organismal system. Similarly, COG characterization of protein showed that core and accessory genes are involved in metabolism, information storages and processing, and cellular processes and signaling. The Naegleria species (n = 6) formed a total of 47 gene clusters; 42 single-copy gene clusters and 5 orthologous gene clusters. It was noted that 100% genes of Naegleria species were present in the orthogroups. We identified 44 single nucleotide polymorphisms (SNP) in the N. fowleri isolate AY27 mtDNA using N. fowleri strain V511 as a reference. Whole mtDNA phylogenetic tree analysis showed that N. fowleri isolates AY27 is closely related to N. fowleri (Accession no. JX174181.1). The ANI (Average Nucleotide Identity) values presented a much clear grouping of the Naegleria species compared to the whole mtDNA based phylogenetic analysis. The current study gives a comprehensive understanding of mtDNA architecture as well as a comparison of Naegleria species (N. fowleri and N. gruberi species) at the mitochondrial genome sequence level.

Genotyping and Molecular Identification of Acanthamoeba Genotype T4 and Naegleria fowleri from Cerebrospinal Fluid Samples of Patients in Turkey: Is it the Pathogens of Unknown Causes of Death?

PURPOSE: This study was aimed to investigate the presence of pathogenic free-living amoebae (FLA) in suspected cases of meningoencephalitis with unknown causes of death in Turkey. METHOD: A total of 92 patients, who were diagnosed as meningoencephalitis, were enrolled. All cerebrospinal fluid (CSF) samples were directly microscopically examined and cultured. Acanthamoeba, N. fowleri and B. mandrillaris were further investigated using molecular diagnostic tools including real-time PCR, sequencing, and phylogenetic analyses. RESULTS: The examined CSF samples were not found positive for the presence of FLA by microscopic examination and culture method. However, two CSF samples were detected positive by real-time PCR assay. Of the positive CSF samples, one was identified as Acanthamoeba genotype T4 and the second positive sample was identified as N. fowleri belonging to genotype II. Furthermore, the pathogens diagnoses was verified through Sanger sequencing. CONCLUSION: This study was significant to report the presence of Acanthamoeba genotype T4 and N. fowleri genotype II in CSF samples by real-time PCR assay. The present study shows the significance of primary amoebic meningoencephalitis (PAM) and granulomatous amoebic encephalitis (GAE) as one of the differential diagnoses to be considered by clinicians during the evaluation of suspected meningoencephalitis or cases of unknown cause in Turkey. Using real-time PCR, this has made the rapid detection, in a short time-frame, of Acanthamoeba and N. fowleri in CSF samples from patients. The problems with qPCR is that it is not available in every laboratory, reagents are expensive, and it requires skilled and expert personnel to set up these assays.

Differential Growth Rates and In Vitro Drug Susceptibility to Currently Used Drugs for Multiple Isolates of Naegleria fowleri.

The free-living amoeba Naegleria fowleri, which typically dwells within warm, freshwater environments, can opportunistically cause primary amoebic meningoencephalitis (PAM), a disease with a mortality rate of >97%. The lack of positive treatment outcomes for PAM has prompted the discovery and development of more effective therapeutics, yet most studies utilize only one or two clinical isolates. The inability to assess possible heterogenic responses to drugs among isolates from various geographical regions hinders progress in the discovery of more effective drugs. Here, we conducted drug efficacy and growth rate determinations for 11 different clinical isolates by applying a previously developed CellTiter-Glo 2.0 screening technique and flow cytometry. We found significant differences in the susceptibilities of these isolates to 7 of 8 drugs tested, all of which make up the cocktail that is recommended to physicians by the U.S. Centers for Disease Control and Prevention. We also discovered significant variances in growth rates among isolates, which draws attention to the differences among the amoeba isolates collected from different patients. Our results demonstrate the need for additional clinical isolates of various genotypes in drug assays and highlight the necessity for more targeted therapeutics with universal efficacy across N. fowleri isolates. Our data establish a needed baseline for drug susceptibility among clinical isolates and provide a segue for future combination therapy studies as well as research related to phenotypic or genetic differences that could shed light on mechanisms of action or predispositions to specific drugs. IMPORTANCE Naegleria fowleri, also known as the brain-eating amoeba, is ubiquitous in warm freshwater and is an opportunistic pathogen that causes primary amoebic meningoencephalitis. Although few cases are described each year, the disease has a case fatality rate of >97%. In most laboratory studies of this organism, only one or two well-adapted lab strains are used; therefore, there is a lack of data to discern if there are major differences in potency of currently used drugs for multiple strains and genotypes of the amoeba. In this study, we found significant differences in the susceptibilities of 11 N. fowleri isolates to 7 of the 8 drugs currently used to treat the disease. The data from this study provide a baseline of drug susceptibility among clinical isolates and suggest that new drugs should be tested on a larger number of isolates in the future.

