Population genetics of Trypanosoma brucei rhodesiense: clonality and diversity within and between foci.

African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda) and Southern (Malawi) Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics.

Phylogeography and taxonomy of Trypanosoma brucei.

BACKGROUND: Characterizing the evolutionary relationships and population structure of parasites can provide important insights into the epidemiology of human disease. METHODOLOGY/PRINCIPAL FINDINGS: We examined 142 isolates of Trypanosoma brucei from all over sub-Saharan Africa using three distinct classes of genetic markers (kinetoplast CO1 sequence, nuclear SRA gene sequence, eight nuclear microsatellites) to clarify the evolutionary history of Trypanosoma brucei rhodesiense (Tbr) and T. b. gambiense (Tbg), the causative agents of human African trypanosomosis (sleeping sickness) in sub-Saharan Africa, and to examine the relationship between Tbr and the non-human infective parasite T. b. brucei (Tbb) in eastern and southern Africa. A Bayesian phylogeny and haplotype network based on CO1 sequences confirmed the taxonomic distinctness of Tbg group 1. Limited diversity combined with a wide geographical distribution suggested that this parasite has recently and rapidly colonized hosts across its current range. The more virulent Tbg group 2 exhibited diverse origins and was more closely allied with Tbb based on COI sequence and microsatellite genotypes. Four of five COI haplotypes obtained from Tbr were shared with isolates of Tbb, suggesting a close relationship between these taxa. Bayesian clustering of microsatellite genotypes confirmed this relationship and indicated that Tbr and Tbb isolates were often more closely related to each other than they were to other members of the same subspecies. Among isolates of Tbr for which data were available, we detected just two variants of the SRA gene responsible for human infectivity. These variants exhibited distinct geographical ranges, except in Tanzania, where both types co-occurred. Here, isolates possessing distinct SRA types were associated with identical COI haplotypes, but divergent microsatellite signatures. CONCLUSIONS/SIGNIFICANCE: Our data provide strong evidence that Tbr is only a phenotypic variant of Tbb; while relevant from a medical perspective, Tbr is not a reproductively isolated taxon. The wide distribution of the SRA gene across diverse trypanosome genetic backgrounds suggests that a large amount of genetic diversity is potentially available with which human-infective trypanosomes may respond to selective forces such as those exerted by drugs.

Human African trypanosomiasis: diagnosis, relapse and survival after severe melarsoprol-induced encephalopathy.

We describe a case of human African trypanosomiasis with a number of unusual features. The clinical presentation was subacute, but the infection was shown to be due to Trypanosoma brucei rhodesiense. The infection relapsed twice following treatment and the patient developed a melarsoprol-associated encephalopathy. Magnetic resonance imaging (MRI) findings were suggestive of microhaemorrhages, well described in autopsy studies of encephalopathy but never before shown on MRI. The patient survived severe encephalopathy with a locked-in syndrome. Our decision to provide ongoing life support may be useful to physicians treating similar cases in a setting where intensive care facilities are available.

Detection of T.b. rhodesiense trypanosomes in humans and domestic animals in south east Uganda by amplification of serum resistance-associated gene.

The human serum resistance-associated (SRA) gene was identified in 28 (80%) of the 35 T.b. rhodesiense trypanosomes from parasitologically confirmed sleeping sickness cases, using the primers designed by Radwanska and in 27 (77.1%) of the same 35 T.b. rhodesiense trypanosomes using the primers designed by Gibson. However, about 20% of the 35 T.b. rhodesiense trypanosomes could not be detected by SRA-polymerase chain reaction (PCR) even when an aliquot of the first PCR was used in the second PCR, indicating that the gene may be absent in those trypanosomes or the trypanosomes could be having another variant of SRA not detectable by these primers since three variants of SRA genes have so far been identified or the amount of trypanosomal DNA extracted from infected blood was too low to be detected. The trypanosome isolates that are SRA gene negative may indicate the presence of some T.b. rhodesiense trypanosomes with modified or lack SRA genes or simple loss of the SRA gene from the expression site in which it resides during antigenic variation. Analysis of trypanosomes derived from domestic animals showed that 79 (90.8%) of the 87 trypanosomes isolated from cattle were positive by Trypanosoma brucei (TBR)-PCR, indicating that they were Trypanozoon while 8 (9.2%) of the trypanosome isolates which were negative by TBR-PCR could be T. vivax, T. congolense, or T. theileri. When subjected to SRA-PCR, 10 (11.5%) of the 87 trypanosomes isolates derived from cattle were positive, indicating that there could be T.b. rhodesiense circulating in cattle, which is similar to the percentage of T.b. rhodesiense previously obtained in cattle in Serere, Soroti district.

