Unravelling the phylogenetic relationships of African trypanosomes of suids

Trypanosomiasis in Introduced Southern White Rhinoceros (Ceratotherium simum simum) Gifts to Ex Situ Habitat in Aitong, Kenya

During the opening of diplomatic relations in the 1990s, South Africa gifted 20 southern white rhinoceros (Ceratotherium simum simum) to Kenya. The species is not indigenous to Kenya, and management of the introduction was not clearly addressed in the legislation. Responsibility was left to the private sector and local authorities. Ten of the animals were introduced to land contiguous with the Maasai Mara National Reserve, an area with tsetse-trypanosomiasis challenges, and with rare cases of human sleeping sickness. Mortalities had been previously documented when indigenous naïve black rhinoceros were introduced to areas with tsetse; hence there was no consensus on the management of this introduction. Feasibility was only explored once before with the introduction of two animals in a monitored and managed translocation from Lewa Downs, Laikipia in 1992-1994. Ultimately, Kenyan experts were co-opted to address risk after trypanosomiasis occurred in many animals. Unfortunately, this finding was followed by gradual mortalities of most rhinoceros with only a few being saved by removal to highland private sanctuaries. This event was complicated by many factors. Samples were only sporadically collected, and mainly from sick animals. With no clear responsibility by government agencies, a collaboration between veterinarians and researchers resulted in characterization of the disease challenge, and when invited, assessment of health status. Laboratory diagnostics revealed common and sometimes severe infections with Trypanosoma brucei, a normally infrequent trypanosome. Infection was associated with disturbances in erythropoiesis, especially anemia. Symptoms varied from sudden death associated with intestinal atony, to a semiparalyzed animal that was partially responsive to treatment for trypanosomes. This event should be used as a caution to future movements of this species that are planned or ongoing in Africa, for conservation or other purposes.

A single test approach for accurate and sensitive detection and taxonomic characterization of Trypanosomes by comprehensive analysis of internal transcribed spacer 1 amplicons

To improve our knowledge on the epidemiological status of African trypanosomiasis, better tools are required to monitor Trypanosome genotypes circulating in both mammalian hosts and tsetse fly vectors. This is important in determining the diversity of Trypanosomes and understanding how environmental factors and control efforts affect Trypanosome evolution. We present a single test approach for molecular detection of different Trypanosome species and subspecies using newly designed primers to amplify the Internal Transcribed Spacer 1 region of ribosomal RNA genes, coupled to Illumina sequencing of the amplicons. The protocol is based on Illumina's widely used 16s bacterial metagenomic analysis procedure that makes use of multiplex PCR and dual indexing. Results from analysis of wild tsetse flies collected from Zambia and Zimbabwe show that conventional methods for Trypanosome species detection based on band size comparisons on gels is not always able to accurately distinguish between T. vivax and T. godfreyi. Additionally, this approach shows increased sensitivity in the detection of Trypanosomes at species level with the exception of the Trypanozoon subgenus. We identified subspecies of T. congolense, T. simiae, T. vivax, and T. godfreyi without the need for additional tests. Results show T. congolense Kilifi subspecies is more closely related to T. simiae than to other T. congolense subspecies. This agrees with previous studies using satellite DNA and 18s RNA analysis. While current classification does not list any subspecies for T. godfreyi, we observed two distinct clusters for these species. Interestingly, sequences matching T. congolense Tsavo (now classified as T. simiae Tsavo) clusters distinctly from other T. simiae Tsavo sequences suggesting the Nannomonas group is more divergent than currently thought thus the need for better classification criteria. This method presents a simple but comprehensive way of identification of Trypanosome species and subspecies-specific using one PCR assay for molecular epidemiology of trypanosomes.

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.