Real-Time PCR Confirmation of a Fatal Case of Primary Amoebic Meningoencephalitis in Turkey Caused by Naegleria fowleri or Brain-Eating Amoeba.

BACKGROUND: Naegleria fowleri, the causative agent of primary amoebic meningoencephalitis (PAM), is a free-living amoeba. It is a water-borne infection usually detected in children and young people with healthy immune system who swim, dive and perform activities in fresh and hot springs. PURPOSE: In this study, it was aimed to raise awareness in the differential diagnosis of meningitis etiopathogenesis by showing that N. fowleri may also be the causative agent, albeit very rarely, in meningitis cases in Turkey. METHODS: Our case was an 18-year-old male patient whose relatives stated that he has gone to the hot spring; his headache complaint started after 2 to 3 days after return from the hot spring. Cerebrospinal fluid (CSF) sample taken from the patient was investigated by direct microscopic examination, real-time PCR method and sequence analysis. RESULTS: The CSF sample collected was taken into distilled water considering the possibility of transformation of trophozoites to intermediate form and incubated at 37 °C for 1 to 2 h, and pear-shaped non-permanent flagellated forms were observed in the direct microscopic examination, and molecular typing was performed to confirm the diagnosis. This study was a comprehensive case of N. fowleri whose etiological agent was isolated and confirmed by real-time PCR in Turkey. CONCLUSION: Clinician awareness would be the key factor in correctly diagnosing PAM. It is also recommended to investigate all likely environmental water sources in Turkey for more detailed information on the distribution and molecular identification of Naegleria species, ultimately to evaluate the potential pathogenic threat to human health and to develop strategies to combat such threats.

A pediatric case of primary amoebic meningoencephalitis due to Naegleria fowleri diagnosed by next-generation sequencing of cerebrospinal fluid and blood samples.

BACKGROUND: Primary amoebic meningoencephalitis (PAM) is a rare, acute and fatal disease of the central nervous system caused by infection with Naegleria fowleri (Heggie, in Travel Med Infect Dis 8:201-6, 2010). Presently, the majority of reported cases in the literature have been diagnosed through pathogen detection pathogens in the cerebrospinal fluid (CSF). This report highlights the first case of pediatric PAM diagnosed with amoeba infiltration within CSF and bloodstream of an 8-year-old male child, validated through meta-genomic next-generation sequencing (mNGS). CASE PRESENTATION: An 8-year-old male child was admitted to hospital following 24 h of fever, headache and vomiting and rapidly entered into a coma. CSF examination was consistent with typical bacterial meningitis. However, since targeted treatment for this condition proved to be futile, the patient rapidly progressed to brain death. Finally, the patient was referred to our hospital where he was confirmed with brain death. CSF and blood samples were consequently analyzed through mNGS. N. fowleri was detected in both samples, although the sequence copy number in the blood was lower than for CSF. The pathogen diagnosis was further verified by PCR and Sanger sequencing. CONCLUSIONS: This is the first reported case of pediatric PAM found in mainland China. The results indicate that N. fowleri may spread outside the central nervous system through a damaged blood-brain barrier.

The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design.

