TcBat a bat-exclusive lineage of Trypanosoma cruzi in the Panama Canal Zone, with comments on its classification and the use of the 18S rRNA gene for lineage identification

Chagas disease in immunocompromised patients

SUMMARYAs Chagas disease remains prevalent in the Americas, it is important that healthcare professionals and researchers are aware of the screening, diagnosis, monitoring, and treatment recommendations for the populations of patients they care for and study. Management of Trypanosoma cruzi infection in immunocompromised hosts is challenging, particularly because, regardless of antitrypanosomal treatment status, immunocompromised patients with Chagas disease are at risk for T. cruzi reactivation, which can be lethal. Evidence-based practices to prevent and manage T. cruzi reactivation vary depending on the type of immunocompromise. Here, we review available data describing Chagas disease epidemiology, testing, and management practices for various populations of immunocompromised individuals, including people with HIV and patients undergoing solid organ and hematopoietic stem cell transplantation.

Apparent absence of Trypanosoma cruzi in Mexican free-tailed bats (Tadarida brasiliensis) from Texas, USA

The Mexican free-tailed bat (Tadarida brasiliensis) is one of the most abundant mammals in North America. Mexican free-tailed bats have a wide geographic range stretching from northern South America to the western United States. Bats are theorized to be the original hosts for Trypanosoma cruzi -the causative agent of Chagas disease- and can serve as a source of infection to triatomine insect vectors that feed upon them. Chagas disease is a neglected tropical disease across the Americas where triatomines are present, including the southern United States, where Texas reports this highest number of locally-acquired human cases. To learn more about the role of bats in the ecology of Chagas disease in Texas, we surveyed a colony of Mexican free-tailed bats from Brazos County, Texas, for T. cruzi using carcasses salvaged after an extreme weather event. A total of 283 Mexican free-tailed bats collected in February 2021 were dissected and DNA from the hearts and kidneys was used for T. cruzi detection via qPCR. None of the bat hearts or kidneys tested positive for T. cruzi; this sample size affords 95% confidence that the true prevalence of T. cruzi in this population does not exceed 1%. Future sampling of multiple bat species as well as migrant and resident colonies of Mexican free-tailed bats across different times of the year over a broader geographic range would be useful in learning more about the role of bats in the ecology of Chagas disease in Texas.

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.

Fifteen Years after the Definition of Trypanosoma cruzi DTUs: What Have We Learned?

Trypanosoma cruzi, the protozoan causative of Chagas disease (ChD), exhibits striking genetic and phenotypic intraspecific diversity, along with ecoepidemiological complexity. Human-pathogen interactions lead to distinct clinical presentations of ChD. In 2009, an international consensus classified T. cruzi strains into six discrete typing units (DTUs), TcI to TcVI, later including TcBat, and proposed reproducible genotyping schemes for DTU identification. This article aims to review the impact of classifying T. cruzi strains into DTUs on our understanding of biological, ecoepidemiological, and pathogenic aspects of T. cruzi. We will explore the likely origin of DTUs and the intrinsic characteristics of each group of strains concerning genome organization, genomics, and susceptibility to drugs used in ChD treatment. We will also provide an overview of the association of DTUs with mammalian reservoirs, and summarize the geographic distribution, and the clinical implications, of prevalent specific DTUs in ChD patients. Throughout this review, we will emphasize the crucial roles of both parasite and human genetics in defining ChD pathogenesis and chemotherapy outcome.

Bat-associated microbes: Opportunities and perils, an overview

The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.

Revisiting gene typing and phylogeny of Trypanosoma cruzi reference strains: Comparison of the relevance of mitochondrial DNA, single-copy nuclear DNA, and the intergenic region of mini-exon gene

Chagas disease is a widespread neglected disease in Latin America. Trypanosoma cruzi, the causative agent of the disease, is currently subdivided into six DTUs (discrete typing units) named TcI-TcVI, and although no clear association has been found between parasite genetics and different clinical outcomes of the disease or different transmission cycles, genetic characterization of T. cruzi strains remains crucial for integrated epidemiological studies. Numerous markers have been used for this purpose, although without consensus. These include mitochondrial genes, single or multiple-copy nuclear genes, ribosomal RNA genes, and the intergenic region of the repeated mini-exon gene. To increase our knowledge of these gene sequences and their usefulness for strain typing, we sequenced fragments of three mitochondrial genes, nine single-copy nuclear genes, and the repeated intergenic part of the mini-exon gene by Next Generation Sequencing (NGS) on a sample constituted of 16 strains representative of T. cruzi genetic diversity, to which we added the corresponding genetic data of the 38 T. cruzi genomes fully sequenced until 2022. Our results show that single-copy nuclear genes remain the gold standard for characterizing T. cruzi strains; the phylogenetic tree from concatenated genes (3959 bp) confirms the six DTUs previously recognized and provides additional information about the alleles present in the hybrid strains. In the tree built from the three mitochondrial concatenated genes (1274 bp), three main clusters are identified, including one with TcIII, TcIV, TcV, and TcVI DTUs which are not separated. Nevertheless, mitochondrial markers remain necessary for detecting introgression and heteroplasmy. The phylogenetic tree built from the sequence alignment of the repeated mini-exon gene fragment (327 bp) displayed six clusters, but only TcI was associated with a single cluster. The sequences obtained from strains belonging to the other DTUs were scattered into different clusters. Therefore, while the mini-exon marker may bring, for some biological samples, some advantages in terms of sensibility due to its repeated nature, mini-exon sequences must be used with caution and, when possible, avoided for T. cruzi typing and phylogenetic studies.

Phylogenetic description of Trypanosoma cruzi isolates from Dipetalogaster maxima: Occurrence of TcI, TcIV, and TcIV-USA

Trypanosoma cruzi is the parasite responsible for Chagas disease. The parasite has been classified into six taxonomic assemblages: TcI-TcVI and TcBat (aka Discrete Typing Units or Near-Clades). No studies have focused on describing the genetic diversity of T. cruzi in the northwestern region of Mexico. Within the Baja California peninsula lives Dipetalogaster maxima, the largest vector species for CD. The study aimed to describe the genetic diversity of T. cruzi within D. maxima. A total of three Discrete Typing Units (DTUs) were found (TcI, TcIV, and TcIV-USA). TcI was the predominant DTU found (∼75% of samples), in concordance with studies from the southern USA, one sample was described as TcIV while the other ∼20% pertained to TcIV-USA, which has recently been proposed to have enough genetic divergence from TcIV, to merit its own DTU. Potential phenotype differences between TcIV and TcIV-USA should be assessed in future studies.

Deep serological profiling of the Trypanosoma cruzi TSSA antigen reveals different epitopes and modes of recognition by Chagas disease patients

BACKGROUND

Trypanosoma cruzi, the agent of Chagas disease, displays a highly structured population, with multiple strains that can be grouped into 6-7 evolutionary lineages showing variable eco-epidemiological traits and likely also distinct disease-associated features. Previous works have shown that antibody responses to 'isoforms' of the polymorphic parasite antigen TSSA enable robust and sensitive identification of the infecting strain with near lineage-level resolution. To optimize the serotyping performance of this molecule, we herein used a combination of immunosignaturing approaches based on peptide microarrays and serum samples from Chagas disease patients to establish a deep linear B-cell epitope profiling of TSSA.

METHODS/PRINCIPLE FINDINGS

Our assays revealed variations in the seroprevalence of TSSA isoforms among Chagas disease populations from different settings, hence strongly supporting the differential distribution of parasite lineages in domestic cycles across the Americas. Alanine scanning mutagenesis and the use of peptides of different lengths allowed us to identify key residues involved in antibody pairing and the presence of three discrete B-cell linear epitopes in TSSAII, the isoform with highest seroprevalence in human infections. Comprehensive screening of parasite genomic repositories led to the discovery of 9 novel T. cruzi TSSA variants and one TSSA sequence from the phylogenetically related bat parasite T. cruzi marinkellei. Further residue permutation analyses enabled the identification of diagnostically relevant or non-relevant substitutions among TSSA natural polymorphisms. Interestingly, T. cruzi marinkellei TSSA displayed specific serorecognition by one chronic Chagas disease patient from Colombia, which warrant further investigations on the diagnostic impact of such atypical TSSA.

