Characterisation of large and small subunit rRNA and mini-exon genes further supports the distinction of six Trypanosoma cruzi lineages

Chagas disease in a naturally-infected dog from Northeast Brazil: a case report

BACKGROUND

Dogs are the main domestic reservoir host of the parasite Trypanosoma cruzi, the causative agent of Chagas disease, and they are considered sentinel animals for the detection of new cases of human infection. Canis familiaris is also a well-established experimental T. cruzi infection model, but little is known about the progression of Chagas disease in naturally-infected dogs, especially during the acute phase in these hosts. Triatomine species infected with discrete typing units (DTUs) I, II and III of T. cruzi have been previously found in many of the municipalities of the state of Rio Grande do Norte. The current study describes the clinical, hematological, biochemical, cardiological and parasitological characteristics of a single dog during the acute phase of its naturally-acquired T. cruzi infection, and characterizes the isolate obtained from this individual host using biological, molecular and phylogenetic methods.

RESULTS

A  juvenile dog exhibiting discomfort during defecation, itchy skin, and enlarged popliteal lymph nodes showed a prolonged period of patent parasitemia, with normocytic and hypochromic anemia. In addition, cardiac damage was suggested by high concentrations of the biomarkers cardiac troponin I and NT-ProBNP, as well as Doppler echocardiography, which showed qualitative segmental hypokinesia. The parasites isolated from this individual canine were genotyped, using three molecular markers and phylogenetic analysis, as the DTU TcIII. First detected in sylvatic environments, our current observations also demonstrate the presence of this DTU in domestic/ peridomestic locations.

CONCLUSIONS

The cardiac alterations that we observed in a naturally-T. cruzi-infected dog contribute to expanding our knowledge of both Chagas disease in Canis familiaris, and the epidemiological scenario in locations where Triatoma brasiliensis is the main triatomine vector of T. cruzi.

Molecular Markers for the Phylogenetic Reconstruction of Trypanosoma cruzi: A Quantitative Review

Trypanosoma cruzi is the parasite responsible for Chagas disease, which has a significant amount of genetic diversification among the species complex. Many efforts are routinely made to characterize the genetic lineages of T. cruzi circulating in a particular geographic area. However, the genetic loci used to typify the genetic lineages of T. cruzi have not been consistent between studies. We report a quantitative analysis of the phylogenetic power that is acquired from the commonly used genetic loci that are employed for the typification of T. cruzi into its current taxonomic nomenclature. Based on three quantitative criteria (the number of phylogenetic informative characters, number of available reference sequences in public repositories, and accessibility to DNA sequences for their use as outgroup sequences), we examine and discuss the most appropriate genetic loci for the genetic typification of T. cruzi. Although the mini-exon gene is by far the locus that has been most widely used, it is not the most appropriate marker for the typification of T. cruzi based on the construction of a resolved phylogenetic tree. Overall, the mitochondrial COII-NDI locus stands out as the best molecular marker for this purpose, followed by the Cytochrome b and the Lathosterol oxidase genes.

Trypanosoma cruzi infection in American black bears (Ursus americanus): A case report in a cub from California and serologic survey for exposure in wild black bears from several states

Trypanosoma cruzi is an important cause of disease and death in humans and dogs, and although wildlife infections are common, less is known about disease manifestations. A 12-week-old male American black bear (Ursus americanus) cub with mild lethargy and anorexia presented to a wildlife rehabilitation center in Lake Tahoe, California. The cub continued to become increasingly weak and showed decreasing interest in play and other activities. The cub was anemic and had increased γ-glutamyltransferase (GGT) liver enzymes. A large number of trypanosomes were noted on a thin blood smear. Trypanosoma cruzi was isolated in culture from a subsequent blood collection. Proliferative bony lesions were noted on radiographs, but this finding was considered unrelated to the T. cruzi infection. The number of parasites observed in thin blood smears dramatically dropped over time, but it remained PCR positive until at least nine months. The cub continued to gain weight and became increasingly active. Serum samples from the cub were positive with three different serologic assays (IFA, ELISA, and ICT). The bear was not treated because of the decreasing parasitemia and the improvement in activity and appetite. Although the bear could not be released due to issues unrelated to T. cruzi, it remains healthy in a captive facility. Sequence analysis of the DHFR-TS and COII-ND1 gene sequences confirmed the bear was infected with DTC TcIV. Following the detection of this clinical case, a serologic survey was conducted to determine the prevalence of T. cruzi exposure of black bears in California, North Carolina, and Pennsylvania. Because no serologic assay has been validated for use in bears, three different assays were used. Marked differences in apparent seroprevalence range from 1% (requiring all three assays to be positive) to ∼20.7% (requiring only one assay to be positive). Black bears are naturally exposed to T. cruzi across the United States. Future studies using PCR testing of tissues or blood would be needed to better understand the prevalence of T. cruzi in wild black bears, lineages most commonly associated with infection, and if T. cruzi represents a health threat to bears.

Diversity of Chagas disease diagnostic antigens: Successes and limitations

Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, remains a public health issue in endemic regions of the Americas, and is becoming globalised due to migration. In the chronic phase, 2 accordant serological tests are required for diagnosis. In addition to "in-house" assays, commercial tests are available (principally ELISA and rapid diagnostic tests). Herein, we discuss the discovery era of defined T. cruzi serological antigens and their utilisation in commercialised tests. A striking feature is the re-discovery of the same antigens from independent studies, and their overlapping use among commonly reported commercial serological tests. We also consider reports of geographical variation in assay sensitivity and areas for refinement including applications to congenital diagnosis, treatment monitoring, and lineage-specific antigens.

Genetic Diversity of Trypanosoma cruzi in the United States of America: The Least Endemic Country for Chagas Disease

Chagas disease (CD), caused by Trypanosoma cruzi and endemic in Latin America, has become an emergent health problem in non-endemic countries due to human migration. The United States (US) is the non-Latin American country with the highest CD burden and cannot be considered as non-endemic, since triatomine vectors and reservoir animals have been found. Populations of T. cruzi are divided into genetic subdivisions, which are known as discrete typing units (DTUs): TcI to TcVI and TcBat. Autochthonous human T. cruzi infection in the US is sporadic, but it may change due to environmental factors affecting the geographic distribution of triatomines. We aimed to perform a literature review of the genetic diversity of T. cruzi in triatomine vectors and mammalian hosts, including human cases, in the US. The 34 analyzed studies revealed the presence of T. cruzi in 18 states, which was mainly concentrated in Texas, Louisiana and New Mexico. TcI and TcIV were the principal DTUs identified, being TcI the most genotyped (42.4%; 917/2164). This study represents a first attempt to compile the molecular epidemiology of T. cruzi in the US, which is fundamental for predicting the progression of the infection in the country and could be of great help in its future management.

Enhancing Trypanosomatid Identification and Genotyping with Oxford Nanopore Sequencing: Development and Validation of an 18S rRNA Amplicon-Based Method

Trypanosomatids, including Trypanosoma and Leishmania species, present significant medical and veterinary challenges, causing substantial economic losses, health complications, and even fatalities. Diagnosing and genotyping these species and their genotypes is often complex, involving multiple steps. This study aimed to develop an amplicon-based sequencing (ABS) method using Oxford Nanopore long-read sequencing to enhance Trypanosomatid detection and genotyping. The 18S rDNA gene was targeted for its inter-species conservation. The Trypanosomatid-ABS method effectively distinguished between 11 Trypanosoma species (including Trypanosoma evansi, Trypanosoma theileri, Trypanosoma vivax, and Trypanosoma rangeli) and 6 Trypanosoma cruzi discrete typing units (TcI to TcVI and TcBat), showing strong concordance with conventional methods (κ index of 0.729, P < 0.001). It detected co-infections between Trypanosomatid genera and T. cruzi, with a limit of detection of one parasite per mL. The method was successfully applied to human, animal, and triatomine samples. Notably, TcI predominated in chronic Chagas samples, whereas TcII and TcIV were found in the acute stage. Triatomine vectors exhibited diverse Trypanosomatid infections, with Triatoma dimidiata mainly infected with TcI and occasional TcBat co-infections, and Rhodnius prolixus showing TcI and TcII infections, along with T. rangeli co-infections and mixed TcII infections. Animals were infected with T. vivax, T. theileri, and T. evansi. The ABS method's high resolution, sensitivity, and accuracy make it a valuable tool for understanding Trypanosomatid dynamics, enhancing disease control strategies, and enabling targeted interventions.

