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Comparative Genomic and Transcriptomic Analysis of Naegleria fowleri Clinical and Environmental Isolates
Sandeep J Joseph1, Subin Park2, Alyssa Kelley2
1Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Preventiongrid.416738.f, Atlanta, Georgia, USA.
Abstract:
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.
Insights
Naegleria fowleri causes a fatal brain infection. This study analyzed its genomes to find unique genes and understand its population structure, aiding in developing new detection methods.
Area of Science:
- Microbiology
- Genomics
- Infectious Diseases
Background:
- Naegleria fowleri is the only Naegleria species that infects humans, causing primary amebic meningoencephalitis (PAM), a devastating brain disease with a high fatality rate.
- Despite extensive research, the specific pathogenic factors enabling N. fowleri to infect humans and breach the blood-brain barrier remain largely unknown.
- Limited information exists regarding the genomic diversity within N. fowleri and among different Naegleria species.
Purpose of the Study:
- To investigate the population structure and genetic relationships of Naegleria species, focusing on N. fowleri.
- To identify potential pathogenic factors by comparing N. fowleri genomes with those of related species.
- To generate novel genomic and transcriptomic data for N. fowleri to facilitate future research and surveillance.
Main Methods:
- Whole-genome sequencing and analysis of 52 novel N. fowleri isolates (clinical and environmental) and one N. lovaniensis strain.
- Comparative genomic analysis of 56 isolates across three Naegleria species (N. fowleri, N. lovaniensis, N. gruberi).
- Transcriptomic analysis of 37 N. fowleri isolates and population structure analysis using whole-nuclear-genome phylogenetic methods.
Main Results:
- Identification of several genes unique to N. fowleri, some previously linked to pathogenicity and others potentially novel virulence factors.
- Population structure analysis revealed 10 distinct populations across the three species, with 7 within N. fowleri.
- Phylogenetic analysis indicated geographical clustering of N. fowleri isolates, offering higher resolution than traditional typing methods. Gene expression analysis showed minimal differences between clinical and environmental isolates.
Conclusions:
- The generated genomic data provide valuable insights into Naegleria species diversity and N. fowleri pathogenicity.
- This resource can support the development of rapid molecular diagnostic assays for N. fowleri surveillance.
- Future population-based genomic studies and integration with environmental metagenomic data can enhance the detection and understanding of this deadly pathogen.