CONCLUSIONS/SIGNIFICANCE

Overall, our findings shed new light into TSSA evolution, epitope landscape and modes of recognition by Chagas disease patients; and have practical implications for the design and/or evaluation of T. cruzi serotyping strategies.

Accessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families

Repetitive elements cause assembly fragmentation in complex eukaryotic genomes, limiting the study of their variability. The genome of Trypanosoma cruzi, the parasite that causes Chagas disease, has a high repetitive content, including multigene families. Although many T. cruzi multigene families encode surface proteins that play pivotal roles in host-parasite interactions, their variability is currently underestimated, as their high repetitive content results in collapsed gene variants. To estimate sequence variability and copy number variation of multigene families, we developed a read-based approach that is independent of gene-specific read mapping and de novo assembly. This methodology was used to estimate the copy number and variability of MASP, TcMUC, and Trans-Sialidase (TS), the three largest T. cruzi multigene families, in 36 strains, including members of all six parasite discrete typing units (DTUs). We found that these three families present a specific pattern of variability and copy number among the distinct parasite DTUs. Inter-DTU hybrid strains presented a higher variability of these families, suggesting that maintaining a larger content of their members could be advantageous. In addition, in a chronic murine model and chronic Chagasic human patients, the immune response was focused on TS antigens, suggesting that targeting TS conserved sequences could be a potential avenue to improve diagnosis and vaccine design against Chagas disease. Finally, the proposed approach can be applied to study multicopy genes in any organism, opening new avenues to access sequence variability in complex genomes. IMPORTANCE Sequences that have several copies in a genome, such as multicopy-gene families, mobile elements, and microsatellites, are among the most challenging genomic segments to study. They are frequently underestimated in genome assemblies, hampering the correct assessment of these important players in genome evolution and adaptation. Here, we developed a new methodology to estimate variability and copy numbers of repetitive genomic regions and employed it to characterize the T. cruzi multigene families MASP, TcMUC, and transsialidase (TS), which are important virulence factors in this parasite. We showed that multigene families vary in sequence and content among the parasite's lineages, whereas hybrid strains have a higher sequence variability that could be advantageous to the parasite's survivability. By identifying conserved sequences within multigene families, we showed that the mammalian host immune response toward these multigene families is usually focused on the TS multigene family. These TS conserved and immunogenic peptides can be explored in future works as diagnostic targets or vaccine candidates for Chagas disease. Finally, this methodology can be easily applied to any organism of interest, which will aid in our understanding of complex genomic regions.

Phylogenetic diversity of two common Trypanosoma cruzi lineages in the Southwestern United States

Trypanosoma cruzi is the causative agent of Chagas disease, a devastating parasitic disease endemic to Central and South America, Mexico, and the USA. We characterized the genetic diversity of Trypanosoma cruzi circulating in five triatomine species (Triatoma gerstaeckeri, T. lecticularia, T.indictiva, T. sanguisuga and T. recurva) collected in Texas and Southern Arizona using multilocus sequence typing (MLST) with four single-copy loci (cytochrome oxidase subunit II- NADH dehydrogensase subunit 1 region (COII-ND1), mismatch-repair class 2 (MSH2), dihydrofolate reductase-thymidylate synthase (DHFR-TS) and a nuclear gene with ID TcCLB.506529.310). All T. cruzi variants fall in two main genetic lineages: 75% of the samples corresponded to T. cruzi Discrete Typing Unit (DTU) I (TcI), and 25% to a North American specific lineage previously labelled TcIV-USA. Phylogenetic and sequence divergence analyses of our new data plus all previously published sequence data from those four loci collected in the USA, show that TcIV-USA is significantly different from any other previously defined T. cruzi DTUs. The significant level of genetic divergence between TcIV-USA and other T. cruzi DTUs should lead to an increased focus on understanding the epidemiological importance of this DTU, as well as its geographical range and pathogenicity in humans and domestic animals. Our findings further corroborate the fact that there is a high genetic diversity of the parasite in North America and emphasize the need for appropriate surveillance and vector control programs for Chagas disease in southern USA and Mexico.

"Visiting old, learn new": taxonomical overview of chiropteran trypanosomes from the morphology to the genes

Bats (the order Chiroptera) account for more than 20% of all mammalian species in the world; remarkably, they are the only mammals capable of true and sustained flight using their wing-like forelimbs. Since the beginning of the twentieth century, various morphotypes (or genotypes in the last decade) of haemoflagellates in the genus Trypanosoma (Euglenozoa: Kinetoplastea: Trypanosomatidae) have been reported worldwide in the blood of bats. Of note, the latent nature of chiropteran trypanosome infection with low levels of parasitaemia, together with the apparent morphological variation of the bloodstream forms related to phenotypical plasticity and the morphological resemblance of different parasite species, has hampered the taxonomic classification of bat trypanosomes based on morphological criteria. This said, 50 years ago, Hoare (1972) provisionally divided bat trypanosomes into two major morphotypes: the megadermae group (corresponding to the subgenus Megatrypanum in the traditional taxonomic system; 8 species) and the vespertilionis group (similar to the subgenus Schizotrypanum; 5 species). Importantly, the biological and biochemical analyses of bat trypanosomes isolated by haemoculture, together with the molecular genetic characterisation using various gene markers, allowed the establishment of clear phylogenetic and taxonomic relationships of various isolates from different continents in the last two decades. Here, we review the historical taxonomic approaches used to define chiropteran trypanosomes, as well as the ones currently employed to shed light on the diversity and evolutional tracks of the globally distributed chiropteran trypanosomes.

Trypanosoma cruzi genetic diversity: impact on transmission cycles and Chagas disease

Trypanosoma cruzi, the agent of Chagas disease (ChD), exhibits remarkable biological and genetic diversity, along with eco-epidemiological complexity. In order to facilitate communication among researchers aiming at the characterisation of biological and epidemiological aspects of T. cruzi, parasite isolates and strains were partitioned into seven discrete typing units (DTUs), TcI-TcVI and TcBat, identifiable by reproducible genotyping protocols. Here we present the potential origin of the genetic diversity of T. cruzi and summarise knowledge about eco-epidemiological associations of DTUs with mammalian reservoirs and vectors. Circumstantial evidence of a connection between T. cruzi genotype and ChD manifestations is also discussed emphasising the role of the host’s immune response in clinical ChD progression. We describe genomic aspects of DTUs focusing on polymorphisms in multigene families encoding surface antigens that play essential functions for parasite survival both in the insect vector and the mammalian host. Such antigens most probably contributed to the parasite success in establishing infections in different hosts and exploring several niches. Gaps in the current knowledge and challenges for future research are pointed out.

Insights from a comprehensive study of Trypanosoma cruzi: A new mitochondrial clade restricted to North and Central America and genetic structure of TcI in the region

More than 100 years since the first description of Chagas Disease and with over 29,000 new cases annually due to vector transmission (in 2010), American Trypanosomiasis remains a Neglected Tropical Disease (NTD). This study presents the most comprehensive Trypanosoma cruzi sampling in terms of geographic locations and triatomine species analyzed to date and includes both nuclear and mitochondrial genomes. This addresses the gap of information from North and Central America. We incorporate new and previously published DNA sequence data from two mitochondrial genes, Cytochrome oxidase II (COII) and NADH dehydrogenase subunit 1 (ND1). These T. cruzi samples were collected over a broad geographic range including 111 parasite DNA samples extracted from triatomines newly collected across North and Central America, all of which were infected with T. cruzi in their natural environment. In addition, we present parasite reduced representation (Restriction site Associated DNA markers, RAD-tag) genomic nuclear data combined with the mitochondrial gene sequences for a subset of the triatomines (27 specimens) collected from Guatemala and El Salvador. Our mitochondrial phylogenetic reconstruction revealed two of the major mitochondrial lineages circulating across North and Central America, as well as the first ever mitochondrial data for TcBat from a triatomine collected in Central America. Our data also show that within mtTcIII, North and Central America represent an independent, distinct clade from South America, named here as mtTcIII_NA-CA, geographically restricted to North and Central America. Lastly, the most frequent lineage detected across North and Central America, mtTcI, was also an independent, distinct clade from South America, noted as mtTcI_NA-CA. Furthermore, nuclear genome data based on Single Nucleotide Polymorphism (SNP) showed genetic structure of lineage TcI from specimens collected in Guatemala and El Salvador supporting the hypothesis that genetic diversity at a local scale has a geographical component. Our multiscale analysis contributes to the understanding of the independent and distinct evolution of T. cruzi lineages in North and Central America regions.