Rediscovery of Trypanosoma (Pycnomonas) suis, a tsetse-transmitted trypanosome closely related to T. brucei

The African tsetse-transmitted trypanosomes are considered to be a well-known group of parasitic protozoa, but in 2008 a novel and distinctive trypanosome related to Trypanosoma brucei was discovered among tsetse isolates from Msubugwe in Tanzania. The host range, distribution and potential pathogenicity of this new trypanosome remain to be elucidated; such studies would be facilitated by a sensitive and specific identification method. Here, we identified two highly repetitive elements in the genome of the new trypanosome: a 177 bp repeat, which was located predominantly on the highly abundant minichromosomes, and a 138 bp repeat, which was widely dispersed in the genome. A PCR test based on each repeat was specific for the new trypanosome and sensitive to <0.1 trypanosome equivalent. These PCR tests were used to identify trypanosomes in archival pig blood smears from the 1950's, confirming the identity of the Msubugwe trypanosome as Trypanosoma (Pycnomonas) suis. We also present data on the molecular karyotype and spliced leader (SL, miniexon) repeat of the new trypanosome, both of which distinguish T. suis from other, better-known African tsetse-transmitted trypanosomes. The rediscovery of T. suis opens new lines of research into the evolution and biology of the African trypanosomes.

Assembling a geospatial database of tsetse-transmitted animal trypanosomosis for Africa

BACKGROUND

African animal trypanosomosis (AAT), or nagana, is widespread within the tsetse-infested belt of sub-Saharan Africa. Although a wealth of information on its occurrence and prevalence is available in the literature, synthesized and harmonized data at the regional and continental scales are lacking. To fill this gap the Food and Agriculture Organization of the United Nations (FAO) launched the Atlas of tsetse and AAT, jointly implemented with the International Atomic Energy Agency (IAEA) in the framework of the Programme Against African Trypanosomosis (PAAT).

METHODS

The Atlas aims to build and regularly update a geospatial database of tsetse species occurrence and AAT at the continental level. The present paper focuses on the methodology to assemble a dynamic database of AAT, which hinges on herd-level prevalence data as estimated using various diagnostic techniques. A range of ancillary information items is also included (e.g. trypanosome species, survey period, species and breed of animals, husbandry system, etc.). Input data were initially identified through a literature review.

RESULTS

Preliminary results are presented for Ethiopia, Kenya and Uganda in East Africa: 122 papers were identified and analyzed, which contained field data collected from January 1990 to December 2013. Information on AAT was extracted and recorded for 348 distinct geographic locations. The presented distribution maps exemplify the range of outputs that can be directly generated from the AAT database.

CONCLUSIONS

Activities are ongoing to map the distribution of AAT in all affected countries and to develop the tsetse component of the Atlas. The presented methodology is also being transferred to partners in affected countries, with a view to developing capacity and strengthening data management, harmonization and sharing. In the future, geospatial modelling will enable predictions to be made within and beyond the range of AAT field observations. This variety of information layers will inform decisions on the most appropriate, site-specific strategies for intervention against AAT. Data on the occurrence of human-infective trypanosomes in non-human hosts will also provide valuable information for sleeping sickness control and elimination.

Trypanosome diversity in wildlife species from the serengeti and Luangwa Valley ecosystems

Background

The importance of wildlife as reservoirs of African trypanosomes pathogenic to man and livestock is well recognised. While new species of trypanosomes and their variants have been identified in tsetse populations, our knowledge of trypanosome species that are circulating in wildlife populations and their genetic diversity is limited.

Methodology/Principal Findings

Molecular phylogenetic methods were used to examine the genetic diversity and species composition of trypanosomes circulating in wildlife from two ecosystems that exhibit high host species diversity: the Serengeti in Tanzania and the Luangwa Valley in Zambia. Phylogenetic relationships were assessed by alignment of partial 18S, 5.8S and 28S trypanosomal nuclear ribosomal DNA array sequences within the Trypanosomatidae and using ITS1, 5.8S and ITS2 for more detailed analysis of the T. vivax clade. In addition to Trypanosoma brucei, T. congolense, T. simiae, T. simiae (Tsavo), T. godfreyi and T. theileri, three variants of T. vivax were identified from three different wildlife species within one ecosystem, including sequences from trypanosomes from a giraffe and a waterbuck that differed from all published sequences and from each other, and did not amplify with conventional primers for T. vivax.

