Draft Chromosome Sequences of a Clinical Isolate of the Free-Living Ameba Naegleria fowleri

Abstract

We present the chromosome sequences of a Naegleria fowleri isolate from a human primary amebic meningoencephalitis (PAM) case. The genome sequences were assembled from Illumina HiSeq and PacBio sequencing data and verified with the optical mapping data. This led to the identification of 37 contigs representing 37 chromosomes in N. fowleri.

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

“…Furthermore, we report the sequence of a portion of the small-subunit (SSU) rRNA gene, ITS1, the 5.8S rRNA gene, ITS2, as well as a portion of the LSU RNA gene of Nf69 that we attained in order to determine the genotype of this isolate. We initially endeavored to ascertain the genotyping parameters by referring to the resource used by Ali et al in their recent publication, in which they defined the TY isolate as genotype III ( 44 ). This guideline, provided by Zhou et al, which uses Roman numerals and defines genotypes I to VI ( 39 ), is outdated, and the repeats and various components of the ITS1 as well as 5.8S rRNA gene are less detailed than in the more recent review by De Jonckheere, which uses Arabic numerals to differentiate types based upon the evolutionary consideration of which type likely appeared first ( 41 ).…”

“…Nf69 (ATCC 30215), a clinical isolate used as a reference strain in these studies and obtained from a 9-year-old boy in Adelaide, Australia, who died in 1969 ( 46 – 49 ), and 6088 (ATCC 30896), obtained from a 9-year-old girl in California who survived in 1978 ( 50 , 51 ), were purchased from the American Type Culture Collection (ATCC). V067, isolated from a 30-year-old male in Arizona who died in 1987 ( 39 , 52 ), V206, isolated from a man in Mexico who died in 1990 ( 39 ), V413, isolated from a 17-year-old boy in Texas who died in 1998 ( 39 , 52 ), V597, isolated from a 10-year-old boy in Florida who died in 2007, V631, isolated from a 28-year-old man in in Louisiana who died in 2011 ( 53 ), Davis, isolated from an individual in Florida who died in 1998 ( 31 ), HB1, isolated from a 16-year-old boy in Florida who died in 1966 ( 25 , 54 – 57 ), HB4, isolated from a female in Virginia who died in 1977 ( 51 , 58 , 59 ), and TY, obtained from a 14-year-old boy in Virginia who died in 1969 ( 31 , 33 , 44 , 51 , 60 ), were all kindly provided by Ibne Ali at the Centers for Disease Control and Prevention (CDC).…”

Naphthyridine Derivatives Induce Programmed Cell Death in Naegleria fowleri

“…The genome data of Naegleria fowleri have recently been published [45,46], showing the presence of DNA topoisomerase 1-like gene (NF0087810 (https://www. uniprot.org/uniprot/A0A6A5BG47 (accessed on 28 September 2021)) [47]. Therefore, the inhibition of one of the key proteins for the viability of the cell could be the reason for the anti-Naegleria activity of the evaluated compounds.…”

Naegleria genus pangenome reveals new structural and functional insights into the versatility of these free-living amoebae

“…For N. lovaniensis , we used our 3 samples plus the reads from the sequencing projects of the strains NL_ATCC 30569 ( Liechti et al, 2018 ) and NL_76-15-250 ( Joseph et al, 2021 ). After a cleaning of raw reads using Cutadapt, Illumina raw reads were first mapped either against the N. fowleri TY “close-to-complete” genome ( Ali et al, 2021 ) or the N. lovaniensis ATCC 30569, using BWA-MEM (version 0.7.17-r1188) software ( Li, 2013 ). BAM mapping files were then converted to pileup format using SAMtools ( Danecek et al, 2021 ) and SNP calling was performed using VarScan ( Koboldt et al, 2012 ) for each sample, using a minimum read coverage of 8X with a Phred quality score of at least 15.…”

“…At the moment, over 60 Naegleria genome sequences are publicly available (with different levels of completeness and using different sequencing methodologies) for the non-pathogenic species N. gruberi ( Fritz-Laylin et al, 2010 ) and N. lovaniensis ( Liechti et al, 2018 ; Joseph et al, 2021 ), and for the pathogenic N. fowleri ( Zysset-Burri et al, 2014 ; Ali et al, 2021 ; Herman et al, 2021 ; Joseph et al, 2021 ). Comparative genomic studies were already performed within N. fowleri species ( Joseph et al, 2021 ) and between Naegleria species ( Liechti et al, 2018 ; Herman et al, 2021 ) but they do not describe the complete gene landscape of a Naegleria species or genus because of the large numbers of variations between accessions.…”