High-throughput analysis of the Trypanosoma cruzi minicirculome (mcDNA) unveils structural variation and functional diversity.

Trypanosoma cruzi causes Chagas disease and has a unique extranuclear genome enclosed in a structure called the kinetoplast, which contains circular genomes known as maxi- and minicircles. While the structure and function of maxicircles are well-understood, many aspects of minicircles remain to be discovered. Here, we performed a high-throughput analysis of the minicirculome (mcDNA) in 50 clones isolated from Colombia's diverse T. cruzi I populations. Results indicate that mcDNA comprises four diverse subpopulations with different structures, lengths, and numbers of interspersed semi-conserved (previously termed ultra-conserved regions mHCV) and hypervariable (mHVPs) regions. Analysis of mcDNA ancestry and inter-clone differentiation indicates the interbreeding of minicircle sequence classes is placed along diverse strains and hosts. These results support evidence of the multiclonal dynamics and random bi-parental segregation. Finally, we disclosed the guide RNA repertoire encoded by mcDNA at a clonal scale, and several attributes of its abundance and function are discussed.

A Survey on Trypanosoma evansi (Kinetoplastida, Trypanosomatidae) Infection in Domestic Animals in a Surra Endemic Area of Southern Algeria.

Background: Trypanosoma (T.) evansi infection is endemic in dromedary camels (Camelus dromedaries) of southern Algeria. Materials and Methods: In order to assess the presence of T. evansi in other domestic animals living together with dromedary camels, a study was conducted in the wilayate of Béchar, El Bayadh, Ouargla and Tamanrasset, between 2015 and 2017. Authorisation to conduct the survey was obtained from the Direction des Services Vétérinaires (DSV, Ministry of Agriculture, Rural Development and Fisheries). A total of 190 animals were sampled, including 42 cattle (Bos taurus), 11 dogs (Canis familiaris), 44 horses (Equus caballus), 3 donkeys (Equus asinus) and 1 mule, 49 goats (Capra hircus) and 40 sheep (Ovis aries). These animals were examined by parasitological (Giemsa stained thin smear, GST), serological (card agglutination test for trypanosomosis (CATT/T. evansi), enzyme-linked immunosorbent assay/Variant Surface Glycoprotein/Rode Trypanozoon antigen type 1.2 [ELISA/VSG RoTat 1.2], immune trypanolysis [TL]) and molecular tests (T. evansi type A specific RoTat 1.2 PCR). Results and Conclusions: The CATT/T. evansi was positive in 10/42 cattle, 0/11 dogs, 2/48 equids, 27/49 goats and 15/40 sheep. On the other hand, 20/38 cattle, 1/9 dogs, 21/42 equids, 17/44 goats and 31/39 sheep were positive in ELISA/VSG RoTat 1.2. However, no single animal was positive in TL. In addition, the T. evansi parasite could not be demonstrated by either GST or RoTat 1.2 PCR in any of the examined animals. This may suggest cross-reactions of CATT/T. evansi and ELISA/VSG RoTat 1.2 with other pathogenic or commensal trypanosome species such as T. vivax or other parasites. Based on these data, in particular taking into account the high specificity of the TL for T. evansi type A, this study does not support the hypothesis that T. evansi circulates in the studied domestic animal species and that they would act as reservoirs for the parasite that causes trypanosomosis in dromedary camels.

Deep kinetoplast genome analyses result in a novel molecular assay for detecting Trypanosoma brucei gambiense-specific minicircles.

The World Health Organization targeted Trypanosoma brucei gambiense (Tbg) human African trypanosomiasis for elimination of transmission by 2030. Sensitive molecular markers that specifically detect Tbg type 1 (Tbg1) parasites will be important tools to assist in reaching this goal. We aim at improving molecular diagnosis of Tbg1 infections by targeting the abundant mitochondrial minicircles within the kinetoplast of these parasites. Using Next-Generation Sequencing of total cellular DNA extracts, we assembled and annotated the kinetoplast genome and investigated minicircle sequence diversity in 38 animal- and human-infective trypanosome strains. Computational analyses recognized a total of 241 Minicircle Sequence Classes as Tbg1-specific, of which three were shared by the 18 studied Tbg1 strains. We developed a minicircle-based assay that is applicable on animals and as specific as the TgsGP-based assay, the current golden standard for molecular detection of Tbg1. The median copy number of the targeted minicircle was equal to eight, suggesting our minicircle-based assay may be used for the sensitive detection of Tbg1 parasites. Annotation of the targeted minicircle sequence indicated that it encodes genes essential for the survival of the parasite and will thus likely be preserved in natural Tbg1 populations, the latter ensuring the reliability of our novel diagnostic assay.

rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects.

