Fluorescent Fragment Length Barcoding Research Articles

Trypanosoma cruzi and Trypanosoma rangeli in Acre, Brazilian Amazonia: Coinfection and Notable Genetic Diversity in an Outbreak of Orally Acquired Acute Chagas Disease in a Forest Community, Wild Reservoirs, and Vectors

Acute Chagas disease (ACD) caused by Trypanosoma cruzi has emerged as a major food-borne disease in Brazilian Amazonia. For the first time, we characterized an outbreak of orally acquired ACD in Acre, in the forest community of Seringal Miraflores, affecting 13 individuals who shared the pulp of açai palm berries: 11 adults and two children (one newborn), all diagnosed by thick-drop blood smears. The fluorescent fragment length barcoding method, which simultaneously identifies species/genotypes of trypanosomes in blood samples, uncovered an unprecedented genetic diversity in patients from a single outbreak of ACD: T. cruzi TcI in all patients, mostly concomitantly with the non-pathogenic Trypanosoma rangeli of genotypes TrA or TrB, and TcI, TcIV, and TrB in the child. The patients presented persistent fever, asthenia, myalgia, edema of the face and lower limbs, hepatosplenomegaly and, rarely, cardiac arrhythmia. The clinical symptoms were not correlated to gender, age, or to trypanosome species and genotypes. The inferred SSU rRNA phylogenetic analyses of trypanosomes from humans, triatomines and sylvatic hosts included the first sequences of T. cruzi and T. rangeli from humans in southwestern (Acre and Rondônia) Amazonia, and the first TcI/TcIV sequences from Rhodnius spp. from Acre. The sylvatic transmission cycles of genetically different trypanosomes in landscapes changed by deforestation for human settlements and increasing açai production is a novel scenario favoring trypanosome transmission to humans in Acre.

Genetic diversity of Trypanosoma cruzi strains isolated from chronic chagasic patients and non-human hosts in the state of São Paulo, Brazil.

Trypanosoma cruzi shows an exuberant genetic diversity. Currently, seven phylogenetic lineages, called discrete typing units (DTUs), are recognised: TcI-TcVI and Tcbat. Despite advances in studies on T. cruzi and its populations, there is no consensus regarding its heterogeneity. This study aimed to perform molecular characterisation of T. cruzi strains, isolated in the state of São Paulo, to identify the DTUs involved and evaluate their genetic diversity. T. cruzi strains were isolated from biological samples of chronic chagasic patients, marsupials and triatomines through culture techniques and subjected to molecular characterisation using the fluorescent fragment length barcoding (FFLB) technique. Subsequently, the results were correlated with complementary information to enable better discrimination between the identified DTUs. It was possible to identify TcI in two humans and two triatomines; TcII/VI in 19 humans, two marsupials and one triatomine; and TcIII in one human host, an individual that also presented a result for TcI, which indicated the possibility of a mixed infection. Regarding the strains characterised by the TcII/VI profile, the correlation with complementary information allowed to suggest that, in general, these parasite populations indeed correspond to the TcII genotype. The TcII/VI profile, associated with domestic cycles and patients with chronic Chagas disease, was the most prevalent among the identified DTUs. Furthermore, the correlation of the study results with complementary information made it possible to suggest that TcII is the predominant lineage of this work.

Genotypic Trypanosoma cruzi distribution and parasite load differ ecotypically and according to parasite genotypes in Triatoma brasiliensis from endemic and outbreak areas in Northeastern Brazil

