Species, Sequence Types and Alleles: Dissecting Genetic Variation in Acanthamoeba

Abstract

<jats:p>Species designations within Acanthamoeba are problematic because of pleomorphic morphology. Molecular approaches, including DNA sequencing, hinted at a resolution that has yet to be fully achieved. Alternative approaches were required. In 1996, the Byers/Fuerst lab introduced the concept of sequence types. Differences between isolates of Acanthamoeba could be quantitatively assessed by comparing sequences of the nuclear 18S rRNA gene, ultimately producing 22 sequence types, designated T1 through T22. The concept of sequence types helps our understanding of Acanthamoeba evolution. Nevertheless, substantial variation in the 18S rRNA gene differentiates many isolates within each sequence type. Because the majority of isolates with sequences in the international DNA databases have been studied for only a small segment of the gene, designated ASA.S1, genetic variation within this hypervariable region of the 18S rRNA gene has been scrutinized. In 2002, we first categorized variation in this region in a sample of T3 and T4 isolates from Hong Kong, observing ten “alleles” within type T4 and five “alleles” within T3. Subsequently, confusion occurred when different labs applied redundant numerical labels to identify different alleles. A more unified approach was required. We have tabulated alleles occurring in the sequences submitted to the international DNA databases, and determined their frequencies. Over 150 alleles have occurred more than once within 3500+ isolates of sequence type T4. Results from smaller samples of other sequence types (T3, T5, T11 and T15, and supergroup T2/6) have also been obtained. Our results provide new insights into the evolutionary history of Acanthamoeba, further illuminating the degree of genetic separation between significant taxonomic units within the genus, perhaps eventually elucidating what constitutes a species of Acanthamoeba.</jats:p>

Immunopathogenicity of Acanthamoeba spp. in the Brain and Lungs

“…Acanthamoeba genotypes are distinguished by a 5% or greater sequence difference between isolates [ 14 , 15 ]. To date, 22 sequence types have been identified, designated T1 through T22 [ 16 ]. However, Booton et al [ 17 ], examining the DF3 subregion of ASA.S1 in the samples of T3 and T4 isolates, observed several unique sequences within T3 and T4 isolates.…”

“…These sequences were designated T3/1–T3/5 and T4/1–T4/10 [ 17 ]. Due to the fact that different laboratories applied redundant numerical labels to identify different sequences, Fuerst and Booton [ 16 ] suggested new subtypes for the T4 genotype, which have been labeled T4A–T4F and T4Neff. The authors also described different sequences within T3 (labeled T3/01–T3/13), T5 (labeled T5/01–T5/15), T11 (labeled T11/01–T11/14), and T15 (labeled T15/01–T15/11).…”

“…The authors also described different sequences within T3 (labeled T3/01–T3/13), T5 (labeled T5/01–T5/15), T11 (labeled T11/01–T11/14), and T15 (labeled T15/01–T15/11). Types T2 and T6 are the most closely related pair of sequence types within Acanthamoeba , and these two types are considered as a supergroup in which five subtypes are formed: T2, T2/6A, T2/6B, T2/6C and T6 [ 16 ].…”

Application of the omics sciences to the study of Naegleria fowleri, Acanthamoeba spp., and Balamuthia mandrillaris: current status and future projections

“…To date, 22 genotypes have been established: T1–T12 [ 70 ], T13 and T14 [ 37 ], T15 [ 36 ], T16 [ 15 ], T17 [ 58 ], T18 [ 64 ] T19 [ 50 ], T20 [ 24 ], T21 and T22 [ 72 ], geographically diversely distributed, so this amoeba has a presence on all continents [ 5 ]. For this reason, and since symptoms during infection vary between genotypes, genetic analyses have been done at the genomic level to identify the origin of these variations [ 23 ]. Acanthamoeba castellanii str.…”

Isolation and Molecular Identification of Acanthamoeba and Naegleria from Agricultural Water Canal in Qazvin, Iran

“…While rare, the importance of infections with FLA in humans emphasizes more comprehensive studies on the prevalence of such opportunistic organisms in our surroundings. Based on 18S rRNA gene sequence, 22 Acanthamoeba genotypes (T1–T22) have been discerned from environmental sources and clinical cases ( http://u.osu.edu/acanthamoeba/genomes-of-acanthamoeba ) ( 9 – 12 ). T4 is the most frequent genotype isolated from environmental samples and AK patients globally, implicating more pathogenic capability of this genotype ( 3 , 13 , 14 ).…”