Neglected Tropical Diseases (NTDs) represents socioeconomic burden in most countries of Latin America. Chagas disease, a NTD, is caused by the parasite Trypanosoma cruzi. The disease can be mild, causing swelling and fever, or it can be long-lasting. Left untreated, it often causes heart failure. This study focused on T. cruzi lineages, emphasizing the gap of information from Central America and complementing what is known in North America. Our diverse collection of kissing bugs from North America (United States and Mexico) and Central America identified two of the major mitochondrial lineages circulating in these regions, both representing distinct clades within the already established three clusters of the T. cruzi parasite (mtTcI-mtTcIII): mtTcI_NA-CA and mtTcIII_NA-CA. At a local scale, population genetic structure of T. cruzi revealed that genetic diversity has a notable geographic component. The important insights into the genetic and evolutionary diversity of T. cruzi in North and Central America provide not only the necessity for referencing genomes to identify lineages but the basis to develop more precise and comprehensive diagnostic assays to better detect T. cruzi infections.

Diversity and Epidemiology of Bat Trypanosomes: A One Health Perspective

Bats (order Chiroptera) have been increasingly recognised as important reservoir hosts for human and animal pathogens worldwide. In this context, molecular and microscopy-based investigations to date have revealed remarkably high diversity of Trypanosoma spp. harboured by bats, including species of recognised medical and veterinary importance such as Trypanosoma cruzi and Trypanosoma evansi (aetiological agents of Chagas disease and Surra, respectively). This review synthesises current knowledge on the diversity, taxonomy, evolution and epidemiology of bat trypanosomes based on both molecular studies and morphological records. In addition, we use a One Health approach to discuss the significance of bats as reservoirs (and putative vectors) of T. cruzi, with a focus on the complex associations between intra-specific genetic diversity and eco-epidemiology of T. cruzi in sylvatic and domestic ecosystems. This article also highlights current knowledge gaps on the biological implications of trypanosome co-infections in a single host, as well as the prevalence, vectors, life-cycle, host-range and clinical impact of most bat trypanosomes recorded to date. Continuous research efforts involving molecular surveillance of bat trypanosomes are required for improved disease prevention and control, mitigation of biosecurity risks and potential spill-over events, ultimately ensuring the health of humans, domestic animals and wildlife globally.

A new Trypanosoma cruzi genotyping method enables high resolution evolutionary analyses

BACKGROUND

Trypanosoma cruzi is an important human pathogen in Latin America with nearly seven million people infected. It has a large degree of genetic diversity, classified into six discrete typing units (DTUs), which probably influences its physiological behavior and clinical manifestations. Several genotyping methods are available, with distinct performance on easiness, cost, resolution and applicability; no method excels in all parameters.

OBJECTIVES AND METHODS

To devise a molecular method for T. cruzi genotyping, based on polymerase chain reaction (PCR) amplification of a single target with multiple copies in the nuclear genome by large scale sequencing. We have applied this method to 29 T. cruzi isolates, comprising all described DTUs.

FINDINGS

We were able to classify all samples into sub DTU level with high robustness. Evolutionary relationship between DTUs were ascertained, suggesting that TcIII and TcIV DTUs are non-hybrid, and DTU IV is more similar to the common ancestral.

CONCLUSION

As the TS-LSS method is based on a single PCR reaction, comprising several copies of the target, it is probably useful for clinical samples, when the amount of DNA is a limiting factor. As large scale sequencing systems become more common, the TS-LSS method can be increasingly applied for T. cruzi genotyping.

Guide RNA Repertoires in the Main Lineages of Trypanosoma cruzi: High Diversity and Variable Redundancy Among Strains

Trypanosoma cruzi, as other kinetoplastids, has a complex mechanism of editing of mitochondrial mRNAs that requires guide RNAs (gRNAs) coded in DNA minicircles in the kinetoplast. There are many variations on this mechanism among species. mRNA editing and gRNA repertoires are almost unknown in T. cruzi. Here, gRNAs were inferred based on deep-sequenced minicircle hypervariable regions (mHVRs) and editing cascades were rebuilt in strains belonging to the six main T. cruzi lineages. Inferred gRNAs were clustered according to their sequence similarity to constitute gRNA classes. Extreme diversity of gRNA classes was observed, which implied highly divergent gRNA repertoires among different lineages, even within some lineages. In addition, a variable gRNA class redundancy (i.e., different gRNA classes editing the same mRNA region) was detected among strains. Some strains had upon four times more gRNA classes than others. Such variations in redundancy affected gRNA classes of all mRNAs in a concerted way, i.e., there are correlated variations in the number of gRNAs classes editing each mRNA. Interestingly, cascades were incomplete for components of the respiratory complex I in several strains. Finally, gRNA classes of different strains may potentially edit mitochondrial mRNAs from other lineages in the same way as they edit their own mitochondrial mRNAs, which is a prerequisite for biparental inheritance of minicircle in hybrids. We propose that genetic exchange and biparental inheritance of minicircles combined with minicircle drift due to (partial) random segregation of minicircles during kDNA replication is a suitable hypothesis to explain the divergences among strains and the high levels of gRNA redundancy in some strains. In addition, our results support that the complex I may not be required in some stages in the life cycle as previously shown and that linkage (in the same minicircle) of gRNAs that edit different mRNAs may prevent gRNA class lost in such stage.

Natural infection with Trypanosoma cruzi in bats captured in Campeche and Yucatán, México

INTRODUCTION

Bats have been reported as hosts of the Trypanosoma cruzi protozoan, the etiologic agent of American trypanosomiasis, an endemic zoonotic disease in México.

OBJECTIVE

To describe T. cruzi infection in bats from the states of Campeche and Yucatán, México.

MATERIALS AND METHODS

Captures were made from March to November, 2017, at three sites in Yucatán and one in Campeche. Up to four mist nets on two consecutive nights were used for the capture. The bats' species were identified and euthanasia was performed to collect kidney and heart samples for total DNA extraction. Trypanosoma cruzi infection was detected by conventional PCR with the amplification of a fragment belonging to the T. cruzi DNA nuclear.

RESULTS

Eighty-six bats belonging to five families (Vespertilionidae, Noctilionidae, Mormoopidae, Phyllostomidae, and Molossidae) and 13 species (Rhogeessa aeneus, Noctilio leporinus, Pteronotus davyi, P. parnellii, Artibeus jamaicensis, A. lituratus, A. phaeotis, Glossophaga soricina, Carollia sowelli, Chiroderma villosum, Uroderma bilobatum, Sturnira parvidens, and Molossus rufus) were captured. Infection frequency by PCR was 30,2% (26/86) detected only in the renal tissue. The infected species were P. parnellii, G. soricina, A. lituratus, A. jamaicensis, S. parvidens, C. villosum, and R. aeneus.

CONCLUSIONS

Our results confirmed the participation of several bat species as hosts in the T. cruzi transmission cycle in the region. Further studies are necessary to establish the importance of these animals in the zoonotic transmission of T. cruzi.

PhyloQuant approach provides insights into Trypanosoma cruzi evolution using a systems-wide mass spectrometry-based quantitative protein profile

The etiological agent of Chagas disease, Trypanosoma cruzi, is a complex of seven genetic subdivisions termed discrete typing units (DTUs), TcI-TcVI and Tcbat. The relevance of T. cruzi genetic diversity to the variable clinical course of the disease, virulence, pathogenicity, drug resistance, transmission cycles and ecological distribution requires understanding the parasite origin and population structure. In this study, we introduce the PhyloQuant approach to infer the evolutionary relationships between organisms based on differential mass spectrometry-based quantitative features. In particular, large scale quantitative bottom-up proteomics features (MS1, iBAQ and LFQ) were analyzed using maximum parsimony, showing a correlation between T. cruzi DTUs and closely related trypanosomes' protein expression and sequence-based clustering. Character mapping enabled the identification of synapomorphies, herein the proteins and their respective expression profiles that differentiate T. cruzi DTUs and trypanosome species. The distance matrices based on phylogenetics and PhyloQuant clustering showed statistically significant correlation highlighting the complementarity between the two strategies. Moreover, PhyloQuant allows the identification of differentially regulated and strain/DTU/species-specific proteins, and has potential application in the identification of specific biomarkers and candidate therapeutic targets.