This study aimed to identify the Trypanosoma cruzi genotypes and their relationship with parasitic load in distinct geographic and ecotypic populations of Triatoma brasiliensis in two sites, including one where a Chagas disease (ChD) outbreak occurred in Rio Grande do Norte state, Brazil. Triatomine captures were performed in peridomestic and sylvatic ecotopes in two municipalities: Marcelino Vieira – affected by the outbreak; and Currais Novos – where high pressure of peridomestic triatomine infestation after insecticide spraying have been reported. The kDNA-PCR was used to select 124 T. cruzi positive triatomine samples, of which 117 were successfully genotyped by fluorescent fragment length barcoding (FFLB). Moreover, the T. cruzi load quantification was performed using a multiplex TaqMan qPCR. Our findings showed a clear ecotypic segregation between TcI and TcII harboured by T. brasiliensis (p<0.001). Although no genotypes were ecotypically exclusive, TcI was predominant in peridomestic ecotopes (86%). In general, T. brasiliensis from Rio Grande do Norte had a higher T. cruzi load varying from 3.94 to 7.66 x 106T. cruzi per insect. Additionally, TcII (median value=299,504 T. cruzi/intestine unit equivalents) had more than twice (p=0.1) the parasite load of TcI (median value=149,077 T. cruzi/intestine unit equivalents), which can be attributed to a more ancient co-evolution with T. brasiliensis. The higher prevalence of TcII in the sylvatic T. brasiliensis (70%) could be associated with a more diversified source of bloodmeals for wild insect populations. Either TcI or TcII may have been responsible for the ChD outbreak that occurred in the city of Marcelino Vieira. On the other hand, a smaller portion of T. brasiliensis was infected by TcIII (3%) in the peridomicile, in addition to T. rangeli genotype A (1%), often found in mixed infections. Our results highlight the need of understanding the patterns of T. cruzi genotype´s development and circulation in insect vectors and reservoirs as a mode of tracking situations of epidemiologic importance, as the ChD outbreak recently recorded for Northeastern Brazil.

Molecular epidemiological insights into Trypanosoma vivax in Argentina: From the endemic Gran Chaco to outbreaks in the Pampas.

Argentina is a home to millions of beef and dairy cattle and is one of the world's major exporters of meat. In the present study, Trypanosoma vivax was prevalent (2016-2018) in two major livestock farming regions, the Gran Chaco and the Pampas. In the Gran Chaco, 29% and 51% of animals (n=72, taurine x zebuine crossbreed) were, respectively, positive by TviCATL-PCR and the more sensitive fluorescent fragment length barcoding (FFLB) method. While 18.4/38.8% of breeding cows (n=49) tested positive by PCR/FFLB, infection increased to 52.2/78.3% in an outbreak of acute infection in steers (n=23, taurine breed) brought from a non-endemic area. In the Pampas, overall infection rates in dairy cows (n=54, taurine breed) were comparable (p>.01) between PCR (66.7%) and FFLB (62.9%) and showed a remarkable increase (PCR / FFLB) from 48.3/44.8% in 2017 to 88/84% in 2018. Infected dairy cattle exhibited anaemia, fever, anorexia, enlarged lymph nodes, emaciation and neurological signs. In contrast, beef cows (taurine x zebuine crossbreed) from the Pampas (n=30) were asymptomatic despite exhibiting 16.7% (PCR) and 53.3% (FFLB) infection rates. Microsatellite genotyping revealed a remarkable microheterogeneity, seven genotypes in the Gran Chaco, nine in the Pampas and five shared between both regions, consistent with regular movement of T. vivax infected livestock. Data gathered in our study support the Gran Chaco being an endemic area for T. vivax, whereas the Pampas emerged as an outbreak area of acute infection in dairy cattle with critical negative impact in milk production. To the best of our knowledge, this is the first molecular study of T. vivax in Argentina, and results indicated the need for preventive measures to control T. vivax spread from the Gran Chaco to vast livestock farming areas across Argentina.

High Trypanosoma vivax infection rates in water buffalo and cattle in the Brazilian Lower Amazon.