New insights into Trypanosoma cruzi genetic diversity, and its influence on parasite biology and clinical outcomes

Chagas disease, caused by Trypanosoma cruzi, remains a serious public health problem worldwide. The parasite was subdivided into six distinct genetic groups, called "discrete typing units" (DTUs), from TcI to TcVI. Several studies have indicated that the heterogeneity of T. cruzi species directly affects the diversity of clinical manifestations of Chagas disease, control, diagnosis performance, and susceptibility to treatment. Thus, this review aims to describe how T. cruzi genetic diversity influences the biology of the parasite and/or clinical parameters in humans. Regarding the geographic dispersion of T. cruzi, evident differences were observed in the distribution of DTUs in distinct areas. For example, TcII is the main DTU detected in Brazilian patients from the central and southeastern regions, where there are also registers of TcVI as a secondary T. cruzi DTU. An important aspect observed in previous studies is that the genetic variability of T. cruzi can impact parasite infectivity, reproduction, and differentiation in the vectors. It has been proposed that T. cruzi DTU influences the host immune response and affects disease progression. Genetic aspects of the parasite play an important role in determining which host tissues will be infected, thus heavily influencing Chagas disease's pathogenesis. Several teams have investigated the correlation between T. cruzi DTU and the reactivation of Chagas disease. In agreement with these data, it is reasonable to suppose that the immunological condition of the patient, whether or not associated with the reactivation of the T. cruzi infection and the parasite strain, may have an important role in the pathogenesis of Chagas disease. In this context, understanding the genetics of T. cruzi and its biological and clinical implications will provide new knowledge that may contribute to additional strategies in the diagnosis and clinical outcome follow-up of patients with Chagas disease, in addition to the reactivation of immunocompromised patients infected with T. cruzi.

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.

Biological characteristics of the Trypanosoma cruzi Arequipa strain make it a good model for Chagas disease drug discovery

Trypanosoma cruzi, the causative agent of Chagas disease (CD), is a genuine parasite with tremendous genetic diversity and a complex life cycle. Scientists have studied this disease for more than 100 years, and CD drug discovery has been a mainstay due to the absence of an effective treatment. Technical advances in several areas have contributed to a better understanding of the complex biology and life cycle of this parasite, with the aim of designing the ideal profile of both drug and therapeutic options to treat CD. Here, we present the T. cruzi Arequipa strain (MHOM/Pe/2011/Arequipa) as an interesting model for CD drug discovery. We characterized acute-phase parasitaemia and chronic-phase tropism in BALB/c mice and determined the in vitro and in vivo benznidazole susceptibility profile of the different morphological forms of this strain. The tropism of this strain makes it an interesting model for the screening of new compounds with a potential anti-Chagas profile for the treatment of this disease.

Consensus Enolase of Trypanosoma Cruzi: Evaluation of Their Immunogenic Properties Using a Bioinformatics Approach

There is currently no vaccine against American trypanosomiasis, caused by the parasite Trypanosoma cruzi. This is due to the genomic variation observed in the six DTUs of T. cruzi. This work aims to propose a consensus sequence of the enolase protein from different strains of T. cruzi and mainly evaluate its immunogenic properties at the bioinformatic level. From specialized databases, 15 sequences of the enolase gene were aligned to obtain a consensus sequence, where this sequence was modeled and then evaluated and validated through different bioinformatic programs to learn their immunogenic potential. Finally, chimeric peptides were designed with the most representative epitopes. The results showed high immunogenic potential with six epitopes for MHC-I, and seven epitopes for MHC-II, all of which were highly representative of the enolase present in strains from the American continent as well as five epitopes for B cells. Regarding the computational modeling, molecular docking with Toll-like receptors showed a high affinity and low constant of dissociation, which could lead to an innate-type immune response that helps to eliminate the parasite. In conclusion, the consensus sequence proposed for enolase is capable of providing an ideal immune response; however, the experimental evaluation of this enolase consensus and their chimeric peptides should be a high priority to develop a vaccine against Chagas disease.

Domiciliation and sympatry of Triatoma maculata and Rhodnius prolixus, risk of Trypanosoma cruzi transmission in villages of Anzoátegui, Venezuela

The domiciliation of Triatoma maculata and Rhodnius prolixus and the entomological risk indicators for the transmission of Trypanosoma cruzi, an etiological agent of Chagas Disease-CD, were studied in rural villages of Anzoátegui state, Venezuela. Nightly home visits were made for 4 months/year, for 2 years, to search for and capture triatomines in human settlements. For six of the evaluated villages, 16.4% (11/67) of houses were found with triatomine infestation; obtaining 151 triatomines in all their ontogenetic stages, of which 54.3% (82/151) corresponded to T. maculata and 45.7% (69/151) to R. prolixus. In 7.5% of the evaluated houses, both species were presented in sympatry. Entomological indicators of transmission risk were higher for T. maculata in relation to R. prolixus. Inoculation of fecal flagellates of triatomines produced 2.92 × 10⁵ flagellates/mL of blood in mean and 100% mortality in the murine model. Molecular tests (satellite DNA, kDNA and DTUs studies) demonstrated the presence of T. cruzi, all compatible with TcI. The food source determined by IESPA, revealed that R. prolixus showed less eclecticism in relation to T. maculata in the use of blood sources. This could be an indicator of an older domiciliation with low dispersion between ecotopes. The sympatry of T. maculata and R. prolixus had been recorded in natural niches, but for the first time it is recorded inside the houses in rural villages of the Anzoátegui state. Human dwellings can constitute an adequate niche, with available food sources for both triatomines species and with the risk of establishing AT/CD as zoonosis or zooanthroponosis.

Variability of the Pr77 sequence of L1Tc retrotransposon among six T. cruzi strains belonging to different discrete typing units (DTUs)

All trypanosomatid genomes are colonized by non-LTR retrotransposons which exhibit a highly conserved 77-nt sequence at their 5' ends, known as the Pr77-hallmark (Pr77). The wide distribution of Pr77 is expected to be related to the gene regulation processes in these organisms as it has promoter and HDV-like ribozyme activities at the DNA and RNA levels, respectively. The identification of Pr77 hallmark-bearing retrotransposons and the study of the associations of mobile elements with relevant genes have been analyzed in the genomes of six strains of Trypanosoma cruzi belonging to different discrete typing units (DTUs) and with different geographical origins and host/vectors. The genomes have been sequenced, assembled and annotated. BUSCO analyses indicated a good quality for the assemblies that were used in comparative analyses. The results show differences among the six genomes in the copy number of genes related to virulence processes, the abundance of retrotransposons bearing the Pr77 sequence and the presence of the Pr77 hallmarks not associated with retroelements. The analyses also show frequent associations of Pr77-bearing retrotransposons and single Pr77 hallmarks with genes coding for trans-sialidases, RHS, MASP or hypothetical proteins, showing variable proportion depending on the type of retroelement, gene class and parasite strain. These differences in the genomic distribution of active retroelements and other Pr77-containing elements have shaped the genome architecture of these six strains and might be contributing to the phenotypic variability existing among them.

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.

First genotyping of Trypanosoma cruzi from naturally infected Triatoma juazeirensis, Triatoma melanica and Triatoma sherlocki from Bahia State, Brazil

Many previous studies have shown a great phylogenetic and biological variability of Trypanosoma cruzi using different molecular and biochemical methods. Populations of T. cruzi were initially clustered into two main lineages called TcI and TcII by the size of the mini-exon PCR product. In the present study, 33 isolates derived from three triatomine taxa, which belong to the Triatoma brasiliensis species complex (Triatoma juazeirensis, Triatoma melanica and Triatoma sherlocki); collected in three distinct areas of Bahia state were characterized by PCR. The isolates were identified by the size of the mini-exon gene, 18S rRNA and 24Sα rRNA amplicons. T. cruzi isolates obtained in sylvatic and intradomiciliar ecotopes, derived from T. juazeirensis and T. melanica, were identified as TcI while the parasites originated from T. sherlocki were characterized as TcI and TcII genotypes, respectively. Those species are present in sylvatic ecotopes but are able to infest intradomiciliar areas. Therefore, it would be important to maintain studies in those localities of Bahia and further investigate the possibilities of Chagas disease transmission. Human disease may occur by any T. cruzi genotype and not only by TcII as it is the case in Amazonia.