Conclusions/Significance

Wildlife carries a wide range of trypanosome species. The failure of the diverse T. vivax in this study to amplify with conventional primers suggests that T. vivax may have been under-diagnosed in Tanzania. Since conventional species-specific primers may not amplify all trypanosomes of interest, the use of ITS PCR primers followed by sequencing is a valuable approach to investigate diversity of trypanosome infections in wildlife; amplification of sequences outside the T. brucei clade raises concerns regarding ITS primer specificity for wildlife samples if sequence confirmation is not also undertaken.

The trypanosomes include a number of species that cause disease in livestock. In recent years, several trypanosomes have been identified which do not fit into the classic trypanosome classification system. However, previous work has focused on trypanosomes identified in the tsetse vector, with little information available on trypanosomes found in their natural hosts, wildlife. We studied trypanosome sequences from wildlife in Serengeti National Park in Tanzania and the Luangwa Valley in Zambia and found a number of trypanosome species pathogenic to livestock were circulating in these areas. For Trypanosoma vivax, one of the causes of trypanosomiasis in cattle, variants were identified in giraffe and waterbuck that were different from all published sequences and from each other. These variants did not test positive with the molecular tests usually used to identify T. vivax suggesting that T. vivax may often be under-diagnosed in Tanzania. The trypanosome classification system is facing challenges as molecular data are incorporated into a system that historically was based on factors such as morphology, host range and geographical distribution.

Multiple Trypanosoma infections are common amongst Glossina species in the new farming areas of Rufiji district, Tanzania

Background

Tsetse flies and trypanosomiasis are among several factors that constrain livestock development in Tanzania. Over the years Rufiji District was excluded from livestock production owing to tsetse fly infestation, however, a few years ago there was an influx of livestock following evictions aimed at conserving the Usangu wetlands.

Methods

A study was conducted to determine the efficiency of available traps for catching tsetse flies, Glossina species infesting the area, their infection rates and Trypanosoma species circulating in the area. Trapping was conducted during the semi dry season for a total of 30 days (ten days each month) during the onset of the dry season of May - July 2009. Harvested flies after every 24 hours were dissected and examined under a light microscope for trypanosome infections and whole fly DNA was extracted from 82 flies and analyzed for trypanosomes by polymerase chain reaction (PCR) using different sets of primers.

Results

The proportions of total tsetse catches per trap were in the following decreasing order S3 (33%), H-Trap (27%), Pyramidal (19%), sticky panel (11%) and biconical trap (10%). Of the 1200 trapped flies, 75.6% were identified as Glossina pallidipes, 11.7% as G. brevipalpis, 9.6% as G. austeni and 3.0% G. morsitans morsitans. Dissections revealed the overall infection rate of 6.6% (13/197). Whole DNA was extracted from 82 tsetse flies and the prevalence of trypanosomes circulating in the area in descending order was 92.7% (76/82) for T. simiae; 70.7% (58/82) for T. brucei types; 48.8% (40/82) for the T. vivax types and 32.9% (27/82) for the T. congolense types as determined by PCR. All trypanosome types were found in all tsetse species analysed except for the T. congolense types, which were absent in G. m. morsitans. None of the T. brucei positive samples contained human infective trypanosomes by SRA - PCR test

Conclusion

All tsetse species found in Rufiji are biologically important in the transmission of animal trypanosomiasis and the absence of T. congolense in G. m. morsitans could be a matter of chance only. Therefore, plans for control should consider all tsetse species.

Managing tsetse transmitted trypanosomosis by insecticide treated nets--an affordable and sustainable method for resource poor pig farmers in Ghana

An outbreak of tsetse-transmitted trypanosomiasis resulted in more than 50% losses of domestic pigs in the Eastern Region of Ghana (source: Veterinary Services, Accra; April 2007). In a control trial from May 4^th–October 10^th 2007, the efficacy of insecticide-treated mosquito fences to control tsetse was assessed. Two villages were selected – one serving as control with 14 pigsties and one experimental village where 24 pigsties were protected with insecticide treated mosquito fences. The 100 cm high, 150denier polyester fences with 100 mg/m² deltamethrin and a UV protector were attached to surrounding timber poles and planks. Bi-monthly monitoring of tsetse densities with 10 geo-referenced bi-conical traps per village showed a reduction of more than 90% in the protected village within two months. Further reductions exceeding 95% were recorded during subsequent months. The tsetse population in the control village was not affected, only displaying seasonal variations. Fifty pigs from each village were ear-tagged and given a single curative treatment with diminazene aceturate (3.5 mg/kg bw) after their blood samples had been taken. The initial trypanosome prevalence amounted to 76% and 72% of protected and control animals, respectively, and decreased to 16% in protected as opposed to 84% in control pigs three months after intervention. After six months 8% of the protected pigs were infected contrasting with 60% in the control group.

