Evaluation of the multispecies coalescent method to explore intra-Trypanosoma cruzi I relationships and genetic diversity

A phased genome assembly of a Colombian Trypanosoma cruzi TcI strain and the evolution of gene families

Chagas is an endemic disease in tropical regions of Latin America, caused by the parasite Trypanosoma cruzi. High intraspecies variability and genome complexity have been challenges to assemble high quality genomes needed for studies in evolution, population genomics, diagnosis and drug development. Here we present a chromosome-level phased assembly of a TcI T. cruzi strain (Dm25). While 29 chromosomes show a large collinearity with the assembly of the Brazil A4 strain, three chromosomes show both large heterozygosity and large divergence, compared to previous assemblies of TcI T. cruzi strains. Nucleotide and protein evolution statistics indicate that T. cruzi Marinkellei separated before the diversification of T. cruzi in the known DTUs. Interchromosomal paralogs of dispersed gene families and histones appeared before but at the same time have a more strict purifying selection, compared to other repeat families. Previously unreported large tandem arrays of protein kinases and histones were identified in this assembly. Over one million variants obtained from Illumina reads aligned to the primary assembly clearly separate the main DTUs. We expect that this new assembly will be a valuable resource for further studies on evolution and functional genomics of Trypanosomatids.

The Low Variability of Tc24 in Trypanosoma cruzi TcI as an Advantage for Chagas Disease Prophylaxis and Diagnosis in Mexico

(1) Background: Chagas disease is the main neglected tropical disease in America. It is estimated that around 6 million people are currently infected with the parasite in Latin America, and 25 million live in endemic areas with active transmission. The disease causes an estimated economic loss of USD 24 billion dollars annually, with a loss of 75,200 working years per year of life; it is responsible for around ~12,000 deaths annually. Although Mexico is an endemic country that recorded 10,186 new cases of Chagas disease during the period of 1990–2017, few studies have evaluated the genetic diversity of genes that could be involved in the prophylaxis and/or diagnosis of the parasite. One of the possible candidates proposed as a vaccine target is the 24 kDa trypomastigote excretory–secretory protein, Tc24, whose protection is linked to the stimulation of T. cruzi-specific CD8+ immune responses. (2) Methods: The aim of the present study was to evaluate the fine-scale genetic diversity and structure of Tc24 in T. cruzi isolates from Mexico, and to compare them with other populations reported in the Americas with the aim to reconsider the potential role of Tc24 as a key candidate for the prophylaxis and improvement of the diagnosis of Chagas disease in Mexico. (3) Results: Of the 25 Mexican isolates analysed, 48% (12) were recovered from humans and 24% (6) recovered from Triatoma barberi and Triatoma dimidiata. Phylogenetic inferences revealed a polytomy in the T. cruzi clade with two defined subgroups, one formed by all sequences of the DTU I and the other formed by DTU II–VI; both subgroups had high branch support. Genetic population analysis detected a single (monomorphic) haplotype of TcI throughout the entire distribution across both Mexico and South America. This information was supported by Nei’s pairwise distances, where the sequences of TcI showed no genetic differences. (4) Conclusions: Given that both previous studies and the findings of the present work confirmed that TcI is the only genotype detected from human isolates obtained from various states of Mexico, and that there is no significant genetic variability in any of them, it is possible to propose the development of in silico strategies for the production of antigens that optimise the diagnosis of Chagas disease, such as quantitative ELISA methods that use this region of Tc24.

Microevolution and subspecific taxonomy of Trypanosoma cruzi

Trypanosoma cruzi, the agent of Chagas disease, is a highly polymorphic species, subdivided into 6 main evolutionary lineages or near-clades (formerly discrete typing units or DTUs). An additional near-clade (TC-bat) has recently been evidenced. This pattern is considered to be the result of predominant clonal evolution (PCE). PCE is compatible with occasional mating/hybridization, which do not break the prevalent pattern of clonal evolution, the main trait of it being the presence of Multigene Bifurcating Trees (MGBTs) at all evolutionary levels ("clonal frame"). The development of highly resolutive genetic (microsatellites*) and genomic (sequencing and multi-single nucleotide polymorphism {SNP}* typing) markers shows that PCE also operates at a microevolutionary* level within each of the near-clades ("Russian doll pattern"), in spite of occasional meiosis and hybridization events. Within each near-clade, one can evidence widespread clonal multilocus genotypes*, linkage disequilibrium*, Multigene Bifurcating Trees and lesser near-clades. The within near-clade population structure is like a miniature picture of that of the whole species, suggesting gradual rather than saltatory evolution. Additional data are required to evaluate the stability of these lesser near-clades in the long run and to evaluate the need for an adequate nomenclature for this microevolutionary level.