Serological Approaches for Trypanosoma cruzi Strain Typing

Trypanosoma cruzi, the protozoan agent of Chagas' disease, displays a complex population structure made up of multiple strains showing a diverse ecoepidemiological distribution. Parasite genetic variability may be associated with disease outcome, hence stressing the need to develop methods for T. cruzi typing in vivo. Serological typing methods that exploit the presence of host antibodies raised against polymorphic parasite antigens emerge as an appealing approach to address this issue. These techniques are robust, simple, cost-effective, and are not curtailed by methodological/biological limitations intrinsic to available genotyping methods. Here, we critically assess the progress towards T. cruzi serotyping and discuss the opportunity provided by high-throughput immunomics to improve this field.

Natural infection with Trypanosoma cruzi in three species of non-human primates in southeastern Mexico: A contribution to reservoir knowledge

The mechanisms of infection and dispersion of Trypanosoma cruzi among animals, especially in the sylvatic environment, are still not entirely clear, and various aspects of the transmission dynamics of this parasite in the sylvatic environment are still unknown. T. cruzi is a parasite with a great biological and genetic diversity that infects a wide variety of hosts, therefore, transmission cycles of this parasite are complex. The objective of this study was to determine the prevalence of T. cruzi infection and analyze the genetic variability of the discrete typing units (DTUs) of the parasite in three non-human primate species (Alouatta palliata, Alouatta pigra, and Ateles geoffroyi) in southeastern Mexico. A total of one hundred sixty-four serum samples (42 samples of A. pigra, 41 samples of A. palliata (free-ranging) and 81 samples of A. geoffroyi (hosted in care centers)) were analyzed for the detection of anti-T. cruzi antibodies by ELISA assays. The seroprevalence of infection was 23.39% in A. palliata, 21.40% in A. pigra and 16.27% in A. geoffroyi. Additionally, presence of parasite DNA was assessed by PCR, and the identification of DTUs was performed by real-time PCR coupled to High Resolution Melting (qPCR-HRM). Different DTUs (TcI, TcII, TcIII, TcV and TcVI) were found in the analyzed monkeys. In addition, infection of monkeys was not associated with age or gender, but it was associated with the species. This study reveals the risk of infection in the study area and that the different DTUs of the parasite can coexist in the same habitat, indicating that T. cruzi transmission in the study area is very complex and involves many ecological factors. However, there is a need for long-term studies of host-parasite interactions to provide a solid understanding of the ecology of these species and to understand the dispersion strategies of T. cruzi.

Trypanosoma Cruzi Genome: Organization, Multi-Gene Families, Transcription, and Biological Implications

Chagas disease caused by the parasite Trypanosoma cruzi affects millions of people. Although its first genome dates from 2005, its complexity hindered a complete assembly and annotation. However, the new sequencing methods have improved genome annotation of some strains elucidating the broad genetic diversity and complexity of this parasite. Here, we reviewed the genomic structure and regulation, the genetic diversity, and the analysis of the principal multi-gene families of the recent genomes for several strains. The telomeric and sub-telomeric regions are sites with high recombination events, the genome displays two different compartments, the core and the disruptive, and the genome plasticity seems to play a key role in the survival and the infection process. Trypanosoma cruzi (T. cruzi) genome is composed mainly of multi-gene families as the trans-sialidases, mucins, and mucin-associated surface proteins. Trans-sialidases are the most abundant genes in the genome and show an important role in the effectiveness of the infection and the parasite survival. Mucins and MASPs are also important glycosylated proteins of the surface of the parasite that play a major biological role in both insect and mammal-dwelling stages. Altogether, these studies confirm the complexity of T. cruzi genome revealing relevant concepts to better understand Chagas disease.

Trypanosoma cruzi Ikiakarora (TcIII) Draft Genome Sequence

Trypanosoma cruzi shows a genetic diversity that has been associated with the variability of clinical manifestations, geographical distribution, and preferential parasite-vector interactions. In an effort to better understand this genetic variability, here, the draft genome of T. cruzi strain Ikiakarora (discrete typing unit TcIII), which has been associated with the sylvatic cycle, is reported.

Draft Genome Sequence of the Trypanosoma cruzi B. M. López Strain (TcIa), Isolated from a Colombian Patient

Trypanosoma cruzi parasite strains are classified into six lineages (discrete typing units TcI to TcVI). The broad genetic diversity of T. cruzi strains has an influence on the development of the host response and pathogenesis, as well as drug susceptibility. Here, the draft genome of the T. cruzi B. M. López strain (TcIa) is reported.

Trypanosoma cruzi parasite strains are classified into six lineages (discrete typing units TcI to TcVI). The broad genetic diversity of T. cruzi strains has an influence on the development of the host response and pathogenesis, as well as drug susceptibility. Here, the draft genome of the T. cruzi B. M. López strain (TcIa) is reported.

Chagas Disease in the United States: a Public Health Approach

Trypanosoma cruzi is the etiological agent of Chagas disease, usually transmitted by triatomine vectors. An estimated 20 to 30% of infected individuals develop potentially lethal cardiac or gastrointestinal disease. Sylvatic transmission cycles exist in the southern United States, involving 11 triatomine vector species and infected mammals such as rodents, opossums, and dogs. Nevertheless, imported chronic T. cruzi infections in migrants from Latin America vastly outnumber locally acquired human cases. Benznidazole is now FDA approved, and clinical and public health efforts are under way by researchers and health departments in a number of states. Making progress will require efforts to improve awareness among providers and patients, data on diagnostic test performance and expanded availability of confirmatory testing, and evidence-based strategies to improve access to appropriate management of Chagas disease in the United States.

Elucidating diversity in the class composition of the minicircle hypervariable region of Trypanosoma cruzi: New perspectives on typing and kDNA inheritance

Background

Trypanosoma cruzi, the protozoan causative of Chagas disease, is classified into six main Discrete Typing Units (DTUs): TcI-TcVI. This parasite has around 10⁵ copies of the minicircle hypervariable region (mHVR) in their kinetoplastic DNA (kDNA). The genetic diversity of the mHVR is virtually unknown. However, cross-hybridization assays using mHVRs showed hybridization only between isolates belonging to the same genetic group. Nowadays there is no methodologic approach with a good sensibility, specificity and reproducibility for direct typing on biological samples. Due to its high copy number and apparently high diversity, mHVR becomes a good target for typing.

Methodology/Principal findings

Around 22 million reads, obtained by amplicon sequencing of the mHVR, were analyzed for nine strains belonging to six T. cruzi DTUs. The number and diversity of mHVR clusters was variable among DTUs and even within a DTU. However, strains of the same DTU shared more mHVR clusters than strains of different DTUs and clustered together. In addition, hybrid DTUs (TcV and TcVI) shared similar percentages (1.9–3.4%) of mHVR clusters with their parentals (TcII and TcIII). Conversely, just 0.2% of clusters were shared between TcII and TcIII suggesting biparental inheritance of the kDNA in hybrids. Sequencing at low depth (20,000–40,000 reads) also revealed 95% of the mHVR clusters for each of the analyzed strains. Finally, the method revealed good correlation in cluster identity and abundance between different replications of the experiment (r = 0.999).

Conclusions/Significance

Our work sheds light on the sequence diversity of mHVRs at intra and inter-DTU level. The mHVR amplicon sequencing workflow described here is a reproducible technique, that allows multiplexed analysis of hundreds of strains and results promissory for direct typing on biological samples in a future. In addition, such approach may help to gain knowledge on the mechanisms of the minicircle evolution and phylogenetic relationships among strains.

Chagas disease is an important public health problem in Latin America showing a wide diversity of clinical manifestations and epidemiological patterns. It is caused by the parasite Trypanosoma cruzi. This parasite is genetically diverse and classified into six main lineages. However, the relationship between intra-specific genetic diversity and clinical or epidemiological features is not clear, mainly because low sensitivity for direct typing on biological samples. For this reason, genetic markers with high copy number are required to achieve sensitivity. Here, we deep sequenced and analyzed a DNA region present in the large mitochondria of the parasite (named as mHVR, 10⁵ copies per parasite) from strains belonging to the six main lineages in order to analyze mHVR diversity and to evaluate its usefulness for typing. Despite the high sequence diversity, strains of the same lineage shared more sequences than strains of different lineages. Curiously, hybrid lineages shared mHVR sequences with both parents suggesting that mHVR (and DNA minicircles from the mitochondria) are inherited from both parentals. The mHVR amplicon sequencing workflow proposed here is reproducible and, potentially, it would be useful for typing hundreds of biological samples at time. It also provides a valuable approach to perform evolutionary and functional studies.

