Widespread heteroplasmy in schistosomes makes an mtVNTR marker "nearsighted"

Population Structure and Dynamics of Helminthic Infection: Schistosomiasis

While disease and outbreaks are mainly clonal for bacteria and other asexually reproducing organisms, sexual reproduction in schistosomes and other helminths usually results in unique individuals. For sexually reproducing organisms, the traits conserved in clones will instead be conserved in the group of organisms that tends to breed together, the population. While the same tools are applied to characterize DNA, how results are interpreted can be quite different at times (see another article in this collection, http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.AME-0002-2018). It is difficult to know what the real effect any control program has on the parasite population without assessing the health of this population, how they respond to the control measure, and how they recover, if they do. This review, part of the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases, concentrates on one approach using pooled samples to study schistosome populations and shows how this and other approaches have contributed to our understanding of this parasite family's biology and epidemiology. *This article is part of a curated collection.

Co-infection and cross-species transmission of divergent Hepatocystis lineages in a wild African primate community

Hemoparasites of the apicomplexan family Plasmodiidae include the etiological agents of malaria, as well as a suite of non-human primate parasites from which the human malaria agents evolved. Despite the significance of these parasites for global health, little information is available about their ecology in multi-host communities. Primates were investigated in Kibale National Park, Uganda, where ecological relationships among host species are well characterized. Blood samples were examined for parasites of the genera Plasmodium and Hepatocystis using microscopy and PCR targeting the parasite mitochondrial cytochrome b gene, followed by Sanger sequencing. To assess co-infection, "deep sequencing" of a variable region within cytochrome b was performed. Out of nine black-and-white colobus (Colobus guereza), one blue guenon (Cercopithecus mitis), five grey-cheeked mangabeys (Lophocebus albigena), 23 olive baboons (Papio anubis), 52 red colobus (Procolobus rufomitratus) and 12 red-tailed guenons (Cercopithecus ascanius), 79 infections (77.5%) were found, all of which were Hepatocystis spp. Sanger sequencing revealed 25 different parasite haplotypes that sorted phylogenetically into six species-specific but morphologically similar lineages. "Deep sequencing" revealed mixed-lineage co-infections in baboons and red colobus (41.7% and 64.7% of individuals, respectively) but not in other host species. One lineage infecting red colobus also infected baboons, but always as the minor variant, suggesting directional cross-species transmission. Hepatocystis parasites in this primate community are a diverse assemblage of cryptic lineages, some of which co-infect hosts and at least one of which can cross primate species barriers.

Schistosoma mansoni population structure and persistence after praziquantel treatment in two villages of Bahia, Brazil

Praziquantel has been used to treat schistosome infections since 1979 and currently is the only chemotherapeutic agent in production for this purpose, raising concerns about the potential for the emergence of drug resistance. In practice, 10-20% of infected patients will continue to excrete eggs after treatment. It is not understood to what degree this represents selection of a resistant population or incomplete elimination due to the presence of immature worms at the time of treatment. We used a population genetics approach to test whether or not persistent Schistosomamansoni parasites were drawn from the same population as susceptible parasites. In this study, stool samples were collected from 96% of individuals in two small Brazilian communities (populations 482 and 367) and examined for S.mansoni eggs. The combined prevalence of S.mansoni infections in the villages was 41%. Total egg DNA was extracted from each sample and was genotyped at 15 microsatellite markers. Day-to-day variation of the infrapopulation from an individual human host was low (median differentiation using Jost's D=0.010), so that a single stool was representative of the genotypes present in stool eggs, at least in the short term. Average pairwise analysis of D among all pre-treatment infrapopulations suggested moderate differentiation (mean D=0.082 and 0.122 for the two villages), whereas the pre-treatment component population differentiation between the two communities was 0.047. The differentiation of the component population remaining after treatment from the fully susceptible component population was low (mean D=0.007 and 0.020 for the two villages), suggesting that the persistent parasites were not selected by praziquantel treatment. We will continue to follow these communities for evidence of selection or changes in population structure.