Sixty million people and more than 70 million livestock live in Africa at risk of contracting trypanosomiasis. The heads of member states of the African Union (AU) declared the year 2000 as the beginning of the Pan African Tsetse and Trypanosomiasis Eradication Campaign to eradicate tsetse flies and the diseases they transmit from the continent. For the first time the social and economic consequences of trypanosomiasis were brought to the attention of the affected populations. Efforts to control the fatal disease in man and livestock are based on treatment of patients and livestock with trypanocidal drugs. Resistance-related drug failures are increasing. Methods to control tsetse flies rely on insecticides. Past tsetse campaigns proved unsustainable due to the public good character of most control techniques such as aerial and ground spraying, traps or targets. Treating livestock with insecticides may be more sustainable and is also controlling ticks, which can transmit economically important and often fatal diseases. Costs per head of livestock and tick resistance against insecticides are seen as a major hindrance to their continuous large-scale use. Insecticide treated nets proved an effective and affordable means protecting pigs against tsetse transmitted trypanosomoses in Ghana.

Landmarks in the evolution of technologies for identifying trypanosomes in tsetse flies

Understanding what the trypanosome pathogens are, their vectors and mode of transmission underpin efforts to control the disease they cause in both humans and livestock. The risk of transmission is estimated by determining what proportion of the vector population is carrying the infectious pathogens. This risk also depends on the infectivity of the trypanosomes to humans and livestock. Most livestock pathogens are not infective to humans, whereas the two sub-species that infect humans also infect livestock. As with other infectious diseases, we can therefore trace the foundation of many continuing disease control programs for trypanosomiasis to the discovery of the pathogens and their vectors more than a century ago. Over this period, methods for detecting and identifying trypanosomes have evolved through various landmark discoveries. This review describes the evolution of methods for identifying African trypanosomes in their tsetse fly vectors.

African trypanosomes: celebrating diversity

Recent advances in molecular identification techniques and phylogenetic analysis have revealed the presence of previously unidentified tsetse-transmitted trypanosomes in Africa. This is surprising in a comparatively well-known group of pathogens that includes the causative agents of human and animal trypanosomiasis. Despite levels of genetic divergence that warrant taxonomic recognition, only one of these new trypanosomes has been named as a new species; the increased diversity is largely ignored or regarded as an inconvenient complication. Yet, some of these trypanosomes have demonstrated pathogenicity, whereas others are closely related to known pathogens, and might share this trait. We should first acknowledge that these novel trypanosomes exist and then take steps to investigate their host range, pathogenicity to livestock and response to chemotherapy.

Trypanosomatid genomes contain several subfamilies of ingi-related retroposons

Retroposons are ubiquitous transposable elements found in the genomes of most eukaryotes, including trypanosomatids. The African and American trypanosomes (Trypanosoma brucei and Trypanosoma cruzi) contain long autonomous retroposons of the ingi clade (Tbingi and L1Tc, respectively) and short nonautonomous truncated versions (TbRIME and NARTc, respectively), as well as degenerate ingi-related retroposons devoid of coding capacity (DIREs). In contrast, Leishmania major contains only remnants of extinct retroposons (LmDIREs) and of short nonautonomous heterogeneous elements (LmSIDERs). We extend this comparative and evolutionary analysis of retroposons to the genomes of two other African trypanosomes (Trypanosoma congolense and Trypanosoma vivax) and another Leishmania sp. (Leishmania braziliensis). Three new potentially functional retroposons of the ingi clade have been identified: Tvingi in T. vivax and Tcoingi and L1Tco in T. congolense. T. congolense is the first trypanosomatid containing two classes of potentially active retroposons of the ingi clade. We analyzed sequences located upstream of these new long autonomous ingi-related elements, which code for the recognition site of the retroposon-encoded endonuclease. The closely related Tcoingi and Tvingi elements show the same conserved pattern, indicating that the Tcoingi- and Tvingi-encoded endonucleases share site specificity. Similarly, the conserved pattern previously identified upstream of L1Tc has also been detected at the same relative position upstream of L1Tco elements. A phylogenetic analysis of all ingi-related retroposons identified so far, including DIREs, clearly shows that several distinct subfamilies have emerged and coexisted, though in the course of trypanosomatid evolution, only a few have been maintained as active elements in modern trypanosomatid (sub)species.