Phenotypic diversity and drug susceptibility of Trypanosoma cruzi TcV clinical isolates

Trypanosoma cruzi is a genetically heterogeneous group of organisms that cause Chagas disease. It has been long suspected that the clinical outcome of the disease and response to therapeutic agents are, at least in part, related to the genetic characteristics of the parasite. Herein, we sought to validate the significance of the genotype of T. cruzi isolates recovered from patients with different clinical forms of Chagas disease living in Argentina on their biological behaviour and susceptibility to drugs. Genotype identification of the newly established isolates confirmed the reported predominance of TcV, with a minor frequency of TcI. Epimastigote sensitivity assays demonstrated marked dissimilar responses to benznidazole, nifurtimox, pentamidine and dihydroartemisinin in vitro. Two TcV isolates exhibiting divergent response to benznidazole in epimastigote assays were further tested for the expression of anti-oxidant proteins. Benznidazole-resistant BOL-FC10A epimastigotes had decreased expression of Old Yellow Enzyme and cytosolic superoxide dismutase, and overexpression of mitochondrial superoxide dismutase and tryparedoxin- 1, compared to benznidazole-susceptible AR-SE23C parasites. Drug sensitivity assays on intracellular amastigotes and trypomastigotes reproduced the higher susceptibility of AR-SE23C over BOL-FC10A parasites to benznidazole observed in epimastigotes assays. However, the susceptibility/resistance profile of amastigotes and trypomastigotes to nifurtimox, pentamidine and dihydroartemisinin varied markedly with respect to that of epimastigotes. C3H/He mice infected with AR-SE23C trypomastigotes had higher levels of parasitemia and mortality rate during the acute phase of infection compared to mice infected with BOL-FC10A trypomastigotes. Treatment of infected mice with benznidazole or nifurtimox was efficient to reduce patent parasitemia induced by either isolate. Nevertheless, qPCR performed at 70 dpi revealed parasite DNA in the blood of mice infected with AR-SE23C but not in BOL-FC10A infected mice. These results demonstrate high level of intra-type diversity which may represent an important obstacle for the testing of chemotherapeutic agents.

Recent advances in trypanosomatid research: genome organization, expression, metabolism, taxonomy and evolution

Unicellular flagellates of the family Trypanosomatidae are obligatory parasites of invertebrates, vertebrates and plants. Dixenous species are aetiological agents of a number of diseases in humans, domestic animals and plants. Their monoxenous relatives are restricted to insects. Because of the high biological diversity, adaptability to dramatically different environmental conditions, and omnipresence, these protists have major impact on all biotic communities that still needs to be fully elucidated. In addition, as these organisms represent a highly divergent evolutionary lineage, they are strikingly different from the common 'model system' eukaryotes, such as some mammals, plants or fungi. A number of excellent reviews, published over the past decade, were dedicated to specialized topics from the areas of trypanosomatid molecular and cell biology, biochemistry, host-parasite relationships or other aspects of these fascinating organisms. However, there is a need for a more comprehensive review that summarizing recent advances in the studies of trypanosomatids in the last 30 years, a task, which we tried to accomplish with the current paper.

Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc-STAMS2)

Background

Chagas disease also known as American trypanosomiasis is caused by the protozoan Trypanosoma cruzi. Over the last 30 years, Chagas disease has expanded from a neglected parasitic infection of the rural population to an urbanized chronic disease, becoming a potentially emergent global health problem. T. cruzi strains were assigned to seven genetic groups (TcI-TcVI and TcBat), named discrete typing units (DTUs), which represent a set of isolates that differ in virulence, pathogenicity and immunological features. Indeed, diverse clinical manifestations (from asymptomatic to highly severe disease) have been attempted to be related to T.cruzi genetic variability. Due to that, several DTU typing methods have been introduced. Each method has its own advantages and drawbacks such as high complexity and analysis time and all of them are based on genetic signatures. Recently, a novel method discriminated bacterial strains using a peptide identification-free, genome sequence-independent shotgun proteomics workflow. Here, we aimed to develop a Trypanosoma cruzi Strain Typing Assay using MS/MS peptide spectral libraries, named Tc-STAMS2.

Methods/Principal findings

The Tc-STAMS2 method uses shotgun proteomics combined with spectral library search to assign and discriminate T. cruzi strains independently on the genome knowledge. The method is based on the construction of a library of MS/MS peptide spectra built using genotyped T. cruzi reference strains. For identification, the MS/MS peptide spectra of unknown T. cruzi cells are identified using the spectral matching algorithm SpectraST. The Tc-STAMS2 method allowed correct identification of all DTUs with high confidence. The method was robust towards different sample preparations, length of chromatographic gradients and fragmentation techniques. Moreover, a pilot inter-laboratory study showed the applicability to different MS platforms.

Conclusions and significance

This is the first study that develops a MS-based platform for T. cruzi strain typing. Indeed, the Tc-STAMS2 method allows T. cruzi strain typing using MS/MS spectra as discriminatory features and allows the differentiation of TcI-TcVI DTUs. Similar to genomic-based strategies, the Tc-STAMS2 method allows identification of strains within DTUs. Its robustness towards different experimental and biological variables makes it a valuable complementary strategy to the current T. cruzi genotyping assays. Moreover, this method can be used to identify DTU-specific features correlated with the strain phenotype.

Chagas disease is one of the most important neglected diseases with an estimated number of 6–7 million infected individuals, the majority living in Central and South America. The Trypanosoma cruzi (T.cruzi) protozoan parasite is the etiological agent of Chagas disease. T.cruzi is highly genetically diverse and a new nomenclature assigned each strain to seven genetic groups (TcI-TcVI and Tcbat), named Discrete Typing Units (DTUs), based on their biochemical, immunological and phenotypical characteristics. T.cruzi DTUs have been correlated to diverse clinical outcomes highlighting the importance of molecular epidemiological screens. Despite the development of T.cruzi typing methods based on genetic signatures, each method presents its own advantages and challenges. The work presented here shows the application of mass spectrometry for Trypanosoma cruzi Strain Typing Assay using MS² peptide spectral libraries (Tc-STAMS2). The novelty of the method is based on the use of peptide fragmentation spectra as strain-specific fingerprints to classify and identify DTUs. Initially, a spectra library is generated from characterized T.cruzi strains. The library is subsequently inspected using MS/MS spectra from unknown strains and confidently assigned to a specific strain in an automated and computationally-driven approach. The Tc-STAMS2 method was challenged to test several variables such as sample type and preparation, instrument setup and identification platform. Tc-STAMS2 provided high confidence and robustness in T.cruzi strain typing. The Tc-STAMS2 method represents a proof-of-concept of a complementary strategy to the current DNA-based T. cruzi genotyping methods. Moreover, the method allows the identification of strain-specific features that could be related to the biology of T.cruzi strains and their clinical outcomes.

Changes of RAPD profile of Trypanosoma cruzi II with Canova and Benznidazole

Chagas disease, caused by the protozoan Trypanosoma cruzi, involves immunomediated processes. Canova (CA) is a homeopathic treatment indicated in the diseases in which the immune system is depressed. This study evaluated the Random Amplification of Polymorphic DNA (RAPD) profile of T. cruzi under the influence of CA and Benznidazole (BZ). Mice infected with the genetic lineage of T. cruzi II (Y strain) were divided into 4 groups:

Infected animals treated with saline solution (control group); treated with CA; treated with BZ; treated with CA and BZ combined.

Treatment was given at the 5th–25th days of infection (D5–25). The parasites were isolated by haemoculture in Liver Infusion Tryptose (LIT) medium: at D5 (before treatment), D13, 15 and 25 (during treatment) and D55 and 295 (after treatment). DNA was extracted from the mass of parasites. RAPD was done with the primers λgt11-F, M13F-40 and L15996, the amplified products were eletrophoresed through a 4% polyacrylamide gel. Data were analyzed by the coefficient of similarity using the DNA-POP program.

163 markers were identified, 5 of them monomorphic. CA did not act against the parasites when used alone. The RAPD profiles of parasites treated with BZ and CA + BZ were different from those in the control group and in the group treated with CA. The actions of the CA and BZ were different and the action of BZ was different from the action of CA + BZ. These data suggest that CA may interact with BZ. The differences in the RAPD profile of the Y strain of T. cruzi produced by BZ, CA + BZ and the natural course of the infection suggest selection/suppression of populations.