Brazilian studies on the genetics of Schistosoma mansoni

The parasite Schistosoma is known to exhibit variations among species, strains and genera, such as, the levels of infectivity, pathogenicity and immunogenicity. These factors may differ among parasite populations according to the local epidemiological conditions. Diversity observed in Schistosoma mansoni from different geographical regions or within individuals of the same region can be determined by differences in the genotype of each parasite strain. However, until recently, finding adequate genetic markers to investigate infectivity or other epidemiological characteristics of a transmission area proved difficult. Several studies have been conducted to evaluate the genetic variability of S. mansoni, using different techniques. Intraspecific variability was observed in morphological characters, isoenzyme studies, mtDNA, ribosomal gene probes, random amplification of polymorphic DNA (RAPD) and microsatellites. The sequencing of the S. mansoni genome was the most important achievement concerning genetic approaches to the study of this parasite and may improve the development of drugs, vaccines and diagnostics of schistosomiasis. The knowledge of the genetic structure of schistosome populations in relation to epidemiological data and host variability is essential for the understanding of the epidemiology of the disease and the design of control strategies.

Genetic diversity and population structuring of Schistosoma mansoni in a Brazilian village

The digenean trematode Schistosoma mansoni is responsible for chronic schistosomiasis worldwide, and in Brazil alone an estimated 35 million people are at risk. To evaluate epidemiological patterns among human definitive hosts, we assessed genetic diversity and population subdivision of S. mansoni infrapopulations in human hosts from the highly endemic village of Virgem das Graças in the state of Minas Gerais, Brazil. We believe this is the largest such survey to date. Genetic diversity of parasites, measured over eight polymorphic microsatellite loci, was relatively high and standard measures of inbreeding indicated that the population was panmictic. Furthermore, there was no significant isolation-by-distance of parasite infrapopulations, and measures of population subdivision indicated significant but low to moderate levels of population differentiation. We conclude that patients within this village sample from a broad range of schistosome genetic diversity and effectively act as "genetic mixing bowls" for the parasites. These results contrast with those previously observed in the Brazilian village of Melqui ades and thus provide the opportunity for comparisons of environmental and epidemiological differences that are likely to influence host-parasite coevolution and parasite transmission.

Genetic filtering and optimal sampling of Schistosoma mansoni populations

Allelic variation in 6 microsatellite markers was compared between frozen Schistosoma mansoni eggs and laboratory-passaged worms originating from the same 5 fecal samples obtained from Brazilian residents. Based on allelic richness values, the number of alleles detected per locus did not differ between egg and worm DNA templates. However, our ability to score loci differed between these DNA templates, with worms providing more scored loci per individual than eggs. Differences also existed between the worms and eggs in the identity of the specific alleles that were detected. Additionally, we observed a reduction in homozygous genotypes among laboratory-passaged worms relative to the eggs. Allelic diversity curves were calculated by genotyping all worms from a representative host sample to determine the relationship between the number of alleles detected at a locus and the number of worms genotyped. Curves for the 5 residents' worm infrapopulations for each of the loci were very similar. The equation y=19.55 x ln(x) + 9.992 explained the association between sampling effort (x) and number of alleles detected (y) with an R(2) of 0.775. In conclusion, egg DNA templates and allelic diversity curves can benefit efforts to discern the sociological, ecological and evolutionary forces impacting the genetic diversity and disease epidemiology of human schistosomes.

A comparison of microsatellite polymorphism and heterozygosity among field and laboratory populations of Schistosoma mansoni

The genetic diversity of a field population (recently collected in Melquiades, Brazil) and two laboratory strains (LE and NMRI) of a human blood fluke, Schistosoma mansoni, were analysed using microsatellite markers. Data from the three groups showed an extreme and consistent discrepancy in the level of polymorphism at all microsatellite loci between the field population and laboratory populations. The numbers of alleles detected in LE and NMRI populations averaged only 14 and 10% of those found in the field population, respectively. Especially apparent was the abundance of rare alleles in the Melquiades population when compared with the laboratory strains. The reduction in allelic diversity in the laboratory strains is most likely due to the founder effect and potential bottlenecks that may have occurred during decades of laboratory maintenance. Surprisingly, a much less drastic difference was found when comparing the average heterozygosity of the field population with the laboratory strains. This apparent anomaly may be explained by observed population substructuring (and a potential resultant Wahlund effect) in the natural population. Our comparison of genetic diversity between laboratory and field populations of S. mansoni emphasizes the need for studies of representative populations in schistosome vaccine development.