Balamuthia mandrillaris, a pathogenic free-living amoeba, causes cutaneous skin lesions as well as granulomatous amoebic encephalitis, a 'brain-eating' disease. As with the other known pathogenic free-living amoebas (Naegleria fowleri and Acanthamoeba species), drug discovery efforts to combat Balamuthia infections of the central nervous system are sparse; few targets have been validated or characterized at the molecular level, and little is known about the biochemical pathways necessary for parasite survival. Current treatments of encephalitis due to B. mandrillaris lack efficacy, leading to case fatality rates above 90%. Using our recently published methodology to discover potential drugs against pathogenic amoebas, we screened a collection of 85 compounds with known antiparasitic activity and identified 59 compounds that impacted the growth of Balamuthia trophozoites at concentrations below 220 µM. Since there is no fully annotated genome or proteome of B. mandrillaris, we sequenced and assembled its transcriptome from a high-throughput RNA-sequencing (RNA-Seq) experiment and located the coding sequences of the genes potentially targeted by the growth inhibitors from our compound screens. We determined the sequence of 17 of these target genes and obtained expression clones for 15 that we validated by direct sequencing. These will be used in the future in combination with the identified hits in structure guided drug discovery campaigns to develop new approaches for the treatment of Balamuthia infections.

Evaluation of molecular characterization and phylogeny for quantification of Acanthamoeba and Naegleria fowleri in various water sources, Turkey.

Free-living amoeba (FLA) is widely distributed in the natural environment. Since these amoebae are widely found in various waters, they pose an important public health problem. The aim of this study was to detect the presence of Acanthamoeba, B. mandrillaris, and N. fowleri in various water resources by qPCR in Izmir, Turkey. A total of (n = 27) 18.24% Acanthamoeba and (n = 4) 2.7% N. fowleri positives were detected in six different water sources using qPCR with ITS regions (ITS1) specific primers. The resulting concentrations varied in various water samples for Acanthamoeba in the range of 3.2x105-1.4x102 plasmid copies/l and for N. fowleri in the range of 8x103-11x102 plasmid copies/l. The highest concentration of Acanthamoeba and N. fowleri was found in seawater and damp samples respectively. All 27 Acanthamoeba isolates were identified in genotype level based on the 18S rRNA gene as T4 (51.85%), T5 (22.22%), T2 (14.81%) and T15 (11.11%). The four positive N. fowleri isolate was confirmed by sequencing the ITS1, ITS2 and 5.8S rRNA regions using specific primers. Four N. fowleri isolates were genotyped (three isolate as type 2 and one isolate as type 5) and detected for the first time from water sources in Turkey. Acanthamoeba and N. fowleri genotypes found in many natural environments are straightly related to human populations to have pathogenic potentials that may pose a risk to human health. Public health professionals should raise awareness on this issue, and public awareness education should be provided by the assistance of civil authorities. To the best of our knowledge, this is the first study on the quantitative detection and distribution of Acanthamoeba and N. fowleri genotypes in various water sources in Turkey.

Comparative Genomic and Transcriptomic Analysis of Naegleria fowleri Clinical and Environmental Isolates.

Out of over 40 species of Naegleria, which are free-living thermophilic amebae found in freshwater and soil worldwide, only Naegleria fowleri infects humans, causing primary amebic meningoencephalitis (PAM), a typically fatal brain disease. To understand the population structure of Naegleria species and the genetic relationships between N. fowleri isolates and to detect pathogenic factors, we characterized 52 novel clinical and environmental N. fowleri genomes and a single Naegleria lovaniensis strain, along with transcriptomic data for a subset of 37 N. fowleri isolates. Whole-genome analysis of 56 isolates from three Naegleria species (N. fowleri, N. lovaniensis, and Naegleria gruberi) identified several genes unique to N. fowleri that have previously been linked to the pathogenicity of N. fowleri, while other unique genes could be associated with novel pathogenicity factors in this highly fatal pathogen. Population structure analysis estimated the presence of 10 populations within the three Naegleria species, of which 7 populations were within N. fowleri. The whole-nuclear-genome (WNG) phylogenetic analysis showed an overall geographical clustering of N. fowleri isolates, with few exceptions, and provided higher resolution in identifying potential clusters of isolates beyond that of the traditional locus typing. There were only 34 genes that showed significant differences in gene expression between the clinical and environmental isolates. Genomic data generated in this study can be used for developing rapid molecular assays and to conduct future population-based global genomic analysis and will also be a valuable addition to genomic reference databases, where shotgun metagenomics data from routine water samples could be searched for the presence of N. fowleri strains. IMPORTANCE N. fowleri, the only known Naegleria species to infect humans, causes fatal brain disease. PAM cases from 1965 to 2016 showed <20 cases per year globally. Out of approximately 150 cases in North America since 1962, only four PAM survivors are known, yielding a >97% case fatality rate, which is critically high. Although the pathogenesis of N. fowleri has been studied for the last 50 years, pathogenetic factors that lead to human infection and breaching the blood-brain barrier remain unknown. In addition, little is known regarding the genomic diversity both within N. fowleri isolates and among Naegleria species. In this study, we generated novel genome sequences and performed comparative genomic and transcriptomic analysis of a set of 52 N. fowleri draft genome sequences from clinical and environmental isolates derived from all over the world in the last 53 years, which will help shape future genome-wide studies and develop sensitive assays for routine surveillance.

Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri.

BACKGROUND: The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. RESULTS: Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system. CONCLUSIONS: In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.

Application of the omics sciences to the study of Naegleria fowleri, Acanthamoeba spp., and Balamuthia mandrillaris: current status and future projections.

In this review, we focus on the sequenced genomes of the pathogens Naegleria fowleri, Acanthamoeba spp. and Balamuthia mandrillaris, and the remarkable discoveries regarding the pathogenicity and genetic information of these organisms, using techniques related to the various omics branches like genomics, transcriptomics, and proteomics. Currently, novel data produced through comparative genomics analyses and both differential gene and protein expression in these free-living amoebas have allowed for breakthroughs to identify genes unique to N. fowleri, genes with active transcriptional activity, and their differential expression in conditions of modified virulence. Furthermore, orthologous genes of the various nuclear genomes within the Naegleria and Acanthamoeba genera have been clustered. The proteome of B. mandrillaris has been reconstructed through transcriptome data, and its mitochondrial genome structure has been thoroughly described with a unique characteristic that has come to light: a type I intron with the capacity of interrupting genes through its self-splicing ribozymes activity. With the integration of data derived from the diverse omic sciences, there is a potential approximation that reflects the molecular complexity required for the identification of virulence factors, as well as crucial information regarding the comprehension of the molecular mechanisms with which these interact. Altogether, these breakthroughs could contribute to radical advances in both the fields of therapy design and medical diagnosis in the foreseeable future.

TITLE: Application des sciences de l'omique à l'étude de Naegleria fowleri, Acanthamoeba spp. et Balamuthia mandrillaris : état actuel et projections futures. ABSTRACT: Dans cette revue, l'accent est mis sur les génomes séquencés des agents pathogènes Naegleria fowleri, Acanthamoeba spp. et Balamuthia mandrillaris, et les découvertes remarquables concernant la pathogénicité et l'information génétique de ces organismes, en utilisant des techniques liées aux diverses branches de l'omique comme la génomique, la transcriptomique et la protéomique. Actuellement, de nouvelles données produites par des analyses génomiques comparatives et l'expression différentielle des gènes et des protéines dans ces amibes libres ont permis des percées pour identifier des gènes uniques à N. fowleri, des gènes avec une activité transcriptionnelle active et leur expression différentielle dans des conditions de virulence modifiée. En outre, les gènes orthologues des divers génomes nucléaires des genres Naegleria et Acanthamoeba ont été regroupés. Le protéome de B. mandrillaris a été reconstruit grâce aux données du transcriptome, et la structure de son génome mitochondrial décrite de manière détaillée, mettant ainsi une caractéristique unique à jour : un intron de type I avec la capacité d'interrompre les gènes par son activité d'auto-épissage des ribozymes. Avec l'intégration des données issues des diverses sciences omiques, il existe une approximation potentielle qui reflète la complexité moléculaire requise pour l'identification des facteurs de virulence, ainsi que des informations cruciales concernant la compréhension des mécanismes moléculaires avec lesquels ceux-ci interagissent. Dans l'ensemble, ces percées pourraient contribuer à des progrès notables à la fois dans les domaines de la conception de la thérapie et du diagnostic médical dans un avenir proche.