Design of a AFLP-PCR and PCR-RFLP test that identify the majority of discrete typing units of Trypanosoma cruzi

Background

Chagas disease, caused by the intracellular parasite Trypanosoma cruzi, is one of the most important parasitological infections in the Americas. It is estimated to infect approximately 6 million people from mostly low income countries in Latin America, although recent infections have been reported in southern US states. Several studies have described an extensive genetic diversity among T. cruzi isolates throughout its geographic distribution in the American continent. This diversity has been correlated with the pathology developed during an infection. However, due to a lack of a single reliable test, current diagnosis practices of the disease are not straightforward since several different tests are applied. The use of current genomic sequence data allows for the selection of molecular markers (MM) that have the ability to identify the Discrete Typing Unit (DTU) of T. cruzi in a given infection, without the need of any sequencing reaction.

Methodology/principal findings

Applying three criteria on the genomic sequencing data of four different phylogenetic lineages of T. cruzi, we designed several molecular tests that can be used for the molecular typing of the parasite. The criteria used were: (1) single-copy orthologs of T. cruzi, (2) T. cruzi unique loci, and (3) T. cruzi polymorphic loci. All criteria combined allowed for the selection of 15 MM, 12 of which were confirmed to be functional and replicable in the laboratory with sylvatic samples. Furthermore, one MM produced distinct polymerase chain reaction (PCR) amplicon sizes among distinct T. cruzi DTUs, allowing the use of a AFLP-PCR test to distinguish DTUs I, II/IV, V and VI. Whereas two MM can differentiate DTUs I, II, IV and V/VI out of the six current DTUs with a PCR-RFLP test.

Conclusions/significance

The designed molecular tests provide a practical and inexpensive molecular typing test for the majority of DTUs of T. cruzi, excluding the need to perform any sequencing reaction. This provides the scientific community with an additional specific, quick and inexpensive test that can enhance the understanding of the correlation between the DTU of T. cruzi and the pathology developed during the infection.

Application of WHO International Biological Reference Standards to evaluate commercial serological tests for chronic Chagas disease

BACKGROUND Chagas disease, resulting from Trypanosoma cruzi infections, continues to be a health concern mainly in Latin American countries where the parasite is endemic. The laboratory diagnosis of a chronic infection is determined through serological assays for antibodies against T. cruzi and several tests are available that differ in key components, formats and methodologies. To date, no single test meets the criteria of a gold standard. The situation is further complicated by the difficulties associated with performance comparisons between different immunoassays or methodologies executed at different times and geographical areas. OBJECTIVE To improve the diagnosis of Chagas disease, the WHO coordinated the development of two International Biological Reference Standards for antibodies against anti-T. cruzi: NIBSC 09/186 and NIBSC 09/188 that respectively represent geographical regions with the highest prevalence of TcII and TcI lineages of the parasite. METHODS The principle goal of this study was to verify the behavior of these standards when assayed by several commercially available serological tests that employ different methods to capture and detect human anti-T. cruzi antibodies. FINDINGS AND MAIN CONCLUSIONS The results reinforce the recommendation that these standards be considered for performance evaluations of commercialised immunoassays and should be an integral step in the development of new test components or assay paradigms.

Trypanosoma cruzi infections and associated pathology in urban-dwelling Virginia opossums (Didelphis virginiana)

Trypanosoma cruzi, a zoonotic protozoan parasite, infects a wide range of mammals. The southern United States has endemic sylvatic transmission cycles maintained by several species of wildlife and domestic dogs. We hypothesized that urban-dwelling opossums (Didelphis virginiana) in South Texas are infected with T. cruzi, and that tissue pathology would be associated with infection. In 2017, we collected blood, heart tissue and anal gland secretions from 100 wild opossums across three seasons that were trapped by animal control in South Texas. In addition, anal gland tissue and intercostal muscle were collected from 43 of the 100 opossums for which time allowed the extra tissue collection. All blood, tissue, and secretion samples were screened for T. cruzi DNA using qPCR with confirmation of positive status achieved through one or more additional PCR assays, including a qPCR to determine the parasite discrete typing unit (DTU). T. cruzi DNA was detected in at least one tissue of 15% of the opossums sampled: blood clot (9%), heart tissue (10%), anal gland secretions (12%), intercostal muscle (16.3%), and anal gland tissue (11.6%). Infection was detected in two or more different tissue types in nine of the opossums. The 35 tissues for which parasite DTU was determined were exclusively 'Tcl'- a DTU previously associated with locally-acquired human disease in the United States. T. cruzi-positive opossums were nearly 14 times more likely to exhibit significant heart lesions on histopathology (lympoplasmacytic inflammation±fibrosis) when compared to negative opossums (OR = 13.56, CI = 1.23-751.28, p-value = 0.03). Three triatomines were opportunistically collected from the study site, of which two were infected (66.7%), and bloodmeal analysis revealed canine, opossum, and human bloodmeals. Given the presence of parasite in opossum blood, unique potential for shedding of parasite in anal glad secretions, and evidence of vectors feeding on opossums, it is likely that opossums serve as wild reservoirs around urban dwellings in South Texas.

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.

Prevalence of Trypanosoma cruzi infection and associated histologic findings in domestic cats (Felis catus)

Trypanosoma cruzi is a zoonotic protozoan parasite transmitted by triatomines that infects a wide range of mammals. South Texas is a hotspot for triatomines, T. cruzi-infected dogs and wildlife, and local transmission to humans also occurs. However, little is known about the infection of domestic cats (Felis catus) in the United States. Given the role cats play in the ecology of T. cruzi in Mexico and South America, we hypothesized that T. cruzi infection occurs in cats from south Texas, sometimes associated with cardiac pathology. In 2017, 167 euthanized cats from a south Texas shelter were sampled across winter, spring, and summer. We collected whole blood and hearts from all cats, with additional tissues from a subset. Serum samples were screened for T. cruzi antibodies using two independent rapid immunochromatographic tests and an indirect fluorescent antibody test. Cats were considered seropositive if they were positive on at least two independent serological tests. Blood clot, heart tissue and other tissues were subjected to qPCR for parasite detection and discrete typing unit (DTU) determination. Tissues from selected seropositive or PCR-positive animals and a subset of negative animals were processed routinely for histopathology and examined by a board-certified pathologist. A total of 19 cats (11.4%) were seropositive and three cats (1.8%) - one of which was seropositive - had one or more PCR-positive tissues. Infected tissues included heart, bicep femoris muscle, sciatic nerve, esophagus, and mesentery. Genotyping of the parastite to the level of DTU showed that exclusively DTU TcI was present, despite past studies showing both TcI and TcIV in vectors of the region. Eight of 19 (42.1%) seropositive cats exhibited lymphoplasmacytic inflammation, sometimes with fibrosis, in cardiac tissue compared to 28.6% of 28 seronegative cats (P = 0.10). Domestic cats are affected hosts in the eco-epidemiology of Chagas disease. Future prospective studies are needed to understand disease progression. Veterinarians in the southern United States should consider T. cruzi in their index of suspicion in cats with exposure to vectors and undetermined cardiac abnormalities.

In Vitro Benznidazole and Nifurtimox Susceptibility Profile of Trypanosoma cruzi Strains Belonging to Discrete Typing Units TcI, TcII, and TcV

We ascertain the in vitro Benznidazole (BZN) and Nifurtimox (NFX) susceptibility pattern of epimastigotes, trypomastigotes, and amastigotes of 21 T. cruzi strains, from patients, reservoir, and triatomine bugs of various geographic origins. Using this panel of isolates, we compute the Epidemiological cut off value (CO_wt). Then, the frequency of the susceptible phenotype (Wild type) towards benznidazole (BZN) and nifurtimox (NFX) within this set of strains belonging to three discrete typing units (DTUs), TcI, TcII, and TcV, was deduced. We observed that the susceptibility status of individual T. cruzi isolates toward BZN and NFX is related to the genetic background and underlying factors that are probably related to the individual life trait history of each strain. Analyzing drug susceptibility in this conceptual framework would offer the possibility to evidence a link between isolates expressing a low susceptibility level (not wild-type) as defined by the CO_wt value and none-curative treatment. It will also permit us to track drug-resistant parasites in the T. cruzi population.