Highly sensitive and accurate molecular diagnostic methods have not yet been employed for livestock trypanosomosis in the Brazilian Lower Amazon although the first reports of Trypanosoma vivax and Trypanosoma evansi in Brazil were in water buffalo (Bubalus bubalis) in this region. The present study assessed trypanosomosis in buffalo and cattle raised in communal and seasonally flooding pastures in the state of Pará using the fluorescent fragment length barcoding (FFLB) method. T. evansi was not detected, but high infection rates of T. vivax and T. theileri were revealed by a simplified FFLB standardized in the present study that discriminates all trypanosome species infective to livestock in South America. T. vivax infection rates detected by TviCATL-PCR were 24.6% for cattle (n = 61) and 28.1% for buffalo (n = 89). Using the FFLB method, overall T. vivax infection rates increased to 59.6% and 44.3% for buffalo and cattle, respectively. Furthermore, the predominance of a single microsatellite-based genotype of T. vivax was reinforced in the Lower Amazon. Relevant T. vivax infection rates detected in clinically healthy buffalo and cattle through the sampled years (2008-2017) highlight the need for systematic studies to demonstrate the endemic steady state of T. vivax in this region. Our findings provide baseline information for livestock management, including control of T. vivax dispersal, and the introduction of naïve animals. The growing international trade of live livestock from this very important livestock breeding region represents a serious risk for T. vivax spreading outside Amazonia and Brazil.

Expanding our knowledge on African trypanosomes of the subgenus Pycnomonas: A novel Trypanosoma suis-like in tsetse flies, livestock and wild ruminants sympatric with Trypanosoma suis in Mozambique

Among the subgenera of African tsetse-transmitted trypanosomes pathogenic to livestock, the least known is the subgenus Pycnomonas, which contains a single species, Trypanosoma suis (TSU), a pathogen of domestic pigs first reported in 1905 and recently rediscovered in Tanzania and Mozambique. Analysis by Fluorescent Fragment Length Barcoding (FFLB) revealed an infection rate of 20.3% (108 out of 530 tsetse flies) in a recent study in the Gorongosa and Niassa wildlife reserves in Mozambique, and demonstrated two groups of Pycnomonas trypanosomes: one (14.1%, 75 flies) showing an FFLB profile identical to the reference TSU from Tanzania, and the other (6.2%, 33 flies) differing slightly from reference TSU and designated Trypanosoma suis-like (TSU-L). Phylogenetic analyses tightly clustered TSU and TSU-L from Mozambique with TSU from Tanzania forming the clade Pycnomonas positioned between the subgenera Trypanozoon and Nannomonas. Our preliminarily exploration of host ranges of Pycnomonas trypanosomes revealed TSU exclusively in warthogs while TSU-L was identified, for the first time for a member of the subgenus Pycnomonas, in ruminants (antelopes, Cape buffalo, and in domestic cattle and goats). The preferential blood meal sources of tsetse flies harbouring TSU and TSU-L were wild suids, and most of these flies concomitantly harboured the porcine trypanosomes T. simiae, T. simiae Tsavo, and T. godfreyi. Therefore, our findings support the link of TSU with suids while TSU-L remains to be comprehensively investigated in these hosts. Our results greatly expand our knowledge of the diversity, hosts, vectors, and epidemiology of Pycnomonas trypanosomes. Due to shortcomings of available molecular diagnostic methods, a relevant cohort of trypanosomes transmitted by tsetse flies to ungulates, especially suids, has been neglected or most likely misidentified. The method employed in the present study enables an accurate discrimination of trypanosome species and genotypes and, hence, a re-evaluation of the “lost” subgenus Pycnomonas and of porcine trypanosomes in general, the most neglected group of African trypanosomes pathogenic to ungulates.