Congenital transmission of Mexican strains of Trypanosoma cruzi TcIa: interaction between parasite and human placental explants

Congenital transmission of Chagas disease plays an important role in endemic countries because it is not a diagnosis that is encountered frequently in prenatal care. Due to limited information regarding congenital transmission of Trypanosoma cruzi in Mexico, the present study aimed to investigate protozoan infectivity and modulation of immune responses in human placental explants infected with T. cruzi Ia Mexican strains. The Inc-5 strain showed increased infectivity and modulated IL-1β, IL-10 and TLR-4, decreasing their expression after 24 h of infection. Both strains (Inc-5 and Ninoa) stimulated the production of TNF-α and decreased IL-6 levels 96 h after infection. An important detachment of the syncytiotrophoblast caused by infection with T. cruzi was observed after 24 h of infection. In this study, ex vivo infection of human placental villi was performed to better understand interactions involving parasitic T. cruzi and human placental tissue. It was concluded that the strains of TcIa present parasitism in placental tissue, modulation of the innate immune system of the placenta, and cause intense detachment of the syncytiotrophoblast, a fact that may be more associated with abortion and premature birth events than the congenital transmission itself, justifying the low rate of this transmission mechanism by this genotype.

Susceptibility dynamics between five Trypanosoma cruzi strains and three triatomine (Hemiptera: Reduviidae) species

American trypanosomiasis is a zoonosis caused by the parasite Trypanosoma cruzi and is transmitted mainly by blood-sucking insects belonging to the subfamily Triatominae. The importance of this parasite lies in its wide geographical distribution, high morbidity, and the fact that there has not yet been an effective treatment or vaccine. Previous studies have detailed the interactions between different triatomine species and T. cruzi strains. However, the factors necessary to establish infection in triatomines have not yet been fully elucidated. Furthermore, it is postulated that the coexistence between the parasite and triatomines could modulate the susceptibility to infection in these insects. Accordingly, in this study, we evaluated the susceptibility to T. cruzi infection in the species Triatoma (Meccus) pallidipennis, Triatoma barberi, and Triatoma lecticularia, which were infected with Ninoa, H8, INC-5, Sontecomapan, and Hueypoxtla strains. The criteria used to establish susceptibility were the amount of blood ingested by the insects, percentage of infected triatomines, concentration of parasites in feces, and percentage of metacyclic trypomastigotes in feces. These parameters were analyzed by fresh examination and differential count with Giemsa-stained smears. Our main findings suggest the following order of susceptibility concerning infection with T. cruzi: T. lecticularia > T. barberi > T. (Meccus) pallidipennis. Furthermore, the study concludes that an increased susceptibility to infection of triatomines that share the same geographic region with different strains of T. cruzi is not always a fact.

UglyTrees: a browser-based multispecies coalescent tree visualizer

SUMMARY

Visualization is a vital task in phylogenetics and yet there is a deficit in programs which visualize the multispecies coalescent (MSC) model. UglyTrees (UT) is an easy-to-use program for visualizing multiple gene trees embedded within a single species trees. The mapping between gene and species nodes is automatically detected allowing for ready access to the program. UT can scrape the contents of a website for MSC analyses, enabling the sharing of interactive MSC figures through optional parameters in the URL. If a posterior distribution is uploaded, the transitions between MSC states are animated allowing the visual tracking of trees throughout the sequence.

AVAILABILITY AND IMPLEMENTATION

UT runs in all major web browsers including mobile devices, and is hosted at www.uglytrees.nz. The MIT-licensed code is available at https://github.com/UglyTrees/uglytrees.github.io.

Trypanosoma cruzi Mexican Strains Differentially Modulate Surface Markers and Cytokine Production in Bone Marrow-Derived Dendritic Cells from C57BL/6 and BALB/c Mice

Dendritic cells (DCs) are a type of antigen-presenting cells that play an important role in the immune response against Trypanosoma cruzi, the causative agent of Chagas disease. In vitro and in vivo studies have shown that the modulation of these cells by this parasite can directly affect the innate and acquired immune response of the host in order to facilitate its biological cycle and the spreading of the species. Many studies show the mechanisms by which T. cruzi modulates DCs, but the interaction of these cells with the Mexican strains of T. cruzi such as Ninoa and INC5 has not yet been properly investigated. Here, we evaluated whether Ninoa and INC5 strains evaded the immunity of their hosts by modulating the biology and function of murine DCs. The CL-Brener strain was used as the reference strain. Herein, it was demonstrated that Ninoa was more infective toward bone marrow-derived dendritic cells (BMDCs) than INC5 and CL-Brener strains in both BMDCs of BALB/c and C57BL/6 mice. Mexican strains of T. cruzi induced different cytokine patterns. In BMDCs obtained from BALB/c mice, Ninoa strain led to the reduction in IL-6 and increased IL-10 production, while in C57BL/6 mice Ninoa strain considerably increased the productions of TNF-α and IL-10. Also, Ninoa and INC5 differentially modulated BMDC expressions of MHC-II, TLR2, and TLR4 in both BALB/c and C57BL/6 mice compared to Brazilian strain CL-Brener. These results indicate that T. cruzi Mexican strains differentially infect and modulate MHC-II, toll-like receptors, and cytokine production in DCs obtained from C57BL/6 and BALB/c mice, suggesting that these strains have developed particular modulatory strategies to disrupt DCs and, consequently, the host immune responses.