BACKGROUND: The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been generated and analyzed, information about the diversity, structure and evolution of their mitochondrial genomes remains fragmentary, mainly because of their extraordinary complexity. Indeed, unicellular flagellates of the order Kinetoplastida contain structurally the most complex mitochondrial genome of all eukaryotes, organized as a giant network of homogeneous maxicircles and heterogeneous minicircles. We recently developed KOMICS, an analysis toolkit that automates the assembly and circularization of the mitochondrial genomes of Kinetoplastid parasites. While this tool overcomes the limitation of extracting mitochondrial assemblies from Next-Generation Sequencing datasets, interpreting and visualizing the genetic (dis)similarity within and between samples remains a time-consuming process. RESULTS: Here, we present a new analysis toolkit-rKOMICS-to streamline the analyses of minicircle sequence diversity in population-scale genome projects. rKOMICS is a user-friendly R package that has simple installation requirements and that is applicable to all 27 trypanosomatid genera. Once minicircle sequence alignments are generated, rKOMICS allows to examine, summarize and visualize minicircle sequence diversity within and between samples through the analyses of minicircle sequence clusters. We showcase the functionalities of the (r)KOMICS tool suite using a whole-genome sequencing dataset from a recently published study on the history of diversification of the Leishmania braziliensis species complex in Peru. Analyses of population diversity and structure highlighted differences in minicircle sequence richness and composition between Leishmania subspecies, and between subpopulations within subspecies. CONCLUSION: The rKOMICS package establishes a critical framework to manipulate, explore and extract biologically relevant information from mitochondrial minicircle assemblies in tens to hundreds of samples simultaneously and efficiently. This should facilitate research that aims to develop new molecular markers for identifying species-specific minicircles, or to study the ancestry of parasites for complementary insights into their evolutionary history.

Trypanosoma brucei gambiense-iELISA: A Promising New Test for the Post-Elimination Monitoring of Human African Trypanosomiasis.

BACKGROUND: The World Health Organization targeted Trypanosoma brucei gambiense human African trypanosomiasis (gHAT) for elimination as a public health problem and for elimination of transmission. To measure gHAT elimination success with prevalences close to zero, highly specific diagnostics are necessary. Such a test exists in the form of an antibody-mediated complement lysis test, the trypanolysis test, but biosafety issues and technological requirements prevent its large-scale use. We developed an inhibition ELISA with high specificity and sensitivity that is applicable in regional laboratories in gHAT endemic countries. METHODS: The T. b. gambiense inhibition ELISA (g-iELISA) is based on the principle that binding of monoclonal antibodies to specific epitopes of T. b. gambiense surface glycoproteins can be inhibited by circulating antibodies of gHAT patients directed against the same epitopes. Using trypanolysis as reference test, the diagnostic accuracy of the g-iELISA was evaluated on plasma samples from 739 gHAT patients and 619 endemic controls and on dried blood spots prepared with plasma of 95 gHAT and 37 endemic controls. RESULTS: Overall sensitivity and specificity on plasma were, respectively, 98.0% (95% CI 96.7-98.9) and 99.5% (95% CI 98.6-99.9). With dried blood spots, sensitivity was 92.6% (95% CI 85.4-97.0), and specificity was 100% (95% CI 90.5-100.0). The g-iELISA is stable for at least 8 months when stored at 2-8°C. CONCLUSION: The g-iELISA might largely replace trypanolysis for monitoring gHAT elimination and for postelimination surveillance. The g-iELISA kit is available for evaluation in reference laboratories in endemic countries.

Assessment of Trypanosoma evansi prevalence and associated risk factors by immune trypanolysis test in camels from Ghardaïa district, southern Algeria.