First report of the prevalence and genotype of Trypanosoma spp. in bats in Yunnan Province, Southwestern China

Trypanosome is considered as one of important parasites in almost all mammalian species, which occurs in Chiroptera throughout the world. Although numerous trypanosome species have been identified in bats in Asia, Africa, South America and Europe, little is known about the genetic diversity and pathogenicity of trypanosomes in Chinese bat. Recently, some human Trypanosoma cruzi infection attributed to a bat-related T. cruzi (TcBat) from the Noctilio spp., Myotis spp. and Artibeus spp was found. Consequently, it is a necessity to know trypanosome species in bats from China. In order to determine the prevalence and genotypes in bat from southwestern China, wehere detected trypanosomes prevalence 227bat brain tissue samples, including 60 Rousettus leschenaultia, 58 Hipposideros Pomona, 69 Rhinolophus pusillus, 40 Myotis daubentonni in Yunnan Province of China using nested PCR based on 18S rRNA. 14 (6.2%) of them were trypanosmes positive including 13 insect-eating bats and 1 fruit bat. The prevalence of trypanosome in R.leschenaultia, H. Pomona, and R.pusillus was 1.67%(1/60), 6.90%(4/58) and 13.0%(9/69), respectively (P < 0.01), suggesting R. pusillus was a main-vector host bat. The positive rate of T.sp, T. dionisii, T.brucei brucei and T.sp ZY-2 was 4.8% (11/227), 0.4%(1/227), 0.4%(1/227), and 0.4% (1/227), resepectively. These results showed that T.sp-Yunnan is the predominant genospecies. To our knowledge, this is the first report about Trypanosome species in bats in Yunnan Province, southwestern China.

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.

Trypanosoma dionisii in insectivorous bats from northern China

Although bats were considered as a major host of trypanosomatid flagellates, information of trypanosomes in bats is unknown in China. We collected bats in 2015 from Shandong Province of China and used PCR to amplify the Trypanosoma glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) gene and 18S rRNA gene from the bat blood samples and heart tissues. The results showed that 10.3% (13/126) of bats (Eptesicus serotinus and Myotis pequinius) were positive for trypanosomatid DNA and DNA sequencing showed that all PCR amplified Trypanosoma DNA belonged to T. dionisii. We concluded that T. dionisii had a infection rate in bats from China. For the first time, Trypanosoma infections were detected in bats from China, providing valuable information on the prevalence of these parasites in Asia. This is also the first report of Trypanosoma dionisii in Myotis pequinius, suggesting that Trypanosoma dionisii has a broad host species.

Trypanosoma cruzi infection, discrete typing units and feeding sources among Psammolestes arthuri (Reduviidae: Triatominae) collected in eastern Colombia

BACKGROUND

Chagas disease (CD) is caused by the protozoan parasite Trypanosoma cruzi, and is transmitted by hematophagous insects of the family Reduviidae. Psammolestes arthuri is a sylvatic triatomine distributed in Colombia and Venezuela which feeds on birds and there are a few studies that have reported Ps. arthuri naturally infected with T. cruzi. In Colombia, Ps. arthuri has been found in dwellings, making it important to evaluate its possible role in the T. cruzi transmission cycle. We aimed to evaluate the presence of T. cruzi and feeding sources of Ps. arthuri to elucidate new possible scenarios of T. cruzi transmission in the country.

METHODS

A total of 60 Ps. arthuri were collected in Arauca and Casanare, Colombia. We detected and genotyped T. cruzi and identified feeding sources. The frequency of the presence of T. cruzi was obtained and compared with different eco-epidemiological variables. Multiple correspondence analysis was conducted to explore associations between eco-epidemiological variables and the presence of T. cruzi; with these results, a logistic regression was used to determine statistical associations.

RESULTS

The infection rate of T. cruzi was 70.7% and was mostly associated with insect stage, sex, bird nest and feeding source. Regarding discrete typing units (DTUs), TcI was found in 54.7% samples, of which 21.7% (5/23) were TcI_Dom, 52.1% (12/23) had mixed infection (TcI_Dom-TcI_Sylv), and single infection with TcI_Sylv was not detected. Mixed infections (TcI/TcII-TcVI) were found in 9.52% (4/42) of the samples; of these, 14.2% (6/42) were TcII-TcVI. A total of 15 feeding sources were identified and the most frequent were: Cranioleuca baroni (35.85%), Homo sapiens (26.42%), Thraupis episcopus (11.32%) and Serinus albogularis (3.77%).

CONCLUSIONS

Although Ps. arthuri is mainly ornithophilic, this species may be feeding on other animals that can be infected with T. cruzi, possibly playing a role maintaining the zoonotic cycle of the parasite. Further studies with molecular techniques and wider sampling are needed to improve information regarding infection rates, ecotopes and habits with the aim of evaluating whether Ps. arthuri could be a potential T. cruzi vector.

High sensitivity and reproducibility of in-house ELISAs using different genotypes of Trypanosoma cruzi

The adequate choice of Trypanosoma cruzi strains as antigen source for the diagnosis of Chagas disease is still controversial due to differences in terms of accuracy reported between different diagnostic tests. In this study was determined if the genetic variability between different genotypes of T. cruzi (TcI, TcII and TcIV) affect the final diagnosis of Chagas disease. The sensitivity and specificity index of in-house ELISA tests prepared with different T. cruzi strains were evaluated with chagasic and non-chagasic control sera and using the TESA-blot as a reference test. The results of this study revealed that the sensitivity index did not vary, with percentages of 100% for all strains in both tests. However, the specificity index for ELISA tests showed differences between 92% and 98%, but were reduced to 78%-89% when Leishmania-positive sera were included. All ELISAs and TESA-blot prepared with different antigens and the recombinant Wiener test were challenged in an endemic community for Chagas disease in Panama. Both ELISAs and TESA-blot recognized the same positive sera, corroborating the sensitivity indexes (100%) found with the control sera. The TESA-blot maintained the specificity index of 100% and did not display false positives. However, the recombinant Wiener test decreased its sensitivity to 81.25%.

Trypanosoma madeirae sp. n.: A species of the clade T. cruzi associated with the neotropical common vampire bat Desmodus rotundus

Molecular phylogenetic studies have revealed the growing diversity of bat trypanosomes. Here, 14 isolates from blood samples of the vampire bat Desmodus rotundus (Phyllostomidae) from Rio de Janeiro, Southeast Brazil, were cultivated, and morphologically and molecularly characterized. All isolates represent a novel species named Trypanosoma madeirae n. sp. positioned in the Neobat lineage of the clade T. cruzi. The Neobat lineage also comprises closely related trypanosomes of clades Neotropic 1, 2 and 3 from diverse phyllostomid species. Trypanosomes of Neotropic 1, found in Trachops cirrhosus and Artibeus jamaicensis (phyllostomids), likely represent a different species or genotype closely related to T. madeirae. Consistent with its phylogenetic positioning, T. madeirae differs from Trypanosoma cruzi in morphology of both epimastigote and trypomastigote culture forms and does not infect Triatoma infestans. Similar to its closest relatives of Neobat lineage, T. madeirae was unable to develop within mammalian cells. To date, PCR-surveys on archived blood/liver samples unveiled T. madeirae exclusively in D. rotundus from Southern to Northern Brazil. The description of a new species of bat trypanosome associated with vampire bats increases the repertoire of trypanosomes infecting D. rotundus, currently comprised of Trypanosoma cruzi, T. cruzi marinkellei, Trypanosoma dionisii, Trypanosoma rangeli, Trypanosoma pessoai, and Trypanosoma madeirae.

