Such a result suggests that the markers
do not share the same genealogy, likely due to extensive recombination or re-assortment Bucladesine price breaking down linkage between markers. The diversity of E. histolytica genome raises a concern in regard to later analysis as it raises the possibility that a rapid rate of evolution may drive any observed differences between E. histolytica genotypes in samples isolated in regions separated even by relatively small geographical distances. Figure 3 Lack of consistent patterns of descent among SNP markers from Bangladeshi E. histolytica isolates suggests they segregate independently. Consensus phylogeny inferred from 100 bootstrap replicates of polymorphic SNP markers, constructed using the MEGA 5 program and the Maximum Likelihood method based on the Tamura-Nei model and using the sequences
shown in Additional file 1: Table 8 . Selleckchem Caspase Inhibitor VI Branches produced in fewer than 50% of the bootstrap phylogenies were collapsed. Sequences from stool have the suffix s; culture c; monthly survey stools begin with MS or CMS, diarrheal DS or CDS, amebic liver abscess samples RUF. The effect of adaptation of to in vitro culture on SNP allele frequencies To examine the potential effect of adaption Go6983 research buy to in vitro culture on the frequency of SNP alleles, and therefore how well transiently or long established cultured trophozoites represent the parasite population, SNP allele frequencies were compared Fludarabine clinical trial between parasites genotyped directly from stool samples and those from cultured trophozoites
(Additional file 1: Table S10). In cultures originating from asymptomatic isolates five linked Non-Reference SNPs at the LCAT EHI_065250/XM_647310.1 locus were detected in 80% of the strains, these same SNPs occurred in only 16% of the E. histolytica positive stool samples from asymptomatic hosts (Figure 4). This suggests that during establishment of E. histolytica cultures a strong selection pressure was exerted on sequence in linkage with the LCAT EHI_065250 gene. This could either cause growth failure of the strains with the Reference allele or the outgrowth of a minority genotype in mixed infections (previous studies using the short tandem repeats have indicated that mixed infections are rare however this possibility cannot be discounted ). Figure 4 Amebic culture effect on the EHI_065250 Entamoeba genotype. Distribution of the EHI_065250 SNP at the 10296 location in field isolates or cultured strains established from asymptomatic disease (p = 0.0166). The distribution of the individual SNPs, which were either Reference (Ref), Non-Reference (Non-Ref) or heterologous was shown on the x-axis. The number of samples of with this genotype isolated from patients with asymptomatic disease was shown on the y-axis.