Trypanosoma evansi (T. evansi) is a flagellated parasite with worldwide distribution, mainly affecting camels, horses, dogs, buffaloes and wild animals. Trypanosomosis caused by T. evansi, known as surra, is a vector borne disease that affects the health and productivity of camels. The aim of our study was to assess the prevalence of trypanosomosis due to T. evansi in camels by the immune trypanolosis test and to identify associated risk factors. Our cross-sectional study was performed on 161 camels from Ghardaïa district, southern Algeria. A structured questionnaire was used to collect data on individual characteristics (age, gender and breed) husbandry management (herd size and activity of animals) and health conditions (history of abortion and clinical symptoms). The immune trypanolysis test revealed an overall seroprevalence of 9.3% (CI 95%, 5.9-14.9). Possible factors associated with T. evansi infection were analysed by univariate and multivariate logistic regression. The results showed that risk factors for camels were history of symptoms (P = 0.002, OR = 21.91, CI95% = 3.48-169.80), racing activities (P = 0.003, OR = 0.01, CI95% = 0.001-0.18) and small herd size (P = 0.013, OR = 8.22, CI95% = 1.64-49.75). In conclusion, this study showed that T. evansi is endemic in camels of Ghardaïa district. To reduce dissemination of the disease to non-endemic areas, it is recommended to minimise risk factors associated with the infection.

Comparison of serological and molecular tests for detection of Trypanosoma evansi in domestic animals from Ghardaïa district, South Algeria.

Trypanosoma evansi (T. evansi) is a hemoflagellate parasite that affects a broad range of mammalian hosts and that causes a disease called surra. Diagnosis of surra based on clinical symptoms alone is inaccurate. Therefore, a variety of serological and molecular diagnostic tests are used to assist in the detection of T. evansi infections. The aim of this study was to compare the diagnostic performance of four serological tests (CATT/T.evansi, immune trypanolysis, ELISA with purified variant surface glycoprotein RoTat 1.2 and with whole cell lysate) and two molecular PCR tests targeting sequences within the ribosomal genes locus (ITS1 TD PCR and 18S qPCR). Tests were carried out on blood samples from 161 dromedary camels, 93 horses, 129 goats, 168 sheep, 127 bovines and 76 dogs. Latent class analysis was carried out to calculate the sensitivity and specificity of each diagnostic test. Cohen's Kappa test was used to assess the concordance between the different diagnostic tests. Overall positivity rates observed with the serological tests were as follows: 3.1 % with CATT/T.evansi, 4.9 % with ELISA/RoTat 1.2, 3.4 % with ELISA/whole lysate and 2.0 % with immune trypanolysis (TL). Among the 754 samples tested with the molecular tests, 1.7 % were positive with 18S qPCR and 1.3 % with ITS1 TD PCR. Cohen's Kappa test showed agreement ranging from fair to substantial (k = 0.2-0.8) between serological diagnostic tests. However, it showed a perfect agreement (k = 0.868) between molecular diagnostic tests. Latent class analysis showed that all serological tests were 100 % sensitive, in contrast to the molecular tests with 47 % sensitivity. All tests, though, were highly specific (≥ 97 %). Given the persistence of circulating antibodies after cure, detectable by serological tests, it is recommend combining a serological and a molecular diagnostic test for accurate diagnosis of infection with T. evansi in domestic animals.

A more sensitive, efficient and ISO 17025 validated Magnetic Capture real time PCR method for the detection of archetypal Toxoplasma gondii strains in meat.

Toxoplasma gondii is a globally prevalent, zoonotic parasite of major importance to public health. Various indirect and direct methods can be used for the diagnosis of toxoplasmosis. Whereas serological tests are useful to prove contact with the parasite has occurred, the actual presence of the parasite in the tissues of a seropositive animal is not demonstrated. For this, a bioassay is still the reference method. As an alternative, various PCR methods have been developed, but due to the limited amount of sample that can be tested, combined with a low tissue cyst density, those have proved to be insufficiently sensitive. A major improvement of the sensitivity was achieved with magnetic capture-based DNA extraction. By combining the hybridization of specific, biotinylated probes with the capture of those probes with streptavidin-coated paramagnetic beads, T. gondii DNA can selectively be "fished out" from a large volume of meat lysate. Still, several studies showed an insufficient sensitivity compared with the mouse bioassay. Here we present a method that is more sensitive (99% limit of detection: 65.4 tachyzoites per 100g of meat), economical and reliable (ISO 17025 validated) by adding a non-competitive PCR inhibition control (co-capture of cellular r18S) and making the release of the target DNA from the streptavidin-coated paramagnetic beads UV-dependent. The presented results demonstrate the potential of the modified Magnetic Capture real time PCR as a full alternative to the mouse bioassay for the screening of various types of tissues and meat, with the additional advantage of being quantitative.