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Trypanosoma madeirae n. sp. was so far only detected in the vampire bat Desmodus rotundus.

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T. madeirae clustered with other Neotropical trypanosomes in the Neobat lineage of the clade T. cruzi.

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Several species of trypanosomes are hosted by Desmodus rotundus.

Triatomines: Trypanosomatids, Bacteria, and Viruses Potential Vectors?

Triatominae bugs are the vectors of Chagas disease, a major concern to public health especially in Latin America, where vector-borne Chagas disease has undergone resurgence due mainly to diminished triatomine control in many endemic municipalities. Although the majority of Triatominae species occurs in the Americas, species belonging to the genus Linshcosteus occur in India, and species belonging to the Triatoma rubrofasciata complex have been also identified in Africa, the Middle East, South-East Asia, and in the Western Pacific. Not all of Triatominae species have been found to be infected with Trypanosoma cruzi, but the possibility of establishing vector transmission to areas where Chagas disease was previously non-endemic has increased with global population mobility. Additionally, the worldwide distribution of triatomines is concerning, as they are able to enter in contact and harbor other pathogens, leading us to wonder if they would have competence and capacity to transmit them to humans during the bite or after successful blood feeding, spreading other infectious diseases. In this review, we searched the literature for infectious agents transmitted to humans by Triatominae. There are reports suggesting that triatomines may be competent vectors for pathogens such as Serratia marcescens, Bartonella, and Mycobacterium leprae, and that triatomine infection with other microrganisms may interfere with triatomine-T. cruzi interactions, altering their competence and possibly their capacity to transmit Chagas disease.

Whole genome sequencing of Trypanosoma cruzi field isolates reveals extensive genomic variability and complex aneuploidy patterns within TcII DTU

BACKGROUND

Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI-TcVI. TcII is among the major DTUs enrolled in human infections in South America southern cone, where it is associated with severe cardiac and digestive symptoms. Despite the importance of TcII in Chagas disease epidemiology and pathology, so far, no genome-wide comparisons of the mitochondrial and nuclear genomes of TcII field isolates have been performed to track the variability and evolution of this DTU in endemic regions.

RESULTS

In the present work, we have sequenced and compared the whole nuclear and mitochondrial genomes of seven TcII strains isolated from chagasic patients from the central and northeastern regions of Minas Gerais, Brazil, revealing an extensive genetic variability within this DTU. A comparison of the phylogeny based on the nuclear or mitochondrial genomes revealed that the majority of branches were shared by both sequences. The subtle divergences in the branches are probably consequence of mitochondrial introgression events between TcII strains. Two T. cruzi strains isolated from patients living in the central region of Minas Gerais, S15 and S162a, were clustered in the nuclear and mitochondrial phylogeny analysis. These two strains were isolated from the other five by the Espinhaço Mountains, a geographic barrier that could have restricted the traffic of insect vectors during T. cruzi evolution in the Minas Gerais state. Finally, the presence of aneuploidies was evaluated, revealing that all seven TcII strains have a different pattern of chromosomal duplication/loss.

CONCLUSIONS

Analysis of genomic variability and aneuploidies suggests that there is significant genomic variability within Minas Gerais TcII strains, which could be exploited by the parasite to allow rapid selection of favorable phenotypes. Also, the aneuploidy patterns vary among T. cruzi strains and does not correlate with the nuclear phylogeny, suggesting that chromosomal duplication/loss are recent and frequent events in the parasite evolution.

A systematic review of the Trypanosoma cruzi genetic heterogeneity, host immune response and genetic factors as plausible drivers of chronic chagasic cardiomyopathy

Chagas disease is a complex tropical pathology caused by the kinetoplastid Trypanosoma cruzi. This parasite displays massive genetic diversity and has been classified by international consensus in at least six Discrete Typing Units (DTUs) that are broadly distributed in the American continent. The main clinical manifestation of the disease is the chronic chagasic cardiomyopathy (CCC) that is lethal in the infected individuals. However, one intriguing feature is that only 30-40% of the infected individuals will develop CCC. Some authors have suggested that the immune response, host genetic factors, virulence factors and even the massive genetic heterogeneity of T. cruzi are responsible of this clinical pattern. To date, no conclusive data support the reason why a few percentages of the infected individuals will develop CCC. Therefore, we decided to conduct a systematic review analysing the host genetic factors, immune response, cytokine production, virulence factors and the plausible association of the parasite DTUs and CCC. The epidemiological and clinical implications are herein discussed.

Discrete typing units of Trypanosoma cruzi detected by real-time PCR in Chilean patients with chronic Chagas cardiomyopathy

Chagas disease is a major public health problem in Latin America and has spread to other countries due to immigration of infected persons. 10-30% of patients with chronic Chagas disease will develop cardiomyopathy. Chagas cardiomyopathy is the worst form of the disease, due to its high morbidity and mortality. Because of its prognostic value and adequate medical monitoring, it is very important to identify infected people who could develop Chagas cardiomyopathy. The aim of this study was to determine if discrete typing units (DTUs) of Trypanosoma cruzi are related to the presence of heart disease in patients with chronic Chagas disease. A total of 86 untreated patients, 41 with cardiomyopathy and 45 without heart involvement were submitted to clinical study. Electrocardiograms and echocardiograms were performed on the group of cardiopaths, in which all important known causes of cardiomyopathy were discarded. Sinus bradycardia and prolonged QTc interval were the most frequent electrocardiographic alterations and patients were classified in group I (46%) and group II (54%) of New York Hearth Association. In all cases real-time PCR genotyping assays were performed. In the group with cardiomyopathy, the most frequent DTU was TcI (56.1%), followed by TcII (19.5%). Mixed infections TcI + TcII were observed in 7.3% of the patients. In the group without cardiac pathologies, TcI and TcII were found at similar rates (28.9 and 31.1%, respectively) and mixed infections TcI + TcII in 17.8% of the cases. TcIII and TcIV were not detected in any sample. Taken together, our data indicate that chronic Chagas cardiomyopathy in Chile can be caused by strains belonging to TcI and TcII.

Trypanosoma cruzi genetic diversity: Something new for something known about Chagas disease manifestations, serodiagnosis and drug sensitivity

The genetic diversity of Trypanosoma cruzi, the protozoan agent of Chagas disease, is widely recognized. At present, T. cruzi is partitioned into seven discrete typing units (DTUs), TcI-TcVI and Tcbat. This article reviews the present knowledge on the parasite population structure, the evolutionary relationships among DTUs and their distinct, but not exclusive ecological and epidemiological associations. Different models for the origin of hybrid DTUs are examined, which agree that genetic exchange among T. cruzi populations is frequent and has contributed to the present parasite population structure. The geographic distribution of the prevalent DTUs in humans from the southern United States to Argentina is here presented and the circumstantial evidence of a possible association between T. cruzi genotype and Chagas disease manifestations is discussed. The available information suggests that parasite strains detected in patients, regardless of the clinical presentation, reflect the principal DTU circulating in the domestic transmission cycles of a particular region. In contrast, in several orally transmitted outbreaks, sylvatic strains are implicated. As a consequence of the genotypic and phenotypic differences of T. cruzi strains and the differential geographic distribution of DTUs in humans, regional variations in the sensitivity of the serological tests are verified. The natural resistance to benznidazole and nifurtimox, verified in vivo and in vitro for some parasite stocks, is not associated with any particular DTU, and does not explain the marked difference in the anti-parasitic efficacy of both drugs in the acute and chronic phases of Chagas disease. Throughout this review, it is emphasized that the interplay between parasite and host genetics should have an important role in the definition of Chagas disease pathogenesis, anti-T. cruzi immune response and chemotherapy outcome and should be considered in future investigations.