Species-specific probes for the identification of the African tsetse-transmitted trypanosomes

The first step in studying the epidemiology of a disease is the accurate identification of the pathogen. Traditional reliance on morphological identification has given way to the use of molecular methods for the detection and identification of pathogens, greatly improving our understanding of epidemiology. For the African tsetse-transmitted trypanosomes, the growth of PCR methods for identification of trypanosomes has led to increased appreciation of trypanosome genetic diversity and discovery of hitherto unknown trypanosome species, as well as greater knowledge about the number and type of trypanosome infections circulating in mammalian hosts and vectors. Sequence data and phylogenetic analysis have provided quantitative information on the relatedness of different trypanosome species and allowed the new trypanosome genotypes discovered through the use of species identification methods in the field to be accurately placed in the phylogenetic tree.

Development of a mathematical model for mechanical transmission of trypanosomes and other pathogens of cattle transmitted by tabanids

Mechanical transmission of pathogens by biting insects is a non-specific phenomenon in which pathogens are transmitted from the blood of an infected host to another host during interrupted feeding of the insects. A large range of pathogens can be mechanically transmitted, e.g. hemoparasites, bacteria and viruses. Some pathogens are almost exclusively mechanically transmitted, while others are also cyclically transmitted. For agents transmitted both cyclically and mechanically (mixed transmission), such as certain African pathogenic trypanosomes, the relative impact of mechanical versus cyclical transmission is essentially unknown. We have developed a mathematical model of pathogen transmission by a defined insect population to evaluate the importance of mechanical transmission. Based on a series of experiments aimed at demonstrating mechanical transmission of African trypanosomes by tabanids, the main parameters of the model were either quantified (host parasitaemia, mean individual insect burden, initial prevalence of infection) or estimated (unknown parameters). This model allows us to simulate the evolution of pathogen prevalence under various predictive circumstances, including control measures and could be used to assess the risk of mechanical transmission under field conditions. If adjustments of parameters are provided, this model could be generalized to other pathogenic agents present in the blood of their hosts (Bovine Leukemia virus, Anaplasma, etc.) or other biting insects such as biting muscids (stomoxyines) and hippoboscids.

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 28Salpha ribosomal DNA. Fluorescently tagged primers, designed in conserved regions of the 18S and 28Salpha 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.

Patterns of co-evolution between trypanosomes and their hosts deduced from ribosomal RNA and protein-coding gene phylogenies

Trypanosomes (genus Trypanosoma) are widespread blood parasites of vertebrates, usually transmitted by arthropod or leech vectors. Most trypanosomes have lifecycles that alternate between a vertebrate host, where they exist in the bloodstream, and an invertebrate host, where they develop in the alimentary tract. This raises the question of whether one type of host has had greater influence on the evolution of the genus. Working from the generally accepted view that trypanosomes are monophyletic, here we examine relationships between trypanosomes using phylogenies based on the genes for the small subunit ribosomal RNA (SSU rRNA) and the glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH). New analysis of a combined dataset of both these genes provides strong support for many known clades of trypanosomes. It also resolves the deepest split within the genus between the Aquatic clade, which mainly contains trypanosomes of aquatic and amphibious vertebrates, and a clade of trypanosomes from terrestrial vertebrates. There is also strengthened support for two deep clades, one comprising a wide selection of mammalian trypanosomes and a tsetse fly-transmitted reptilian trypanosome, and the other combining two bird trypanosome subclades. Considering the vertebrate and invertebrate hosts of each clade, it is apparent that co-speciation played little role in trypanosome evolution. However most clades are associated with a type of vertebrate or invertebrate host, or both, indicating that 'host fitting' has been the principal mechanism for evolution of trypanosomes.