Trypanosoma evansi: genetic variability detected using amplified restriction fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) analysis of Kenyan isolates.

We compared two methods to generate polymorphic markers to investigate the population genetics of Trypanosoma evansi; random amplified polymorphic DNA (RAPD) and amplified restriction fragment length polymorphism (AFLP) analyses. AFLP accessed many more polymorphisms than RAPD. Cluster analysis of the AFLP data showed that 12 T.evansi isolates were very similar ('type A') whereas 2 isolates differed substantially ('type B'). Type A isolates have been generally regarded as genetically identical but AFLP analysis was able to identify multiple differences between them and split the type A T. evansi isolates into two distinct clades.

Sleeping sickness in Uganda: a thin line between two fatal diseases.

OBJECTIVE: To determine, through the use of molecular diagnostic tools, whether the two species of parasite that cause human African trypanosomiasis have become sympatric. DESIGN: Blood sampling of all available patients between June 2001 and June 2005 in central Uganda and between July and September 2003 in northwest Uganda and analysis of subcounty sleeping sickness records in Uganda between 1985 and 2005. SETTING: Sleeping sickness treatment centres in central and northwest Uganda and in south Sudan. PARTICIPANTS: Patients presenting at the treatment centres and diagnosed as having sleeping sickness. MAIN OUTCOME MEASURE: Classification of parasites from patients from each disease focus as either Trypanosoma brucei rhodesiense (acute form) or T b gambiense (chronic form). RESULTS: Blood from 231 patients with sleeping sickness in central Uganda and from 91 patients with sleeping sickness in northwest Uganda and south Sudan were screened for T b rhodesiense (detection of SRA gene) and T b gambiense (detection of TgsGP gene). All samples from central Uganda were classified as T b rhodesiense, and all samples from northwest Uganda and south Sudan were identified as T b gambiense. CONCLUSIONS: The two focuses of human African trypanosomiasis remain discrete, but the area of Uganda affected by the acute form of human sleeping sickness has increased 2.5-fold since 1985, spreading to three new districts within the past five years through movement of infected livestock. Without preventive action targeted at the livestock reservoir of this zoonotic disease, it is likely that the two disease focuses will converge. This will have a major impact on diagnosis and treatment of this neglected disease. Real time monitoring is recommended, using molecular diagnostic tools (at a regional surveillance centre, for example) targeted at both livestock and human patients.

[Analysis of molecular profiles among Trypanozoon species and subspecies by MGE-PCR method].

OBJECTIVE: To analyze the relationship between genetic variability and evolution among Trypanosoma brucei (including T. b. brucei, T. b. rhodesiense and T. b. gambiense), T. evansi and T. equiperdum isolates. METHODS: Genomic DNAs of 26 trypanosome isolates were amplified by a mobile genetic elements (MGE) -PCR technique and cluster analysis was performed based on the molecular profiles with Neighbor-Joining method. RESULTS: The genetic variability among trypanosome isolates examined was obvious with an average genetic distance of 41.2% (ranged from 0 to 100%). Similarity coefficient among T. brucei isolates was 41.15% which was lower than that between T. evansi and T. equiperdum isolates. The closest relationship was found between T. evansi and T. brucei isolates with a similarity coefficient of 62.94%. The genetic variability between T. b. rhodesiense and T. b. brucei isolates was higher than that among T. b. gambiense isolates. CONCLUSION: Species and subspecies in Trypanozoon displayed a higher genetic variability; T. equiperdum isolates collected from China and from South America, and T. evansi isolates from China and from South America, should have a similar origin.

Severity of human african trypanosomiasis in East Africa is associated with geographic location, parasite genotype, and host inflammatory cytokine response profile.