Molecular eco-epidemiology on the sympatric Chagas disease vectors Triatoma brasiliensis and Triatoma petrocchiae: Ecotopes, genetic variation, natural infection prevalence by trypanosomatids and parasite genotyping

Triatoma petrocchiae is the newly member of the Triatoma brasiliensis species complex. This species overlaps with T. brasiliensis in geographic and ecotypic occupation in the sylvatic habitat because both inhabit rocky outcrops in the semi-arid portion of Brazilian northeast. In this region T. brasiliensis is the most important Chagas disease vector because it constantly colonizes domiciles. In contrast, T. petrocchiae is rarely found in peri or intradomiciliary habitats – reason why little is known about this species. Therefore, Here, we present information for the first time on. the T. petrocchiae ecotopes, genetic diversity, Trypanosoma cruzi prevalence/genotyping in comparison to T. brasiliensis. We found T. brasilensis (N = 223) and T. petrocchiae (N = 69) in co-habitation in rocky outcrops in three Districts of Paraíba and Rio Grande do Norte states. Forty-tree T. petrocchiae insects of eleven sampling spots (composing three geographic populations) were genotyped for the mitochondrial Cyt B gene and little geographic structure was observed. Tajima's D test suggested that species is evolving toward a mutation-drift equilibrium in our collection range. Sylvatic T. petrocchiae had 4% (3/68) of infected insects by T. cruzi, whereas T. brasiliensis had 26% (59/223). Fluorescent Fragment Length Barcoding demonstrated that all three T. petrocchiae harbored TcI whereas T. brasiliensis had TcI, but also TcIII, TcII/TcVI and T. rangeli genotype A, sometimes under mixed infections. None of infected T. petrocchiae were carrying mixed infections. However, this result should be confirmed using a larger pool of infected bugs. We here presented the first documentation of T. rangeli infecting T. brasiliensis. The finding of infected T. petrocchiae calls for constant vector monitoring because the epidemiologic scenario is dynamic and sylvatic vectors are progressively found in adaptation to anthropic environments.

Zoonotic Trypanosomes in Rats and Fleas of Venezuelan Slums.

Rattus spp. are reservoirs of many human zoonoses, but their role in domestic transmission cycles of human trypanosomiasis is underestimated. In this study, we report trypanosome-infected Rattus norvegicus and Rattus rattus in human dwellings in slums neighboring Maracay, a large city near Caracas, the capital of Venezuela. Blood samples of R. norvegicus and R. rattus examined by PCR and FFLB (fluorescent fragment length barcoding) revealed a prevalence of 6.3% / 31.1% for Trypanosoma lewisi (agent of rat- and flea-borne human emergent zoonosis), and 10.5% / 24.6% for Trypanosoma cruzi (agent of Chagas disease). Detection in flea guts of T. lewisi (76%) and, unexpectedly, T. cruzi (21.3%) highlighted the role of fleas as carriers and vectors of these trypanosomes. A high prevalence of rats infected with T. lewisi and T. cruzi and respective flea and triatomine vectors poses a serious risk of human trypanosomiasis in Venezuelan slums. Anthropogenic activities responsible for growing rat and triatomine populations within human dwellings drastically increased human exposure to trypanosomes. This scenario has allowed for the reemergence of Chagas disease as an urban zoonosis in Venezuela and can propitiate the emergence of atypical T. lewisi infection in humans.

Genetic diversity of trypanosomes pathogenic to livestock in tsetse flies from the Nech Sar National Park in Ethiopia: A concern for tsetse suppressed area in Southern Rift Valley?

