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Nanopore sequencing improves the draft genome of the human pathogenic amoeba Naegleria fowleri
Nicole Liechti1,2,3, Nadia Schürch2, Rémy Bruggmann1
1Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland.
Abstract:
Naegleria fowleri is an environmental protist found in soil and warm freshwater sources worldwide and is known for its ability to infect humans and causing a rapid and mostly fatal primary amoebic meningoencephalitis. When contaminated water enters the nose, the facultative parasite follows the olfactory nerve and enters the brain by crossing the cribriform plate where it causes tissue damage and haemorrhagic necrosis. Although N. fowleri has been studied for several years, the mechanisms of pathogenicity are still poorly understood. Furthermore, there is a lack of knowledge on the genomic level and the current reference assembly is limited in contiguity. To improve the draft genome and to investigate pathogenicity factors, we sequenced the genome of N. fowleri using Oxford Nanopore Technology (ONT). Assembly and polishing of the long reads resulted in a high-quality draft genome whose N50 is 18 times higher than the previously published genome. The prediction of potentially secreted proteins revealed a large proportion of enzymes with a hydrolysing function, which could play an important role during the pathogenesis and account for the destructive nature of primary amoebic meningoencephalitis. The improved genome provides the basis for further investigation unravelling the biology and the pathogenic potential of N. fowleri.
Insights
Naegleria fowleri causes fatal brain infections. Researchers improved its genome assembly, revealing enzymes linked to its destructive nature and paving the way for understanding this dangerous amoeba.
Area of Science:
- Microbiology
- Genomics
- Pathogen Biology
Background:
- Naegleria fowleri is an environmental amoeba causing primary amoebic meningoencephalitis (PAM), a severe brain infection.
- The mechanisms of N. fowleri pathogenicity and its genomic information are poorly understood.
- Previous genome assemblies lacked contiguity, hindering research into virulence factors.
Purpose of the Study:
- To improve the draft genome of Naegleria fowleri.
- To investigate potential pathogenicity factors using genomic data.
- To enhance understanding of N. fowleri biology and its disease-causing potential.
Main Methods:
- Genome sequencing of N. fowleri using Oxford Nanopore Technology (ONT).
- Assembly and polishing of long-read sequencing data.
- Prediction and analysis of potentially secreted proteins, focusing on enzymatic functions.
Main Results:
- A high-quality draft genome of N. fowleri was generated with significantly improved contiguity (N50 18x higher).
- A large proportion of predicted secreted proteins were identified as hydrolytic enzymes.
- These enzymes are hypothesized to contribute to the tissue damage observed in PAM.
Conclusions:
- The enhanced N. fowleri genome provides a valuable resource for studying its biology.
- The identified hydrolytic enzymes offer insights into the pathogenic mechanisms of N. fowleri.
- Further research using the improved genome can elucidate the virulence potential of this amoeba.