The mechanisms underlying virulence in human African trypanosomiasis are poorly understood, although studies with experimental mice suggest that unregulated host inflammatory responses are associated with disease severity. We identified two trypanosomiasis foci with dramatically different disease virulence profiles. In Uganda, infections followed an acute profile with rapid progression to the late stage (meningoencephalitic infection) in the majority of patients (86.8%). In contrast, infections in Malawi were of a chronic nature, in which few patients progressed to the late stage (7.1%), despite infections of several months' duration. All infections were confirmed to be Trypanosoma brucei rhodesiense by testing for the presence of the serum resistance-associated (SRA) gene, but trypanosomes isolated from patients in Uganda or Malawi were distinguished by an SRA gene polymorphism. The two disease profiles were associated with markedly different levels of tumor necrosis factor alpha (TNF-alpha) and transforming growth factor beta (TGF-beta) in plasma. In Uganda but not Malawi early-stage TNF-alpha was elevated, while in Malawi but not Uganda early-stage TGF-beta was elevated. Thus, rapid disease progression in Uganda is associated with TNF-alpha-mediated inflammatory pathology, whereas in the milder disease observed in Malawi this may be ameliorated by counterinflammatory cytokines. These differing host responses may result either from differing virulence phenotypes of northern and southern trypanosomes or from immune response polymorphisms in the different host populations.

Will the real Trypanosoma brucei rhodesiense please step forward?

The sleeping sickness trypanosomes Trypanosoma brucei rhodesiense and T. brucei gambiense are morphologically indistinguishable from each other and from T. brucei brucei, which does not infect humans. The relationships between these three subspecies have been controversial. Several years ago, the characterization of T. brucei gambiense was reviewed in an attempt to clarify and draw together the results, and to put them in the context of the biology of the organism. The discovery of a gene associated with human-serum resistance in T. brucei rhodesiense and the consequent reappraisal of the identity of this trypanosome prompt this companion article.

Molecular characterization of field isolates of human pathogenic trypanosomes.

The accurate identification of each of the three subspecies of Trypanosoma brucei remains a challenging problem in the epidemiology of sleeping sickness. Advances in molecular characterization have revealed a much greater degree of heterogeneity within the species than previously supposed. Only group 1 T. b. gambiense stands out as a separate entity, defined by several molecular markers. T. b. rhodesiense is generally too similar to sympatric T. b. brucei strains to be distinguished from them by any particular molecular markers. Nevertheless, characterization of trypanosome isolates from humans and other animals has allowed the identification of potential reservoir hosts of T. b. rhodesiense. The recent discovery of a gene for human serum resistance may provide a useful marker for T. b. rhodesiense in the future. There have been few attempts to find associations between genetic markers and other biological characters, except human infectivity. However, virulence or fly transmissibility have been correlated with molecular markers in some instances.

Trypanosoma brucei: comparison of circulating strains in an endemic and an epidemic area of a sleeping sickness focus.

Human sleeping sickness in East Africa is characterized by periods of long-term endemicity interspersed with short-term epidemics. The factors generating these huge changes are largely uncharacterized but probably reflect complex interactions among socioeconomic factors, ecological factors, and the movement and diversity of trypanosome strains. To investigate the role of trypanosome strains in the generation of these epidemics, we addressed two important questions. (1) Are the trypanosome strains circulating within a focus the same during times of endemicity and during an epidemic? (2) How stable are trypanosome strains within a single animal reservoir host? Using restriction fragment length polymorphism analysis of repetitive DNA, we have examined the relationship between Trypanosoma brucei isolates, taken from the Busoga focus of human sleeping sickness, during an endemic period (Busia, Kenya, 1993-1994) and stocks isolated during an epidemic period (Tororo, Uganda, 1988-1990). We show that similar strains, including human infective strains, are circulating in domestic cattle (the most significant animal reservoir) in both epidemic and endemic areas of the Busoga focus. Furthermore, we show the important finding that individual animals harbor the same genotype of T. brucei for a period of time and may be clonal for a given parasite strain.

Genetic diversity among Trypanosoma brucei rhodesiense isolates from Tanzania.