Resolution of the species problem in African trypanosomes

There is a general assumption that eukaryote species are demarcated by morphological or genetic discontinuities. This stems from the idea that species are defined by the ability of individuals to mate and produce viable progeny. At the microscopic level, where organisms often proliferate more by asexual than sexual reproduction, this tidy classification system breaks down and species definition becomes messy and problematic. The dearth of morphological characters to distinguish microbial species has led to the widespread application of molecular methods for identification. As well as providing molecular markers for species identification, gene sequencing has generated the data for accurate estimation of relatedness between different populations of microbes. This has led to recognition of conflicts between current taxonomic designations and phylogenetic placement. In the case of microbial pathogens, the extent to which taxonomy has been driven by utilitarian rather than biological considerations has been made explicit by molecular phylogenetic analysis. These issues are discussed with reference to the taxonomy of the African trypanosomes, where pathogenicity, host range and distribution have been influential in the designation of species and subspecies. Effectively, the taxonomic units recognised are those that are meaningful in terms of human or animal disease. The underlying genetic differences separating the currently recognised trypanosome taxa are not consistent, ranging from genome-wide divergence to presence/absence of a single gene. Nevertheless, if even a minor genetic difference reflects adaptation to a particular parasitic niche, for example, in Trypanosoma brucei rhodesiense, the presence of a single gene conferring the ability to infect humans, then it can prove useful as an identification tag for the taxon occupying that niche. Thus, the species problem can be resolved by bringing together considerations of utility, genetic difference and adaptation.

Phylogeny of Trypanosoma ( Megatrypanum ) theileri and related trypanosomes reveals lineages of isolates associated with artiodactyl hosts diverging on SSU and ITS ribosomal sequences

SSU ribosomal sequences of trypanosomes from Brazilian cattle and water buffalo were used to infer phylogenetic relationships between non-pathogenic T. theileri and allied species parasitic in artiodactyls. T. theileri trypanosomes from distinct geographical regions in Brazil and from other countries were tightly clustered into the 'clade T. theileri' distant from the 'T. brucei clade' of pathogenic parasites of artiodactyls, and also distinct from trypanosomes of other mammals. The existence of this monophyletic assemblage (T. theileri clade) composed only by isolates from artiodactyl species justifies the continued recognition of the subgenus T. (Megatrypanum) with T. theileri as its type species. Phylogenies based on SSU and ITS1 ribosomal sequences produced the same branching pattern with isolates from different mammalian hosts clustered in 5 lineages: A, related to water buffalo; B, C and D, to cattle; E, to fallow deer. The pattern of host specificity allied to some congruence between host and parasite phylogenies suggested association of these trypanosomes with their respective hosts. Segregation of cattle isolates into three lineages revealed an overall geographical structure. Moreover, positioning of trypanosomes infecting tabanids in the T. theileri clade is consistent with the role of these flies as important vectors of these trypanosomes.