In Ethiopia, home to the largest African herd of cattle, animal trypanosomiasis is a major constraint to the efforts made for food self-sufficiency. We searched for trypanosomes in tsetse flies caught in the Nech Sar National Park (NSNP), Southern Rifty Valley, Ethiopia, at the district of Arba Minch where intensive tsetse control is successfully improving cattle productivity. Despite narrow geographical and temporal scales of our survey, we found a remarkable diversity of trypanosomes using the sensitive and discriminative method of fluorescent fragment length barcoding. We also found a high density of Glossina pallidipes (47.8 flies/trap/day) showing relevant cytochrome oxidase I gene variability. The identification of blood meal sources through cytochrome b gene sequences revealed cattle and warthog as preferential ungulate hosts of tsetse flies in the study area. Our survey identified trypanosomes in 38% of the 287 flies examined (42% of proboscises and 32% of guts), and the following infection rates for each species: Trypanosoma vivax 23%, T. simiae 23%, T. congolense 22%, T. theileri 19.9%, T. (Trypanozoon) spp. 10.5%, T. godfreyi 9.4%, T. simiae Tsavo 6.3%, and mixed infections in proboscises (30%) and guts (61%). Phylogenetic analysis revealed T. vivax of the “West African-South American” genotype, T. congolense of Savannah (16.7%), Kilifi (3.5%) and Forest (2.1%) lineages, and new genotypes of T. simiae. To our knowledge, this is the first survey of trypanosomes in the NSNP, and the most comprehensive molecular characterisation of trypanosomes in tsetse flies of Ethiopia, including the comparison with samples from West and other East African countries. Our results support the diversification of T. vivax in East Africa, and the dispersion of the genotype herein identified in Ethiopia across West Africa and then in South America. Altogether, tsetse density and infection rate, repertoire of trypanosomes and feeding behavior indicate a high risk of transmission of trypanosomes pathogenic to ungulates by tsetse flies from the NSNP, a hotspot of tsetse infestation and trypanosome diversity. Our findings reinforce the need for constant surveillance, and the reliance on community efforts to prevent reinvasion of tsetse and animal trypanosomiasis in suppressed areas of Southern Rift Valley.

Remarkable richness of trypanosomes in tsetse flies (Glossina morsitans morsitans and Glossina pallidipes) from the Gorongosa National Park and Niassa National Reserve of Mozambique revealed by fluorescent fragment length barcoding (FFLB)

Trypanosomes of African wild ungulates transmitted by tsetse flies can cause human and livestock diseases. However, trypanosome diversity in wild tsetse flies remains greatly underestimated. We employed FFLB (fluorescent fragment length barcoding) for surveys of trypanosomes in tsetse flies (3086) from the Gorongosa National Park (GNP) and Niassa National Reserve (NNR) in Mozambique (MZ), identified as Glossina morsitans morsitans (GNP/NNR=77.6%/90.5%) and Glossina pallidipes (22.4%/9.5%). Trypanosomes were microscopically detected in 8.3% of tsetse guts. FFLB of gut samples revealed (GNP/NNR): Trypanosoma congolense of Savannah (27%/63%), Kilifi (16.7%/29.7%) and Forest (1.0%/0.3%) genetic groups; T. simiae Tsavo (36.5%/6.1%); T. simiae (22.2%/17.7%); T. godfreyi (18.2%/7.0%); subgenus Trypanozoon (20.2%/25.7%); T. vivax/T. vivax-like (1.5%/5.2%); T. suis/T. suis-like (9.4%/11.9%). Tsetse proboscises exhibited similar species composition, but most prevalent species were (GNP/NNR): T. simiae (21.9%/28%), T. b. brucei (19.2%/31.7%), and T. vivax/T. vivax-like (19.2%/28.6%). Flies harboring mixtures of trypanosomes were common (~ 64%), and combinations of more than four trypanosomes were especially abundant in the pristine NNR. The non-pathogenic T. theileri was found in 2.5% while FFLB profiles of unknown species were detected in 19% of flies examined. This is the first report on molecular diversity of tsetse flies and their trypanosomes in MZ; all trypanosomes pathogenic for ungulates were detected, but no human pathogens were detected. Overall, two species of tsetse flies harbor 12 species/genotypes of trypanosomes. This notable species richness was likely uncovered because flies were captured in wildlife reserves and surveyed using the method of FFLB able to identify, with high sensitivity and accuracy, known and novel trypanosomes. Our findings importantly improve the knowledge on trypanosome diversity in tsetse flies, revealed the greatest species richness so far reported in tsetse fly of any African country, and indicate the existence of a hidden trypanosome diversity to be discovered in African wildlife protected areas.