Genome and genomics of schistosomes

Schistosomes infect over 200 million people and 600 million are at risk. Genomics and post-genomic studies of schistosomes will contribute greatly to developing new reagents for diagnostic purposes and new vaccines that are of interest to the biotechnology industry. In this review, the most recent advances in these fields as well as new projects and future perspectives will de described. A vast quantity of data is publicly available, including short cDNA and genomic sequences, complete large genomic fragments, and the mitochondrial genomes of three species of the genus Schistosoma. The physical structure of the genome is being studied by physically mapping large genomic fragments and characterizing the highly abundant repetitive DNA elements. Bioinformatic manipulations of the data have already been carried out, mostly dealing with the functional analysis of the genes described. Specific search tools have also been developed. Sequence variability has been used to better understand the phylogeny of the species and for population studies, and new polymorphic genomic markers are currently being developed. The information generated has been used for the development of post-genomic projects. A small microarray detected genes that were differentially expressed between male and female worms. The identification of two-dimensional spots by mass spectrometry has also been demonstrated.

Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers

Blood flukes in the genus Schistosoma are important human parasites in tropical regions. A substantial amount of genetic diversity has been described in populations of these parasites using molecular markers. We first consider the extent of genetic variation found in Schistosoma mansoni and some factors that may be contributing to this variation. Recently, though, attempts have been made to analyze not only the genetic diversity but how that diversity is partitioned within natural populations of schistosomes. Studies with non-allelic molecular markers (e.g. RAPDs and mtVNTRs) have indicated that schistosome populations exhibit varying levels of gene flow among component subpopulations. The recent characterization of microsatellite markers for S. mansoni provided an opportunity to study schistosome population structure within a population of schistosomes from a single Brazilian village using allelic markers. Whereas the detection of population structure depends strongly on the type of analysis with a mitochondrial marker, analyses with a set of seven microsatellite loci consistently revealed moderate genetic differentiation when village boroughs were used to define parasite subpopulations and greater subdivision when human hosts defined subpopulations. Finally, we discuss the implications that such strong population structure might have on schistosome epidemiology.

Mitochondrial genomes of parasitic flatworms

Complete or near-complete mitochondrial genomes are now available for 11 species or strains of parasitic flatworms belonging to the Trematoda and the Cestoda. The organization of these genomes is not strikingly different from those of other eumetazoans, although one gene (atp8) commonly found in other phyla is absent from flatworms. The gene order in most flatworms has similarities to those seen in higher protostomes such as annelids. However, the gene order has been drastically altered in Schistosoma mansoni, which obscures this possible relationship. Among the sequenced taxa, base composition varies considerably, creating potential difficulties for phylogeny reconstruction. Long non-coding regions are present in all taxa, but these vary in length from only a few hundred to approximately 10000 nucleotides. Among Schistosoma spp., the long non-coding regions are rich in repeats and length variation among individuals is known. Data from mitochondrial genomes are valuable for studies on species identification, phylogenies and biogeography.

Distribution of schistosome infections in molluscan hosts at different levels of parasite prevalence

Biomphalaria glabrata snails infected with Schistosoma mansoni were collected during consecutive seasons from a site in Brazil known to have a very high percentage of infected snails. Schistosoma mansoni cercariae from single snails were used to infect individual mice, and the recovered adult worms were genetically assessed using a mtVNTR marker. The number of unique parasite genotypes found per snail was compared to expected abundance values, based on the infection prevalence at the site, to determine the distribution of S. mansoni infections within the snail population. The observed distributions and those from previous studies were used to examine the relationship between schistosome prevalence and aggregation across a wide range of prevalence values. Our analysis showed that prevalence was inversely related to the degree of parasite overdispersion, and at high prevalence, S. mansoni infections were randomly distributed among snails.

Defining and interpreting intraspecific molecular variation

Defining the extent and character of intraspecific genetic variation provides important information about gene function and organismal history. Powerful tests may be applied to sequenced alleles in order to critically examine whether natural selection is responsible for limiting or elevating intraspecific polymorphism in particular genes. Unconventional patterns of sequence variation and unusual allelic frequency distributions can be used to test whether genes encoding parasite antigens are being diversified by immune selection. The strikingly limited genetic variation in the falciparum malaria genome, and in human chromosomes encoding resistance to severe malaria, date the emergence of this disease to within the last few thousand years, illustrating the power of population genetic analysis to elucidate the history of host-parasite interactions. Coupling phylogenetic and geographic information and analyzing the rate of diversification in intraspecific gene trees provides new and rich sources of information on microbial evolution and epidemiology.