Combined parasitological and molecular-based diagnostic tools improve the detection of Trypanosoma cruzi in single peripheral blood samples from patients with Chagas disease

INTRODUCTION

In order to detect Trypanosoma cruzi and determine the genetic profiles of the parasite during the chronic phase of Chagas disease (ChD), parasitological and molecular diagnostic methods were used to assess the blood of 91 patients without specific prior treatment.

METHODS

Blood samples were collected from 68 patients with cardiac ChD and 23 patients with an indeterminate form of ChD, followed by evaluation using blood culture and polymerase chain reaction. T . cruzi isolates were genotyped using three different genetic markers.

RESULTS:

Blood culture was positive in 54.9% of all patients, among which 60.3% had the cardiac form of ChD, and 39.1% the indeterminate form of ChD. There were no significant differences in blood culture positivity among patients with cardiac and indeterminate forms. Additionally, patient age and clinical forms did not influence blood culture results. Polymerase chain reaction (PCR) was positive in 98.9% of patients, although comparisons between blood culture and PCR results showed that the two techniques did not agree. Forty-two T . cruzi stocks were isolated, and TcII was detected in 95.2% of isolates. Additionally, one isolate corresponded to TcIII or TcIV, and another corresponded to TcV or TcVI.

CONCLUSIONS

Blood culture and PCR were both effective for identifying T. cruzi using a single blood sample, and their association did not improve parasite detection. However, we were not able to establish an association between the clinical form of ChD and the genetic profile of the parasite.

The diversity of the Chagas parasite, Trypanosoma cruzi, infecting the main Central American vector, Triatoma dimidiata, from Mexico to Colombia

Little is known about the strains of Trypanosoma cruzi circulating in Central America and specifically in the most important vector in this region, Triatoma dimidiata. Approximately six million people are infected with T. cruzi, the causative agent of Chagas disease, which has the greatest negative economic impact and is responsible for ~12,000 deaths annually in Latin America. By international consensus, strains of T. cruzi are divided into six monophyletic clades called discrete typing units (DTUs TcI-VI) and a seventh DTU first identified in bats called TcBat. TcI shows the greatest geographic range and diversity. Identifying strains present and diversity within these strains is important as different strains and their genotypes may cause different pathologies and may circulate in different localities and transmission cycles, thus impacting control efforts, treatment and vaccine development. To determine parasite strains present in T. dimidiata across its geographic range from Mexico to Colombia, we isolated abdominal DNA from T. dimidiata and determined which specimens were infected with T. cruzi by PCR. Strains from infected insects were determined by comparing the sequence of the 18S rDNA and the spliced-leader intergenic region to typed strains in GenBank. Two DTUs were found: 94% of infected T. dimidiata contained TcI and 6% contained TcIV. TcI exhibited high genetic diversity. Geographic structure of TcI haplotypes was evident by Principal Component and Median-Joining Network analyses as well as a significant result in the Mantel test, indicating isolation by distance. There was little evidence of association with TcI haplotypes and host/vector or ecotope. This study provides new information about the strains circulating in the most important Chagas vector in Central America and reveals considerable variability within TcI as well as geographic structuring at this large geographic scale. The lack of association with particular vectors/hosts or ecotopes suggests the parasites are moving among vectors/hosts and ecotopes therefore a comprehensive approach, such as the Ecohealth approach that makes houses refractory to the vectors will be needed to successfully halt transmission of Chagas disease.

Identifying Trypanosoma cruzi discreet typing units in triatomines collected in different natural regions of Perú

INTRODUCTION

Trypanosoma cruzi has been divided by international consensus into six discrete typing units (DTU): TcI, TcII, TcIII, TcIV, TcV y TcVI. The factors determining the dynamics of T. cruzi genotypes vector transmission of Chagas' disease in the different geographical regions of Perú are still unknown.

OBJECTIVE

To detect and type T. cruzi DTUs from the faeces of seven species of triatomines (Panstrongylus chinai, P. geniculatus, P. herreri, Rhodnius robustus, R. pictipes, Triatoma carrioni and T. infestans) captured in eight departments from different natural regions of Perú.

MATERIALS AND METHODS

We examined 197 insects for detecting trypanosomes. DNA was extracted from each insect intestinal contents and PCR amplification of kDNA, SL-IR, 24Sα rRNA and 18Sα RNA was performed for detecting T. cruzi DTUs.

RESULTS

Five T. rangeli and 113 T. cruzi infections were detected; 95 of the latter were identified as TcI (two in P. chinai, one in P. geniculatus, 68 in P. herreri, four in R. pictipes, seven in R. robustus, one in T. carrioni, 12 in T. infestans), five as TcII (four in P. herreri, one in T. infestans), four as TcIII (three in P. herreri, one in R. robustus) and four TcIV infections in P. herreri.

CONCLUSIONS

This is the first study which has attempted a large-scale characterization of T. cruzi found in the intestine of epidemiologically important vectors in Perú, thus providing basic information that will facilitate a better understanding of the dynamics of T. cruzi vector transmission in Perú.

Frequency of Trypanosoma cruzi parasitemia among infected blood donors with a potential association between parasite lineage and transfusion transmission

BACKGROUND

Trypanosoma cruzi is endemic to the Americas where it demonstrates multiple lineages over a vast geographic range (i.e., United States to Argentina). These lineages possess divergent geographic and biologic characteristics, including variations in disease manifestations. Herein, we report the frequency of parasitemia among seropositive US blood donors and the potential association between parasite lineage and transfusion transmission.

STUDY DESIGN AND METHODS

Blood donors identified as T. cruzi seropositive during screening were enrolled in follow-up studies, including hemoculture testing and a risk factor questionnaire. Positive hemocultures were expanded to obtain sufficient parasites for molecular lineage determination and analysis. Country of birth, obtained from the questionnaire, was used to predict parasite lineage in the absence of demonstrable parasitemia for infected donors.

RESULTS

Eighteen (6.8%) of 263 seropositive donors were hemoculture positive. Among the 17 hemocultures expanded for lineage determination, TcV was identified more frequently (n = 12), compared to TcI (n = 2), TcII (n = 1), and TcVI (n = 2). When presumptive parasite lineages were compared to hemoculture results, only two of 157 (1.3%) TcI versus 13 of 38 (34.2%) TcII/TcV/TcVI non-US donors were parasitemic; three of 44 (6.8%) US donors were TcV or TcVI.

CONCLUSIONS

Based on lineage determination for donors with parasitemia; hemoculture positivity associated with presumptive parasite lineage; and implicated donors from US, Canadian, and Spanish transfusion cases, donors from Southern South America are significantly more likely to have parasitemia and transmit infection to blood recipients (TcII, TcV, or TcVI vs. TcI). Thus, parasite lineage may be associated with risk of transfusion-transmitted T. cruzi.

Cynomolgus macaques naturally infected with Trypanosoma cruzi-I exhibit an overall mixed pro-inflammatory/modulated cytokine signature characteristic of human Chagas disease

Background

Non-human primates have been shown to be useful models for Chagas disease. We previously reported that natural T. cruzi infection of cynomolgus macaques triggers clinical features and immunophenotypic changes of peripheral blood leukocytes resembling those observed in human Chagas disease. In the present study, we further characterize the cytokine-mediated microenvironment to provide supportive evidence of the utility of cynomolgus macaques as a model for drug development for human Chagas disease.

Methods and findings

In this cross-sectional study design, flow cytometry and systems biology approaches were used to characterize the ex vivo and in vitro T. cruzi-specific functional cytokine signature of circulating leukocytes from TcI-T. cruzi naturally infected cynomolgus macaques (CH). Results showed that CH presented an overall CD4⁺-derived IFN-γ pattern regulated by IL-10-derived from CD4⁺ T-cells and B-cells, contrasting with the baseline profile observed in non-infected hosts (NI). Homologous TcI-T. cruzi-antigen recall in vitro induced a broad pro-inflammatory cytokine response in CH, mediated by TNF from innate/adaptive cells, counterbalanced by monocyte/B-cell-derived IL-10. TcIV-antigen triggered a more selective cytokine signature mediated by NK and T-cell-derived IFN-γ with modest regulation by IL-10 from T-cells. While NI presented a cytokine network comprised of small number of neighborhood connections, CH displayed a complex cross-talk amongst network elements. Noteworthy, was the ability of TcI-antigen to drive a complex global pro-inflammatory network mediated by TNF and IFN-γ from NK-cells, CD4⁺ and CD8⁺ T-cells, regulated by IL-10⁺CD8⁺ T-cells, in contrast to the TcIV-antigens that trigger a modest network, with moderate connecting edges.