Trypanosoma livingstonei: a new species from African bats supports the bat seeding hypothesis for the Trypanosoma cruzi clade

BackgroundBat trypanosomes have been implicated in the evolutionary history of the T. cruzi clade, which comprises species from a wide geographic and host range in South America, Africa and Europe, including bat-restricted species and the generalist agents of human American trypanosomosis T. cruzi and T. rangeli.MethodsTrypanosomes from bats (Rhinolophus landeri and Hipposideros caffer) captured in Mozambique, southeast Africa, were isolated by hemoculture. Barcoding was carried out through the V7V8 region of Small Subunit (SSU) rRNA and Fluorescent Fragment Length barcoding (FFLB). Phylogenetic inferences were based on SSU rRNA, glyceraldehyde phosphate dehydrogenase (gGAPDH) and Spliced Leader (SL) genes. Morphological characterization included light, scanning and transmission electron microscopy.ResultsNew trypanosomes from bats clustered together forming a clade basal to a larger assemblage called the T. cruzi clade. Barcoding, phylogenetic analyses and genetic distances based on SSU rRNA and gGAPDH supported these trypanosomes as a new species, which we named Trypanosoma livingstonei n. sp. The large and highly polymorphic SL gene repeats of this species showed a copy of the 5S ribosomal RNA into the intergenic region. Unique morphological (large and broad blood trypomastigotes compatible to species of the subgenus Megatrypanum and cultures showing highly pleomorphic epimastigotes and long and slender trypomastigotes) and ultrastructural (cytostome and reservosomes) features and growth behaviour (when co-cultivated with HeLa cells at 37°C differentiated into trypomastigotes resembling the blood forms and do not invaded the cells) complemented the description of this species.ConclusionPhylogenetic inferences supported the hypothesis that Trypanosoma livingstonei n. sp. diverged from a common ancestral bat trypanosome that evolved exclusively in Chiroptera or switched at independent opportunities to mammals of several orders forming the clade T. cruzi, hence, providing further support for the bat seeding hypothesis to explain the origin of T. cruzi and T. rangeli.

Trypanosoma evansi kDNA minicircle found in the Venezuelan nectar-feeding bat Leptonycteris curasoae (Glossophaginae), supports the hypothesis of multiple origins of that parasite in South America

Trypanosoma evansi is a mammal generalist protozoon which causes negative effects on health and productivity in bovine and equine herds in South America, Europe, Asia and Africa. By molecular methods, we screened the presence of that parasite together with other trypanosome species in 105 bats of 10 species collected in arid zones of northern Venezuela. The first molecular approach was fluorescent fragment length barcoding (FFLB), which relies on amplification of relative small regions of rRNA genes (four loci) and fluorescence detection. By FFLB, 17 samples showed patterns of possible trypanosomatid infections. These samples were used to test presence of trypanosomes by PCR using the following DNA markers: V7–V8 SSU rRNA, gGAPDH and kDNA minicircle regions. Only in one individual of the nectar-feeding bat, Leptonycteris curasoae, we were able to amplify 1000bp of the trypanosome kDNA minicircle. That PCR product was sequenced and the parasite species was determined by NCBI-BLAST and phylogenetic analysis. Both analyses showed that the minicircle sequence corresponds to Trypanosoma evansi. The phylogenetic analysis of the sequence obtained in this study clustered with a T. evansi sequence obtained in a Venezuelan capybara, Hydrochoerus hydrochaeris, and distant of others two T. evansi sequences obtained in a Colombian capybara and horse. This result supports the hypothesis of multiple origins of T. evansi in South America.