We compared 19 stocks of Trypanosoma brucei rhodesiense collected in 1991 and 1994 from Tanzania with representative stocks from other foci of Rhodesian sleeping sickness in Zambia, Kenya and Uganda. Stocks were characterized by isoenzyme electrophoresis, restriction fragment length polymorphisms in variant surface glycoprotein genes and random amplification of polymorphic DNA; the banding patterns obtained were coded for numerical analysis. In addition, the Tanzanian stocks were compared by pulsed field gel electrophoresis. Overall the Tanzanian stocks formed a homogeneous group and the predominant genotype isolated in 1991 was still present in the 1994 sample, although at a reduced level. The Tanzanian stocks were distinct from representative stocks from other East African foci. This observation does not support the proposal that there are northern and southern strains of T. b. rhodesiense, but is consistent with the view that T. b. rhodesiense stocks form a mosaic of different genotypes varying from focus to focus in East Africa.

The subspecific taxonomy of Trypanosoma brucei.

Trypanosoma brucei was first seen by David Bruce in 1894, in the blood of a cow in South Africa, and named in his honour in 1899. Trypanosomes seen in the blood of an Englishman in The Gambia in 1901 were named T. gambiense in 1902. Finally, in 1909, trypanosomes from the blood of an Englishman in Zambia ("Rhodesia") were named T. rhodesiense. Since then there has been continuous debate about the interrelationships of these three "species". Studies of the molecular biology of these trypanosomes, mainly analyses of their isoenzymes and deoxyribonucleic acid, now appear to have shown that T. "rhodesiense" cannot be distinguished from T. brucei brucei by any valid and consistent criterion, while T. "gambiense" probably does constitute a valid subspecies of T. brucei. There is still doubt whether populations of T. brucei are predominantly clonal or sexual. While some form of genetic exchange undoubtedly can occur in this species, its nature and frequency are unknown and there is evidence that the population structure of T. brucei is essentially clonal.

Identification of trypanosomes in animals, humans and Glossina.

A number of biochemical methods are now available for the identification of African trypanosomes. The method of choice depends on the number of trypanosomes present in the sample and the taxonomic level required. DNA probes based on repetitive DNA elements allow identification to subgeneric (e.g. Trypanozoon), species (e.g. Trypanosoma congolense, T. simiae) or subspecific (e.g. T. congolense savannah) levels. These probes are particularly useful for identification of trypanosomes in the fly midgut, where sufficient numbers are present to allow simple dot blot hybridization to be used (> 100). Greater sensitivity has been achieved by amplification of these repetitive DNA sequences by PCR (polymerase chain reaction), so enabling the small numbers of trypanosomes found in the fly mouthparts to be identified (> 1). At the subspecific level, isoenzyme analysis and latterly RFLP (restriction fragment length polymorphism) analysis have been widely used to characterize isolates within the T. brucei species. Two other techniques, karyotype analysis and RAPD analysis, are also useful for fingerprinting isolates. Molecular karyotypes are produced by size fractionation of chromosomal DNAs by PFGE (pulsed field gel electrophoresis). RAPD (random amplified polymorphic DNA) is a PCR-based technique, using arbitrary primers to generate a fingerprint consisting of 20 or so bands.

Isoenzyme comparison of Trypanozoon isolates from two sleeping sickness areas of south-eastern Uganda.

The study characterized 151 Trypanozoon isolates from south-east Uganda by isoenzyme electrophoresis. Stocks were from a range of hosts, including man, cattle, pigs, dogs and Glossina fuscipes fuscipes: 104 isolates were from the Busoga area, 47 were from the Tororo district. Stocks were characterized on thin layer starch gel using eight enzyme systems: ALAT, ASAT, ICD, MDH, ME, NHD, NHI, PGM. Enzyme profiles were generally typical of East Africa; new patterns for ICD and ME were detected. Trypanosomes were classified on the basis of their profile by similarity coefficient analysis and the unweighted pair-group method using arithmetic averages (UPGMA). The majority of trypanosomes were classified in one or other of two genetically distinct groups which corresponded to the strain groups busoga and zambezi, both of which are associated with Rhodesian sleeping sickness in East Africa. Contingency table analyses indicated associations between certain isoenzymes of ICD and PGM, according to host and geographical origin. Significant relationships between trypanosome strain group and geographic origin were also demonstrated for some host groups.