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.

Center for Autoimmune Genomics and Etiology and Divisions of Biomedical Informatics and Developmental Biology Cincinnati Children's Hospital Medical Center Cincinnati OH USA

Centre for Genomic Regulation 08003 Barcelona Catalonia Spain

Centre for Organelle Research Department of Chemistry Bioscience and Environmental Engineering University of Stavanger Stavanger Norway

CSIRO Indian Oceans Marine Research Centre Environomics Future Science Platform Crawley WA Australia

CSIRO Land and Water Black Mountain Laboratories Canberra Australia

CSIRO Land and Water Centre for Environment and Life Sciences Private Bag No 5 Wembley Western Australia 6913 Australia

Department of Agricultural Food and Nutritional Science University of Alberta Edmonton Alberta Canada

Department of Biochemistry and Molecular Biology Centre for Comparative Genomics and Evolutionary Bioinformatics Dalhousie University Halifax Canada

Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic

Department of Biology University of Massachusetts Amherst UK

Department of Cardiology Hospital Clinico Universitario Virgen de la Arrixaca Instituto Murciano de Investigación Biosanitaria Centro de Investigación Biomedica en Red Enfermedades Cardiovasculares Madrid Spain

Department of Laboratory Medicine University of Washington Medical Center Montlake USA

Department of Life Sciences The Natural History Museum London UK

Department of Medicine Faculty of Medicine and Dentistry University of Alberta Edmonton Canada

Department of Microbiology and Immunology Virginia Commonwealth University School of Medicine Richmond Virginia USA

Department of Ophthalmology Inselspital Bern University Hospital University of Bern Bern Switzerland

Department of Pediatrics University of Cincinnati College of Medicine Cincinnati USA

Division of Infectious Disease Department of Medicine Faculty of Medicine and Dentistry University of Alberta Edmonton Canada

Faculty of Science Charles University BIOCEV Prague Czech Republic

Institut de Biologia Evolutiva Barcelona Spain

Institute of Parasitology Biology Centre Czech Academy of Sciences České Budějovice Czech Republic

Institute of Parasitology Vetsuisse Faculty Bern University of Bern Bern Switzerland

Laboratory Medicine and Medicine Infectious Diseases UCSF Abbott Viral Diagnostics and Discovery Center UCSF Clinical Microbiology Laboratory UCSF School of Medicine San Francisco USA

School of Applied Sciences Department of Biological and Geographical Sciences University of Huddersfield Huddersfield UK

School of Biosciences University of Kent Canterbury UK

Spiez Laboratory Federal Office for Civil Protection Austrasse Spiez Switzerland

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Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes

Copper Metabolism in Naegleria gruberi and Its Deadly Relative Naegleria fowleri

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