The use of ITS1 rDNA PCR in detecting pathogenic African trypanosomes

There are 11 different pathogenic trypanosomes in trypanosomiasis endemic regions of Africa. Their detection and characterisation by molecular methods relies on species-specific primers; consequently several PCR tests have to be made on each sample. Primers ITS1 CF and ITS1 BR, previously designed to amplify the internal transcribed spacer (ITS1) of rDNA, have been evaluated for use in a universal diagnostic test for all pathogenic trypanosomes. Blood was collected from 373 cattle and 185 camels. The primers gave constant PCR products with the stocks of each taxon tested. Members of subgenus Trypanozoon (T. brucei brucei, T. evansi, T. b. rhodesiense and T. b. gambiense) gave a constant product of approximately 480 bp; T. congolense, savannah 700 bp, T. congolense kilifi 620 bp and T. congolense forest 710 bp: T. simiae 400 bp, T. simiae tsavo 370 bp, T. godfreyi 300 bp and T. vivax 250 bp. The sensitivity of the test ranged from 10 pg for Trypanozoon, T. congolense clade and T. vivax to 100 pg for T. simiae and T. godfreyi. The primers detected cases of multi-taxa samples, although the sensitivity was reduced with an increase in the combinations. A better detection rate of trypanosome DNA was recorded with buffy coats than from direct blood. With the field samples, the diagnostic sensitivity was close to the sensitivity obtained using single reactions with species-specific primers for Trypanozoon 38/40 (95%) and T. congolense savannah 30/33 (90.9%) but was lower with T. vivax 25/31 (77.4%). The primers offer promise as a routine diagnostic tool through the use of a single PCR; however, further evaluation is recommended.

Identification of trypanosomes in Glossina pallidipes and G. longipennis in Kenya

The polymerase chain reaction (PCR) was used to identify trypanosomes in Glossina pallidipes and G. longipennis caught in Kenya. Of 3826 flies dissected, 188 (4.9%) were parasitologically positive overall. The infection rate in G. pallidipes was 5.7% (187 of 3301 flies), but only one of 525 G. longipennis was infected (infection rate 0.2%). There was a higher infection rate in female G. pallidipes flies than male flies (chi(2) = 18.5, P < 0.001) and odds ratio = 2.5 (95% 1.6, 3.7). The infected flies were analysed by PCR using 10 sets of primers specific for species and subgroups within the subgenera Nannomonas, Trypanozoon and Duttonella. Of 188 parasitologically positive samples, PCR identified 137 (72.9%), leaving 51 (27.1%) non-identified. We recorded infection rates of 47.2% for Trypanosoma congolense savannah, forest and kilifi subgroups, 20.9% for T. simiae/T. simiae tsavo/T. godfreyi, 14.9% for T. brucei ssp. and 13.8% for T. vivax. Thirty-nine (26.7%) flies had mixed infections, with a minor association between T. congolense savannah/T. simiae tsavo/T. godfreyi (chi(2) = 6.93, d.f. = 1, P < 0.05). The relative proportion of each trypanosome species or subgroup varied between fly belts with T. congolense (all subgroups) being the most abundant and T. godfreyi the least. Statistical analysis showed that dissection method and PCR test classified infections independently (chi(2) = 10.5, d.f. = 1, P < 0.05 and kappa = 0.38). This study shows that pathogenic trypanosomes are widespread in all sampled testes fly belts with G. pallidipes as the main vector. Further, PCR test is more reliable in detecting and identifying trypanosomes than dissection method.

The use of specific and generic primers to identify trypanosome infections of wild tsetse flies in Tanzania by PCR

The accurate identification of trypanosome species and subspecies remains a challenging task in the epidemiology of human and animal trypanosomiasis in tropical Africa. Currently, there are specific PCR tests to identify about 10 different species, subspecies or subgroups of African tsetse-transmitted trypanosomes. These PCR tests have been used here to identify trypanosomes in four species of tsetse (Glossina brevipalpis, G. pallidipes, G. swynnertoni, G. morsitans morsitans) from two areas of Tanzania. PCR using species-specific primers was performed on 1041 dissection-positive proboscides, giving an overall positive identification in 254 (24%). Of these, 61 proboscides (24%) contained two or more trypanosomes. The trypanosome with the greatest overall prevalence at both field sites was Trypanosoma simiae Tsavo, which was identified in a total of 118 infected tsetse proboscides (46%). At Pangani, T. godfreyi was found in G. pallidipes but not in G. brevipalpis, suggesting that these flies might have different susceptibility to this trypanosome or might have fed on a different range of hosts. A high proportion (about 75%) of trypanosome infections remained unidentified. To investigate the identity of these unidentified samples, we used primers complementary to the conserved regions of trypanosomal small subunit ribosomal RNA (ssu rRNA) genes to amplify variable segments of the gene. Amplified DNA fragments were cloned, sequenced and compared with ssu rRNA genes on database of known trypanosome species. In this way, we have tentatively identified two new trypanosomes: a trypanosome related to Trypanosoma vivax and a trypanosome related to T. godfreyi. The T. godfreyi-related trypanosome occurred frequently in the Tanzanian field samples and appears to be widespread. Molecular identification of these two new trypanosomes should now facilitate their isolation and full biological characterisation.