Conclusions

Altogether, our findings demonstrated that CH present a pro-inflammatory/regulatory cytokine signature similar to that observed in human Chagas disease. These data bring additional insights that further validate these non-human primates as experimental models for Chagas disease.

Trypanosoma cruzi is the causative agent of Chagas disease; millions of people are infected with this parasite. One of the major challenges to manage infected patients is the low efficacy of currently available treatments, especially during chronic infection. Different T. cruzi genotypes are known to differ in response to existing drugs (e.g., TcI is quite resistant), and differences among individuals in immune response also are believed to play a role determining therapeutic efficacy. Experimental models and in vitro systems have been proposed for rational searches for new compounds for treating infected individuals, optimally before the infection becomes clinically manifested as Chagas disease. In the field of drug development, the non-human primate models offer a unique and valuable contribution, as a consequence of patho-physiological similarities that mimic many human diseases, including Chagas disease. In the present study, we further investigated the functional features of the immune response triggered by TcI T. cruzi-infection, characterizing the ex vivo as well as the in vitro cytokine microenvironment, upon T. cruzi-antigen recall. Our results revealed that chronically infected cynomolgus macaques display a similar ex vivo cytokine signature to that observed in chronic human Chagas disease. Moreover, CH macaques display a complex cross-talk among the cytokine⁺ leukocyte subsets, enhanced by TcI T. cruzi-antigen recall in vitro. These findings provide additional insights that further validate these non-human primates as experimental models for rational development of new therapeutic agents for Chagas disease.

Real-time PCR strategy for the identification of Trypanosoma cruzi discrete typing units directly in chronically infected human blood

The protozoan Trypanosoma cruzi is the causative agent of Chagas disease, a major public health problem in Latin America. This parasite has a complex population structure comprised by six or seven major evolutionary lineages (discrete typing units or DTUs) TcI-TcVI and TcBat, some of which have apparently resulted from ancient hybridization events. Because of the existence of significant biological differences between these lineages, strain characterization methods have been essential to study T. cruzi in its different vectors and hosts. However, available methods can be laborious and costly, limited in resolution or sensitivity. In this study, a new genotyping strategy by real-time PCR to identify each of the six DTUs in clinical blood samples have been developed and evaluated. Two nuclear (SL-IR and 18S rDNA) and two mitochondrial genes (COII and ND1) were selected to develop original primers. The method was evaluated with eight genomic DNA of T. cruzi populations belonging to the six DTUs, one genomic DNA of Trypanosoma rangeli, and 53 blood samples from individuals with chronic Chagas disease. The assays had an analytical sensitivity of 1-25fg of DNA per reaction tube depending on the DTU analyzed. The selectivity of trials with 20fg/μL of genomic DNA identified each DTU, excluding non-targets DTUs in every test. The method was able to characterize 67.9% of the chronically infected clinical samples with high detection of TcII followed by TcI. With the proposed original genotyping methodology, each DTU was established with high sensitivity after a single real-time PCR assay. This novel protocol reduces carryover contamination, enables detection of each DTU independently and in the future, the quantification of each DTU in clinical blood samples.

Identification of Trypanosoma cruzi Discrete Typing Units (DTUs) in Latin-American migrants in Barcelona (Spain)

Trypanosoma cruzi, the causative agent of Chagas disease, is divided into six Discrete Typing Units (DTUs): TcI-TcVI. We aimed to identify T. cruzi DTUs in Latin-American migrants in the Barcelona area (Spain) and to assess different molecular typing approaches for the characterization of T. cruzi genotypes. Seventy-five peripheral blood samples were analyzed by two real-time PCR methods (qPCR) based on satellite DNA (SatDNA) and kinetoplastid DNA (kDNA). The 20 samples testing positive in both methods, all belonging to Bolivian individuals, were submitted to DTU characterization using two PCR-based flowcharts: multiplex qPCR using TaqMan probes (MTq-PCR), and conventional PCR. These samples were also studied by sequencing the SatDNA and classified as type I (TcI/III), type II (TcII/IV) and type I/II hybrid (TcV/VI). Ten out of the 20 samples gave positive results in the flowcharts: TcV (5 samples), TcII/V/VI (3) and mixed infections by TcV plus TcII (1) and TcV plus TcII/VI (1). By SatDNA sequencing, we classified the 20 samples, 19 as type I/II and one as type I. The most frequent DTU identified by both flowcharts, and suggested by SatDNA sequencing in the remaining samples with low parasitic loads, TcV, is common in Bolivia and predominant in peripheral blood. The mixed infection by TcV-TcII was detected for the first time simultaneously in Bolivian migrants. PCR-based flowcharts are very useful to characterize DTUs during acute infection. SatDNA sequence analysis cannot discriminate T. cruzi populations at the level of a single DTU but it enabled us to increase the number of characterized cases in chronically infected patients.

Molecular Diagnosis of Chagas Disease in Colombia: Parasitic Loads and Discrete Typing Units in Patients from Acute and Chronic Phases

BACKGROUND

The diagnosis of Chagas disease is complex due to the dynamics of parasitemia in the clinical phases of the disease. The molecular tests have been considered promissory because they detect the parasite in all clinical phases. Trypanosoma cruzi presents significant genetic variability and is classified into six Discrete Typing Units TcI-TcVI (DTUs) with the emergence of foreseen genotypes within TcI as TcIDom and TcI Sylvatic. The objective of this study was to determine the operating characteristics of molecular tests (conventional and Real Time PCR) for the detection of T. cruzi DNA, parasitic loads and DTUs in a large cohort of Colombian patients from acute and chronic phases.

METHODOLOGY/PRINCIPAL FINDINGS

Samples were obtained from 708 patients in all clinical phases. Standard diagnosis (direct and serological tests) and molecular tests (conventional PCR and quantitative PCR) targeting the nuclear satellite DNA region. The genotyping was performed by PCR using the intergenic region of the mini-exon gene, the 24Sa, 18S and A10 regions. The operating capabilities showed that performance of qPCR was higher compared to cPCR. Likewise, the performance of qPCR was significantly higher in acute phase compared with chronic phase. The median parasitic loads detected were 4.69 and 1.33 parasite equivalents/mL for acute and chronic phases. The main DTU identified was TcI (74.2%). TcIDom genotype was significantly more frequent in chronic phase compared to acute phase (82.1% vs 16.6%). The median parasitic load for TcIDom was significantly higher compared with TcI Sylvatic in chronic phase (2.58 vs.0.75 parasite equivalents/ml).

CONCLUSIONS/SIGNIFICANCE

The molecular tests are a precise tool to complement the standard diagnosis of Chagas disease, specifically in acute phase showing high discriminative power. However, it is necessary to improve the sensitivity of molecular tests in chronic phase. The frequency and parasitemia of TcIDom genotype in chronic patients highlight its possible relationship to the chronicity of the disease.

Ecological scenario and Trypanosoma cruzi DTU characterization of a fatal acute Chagas disease case transmitted orally (Espírito Santo state, Brazil)

BACKGROUND

Trypanosoma cruzi infection via oral route results in outbreaks or cases of acute Chagas disease (ACD) in different Brazilian regions and poses a novel epidemiological scenario. In the Espírito Santo state (southeastern Brazil), a fatal case of a patient with ACD led us to investigate the enzootic scenario to avoid the development of new cases. At the studied locality, Triatoma vitticeps exhibited high T. cruzi infection rates and frequently invaded residences.

METHODS

Sylvatic and domestic mammals in the Rio da Prata locality, where the ACD case occurred, and in four surrounding areas (Baia Nova, Buenos Aires, Santa Rita and Todos os Santos) were examined and underwent parasitological and serological tests. Triatomines were collected for a fecal material exam, culturing and mini-exon gene molecular characterization, followed by RFLP-PCR of H3/Alul. Paraffin-embedded cardiac tissue of a patient was washed with xylene to remove paraffin and DNA was extracted using the phenol-chloroform method. For genotype characterization, PCR was performed to amplify the 1f8, GPI and 18S rRNA genes. In the case of V7V8 SSU rRNA, the PCR products were molecularly cloned. PCR products were sequenced and compared to sequences in GenBank. Phylogenetic analysis using maximum likelihood method with 1000 bootstrap replicates was performed.