Identification and lineage genotyping of South American trypanosomes using fluorescent fragment length barcoding

Trypanosoma cruzi and Trypanosoma rangeli are human-infective blood parasites, largely restricted to Central and South America. They also infect a wide range of wild and domestic mammals and are transmitted by a numerous species of triatomine bugs. There are significant overlaps in the host and geographical ranges of both species. The two species consist of a number of distinct phylogenetic lineages. A range of PCR-based techniques have been developed to differentiate between these species and to assign their isolates into lineages. However, the existence of at least six and five lineages within T. cruzi and T. rangeli, respectively, makes identification of the full range of isolates difficult and time consuming. Here we have applied fluorescent fragment length barcoding (FFLB) to the problem of identifying and genotyping T. cruzi, T. rangeli and other South American trypanosomes. This technique discriminates species on the basis of length polymorphism of regions of the rDNA locus. FFLB was able to differentiate many trypanosome species known from South American mammals: T. cruzi cruzi, T. cruzi marinkellei, T. dionisii-like, T. evansi, T. lewisi, T. rangeli, T. theileri and T. vivax. Furthermore, all five T. rangeli lineages and many T. cruzi lineages could be identified, except the hybrid lineages TcV and TcVI that could not be distinguished from lineages III and II respectively. This method also allowed identification of mixed infections of T. cruzi and T. rangeli lineages in naturally infected triatomine bugs. The ability of FFLB to genotype multiple lineages of T. cruzi and T. rangeli together with other trypanosome species, using the same primer sets is an advantage over other currently available techniques. Overall, these results demonstrate that FFLB is a useful method for species diagnosis, genotyping and understanding the epidemiology of American trypanosomes.

NewTrypanosoma (Duttonella) vivaxgenotypes from tsetse flies in East Africa

Salivarian trypanosomes pose a substantial threat to livestock, but their full diversity is not known. To survey trypanosomes carried by tsetse in Tanzania, DNA samples from infected proboscides of Glossina pallidipes and G. swynnertoni were identified using fluorescent fragment length barcoding (FFLB), which discriminates species by size polymorphisms in multiple regions of the ribosomal RNA locus. FFLB identified the trypanosomes in 65 of 105 (61.9%) infected proboscides, revealing 9 mixed infections. Of 7 different FFLB profiles, 2 were similar but not identical to reference West African Trypanosoma vivax; 5 other profiles belonged to known species also identified in fly midguts. Phylogenetic analysis of the glycosomal glyceraldehyde phosphate dehydrogenase gene revealed that the Tanzanian T. vivax samples fell into 2 distinct groups, both outside the main clade of African and South American T. vivax. These new T. vivax genotypes were common and widespread in tsetse in Tanzania. The T. brucei-like trypanosome previously described from tsetse midguts was also found in 2 proboscides, demonstrating a salivarian transmission route. Investigation of mammalian host range and pathogenicity will reveal the importance of these new trypanosomes for the epidemiology and control of animal trypanosomiasis in East Africa.

Phylogenetic analysis reveals the presence of the Trypanosoma cruzi clade in African terrestrial mammals

Despite the impact of some trypanosome species on human and livestock health, the full diversity of trypanosomes in Africa is poorly understood. A recent study examined the prevalence of trypanosomes among a wide variety of wild vertebrates in Cameroon using species-specific PCR tests, but six trypanosome isolates remained unidentified. Here they have been re-examined using fluorescent fragment length barcoding (FFLB) and phylogenetic analysis of glycosomal glyceraldehyde phosphate dehydrogenase gGAPDH and 18S ribosomal RNA (rDNA) genes. Isolates from a monkey ( Cercopithecus nictitans) and a palm civet ( Nandinia binotata) belonged to the Trypanosoma cruzi clade, known previously only from New World and Australian terrestrial mammals, and bats from Africa, Europe and South America. Of the four other isolates, three from antelope were identified as Trypanosoma theileri, and one from a crocodile as T. grayi. This is the first report of trypanosomes of the T. cruzi clade in African terrestrial mammals and expands the clade's known global distribution in terrestrial mammals. Previously it has been hypothesized that African and New World trypanosomes diverged after continental separation, dating the divergence to around 100 million years ago. The new evidence instead suggests that intercontinental transfer occurred well after this, possibly via bats or rodents, allowing these trypanosomes to establish and evolve in African terrestrial mammals, and questioning the validity of calibrating trypanosome molecular trees using continental separation.