Species concepts for trypanosomes: from morphological to molecular definitions?

The way species and subspecies names are applied in African trypanosomes of subgenera Trypanozoon and Nannomonas is reviewed in the light of data from molecular taxonomy. In subgenus Trypanozoon the taxonomic importance of pathogenicity, host range and distribution appear to have been inflated relative to actual levels of genetic divergence. The opposite is true for subgenus Nannomonas, where current taxonomic usage badly underrepresents genetic diversity. Data from molecular characterisation studies are revealing a growing number of genotypes, which may represent distinct taxa. Unfortunately few of these genotypes are yet supported by sufficient biological data to be recognized taxonomically. But we may be missing fundamental epidemiological information, because of our inability to distinguish these trypanosomes in host blood morphologically or in tsetse by their developmental cycle. Molecular taxonomy has led the way in identifying these new genotypes and now offers the key to elucidating the biology of these organisms.

Applications of PCR-based tools for detection and identification of animal trypanosomes: a review and perspectives

This paper aims to review the applications of the polymerase chain reaction (PCR) for the detection and identification of trypanosomes in animals. The diagnosis of trypanosomes, initially based on microscopic observations and the host range of the parasites, has been improved, since the 1980s, by DNA-based identification. These diagnostic techniques evolved successively through DNA probing, PCR associated to DNA probing, and currently to PCR alone. Several DNA sequences have been investigated as possible targets for diagnosis, especially multi-copy genes such as mini-exon, kinetoplastid mini-circles, etc., but the most favoured target is the nuclear satellite DNA of mini-chromosomes, which presents the advantages, and the drawbacks, of highly repetitive short sequences (120-600 bp). Several levels of specificity have been achieved from sub-genus to species, sub-species and even types. Random priming of trypanosome DNA has even allowed "isolate specific" identification. Other work based on microsatellite sequences has provided markers for population genetic studies. For regular diagnosis, the sensitivity of PCR has increased with the advancement of technologies for sample preparation, to reach a level of 1 trypanosome/ml of blood, which has brought to field samples a sensitivity two to three times higher than microscopic observation of the buffy coat. Similarly, PCR has allowed an increase in the specificity and sensitivity of diagnosis in vectors such as tsetse flies. However, because of the diversity of Trypanosoma species potentially present in a single host, PCR diagnosis carried out on host material requires several PCR reactions; for example, in cattle, up to five reactions per sample may be required. Research is now focusing on a diagnosis based on the amplification of the internal transcribed spacer-1 (ITS-1) of ribosomal DNA which presents the advantages of being a multi-copy locus (100-200), having a small size (300-800 bp), which varies from one taxon to another but is conserved in size in a given taxon. This may lead to the development of a multi-species-specific diagnostic protocol using a single PCR. By reducing the cost of the PCR diagnosis, this technique would allow a greater number of field samples to be tested in epidemiological studies and/or would increase the variety of Trypanosoma species that could be detected. Further investigations are required to develop and optimise multi-species-specific diagnostic tools for trypanosomes, which could also serve as a model for such tools in other pathogens.

Evolutionary rate differences in trypanosomes

Ribosomal RNA-based studies of trypanosome phylogenies have highlighted considerable differences in genetic diversity within clades in the genus Trypanosoma and several-fold substitution rate differences between clades have been identified. While early 18S rRNA-based studies were hampered by highly variable substitution rates and long-branch attraction, it is apparent that genuine differences in evolution rates within localized clades do exist and questions remain regarding what rate or rates such clades are evolving at and why is the application of a single clock to trypanosome evolution so inappropriate? In this study, we explore rate heterogeneity in the commonly used 18S rRNA gene across genus Trypanosoma, using a maximum likelihood (ML) approach to explore local rate variations in clades of biological interest.