RESULTS

None of the animals showed positive hemocultures. Three rodents and two dogs showed signs of infection, as inferred from borderline serological titers. T. vitticeps was the only triatomine species identified and showed T. cruzi infection by DTUs TcI and TcIV. The analysis of cardiac tissue DNA showed mixed infection by T. cruzi (DTUs I, II, III and IV) and Trypanosoma dionisii.

CONCLUSIONS

Each case or outbreak of ACD should be analyzed as a particular epidemiological occurrence. The results indicated that mixed infections in humans may play a role in pathogenicity and may be more common than is currently recognized. Direct molecular characterization from biological samples is essential because this procedure avoids parasite selection. T. dionisii may under certain and unknown circumstances infect humans. The distribution of T. cruzi DTUS TcIII and TcIV in Brazilian biomes is broader than has been assumed to date.

Over Six Thousand Trypanosoma cruzi Strains Classified into Discrete Typing Units (DTUs): Attempt at an Inventory

Trypanosoma cruzi, the causative agent of Chagas disease, presents wide genetic diversity. Currently, six discrete typing units (DTUs), named TcI to TcVI, and a seventh one called TcBat are used for strain typing. Beyond the debate concerning this classification, this systematic review has attempted to provide an inventory by compiling the results of 137 articles that have used it. A total of 6,343 DTU identifications were analyzed according to the geographical and host origins. Ninety-one percent of the data available is linked to South America. This sample, although not free of potential bias, nevertheless provides today's picture of T. cruzi genetic diversity that is closest to reality. DTUs were genotyped from 158 species, including 42 vector species. Remarkably, TcI predominated in the overall sample (around 60%), in both sylvatic and domestic cycles. This DTU known to present a high genetic diversity, is very widely distributed geographically, compatible with a long-term evolution. The marsupial is thought to be its most ancestral host and the Gran Chaco region the place of its putative origin. TcII was rarely sampled (9.6%), absent, or extremely rare in North and Central America, and more frequently identified in domestic cycles than in sylvatic cycles. It has a low genetic diversity and has probably found refuge in some mammal species. It is thought to originate in the south-Amazon area. TcIII and TcIV were also rarely sampled. They showed substantial genetic diversity and are thought to be composed of possible polyphyletic subgroups. Even if they are mostly associated with sylvatic transmission cycles, a total of 150 human infections with these DTUs have been reported. TcV and TcVI are clearly associated with domestic transmission cycles. Less than 10% of these DTUs were identified together in sylvatic hosts. They are thought to originate in the Gran Chaco region, where they are predominant and where putative parents exist (TcII and TcIII). Trends in host-DTU specificities exist, but generally it seems that the complexity of the cycles and the participation of numerous vectors and mammal hosts in a shared area, maintains DTU diversity.

Acute Chagas outbreaks: molecular and biological features of Trypanosoma cruzi isolates, and clinical aspects of acute cases in Santander, Colombia

BACKGROUND

Outbreaks of acute Chagas disease associated with oral transmission are easily detected nowadays with trained health personnel in areas of low endemicity, or in which the vector transmission has been interrupted. Given the biological and genetic diversity of Trypanosoma cruzi, the high morbidity, mortality, and the observed therapeutic failure, new characteristics of these outbreaks need to be addressed at different levels, both in Trypanosoma cruzi as in patient response. The aim of this work was to evaluate the patient's features involved in six outbreaks of acute Chagas disease which occurred in Santander, Colombia, and the characteristics of Trypanosoma cruzi clones isolated from these patients, to establish the potential relationship between the etiologic agent features with host behavior.

METHODS

The clinical, pathological and epidemiological aspects of outbreaks were analyzed. In addition, Trypanosoma cruzi clones were biologically characterized both in vitro and in vivo, and the susceptibility to the classical trypanocidal drugs nifurtimox and benznidazole was evaluated. Trypanosoma cruzi clones were genotyped by means of mini-exon intergenic spacer and cytochrome b genes sequencing.

RESULTS

All clones were DTU I, and based on the mini-exon intergenic spacer, belong to two genotypes: G2 related with sub-urban, and G11 with rural outbreaks. Girón outbreak clones with higher susceptibility to drugs presented G2 genotype and C/T transition in Cyt b. The outbreaks affected mainly young population (±25.9 years), and the mortality rate was 10 %. The cardiac tissue showed intense inflammatory infiltrate, myocardial necrosis and abundant amastigote nests. However, although the gastrointestinal tissue was congestive, no inflammation or parasites were observed.

CONCLUSIONS

Although all clones belong to DTU I, two intra-DTU genotypes were found with the sequencing of the mini-exon intergenic spacer, however there is no strict correlation between genetic groups, the cycles of the parasite or the clinical forms of the disease. Trypanosoma cruzi clones from Girón with higher sensitivity to nifurtimox presented a particular G2 genotype and C/T transition in Cyt b. When the diagnosis was early, the patients responded well to antichagasic treatment, which highlights the importance of diagnosis and treatment early to prevent fatal outcomes associated with these acute episodes.

Trypanosoma cruzi DTU TcII presents higher blood parasitism than DTU TcI in an experimental model of mixed infection

Trypanosoma cruzi (Tc), the causative agent of Chagas disease, affects millions of people worldwide. One of the major characteristics of T. cruzi is related to its heterogeneity due to the variability of its biological properties, parasite growth rates, infectivity, tissue tropism, morbidity and virulence among different isolates observed during experimental or human infection. Moreover, presence of mixed infections in the same host in endemic areas is a matter of study due to its impact on clinical manifestations and disease progression. In this study, we evaluated the biological behavior of two Tc I strains AQ1-7 (AQ) and MUTUM (MT) and one Tc II strain (JG) during the acute phase of infection, in unique and mixed infections. A patent blood parasitism was detected only in mice inoculated with JG strain . In addition blood parasitism parameters (peak and average blood parasitism) were positively associated when JG and AQ strains were combined. In contrast, a negative association was observed in the JG+MUTUM group. The predominance of TcII strain over TcI strains was highlighted using the LSSP-PCR technique, which was performed in samples from hemoculture. Thus, this study showed important biological differences between different T. cruzi strains and discrete typing units (DTUs) in acute phase. Finally, we observed that blood parasitism during early period of infection seems to be more related to DTU than to a specific strain.

Between a bug and a hard place: Trypanosoma cruzi genetic diversity and the clinical outcomes of Chagas disease

Over the last 30 years, concomitant with successful transnational disease control programs across Latin America, Chagas disease has expanded from a neglected, endemic parasitic infection of the rural poor to an urbanized chronic disease, and now a potentially emergent global health problem. Trypanosoma cruzi infection has a highly variable clinical course, ranging from complete absence of symptoms to severe and often fatal cardiovascular and/or gastrointestinal manifestations. To date, few correlates of clinical disease progression have been identified. Elucidating a putative role for T. cruzi strain diversity in Chagas disease pathogenesis is complicated by the scarcity of parasites in clinical specimens and the limitations of our contemporary genotyping techniques. This article systematically reviews the historical literature, given our current understanding of parasite genetic diversity, to evaluate the evidence for any association between T. cruzi genotype and chronic clinical outcome, risk of congenital transmission or reactivation and orally transmitted outbreaks.

Multiplex Real-Time PCR Assay Using TaqMan Probes for the Identification of Trypanosoma cruzi DTUs in Biological and Clinical Samples

BACKGROUND

Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI-TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR).

METHODS/PRINCIPAL FINDINGS

The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm.

CONCLUSIONS/SIGNIFICANCE

Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production.

Infection with Trypanosoma cruzi TcII and TcI in free-ranging population of lion tamarins (Leontopithecus spp): an 11-year follow-up

Here, we present a review of the dataset resulting from the 11-years follow-up of Trypanosoma cruzi infection in free-ranging populations of Leontopithecus rosalia (golden lion tamarin) and Leontopithecus chrysomelas (golden-headed lion tamarin) from distinct forest fragments in Atlantic Coastal Rainforest. Additionally, we present new data regarding T. cruzi infection of small mammals (rodents and marsupials) that live in the same areas as golden lion tamarins and characterisation at discrete typing unit (DTU) level of 77 of these isolates. DTU TcII was found to exclusively infect primates, while TcI infected Didelphis aurita and lion tamarins. The majority of T. cruzi isolates derived from L. rosalia were shown to be TcII (33 out 42) Nine T. cruzi isolates displayed a TcI profile. Golden-headed lion tamarins demonstrated to be excellent reservoirs of TcII, as 24 of 26 T. cruzi isolates exhibited the TcII profile. We concluded the following: (i) the transmission cycle of T. cruzi in a same host species and forest fragment is modified over time, (ii) the infectivity competence of the golden lion tamarin population fluctuates in waves that peak every other year and (iii) both golden and golden-headed lion tamarins are able to maintain long-lasting infections by TcII and TcI.

