High-throughput sequencing to explore the extrachromosomal plasmid rDNA
of Naegleria fowleri AY27 genotype II: A human brain-eating Amoeba
Abstract
Naegleria fowleri is the only known Naegleria spp. that
cause acute, fulminant, and rapidly fatal infection in the central
nervous system of humans called primary amebic meningoencephalitis
(PAM). We report a 28 years-old suspected PAM patient hospitalized in
Karachi, Pakistan, with no earlier memoire of recreational activities
but daily ritual ablution. Wet film observation of CSF showed amoebic
trophozoites and confirmation of N. fowleri was done using
Internal Transcribed Spacers detection method ((ITS-PCR). Clinical
isolate of N. fowleri from patient CSF was sequenced for
circular extrachromosomal ribosomal DNA (CERE - rDNA). The CERE contains
18S, 5.8S and 28S ribosomal subunits separated by internal transcribed
spacers, 5 open reading frames (ORF’s), and mostly repeat elements
comprising 7268bp out of 15786bp (46%). A wide variety of variations
and recombination events were observed. Finally, the ORF’s that
comprised of only 4 hypothetical proteins were modelled and screened
against Zinc drug-like compounds. Two compounds [ZINC77564275 (ethyl
2-(((4-isopropyl-4H-1,2,4-triazol-3-yl)methyl)(methyl)amino)oxazole-4-carboxylate)
and ZINC15022129
(5-(2-methoxyphenoxy)-[2,2’-bipyrimidine]-4,6(1H,5H)-dione)] were
finalized as potential druggable compounds based on ADME toxicity
analysis. We propose that the compounds showing least toxicity would be
potential drug candidates after laboratory experimental validation is
performed.