Limit of detection of PCR/RFLP analysis of cytochrome oxidase II for the identification of genetic groups of Trypanosoma cruzi and Trypanosoma rangeli in biological material from vertebrate hosts

Mixed infections with Trypanosoma cruzi and Trypanosoma rangeli and their different genetic groups occur frequently in vertebrate hosts and are difficult to detect by serology. In the present study, we evaluated the limit of detection of polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) analysis of cytochrome oxidase II (COII) for the identification of genetic groups of these two parasites in blood and tissue from vertebrate hosts. Reconstitution experiments were performed using human blood (TcI/TcII and KP1+/KP1-) and mouse tissue (TcI/TcII). We tested blood from patients who were in the chronic phase of Chagas disease and tissue from animals that were experimentally infected with all possible combinations of six discrete typing units. In blood samples, T. cruzi and T. rangeli were detected when 5 parasites (pa) were present in the sample, and genetic groups were identified when at least 50 pa were present in the sample. T. cruzi alone could be detected with 1 pa and genotyped (TcI/TcII) with 2 pa. T. rangeli was detected with 2 pa and genotyped (KP+/KP1-) with 25 pa. The present method more readily detected TcII and KP1- in both admixtures and alone. In mouse tissue, TcI and TcII were detected with at least 25 pa. The analysis of blood samples from patients and tissue from animals that were experimentally infected revealed low parasite loads in these hosts, which were below the limit of detection of the present method and could not be genotyped. Our findings indicate that the performance of PCR/RFLP analysis of COII is directly related to the amount and proportion of parasites that are present in the sample and the genetic groups to which the parasites belong.

Trypanosoma rangeli is phylogenetically closer to Old World trypanosomes than to Trypanosoma cruzi

Trypanosoma rangeli and Trypanosoma cruzi are generalist trypanosomes sharing a wide range of mammalian hosts; they are transmitted by triatomine bugs, and are the only trypanosomes infecting humans in the Neotropics. Their origins, phylogenetic relationships, and emergence as human parasites have long been subjects of interest. In the present study, taxon-rich analyses (20 trypanosome species from bats and terrestrial mammals) using ssrRNA, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH), heat shock protein-70 (HSP70) and Spliced Leader RNA sequences, and multilocus phylogenetic analyses using 11 single copy genes from 15 selected trypanosomes, provide increased resolution of relationships between species and clades, strongly supporting two main sister lineages: lineage Schizotrypanum, comprising T. cruzi and bat-restricted trypanosomes, and Tra[Tve-Tco] formed by T. rangeli, Trypanosoma vespertilionis and Trypanosoma conorhini clades. Tve comprises European T. vespertilionis and African T. vespertilionis-like of bats and bat cimicids characterised in the present study and Trypanosoma sp. Hoch reported in monkeys and herein detected in bats. Tco included the triatomine-transmitted tropicopolitan T. conorhini from rats and the African NanDoum1 trypanosome of civet (carnivore). Consistent with their very close relationships, Tra[Tve-Tco] species shared highly similar Spliced Leader RNA structures that were highly divergent from those of Schizotrypanum. In a plausible evolutionary scenario, a bat trypanosome transmitted by cimicids gave origin to the deeply rooted Tra[Tve-Tco] and Schizotrypanum lineages, and bat trypanosomes of diverse genetic backgrounds jumped to new hosts. A long and independent evolutionary history of T. rangeli more related to Old World trypanosomes from bats, rats, monkeys and civets than to Schizotrypanum spp., and the adaptation of these distantly related trypanosomes to different niches of shared mammals and vectors, is consistent with the marked differences in transmission routes, life-cycles and host-parasite interactions, resulting in T. cruzi (but not T. rangeli) being pathogenic to humans.

Identification of bat trypanosomes from Minas Gerais state, Brazil, based on 18S rDNA and Cathepsin-L-like targets

Several bat species can be infected by trypanosomes, but there is not much information about which of these parasites infect bats from Triângulo Mineiro and Alto Paranaíba, Minas Gerais state, Brazil, a formerly endemic region for Trypanosoma cruzi, the causative agent of Chagas disease. The aim of this study was to describe, characterize, and identify the presence of trypanosomes in bats. The captured bats (448) belong to four families and to 19 different species. Of those, 37 bats were found to be positive for trypanosomes by microhematocrit, (infection rate 8.3%) and 27 were positive after hemoculture analysis. Initially, the isolates were identified by PCR (18S rDNA, 24Sα rDNA, spliced leader, COII RFLP-PCR) using primers originally designed for T. cruzi. PCRs (18S rDNA, 24Sα rDNA) showed compatible bands for TcI, whereas COII RFLP-PCR showed a similar pattern associated to TcII. However, there was no DNA amplification using spliced leader as a target, revealing a discrepancy between the results. Phylogenetic analysis of Cathepsin L-like and 18S rDNA sequences proved that 15 of the isolates corresponded to Trypanosoma cruzi marinkellei and one to Trypanosoma dionisii. These results revealed that the diversity of trypanosome species in a region considered endemic for Chagas disease is greater than previous descriptions. All this can confirm the necessity of using DNA sequencing approaches in order to determinate trypanosomes species isolated from bats.

American trypanosomiasis, or Chagas disease, in Panama: a chronological synopsis of ecological and epidemiological research

American trypanosomiasis, or Chagas disease, is a growing public health problem in Panama, and further forest degradation due to human population growth is expected to worsen the situation. Most people infected with the parasite Trypanosoma cruzi are silently ill, and their life expectancy is severely compromised, which contributes to further deterioration of living conditions in endemic regions. Here, we review the outcomes of nearly 100 years of ecological and epidemiological investigation about Chagas disease in Panama, in an attempt to highlight progress, identify needs, and re-orient future efforts. Rhodnius pallescens and Triatoma dimidiata are both primary vectors of T. cruzi in Panama, but R. pallescens seems more efficient in human-altered forest ecosystems due to a greater degree of association with Attalea butyracea. In contrast, T. dimidiata transmits T. cruzi efficiently under more sylvatic conditions (e.g. settlements inside old-growth or secondary forest patches), where its populations reach considerable numbers irrespective of the absence of A. butyracea. A trend of increasing forest degradation, suburbanization, and development of tourism in Panama favoring the establishment of A. butyracea and other palm tree species (Acrocomia sp.) suggests that a colonist species like R. pallescens will continue to play a more prominent role in the transmission of T. cruzi than a forest specialist like T. dimidiata. However, studies about the taxonomic status and ecology of these vectors are still needed in Panama to address their transmission potential fully. The implementation of an active surveillance system and education programs could greatly minimize the risk of Chagas disease transmission in Panama, preventing fatal infections in children from endemic areas.

Biological factors that impinge on Chagas disease drug development

Chagas disease is caused by infection with the insect-transmitted protozoan Trypanosoma cruzi, and is the most important parasitic infection in Latin America. The current drugs, benznidazole and nifurtimox, are characterized by limited efficacy and toxic side-effects, and treatment failures are frequently observed. The urgent need for new therapeutic approaches is being met by a combined effort from the academic and commercial sectors, together with major input from not-for-profit drug development consortia. With the disappointing outcomes of recent clinical trials against chronic Chagas disease, it has become clear that an incomplete understanding of parasite biology and disease pathogenesis is impacting negatively on the development of more effective drugs. In addition, technical issues, including difficulties in establishing parasitological cure in both human patients and animal models, have greatly complicated the assessment of drug efficacy. Here, we outline the major questions that need to be addressed and discuss technical innovations that can be exploited to accelerate the drug development pipeline.

Small subunit ribosomal metabarcoding reveals extraordinary trypanosomatid diversity in Brazilian bats

BACKGROUND

Bats are a highly successful, globally dispersed order of mammals that occupy a wide array of ecological niches. They are also intensely parasitized and implicated in multiple viral, bacterial and parasitic zoonoses. Trypanosomes are thought to be especially abundant and diverse in bats. In this study, we used 18S ribosomal RNA metabarcoding to probe bat trypanosome diversity in unprecedented detail.

METHODOLOGY/PRINCIPAL FINDINGS

Total DNA was extracted from the blood of 90 bat individuals (17 species) captured along Atlantic Forest fragments of Espírito Santo state, southeast Brazil. 18S ribosomal RNA was amplified by standard and/or nested PCR, then deep sequenced to recover and identify Operational Taxonomic Units (OTUs) for phylogenetic analysis. Blood samples from 34 bat individuals (13 species) tested positive for infection by 18S rRNA amplification. Amplicon sequences clustered to 14 OTUs, of which five were identified as Trypanosoma cruzi I, T. cruzi III/V, Trypanosoma cruzi marinkellei, Trypanosoma rangeli, and Trypanosoma dionisii, and seven were identified as novel genotypes monophyletic to basal T. cruzi clade types of the New World. Another OTU was identified as a trypanosome like those found in reptiles. Surprisingly, the remaining OTU was identified as Bodo saltans-closest non-parasitic relative of the trypanosomatid order. While three blood samples featured just one OTU (T. dionisii), all others resolved as mixed infections of up to eight OTUs.