Characterization of the microbiota in the guts of Triatoma brasiliensis and Triatoma pseudomaculata infected by Trypanosoma cruzi in natural conditions using culture independent methods

Background

Chagas disease is caused by Trypanosoma cruzi, which is transmitted by triatomine vectors. The northeastern region of Brazil is endemic for Chagas disease and has the largest diversity of triatomine species. T. cruzi development in its triatomine vector depends on diverse factors, including the composition of bacterial gut microbiota.

Methods

We characterized the triatomines captured in the municipality of Russas (Ceará) by sequencing the cytochrome c oxidase subunit I (COI) gene. The composition of the bacterial community in the gut of peridomestic Triatoma brasiliensis and Triatoma pseudomaculata was investigated using culture independent methods based on the amplification of the 16S rRNA gene by polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), DNA fragment cloning, Sanger sequencing and 454 pyrosequencing. Additionally, we identified TcI and TcII types of T. cruzi by sequencing amplicons from the gut metagenomic DNA with primers for the mini-exon gene.

Results

Triatomines collected in the peridomestic ecotopes were diagnosed as T. pseudomaculata and T. brasiliensis by comparing their COI sequence with GenBank. The rate of infection by T. cruzi in adult triatomines reached 80% for T. pseudomaculata and 90% for T. brasiliensis. According to the DNA sequences from the DGGE bands, the triatomine gut microbiota was primarily composed of Proteobacteria and Actinobacteria. However, Firmicutes and Bacteroidetes were also detected, although in much lower proportions. Serratia was the main genus, as it was encountered in all samples analyzed by DGGE and 454 pyrosequencing. Members of Corynebacterinae, a suborder of the Actinomycetales, formed the next most important group. The cloning and sequencing of full-length 16S rRNA genes confirmed the presence of Serratia marcescens, Dietzia sp., Gordonia terrae, Corynebacterium stationis and Corynebacterium glutamicum.

Conclusions

The study of the bacterial microbiota in the triatomine gut has gained increased attention because of the possible role it may play in the epidemiology of Chagas disease by competing with T. cruzi. Culture independent methods have shown that the bacterial composition of the microbiota in the guts of peridomestic triatomines is made up by only few bacterial species.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-015-0836-z) contains supplementary material, which is available to authorized users.

Are Members of the Triatoma brasiliensis (Hemiptera, Reduviidae) Species Complex Able to Alter the Biology and Virulence of a Trypanosoma cruzi Strain?

Trypanosoma cruzi is the causative agent of Chagas disease, transmitted to humans and mammals by blood-sucking hemipteran insects belonging to the Triatominae subfamily. The two main genotypes of T. cruzi (TcI and TcII) differ in many characteristics concerning their genetic profile. Despite the extensive literature on vectors and the etiologic agent, several interactive aspects between these two elements of Chagas disease are still waiting to be further clarified. Here, biological and histological features resulting from the interaction between Albino Swiss mice and T. cruzi isolate PB913 after passages through vectors of the Triatoma brasiliensis species complex were evaluated. Comparing the four members of the T. brasiliensis species complex-Triatoma brasiliensis brasiliensis Neiva, Triatoma brasiliensis macromelasoma Galvão, Triatoma melanica Neiva & Lent, and Triatoma juazeirensis Costa & Felix-no significant differences in parasitemia of the infected mice were observed. At 20 days post-infection, the highest number of parasites was observed in the group of mice that were infected with parasites obtained from T. b. macromelasoma. Tropism of the parasites to different organs such as heart, bladder, and skeletal muscles followed by inflammatory cell infiltrates was observed with quantitative and qualitative differences. Even though the four members of the T. brasiliensis species complex differ in their geographical distribution, morphology, biology, ecology, and genetics, no significant influence on the parasitemia of the T. cruzi PB913 isolate was detected. After evaluation of the tissue samples, a higher pathogenicity of parasites obtained from T. b. brasiliensis was noticeable.

The identification of two Trypanosoma cruzi I genotypes from domestic and sylvatic transmission cycles in Colombia based on a single polymerase chain reaction amplification of the spliced-leader intergenic region

A single polymerase chain reaction (PCR) reaction targeting the spliced-leader intergenic region of Trypanosoma cruzi I was standardised by amplifying a 231 bp fragment in domestic (TcI_DOM) strains or clones and 450 and 550 bp fragments in sylvatic strains or clones. This reaction was validated using 44 blind coded samples and 184 non-coded T. cruzi I clones isolated from sylvatic triatomines and the correspondence between the amplified fragments and their domestic or sylvatic origin was determined. Six of the nine strains isolated from acute cases suspected of oral infection had the sylvatic T. cruzi I profile. These results confirmed that the sylvatic T. cruzi I genotype is linked to cases of oral Chagas disease in Colombia. We therefore propose the use of this novel PCR reaction in strains or clones previously characterised as T. cruzi I to distinguish TcI_DOMfrom sylvatic genotypes in studies of transmission dynamics, including the verification of population selection within hosts or detection of the frequency of mixed infections by both T. cruzi I genotypes in Colombia.

Molecular genotyping of Trypanosoma cruzi for lineage assignment and population genetics

Trypanosoma cruzi, the etiological agent of Chagas disease, remains a major public health problem in Latin America. Infection with T. cruzi is lifelong and can lead to a spectrum of pathological sequelae ranging from subclinical to lethal cardiac and/or gastrointestinal complications. Isolates of T. cruzi can be assigned to six genetic lineages or discrete typing units (DTUs), which are broadly associated with disparate ecologies, transmission cycles, and geographical distributions. This extensive genetic diversity is also believed to contribute to the clinical variation observed among chagasic patients. Unravelling the population structure of T. cruzi is fundamental to understanding Chagas disease epidemiology, developing control strategies, and resolving the relationship between parasite genotype and clinical prognosis. To date, no single, widely validated, genetic target allows unequivocal resolution to DTU-level. In this chapter we present standardized methods for strain DTU assignment using PCR-restriction fragment length polymorphism analysis (PCR-RFLP) and nuclear multilocus sequence typing (MLST). PCR-RFLPs have the advantages of simplicity and reproducibility, requiring limited expertise and few laboratory consumables. MLST data are more laborious to generate but more informative; DNA sequences are readily transferable between research groups and amenable to recombination detection and intra-lineage analyses. We also recommend a mitochondrial (maxicircle) MLST scheme and a panel of 28 microsatellite loci for higher resolution population genetics studies. Due to the scarcity of T. cruzi in blood and tissue, all of these genotyping techniques have limited sensitivity when applied directly to clinical or biological specimens, particularly when targets are single (MLST) or low copy number (PCR-RFLPs). We therefore describe essential protocols to isolate parasites, derive biological clones, and extract T. cruzi genomic DNA from field and clinical samples.

Immunoregulatory networks in human Chagas disease

Chagas disease, caused by the infection with Trypanosoma cruzi, is endemic in all Latin America. Due to the increase in population migration, Chagas disease has spread worldwide and is now considered a health issue not only in endemic countries. While most chronically infected individuals remain asymptomatic, approximately 30% of the patients develop a potentially deadly cardiomyopathy. The exact mechanisms that underlie the establishment and maintenance of the cardiac pathology are not clear. However, there is consistent evidence that immunoregulatory cytokines are critical for orchestrating the immune response and thus influence disease development or control. While the asymptomatic (indeterminate) form represents a state of balance between the host and the parasite, the establishment of the cardiac form represents the loss of this balance. Analysis of data obtained from several studies has led to the hypothesis that the indeterminate form is associated with an anti-inflammatory cytokine profile, represented by high expression of IL-10, while cardiac form is associated with a high production of IFN-gamma and TNF-alpha in relation to IL-10, leading to an inflammatory profile. Here, we discuss the immunoregulatory events that might influence disease outcome, as well as the mechanisms that influence the establishment of these complex immunoregulatory networks.