New Molecular Tools for the Identification of Trypanosome Species

Trypanosomes are the causative agents of many diseases of medical and veterinary importance, including sleeping sickness and nagana in Africa, and Chagas disease in South America. Accurate identification of trypanosome species is essential, as some species are morphologically indistinguishable, yet differ greatly in their pathogenicity. A range of molecular tools has been developed for identification of species and strains of trypanosomes. PCR, using primer sets designed to amplify a specific DNA fragment from each trypanosome species, is frequently used. More recently, generic systems have been developed that can potentially recognize all trypanosome species, such as amplification of the internal transcribed spacer and fluorescent fragment length barcoding, both of which use interspecies size variation in PCR fragments amplified from the ribosomal RNA locus. Loop-mediated isothermal amplification is a promising technique and is able to detect trypanosomes in blood, serum and cerebrospinal fluid. The advantages of these techniques for high-throughput and sensitive molecular identification will be discussed.

A novel, high-throughput technique for species identification reveals a new species of tsetse-transmitted trypanosome related to the Trypanosoma brucei subgenus, Trypanozoon

We describe a novel method of species identification, fluorescent fragment length barcoding, based on length variation in regions of the 18S and 28Sα ribosomal DNA. Fluorescently tagged primers, designed in conserved regions of the 18S and 28Sα ribosomal DNA, were used to amplify fragments with inter-species size variation, and sizes determined accurately using an automated DNA sequencer. By using multiple regions and different fluorochromes, a barcode unique to each species was generated. The technique was developed for the identification of African tsetse-transmitted trypanosomes and validated using DNA from laboratory isolates representing known species, subspecies and subgroups. To test the methodology, we examined 91 trypanosome samples from infected tsetse fly midguts from Tanzania, most of which had already been identified by species-specific and generic PCR tests. Identifications were mainly in agreement, but the presence of an unknown trypanosome in several samples was revealed by its unique barcode. Phylogenetic analyses based on 18S rDNA and glycosomal glyceraldehyde phosphate dehydrogenase gene sequences confirmed that this trypanosome is a new species and it is within the Trypanosoma brucei clade, as a sister group of subgenus Trypanozoon. The overall identification rate of trypanosome-infected midgut samples increased from 78 to 96% using FFLB instead of currently available PCR tests. This was due to the high sensitivity of FFLB as well as its capacity to identify previously unrecognised species. FFLB also allowed the identification of multiple species in mixed infections. The method enabled high-throughput and accurate species identification and should be applicable to any group of organisms where there is length variation in regions of rDNA.

The identification, diversity and prevalence of trypanosomes in field caught tsetse in Tanzania using ITS-1 primers and fluorescent fragment length barcoding

We report on the development of two generic, PCR-based methods, which replace the multiple species-specific PCR tests used previously to identify the trypanosome species carried by individual tsetse flies. The first method is based on interspecies size variation in the PCR product of the ITS-1 region of the ribosomal RNA (rRNA) locus. In the second approach, length variation of multiple fragments within the 18S and 28S rRNA genes is assayed by PCR amplification with fluorescent primers; products are subsequently sized accurately and rapidly by the use of an automated DNA sequencer. Both methods were used to identify samples collected during large-scale field studies of trypanosome-infected tsetse in Tanzania in the National Parks of Tarangire and Serengeti, and the coastal forest reserve of Msubugwe. The fluctuations of trypanosome prevalence over time and two different field seasons are discussed. As well as facilitating the identification of trypanosome species with increased speed, precision and sensitivity, these generic systems have enabled us to identify two new species of trypanosome.