The Evolutionary History of the Genus Acanthamoeba and the Identification of Eight New 18S rRNA Gene Sequence Types

ABSTRACT The 18S rRNA gene ( Rns ) phylogeny of Acanthamoeba is being investigated as a basis for improvements in the nomenclature and taxonomy of the genus. We previously analyzed Rns sequences from 18 isolates from morphological groups 2 and 3 and found that they fell into four distinct evolutionary lineages we called sequence types T1-T4. Here, we analyzed sequences from 53 isolates representing 16 species and including 35 new strains. Eight additional lineages (sequence types T5-T12) were identified. Four of the 12 sequence types included strains from more than one nominal species. Thus, sequence types could be equated with species in some cases or with complexes of closely related species in others. The largest complex, sequence type T4, which contained six closely related nominal species, included 24 of 25 keratitis isolates. Rns sequence variation was insufficient for full phylogenetic resolution of branching orders within this complex, but the mixing of species observed at terminal nodes confirmed that traditional classification of isolates has been inconsistent. One solution to this problem would be to equate sequence types and single species. Alternatively, additional molecular information will be required to reliably differentiate species within the complexes. Three sequence types of morphological group 1 species represented the earliest divergence in the history of the genus and, based on their genetic distinctiveness, are candidates for reclassification as one or more novel genera.     

Spatial and temporal population genetic survey of Bulinus globosus from Zanzibar: an intermediate host of Schistosoma haematobium

In Zanzibar, the freshwater hermaphroditic snail Bulinus globosus is the intermediate host of the human parasite Schistosoma haematobium . To shed light on the patterns of genetic variation within Bu. globosus , variation at six polymorphic microsatellite loci was assessed to quantify spatial genetic structure within eight populations and temporal changes in a further four populations of the snails. Limited genetic variation was observed within populations, possibly reflecting both partial-selfing and fluctuations in population size. Although a statistically significant heterozygote deficiency was observed, Bu. globosus appears to be a preferential out-crosser, which was consistent with the absence of genotypic linkage disequilibria. Genetic variation across populations was substantial, illustrating significant isolation-by-distance on a regional scale and that gene flow was restricted to nearby populations. The temporal survey showed that levels of genetic variation and inbreeding changed over a 1-year period, consistent with field observations of seasonal change. The results strongly support a snail demographic model of population expansion and contraction throughout the year with habitats re-colonized by aestivating or surviving snails from local refugia. This model might help explain co-evolution of snails and schistosomes in Zanzibar as local populations of Bu. globosus have varying degrees of susceptibility to S. haematobium .     

Circular genome visualization and exploration using CGView

SUMMARY: CGView (Circular Genome Viewer) is a Java application and library for generating high-quality, zoomable maps of circular genomes. It converts XML or tab-delimited input into a graphical map (PNG, JPG or Scalable Vector Graphics format), complete with sequence features, labels, legends and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any Web browser, allowing rapid genome browsing and facilitating data sharing. AVAILABILITY: CGView (the standalone application, library or applet), sample input, sample maps and documentation can be obtained from http://wishart.biology.ualberta.ca/cgview/ CONTACT: david.wishart@ualberta.ca.     

Urinary schistosomiasis on Zanzibar: application of two novel assays for the detection of excreted albumin and haemoglobin in urine

As part of a urinary schistosomiasis control programme on Zanzibar, an aged cross-sectional survey of 305 children from three schools on Unguja was conducted to investigate the relationships between levels of excreted albumin and haemoglobin in urine and Schistosoma haematobium infection status. Diagnosis was determined by standard parasitological methods, dipstick reagents for microhaematuria, visual inspection for macrohaematuria as well as collection of case-history questionnaire data for self-diagnosis. Prevalence of infection as determined by parasitology was 53.9% and approximately, one quarter of the children examined were anaemic (<11 g dl(-1)). A statistically significant negative association of blood haemoglobin levels of boys and S. haematobium infection intensity status was observed (rs=-0.23, P=0.005). Through sensitivity analysis of urine-albumin values it was determined that a concentration of above >40 mg l(-1), as measured with the HemoCue urine-albumin photometer, had sensitivity, specificity, positive and negative predictive values of 0.90, 0.83, 0.86 and 0.89 respectively against 'gold-standard' parasitology. There was a clear association of reported pain upon micturition for children with elevated urine-albumin levels, with an odds ratio of 20 to 1. Levels of excreted blood in urine were quantified with the HemoCue Plasma/Low Hb photometer. However, dipsticks remain the method of choice for urine-haemoglobin of 0.1 g l(-1) and below. Urine parameters over a 24-h period were assessed in a small sub-sample. Reductions in both albumin and haemoglobin excretion were observed in 11 children 54 days after praziquantel treatment. It was concluded that these rapid, high-through-put, portable HemoCue assays could play a role in better describing and monitoring the occurrence, severity and evolution of urinary schistosomiasis disease. The urine-albumin assay has particular promise as a biochemical marker of S. haematobium induced kidney- and upper urinary tract-morbidity.     

Schistosoma bovis in western Uganda

During routine parasitological surveillance and monitoring activities within a National Control Programme for control of human schistosomiasis in Uganda, it was noted that cattle grazing in a water meadow immediately adjacent to Tonya primary school, where the prevalence of intestinal schistosomiasis in children was in excess of 90%, were unusually emaciated. To test the hypothesis that there may have been an anthropozoonotic focus of Schistosoma mansoni within the local herd, a young female heifer, clearly emaciated and c. 8 months old, was slaughtered from which schistosome worms were later recovered by dissection. As female worms inspected by microscopy were not gravid, morphological identification proved inconclusive but analysis of cytochrome oxidase subunit I (COI) and small subunit (SSU) ribosomal DNA sequences from these worms identified them as Schistosoma bovis Sonsino, 1876. This is the first substantiated report of S. bovis from Lake Albert, western Uganda. Further epidemiological surveys are needed to clarify the extent of bovine schistosomiasis within this region, particularly so since this lakeside plain has been earmarked as a future game reserve.     

Genetic Diversity within Schistosoma haematobium: DNA Barcoding Reveals Two Distinct Groups

Background

Schistosomiasis in one of the most prevalent parasitic diseases, affecting millions of people and animals in developing countries. Amongst the human-infective species S. haematobium is one of the most widespread causing urogenital schistosomiasis, a major human health problem across Africa, however in terms of research this human pathogen has been severely neglected.

Methodology/Principal Findings

To elucidate the genetic diversity of Schistosoma haematobium, a DNA ‘barcoding’ study was performed on parasite material collected from 41 localities representing 18 countries across Africa and the Indian Ocean Islands. Surprisingly low sequence variation was found within the mitochondrial cytochrome oxidase subunit I (cox1) and the NADH-dehydrogenase subunit 1 snad1). The 61 haplotypes found within 1978 individual samples split into two distinct groups; one (Group 1) that is predominately made up of parasites from the African mainland and the other (Group 2) that is made up of samples exclusively from the Indian Ocean Islands and the neighbouring African coastal regions. Within Group 1 there was a dominance of one particular haplotype (H1) representing 1574 (80%) of the samples analyzed. Population genetic diversity increased in samples collected from the East African coastal regions and the data suggest that there has been movement of parasites between these areas and the Indian Ocean Islands.

Conclusions/Significance

The high occurrence of the haplotype (H1) suggests that at some point in the recent evolutionary history of S. haematobium in Africa the population may have passed through a genetic ‘bottleneck’ followed by a population expansion. This study provides novel and extremely interesting insights into the population genetics of S. haematobium on a large geographic scale, which may have consequence for control and monitoring of urogenital schistosomiasis.