CONCLUSIONS/SIGNIFICANCE

This study demonstrates the utility of next-generation barcoding methods to screen parasite diversity in mammalian reservoir hosts. We exposed high rates of local bat parasitism by multiple trypanosome species, some known to cause fatal human disease, others non-pathogenic, novel or yet little understood. Our results highlight bats as a long-standing nexus among host-parasite interactions of multiple niches, sustained in part by opportunistic and incidental infections of consequence to evolutionary theory as much as to public health.

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.

The Prevalence of Trypanosoma cruzi, the Causal Agent of Chagas Disease, in Texas Rodent Populations

Rodent species were assessed as potential hosts of Trypanosoma cruzi, the etiologic agent of Chagas disease, from five sites throughout Texas in sylvan and disturbed habitats. A total of 592 rodents were captured, resulting in a wide taxonomic representation of 11 genera and 15 species. Heart samples of 543 individuals were successfully analyzed by SybrGreen-based quantitative PCR (qPCR) targeting a 166 bp fragment of satellite DNA of T. cruzi. Eight rodents representing six species from six genera and two families were infected with T. cruzi. This is the first report of T. cruzi in the pygmy mouse (Baiomys taylori) and the white-footed mouse (Peromyscus leucopus) for the USA. All infected rodents were from the southernmost site (Las Palomas Wildlife Management Area). No differences in pathogen prevalence existed between disturbed habitats (5 of 131 tested; 3.8%) and sylvan habitats (3 of 40 tested; 7.5%). Most positives (n = 6, 16% prevalence) were detected in late winter with single positives in both spring (3% prevalence) and fall (1% prevalence). Additionally, 30 Triatoma insects were collected opportunistically from sites in central Texas. Fifty percent of these insects, i.e., 13 T. gerstaeckeri (68%), and two T. lecticularia (100%) were positive for T. cruzi. Comparative sequence analyses of 18S rRNA of samples provided identical results with respect to detection of the presence or absence of T. cruzi and assigned T. cruzi from rodents collected in late winter to lineage TcI. T. cruzi from Triatoma sp. and rodents from subsequent collections in spring and fall were different, however, and could not be assigned to other lineages with certainty.

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.

Trypanosome species, including Trypanosoma cruzi, in sylvatic and peridomestic bats of Texas, USA

In contrast to other mammalian reservoirs, many bat species migrate long-distances and have the potential to introduce exotic pathogens to new areas. Bats have long been associated with blood-borne protozoal trypanosomes of the Schizotrypanum subgenus, which includes the zoonotic parasite Trypanosoma cruzi, agent of Chagas disease. Another member of the subgenus, Trypanosoma dionisii, infects bats of Europe and South America, and genetic similarities between strains from the two continents suggest transcontinental movement of this parasite via bats. Despite the known presence of diverse trypanosomes in bats of Central and South America, and the presence of T. cruzi-infected vectors and wildlife in the US, the role of bats in maintaining and dispersing trypanosomes in the US has not yet been reported. We collected hearts and blood from 8 species of insectivorous bats from 30 counties across Texas. Using PCR and DNA sequencing, we tested 593 bats for trypanosomes and found 1 bat positive for T. cruzi (0.17%), 9 for T. dionisii (1.5%), and 5 for Blastocrithidia spp. (0.8%), a group of insect trypanosomes. The T. cruzi-infected bat was carrying TcI, the strain type associated with human disease in the US. In the T. dionisii-infected bats, we detected three unique variants associated with the three infected bat species. These findings represent the first report of T. cruzi in a bat in the US, of T. dionisii in North America, and of Blastocrithidia spp. in mammals, and underscore the importance of bats in the maintenance of trypanosomes, including agents of human and animal disease, across broad geographic locales.

Impact of Anthropogenic Disturbance on Native and Invasive Trypanosomes of Rodents in Forested Uganda

Habitat disturbance and anthropogenic change are globally associated with extinctions and invasive species introductions. Less understood is the impact of environmental change on the parasites harbored by endangered, extinct, and introduced species. To improve our understanding of the impacts of anthropogenic disturbance on such host-parasite interactions, we investigated an invasive trypanosome (Trypanosoma lewisi). We screened 348 individual small mammals, representing 26 species, from both forested and non-forested habitats in rural Uganda. Using microscopy and PCR, we identified 18% of individuals (order Rodentia) as positive for trypanosomes. Further phylogenetic analyses revealed two trypanosomes circulating-T. lewisi and T. varani. T. lewisi was found in seven species both native and invasive, while T. varani was identified in only three native forest species. The lack of T. varani in non-forested habitats suggests that it is a natural parasite of forest-dwelling rodents. Our findings suggest that anthropogenic disturbance may lead to spillover of an invasive parasite (T. lewisi) from non-native to native species, and lead to local co-extinction of a native parasite (T. varani) and native forest-dwelling hosts.

Diversity of bats trypanosomes in hydroeletric area of Belo Monte in Brazilian Amazonia

The Trypanosoma comprises flagellates able to infect many mammalian species and is transmitted by several groups of invertebrates. The order Chiroptera can be infected by the subgenera Herpetosoma, Schizotrypanum, Megatrypanum and Trypanozoon. In this study, we described the diversity of bats trypanosomes, inferring the phylogenetic relationships among the trypanosomes from bats caught Belo Monte Hydroeletric area (Brazilian Amazonia). Trypanosomes from bats were isolated by haemoculture, and the molecular phylogeny based on small subunit rDNA (SSU rDNA) and glycosomal-3-phosphate dehydrogenase (gGAPDH) gene sequences. Morphological characterization included light and scanning electron microscopy. A total of 157 bats were caught in the area belonging 6 Families (Emballonuridae, Furipteridae, Mormoopidae, Natalidae, Phyllostomidae and Vespertilionidae) and 34 species. The bat trypanosome prevalence, as evaluated through haemoculture, was 5,7%. Phylogenetic trees grouped the isolates in T. cruzi branch (TCI and TCbat lineage), T. cruzi marinkellei and Trypanosoma wauwau from Pteronotus parnellii. This is the first isolate from T. wauwau in Para state. The occurrence of T. cruzi in the ​​ Belo Monte Hydroeletric area (UHE Belo Monte) in Amazon/Brazil attentive to the risk of migration human population required for the works of the dam and new cities that grow in the vicinity of these businesses, but it is a zoonosis already known to the Amazon region, and the presence of unclassified Trypanosoma species, attend to the large parasitic biodiversity still unknown.

Chagas Disease Diagnostic Applications: Present Knowledge and Future Steps

Chagas disease, caused by the protozoan Trypanosoma cruzi, is a lifelong and debilitating illness of major significance throughout Latin America and an emergent threat to global public health. Being a neglected disease, the vast majority of Chagasic patients have limited access to proper diagnosis and treatment, and there is only a marginal investment into R&D for drug and vaccine development. In this context, identification of novel biomarkers able to transcend the current limits of diagnostic methods surfaces as a main priority in Chagas disease applied research. The expectation is that these novel biomarkers will provide reliable, reproducible and accurate results irrespective of the genetic background, infecting parasite strain, stage of disease, and clinical-associated features of Chagasic populations. In addition, they should be able to address other still unmet diagnostic needs, including early detection of congenital T. cruzi transmission, rapid assessment of treatment efficiency or failure, indication/prediction of disease progression and direct parasite typification in clinical samples. The lack of access of poor and neglected populations to essential diagnostics also stresses the necessity of developing new methods operational in point-of-care settings. In summary, emergent diagnostic tests integrating these novel and tailored tools should provide a significant impact on the effectiveness of current intervention schemes and on the clinical management of Chagasic patients. In this chapter, we discuss the present knowledge and possible future steps in Chagas disease diagnostic applications, as well as the opportunity provided by recent advances in high-throughput methods for biomarker discovery.

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.