Multilocus Sequence Typing (MLST) for Lineage Assignment and High Resolution Diversity Studies in Trypanosoma cruzi

Yeo, Matthew; Maurício, Isabel; Messenger, Louisa A.; Lewis, Michael D.; Llewellyn, Martin S.; Acosta, Nidia; Bhattacharyya, Tapan; Diosque, Patricio; Carrasco, Hernán J.; Miles, Michael A.

doi:10.1371/journal.pntd.0001049

Cited by 101 publications

(140 citation statements)

References 61 publications

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“…Nonetheless, it is clear that cross-fertilization was common, highlighting the efficiency with which E. tenella can hybridize and indicating the ease with which vaccine-or drug-resistant alleles may be disseminated and mixed in field parasite populations. Corroboratory data from field parasite populations is scarce, but the large number of singleton haplotypes from Southern India and Nigeria is characteristic of populations with high rates of recombination (52).…”

Section: Discussionmentioning

confidence: 99%

Population, genetic, and antigenic diversity of the apicomplexanEimeria tenellaand their relevance to vaccine development

Blake

Clark

Macdonald

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

100

102

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The phylum Apicomplexa includes serious pathogens of humans and animals. Understanding the distribution and population structure of these protozoan parasites is of fundamental importance to explain disease epidemiology and develop sustainable controls. Predicting the likely efficacy and longevity of subunit vaccines in field populations relies on knowledge of relevant preexisting antigenic diversity, population structure, the likelihood of coinfection by genetically distinct strains, and the efficiency of cross-fertilization. All four of these factors have been investigated for Plasmodium species parasites, revealing both clonal and panmictic population structures with exceptional polymorphism associated with immunoprotective antigens such as apical membrane antigen 1 (AMA1). For the coccidian Toxoplasma gondii only genomic diversity and population structure have been defined in depth so far; for the closely related Eimeria species, all four variables are currently unknown. Using Eimeria tenella, a major cause of the enteric disease coccidiosis, which exerts a profound effect on chicken productivity and welfare, we determined population structure, genotype distribution, and likelihood of crossfertilization during coinfection and also investigated the extent of naturally occurring antigenic diversity for the E. tenella AMA1 homolog. Using genome-wide Sequenom SNP-based haplotyping, targeted sequencing, and single-cell genotyping, we show that in this coccidian the functionality of EtAMA1 appears to outweigh immune evasion. This result is in direct contrast to the situation in Plasmodium and most likely is underpinned by the biology of the direct and acute coccidian life cycle in the definitive host.Eimeria | coccidiosis | population structure | chickens | food security

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Section: Discussionmentioning

confidence: 99%

Population, genetic, and antigenic diversity of the apicomplexanEimeria tenellaand their relevance to vaccine development

Blake

Clark

Macdonald

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

100

102

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“…The level of nuclear sequence divergence between major T. cruzi DTUs is equivalent to interspecies diversity among New World Leishmania species (Yeo et al . 2011; Boité et al . 2012).…”

Section: Introductionmentioning

confidence: 99%

Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure, hybridization and a role for humans in Andean parasite dispersal

et al. 2015

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An improved understanding of how a parasite species exploits its genetic repertoire to colonize novel hosts and environmental niches is crucial to establish the epidemiological risk associated with emergent pathogenic genotypes. Trypanosoma cruzi, a genetically heterogeneous, multi‐host zoonosis, provides an ideal system to examine the sylvatic diversification of parasitic protozoa. In Bolivia, T. cruzi I, the oldest and most widespread genetic lineage, is pervasive across a range of ecological clines. High‐resolution nuclear (26 loci) and mitochondrial (10 loci) genotyping of 199 contemporaneous sylvatic TcI clones was undertaken to provide insights into the biogeographical basis of T. cruzi evolution. Three distinct sylvatic parasite transmission cycles were identified: one highland population among terrestrial rodent and triatomine species, composed of genetically homogenous strains (A r = 2.95; PA/L = 0.61; DAS = 0.151), and two highly diverse, parasite assemblages circulating among predominantly arboreal mammals and vectors in the lowlands (A r = 3.40 and 3.93; PA/L = 1.12 and 0.60; DAS = 0.425 and 0.311, respectively). Very limited gene flow between neighbouring terrestrial highland and arboreal lowland areas (distance ~220 km; FST = 0.42 and 0.35) but strong connectivity between ecologically similar but geographically disparate terrestrial highland ecotopes (distance >465 km; FST = 0.016–0.084) strongly supports ecological host fitting as the predominant mechanism of parasite diversification. Dissimilar heterozygosity estimates (excess in highlands, deficit in lowlands) and mitochondrial introgression among lowland strains may indicate fundamental differences in mating strategies between populations. Finally, accelerated parasite dissemination between densely populated, highland areas, compared to uninhabited lowland foci, likely reflects passive, long‐range anthroponotic dispersal. The impact of humans on the risk of epizootic Chagas disease transmission in Bolivia is discussed.

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“…Moreover, the portability of MLST data allows results from different laboratories to be compared (33,34). MLST was first utilized to genetically characterize pathogenic bacteria but has now been expanded for use in genetic and population studies of fungi and protozoa (48,67).…”

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confidence: 99%

Genetic Characterization of Trichomonas vaginalis Isolates by Use of Multilocus Sequence Typing

et al. 2012

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dIn this study, we introduce a multilocus sequence typing (MLST) scheme, comprised of seven single-copy housekeeping genes, to genetically characterize Trichomonas vaginalis. Sixty-eight historical and recent isolates of T. vaginalis were sampled from the American Type Culture Collection and female patients at area health care facilities, respectively, to assess the usefulness of this typing method. Forty-three polymorphic nucleotide sites, 51 different alleles, and 60 sequence types were distinguished among the 68 isolates, revealing a diverse T. vaginalis population. Moreover, this discriminatory MLST scheme retains the ability to identify epidemiologically linked isolates such as those collected from sexual partners. Population genetic and phylogenetic analyses determined that T. vaginalis population structure is strongly influenced by recombination and is composed of two separate populations that may be nonclonal. MLST is useful for investigating the epidemiology, genetic diversity, and population structure of T. vaginalis.

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Multilocus Sequence Typing (MLST) for Lineage Assignment and High Resolution Diversity Studies in Trypanosoma cruzi

Cited by 101 publications

References 61 publications

Population, genetic, and antigenic diversity of the apicomplexanEimeria tenellaand their relevance to vaccine development

Population, genetic, and antigenic diversity of the apicomplexanEimeria tenellaand their relevance to vaccine development

Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure, hybridization and a role for humans in Andean parasite dispersal

Genetic Characterization of Trichomonas vaginalis Isolates by Use of Multilocus Sequence Typing

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