However, based on the composition of highly repetitive tRNA arrays, E. histolytica has been shown to have distinct genotypes with different potentials to cause disease [23–27]. E. histolytica tRNA genes are unusually organized in 25 arrays containing up to 5 tRNA genes in each array, with intergenic regions between tRNA genes containing

short Go6983 in vitro tandem repeats (STRs) [27]. A 6-locus (D-A, S-Q, R-R, A-L, STGA-D, and N-K) tRNA gene-linked genotyping system has shown that the number of STRs at these loci differ in parasite populations isolated from three clinical groups (asymptomatic, diarrhea/dysentery and liver abscess) [24, 26]. The variations occurring in tRNA genotypes, even between the ameba strains isolated from the intestine and in the liver abscess of the same patient, suggest that not all strains of E. histolytica have the same capacity to reach the liver of the infected host [28]. However, the

diversity of tRNA linked STR genotypes occurring even in a restricted geographic region, and the frequent occurrence of novel genotypes, limit their usefulness to predict infection outcome or to probe the population structure of E. histolytica [25, 29, 30]. The extensive genetic polymorphism in the repeat sequences of SREHP, chitinase and tRNA arrays for instance could reflect slippage occurring during E. histolytica DNA replication as Tibayrenc et al. hypothesize that the parasites exist as clonal populations that are stable over large geographical areas and long periods of time [31, 32]. Compared with other DNA markers, single nucleotide ABT-737 nmr polymorphisms (SNPs) are genetically stable, amenable to future automated methods of detection, and in contrast to the highly repetitive tRNA arrays, their location can be mapped in the E. histolytica genome [33–35]. After the first sequencing and assembly of Entamoeba histolytica HM-1:IMSS genome was published by Loftus et al. Bhattacharya et al. amplified and sequenced 9 kb of coding and non-coding DNA to evaluate the variability of E. histolytica SNPs in 14 strains

and identified a link between some genotypes and clinical outcome [36]. The advent of the next 3-oxoacyl-(acyl-carrier-protein) reductase generation of high throughput genomic sequencing (NGS) technologies has provided more comprehensive opportunities to investigate variation in the genome of E. histolytica and clinical outcome by allowing the fast and efficient way to sequence laboratory-cultured ameba of clinical relevance [35, 37]. These cultured strains were isolated from different geographical areas endemic for amebiasis and contained large numbers of “strain-specific” SNPs in addition to SNPs present in more than one strain [35]. The sequence variations associated with virulence strains previously identified in the sequenced 9 kb DNA (a synonomous SNP in XM_001913658.1the heavy subunit of the Gal/GalNAc lectin gene (894A/G), and SNPs in the non-coding DNA either between XM_652295.