Phylogenetic Analysis and the Evolution of the 18S rRNA Gene Typing System of Acanthamoeba

Abstract

Species of Acanthamoeba were first described using morphological characters including cyst structure and cytology of nuclear division. More than 20 nominal species were proposed using these methods. Morphology, especially cyst shape and size, has proven to be plastic and dependent upon culture conditions. The DNA sequence of the nuclear small-subunit (18S) rRNA, the Rns gene, has become the most widely accepted method for rapid diagnosis and classification of Acanthamoeba. The Byers-Fuerst lab first proposed an Rns typing system in 1996. Subsequent refinements, with an increasing DNA database and analysis of diagnostic fragments within the gene, have become widely accepted by the Acanthamoeba research community. The development of the typing system, including its current state of implementation is illustrated by three cases: (i) the division between sequence types T13 and T16; (ii) the diversity within sequence supertype T2/T6, and (iii) verification of a new sequence type, designated T20. Molecular studies make clear the disconnection between phylogenetic relatedness and species names, as applied for the genus Acanthamoeba. Future reconciliation of genetic types with species names must become a priority, but the possible shortcomings of the use of a single gene when reconstructing the evolutionary history of the acanthamoebidae must also be resolved.

Genotyping of Acanthamoeba spp. and characterization of the prevalent T4 type along with T10 and unassigned genotypes from amoebic keratitis patients in India

“…The genus Acanthamoeba is divided in 20 genotypes (T1-T20) on the basis of variation in nucleotide sequences of the 18S rRNA gene (Fuerst et al, 2015). Amongst all the known genotypes, T3, T4, T5, T6, T10, T11, T13 and T15 are known to cause Acanthamoeba keratitis in humans (Siddiqui & Khan, 2012).…”

“…Rns genotyping has placed Acanthamoeba spp. in 20 different genotypes (T1-T20) on the basis of the gene encoding the 18S rRNA sequence (Fuerst et al, 2015). Out of the 20 genotypes, T4 is the most common and predominant genotype involved in Acanthamoeba keratitis infections, as reported from several studies across the world (Booton et al, 2002;Schroeder et al, 2001;Zhao et al, 2010).…”

Isolates from ancient permafrost help to elucidate species boundaries in Acanthamoeba castellanii complex (Amoebozoa: Discosea)

“…Both BI and ML analyses produce seven subtypes, T4 A through T4 E and T4 Neff , previously mentioned by Fuerst (2014) and Fuerst et al (2015), further referred to as A-E and Neff. All but A and B receive maximum support in both analyses; B is highly supported (0.9) and A moderately supported (0.78) in the BI analysis.…”

“…This particularly concerns type T4, the most frequently isolated one in both clinics and nature (Maciver et al , 2013). Internally, type T4 is also heterogeneous, which has been noted since the beginning of comparative studies of the 18S rDNA in Acanthamoeba (Gast et al , 1996;Fuerst, Booton, & Crary, 2015), though genetic distances between clusters inside T4 are smaller than those between this and the other types (Stothard et al , 1998). Here belong the type strains of most of the species described on the basis of morphology, including the generic type, Acanthamoeba castellanii (Douglas, 1930) and thoroughly redescribed by Page (1967) Acanthamoeba polyphaga (Puschkarew, 1913).…”

“…The distinctiveness of different clades inside type T4 has begun to manifest itself since the first works on Acanthamoeba rDNA diversity (Gast et al , 1996;Stothard et al , 1998;Chung et al , 1998;Booton et al , 2002;Kong, 2009;Fuerst et al , 2015;Martín-Pérez et al , 2017). Subtypes T4 C , T4 D , T4 E , T4 F , and T4 Neff , when represented by several sequences, were usually well-supported, while T4 B was sometimes mixed with T4 A , and the latter mostly paraphyletic.…”