Genetic diversity among Trypanosoma brucei rhodesiense isolates from Tanzania

Population genetic structure and temporal stability among Trypanosoma brucei rhodesiense isolates in Uganda

Background

The population structure and role of genetic exchange in African trypanosomes have been previously analyzed albeit with contradictory findings. To further investigate the role of genetic polymorphism on the population genetic structure of Trypanosoma b. rhodesiense, we hypothesized that parasite genotypes are clonal and stable over time.

Methods

We have undertaken a microsatellite marker analysis of T. b. rhodesiense isolates in a relatively new active HAT focus in Uganda (Kaberamaido-Dokolo-Amolatar) over a six-year period (2006–2012). We amplified six microsatellite markers by PCR directly from blood spotted FTA cards following whole genome amplification.

Results

The majority of loci demonstrated an excess of heterozygosity (Ho > He, F_IS < 0). We identified 26 unique genotypes among the 57 isolates, accounting for 45.6 % genotypic polymorphism. The presence of a high proportion of samples with repeated genotypes (54.4 %, 31/57), disagreement with Hardy-Weinberg equilibrium, and significant linkage disequilibrium between loci pairs, provide evidence that T. b. rhodesiense isolates from this focus are clonal. Our results show low values of F_ST’ (0–0.115) indicating negligible genetic differentiation across temporal isolates. Furthermore, predominant genotypes isolated in 2006 were still detectable in 2012.

Conclusions

Our findings confirm the notion that endemicity is maintained by stable genotypes rather than an influx of new genotypes. Our results have considerable importance in understanding and tracking the spread of sleeping sickness with significant implication to disease control.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1542-1) contains supplementary material, which is available to authorized users.

Genetic recombination between human and animal parasites creates novel strains of human pathogen

Genetic recombination between pathogens derived from humans and livestock has the potential to create novel pathogen strains, highlighted by the influenza pandemic H1N1/09, which was derived from a re-assortment of swine, avian and human influenza A viruses. Here we investigated whether genetic recombination between subspecies of the protozoan parasite, Trypanosoma brucei, from humans and animals can generate new strains of human pathogen, T. b. rhodesiense (Tbr) responsible for sleeping sickness (Human African Trypanosomiasis, HAT) in East Africa. The trait of human infectivity in Tbr is conferred by a single gene, SRA, which is potentially transferable to the animal pathogen Tbb by sexual reproduction. We tracked the inheritance of SRA in crosses of Tbr and Tbb set up by co-transmitting genetically-engineered fluorescent parental trypanosome lines through tsetse flies. SRA was readily transferred into new genetic backgrounds by sexual reproduction between Tbr and Tbb, thus creating new strains of the human pathogen, Tbr. There was no evidence of diminished growth or transmissibility of hybrid trypanosomes carrying SRA. Although expression of SRA is critical to survival of Tbr in the human host, we show that the gene exists as a single copy in a representative collection of Tbr strains. SRA was found on one homologue of chromosome IV in the majority of Tbr isolates examined, but some Ugandan Tbr had SRA on both homologues. The mobility of SRA by genetic recombination readily explains the observed genetic variability of Tbr in East Africa. We conclude that new strains of the human pathogen Tbr are being generated continuously by recombination with the much larger pool of animal-infective trypanosomes. Such novel recombinants present a risk for future outbreaks of HAT.

Genetic recombination allows transfer of harmful traits between different strains of the same pathogen and enables the emergence of genetically novel pathogen strains that the host population has not previously encountered. This can be particularly important when a pathogen acquires a virulence trait that allows it to spread beyond its normal host population. Here we show that this happens among the single-celled parasites—trypanosomes—that cause human African trypanosomiasis (HAT) or sleeping sickness carried by the tsetse fly. Genetic recombination readily occurs between the human and animal parasites when they are co-transmitted by the tsetse fly, creating new pathogen genotypes or strains. There is a single gene that confers human infectivity and each of the genotypes that inherits this gene is potentially capable of infecting humans. In this way new strains of the human pathogen can be generated by recombination between the human-infective and animal-infective trypanosomes. Such novel recombinants present a risk for future outbreaks of HAT.

Genetic diversity and population structure of Trypanosoma brucei in Uganda: implications for the epidemiology of sleeping sickness and Nagana

Background

While Human African Trypanosomiasis (HAT) is in decline on the continent of Africa, the disease still remains a major health problem in Uganda. There are recurrent sporadic outbreaks in the traditionally endemic areas in south-east Uganda, and continued spread to new unaffected areas in central Uganda. We evaluated the evolutionary dynamics underpinning the origin of new foci and the impact of host species on parasite genetic diversity in Uganda. We genotyped 269 Trypanosoma brucei isolates collected from different regions in Uganda and southwestern Kenya at 17 microsatellite loci, and checked for the presence of the SRA gene that confers human infectivity to T. b. rhodesiense.

Results

Both Bayesian clustering methods and Discriminant Analysis of Principal Components partition Trypanosoma brucei isolates obtained from Uganda and southwestern Kenya into three distinct genetic clusters. Clusters 1 and 3 include isolates from central and southern Uganda, while cluster 2 contains mostly isolates from southwestern Kenya. These three clusters are not sorted by subspecies designation (T. b. brucei vs T. b. rhodesiense), host or date of collection. The analyses also show evidence of genetic admixture among the three genetic clusters and long-range dispersal, suggesting recent and possibly on-going gene flow between them.

Conclusions

Our results show that the expansion of the disease to the new foci in central Uganda occurred from the northward spread of T. b. rhodesiense (Tbr). They also confirm the emergence of the human infective strains (Tbr) from non-infective T. b. brucei (Tbb) strains of different genetic backgrounds, and the importance of cattle as Tbr reservoir, as confounders that shape the epidemiology of sleeping sickness in the region.

Human African Trypanosomiasis (HAT) is a major health problem in Uganda, as there are recurrent sporadic outbreaks of the disease in traditionally endemic areas in south-east Uganda, and continued spread to new unaffected areas in central Uganda. In this study, we evaluate the evolutionary dynamics underpinning the origin of new disease foci and the impact of host species on parasite genetic diversity in Uganda. We found three distinct genetic clusters of T. brucei in Uganda and southwestern Kenya. Clusters 1 and 3 include isolates from central and southern Uganda, while cluster 2 contains mostly isolates from southwestern Kenya. These three clusters are not sorted by subspecies designation (T. b. brucei vs T. b. rhodesiense), host or date of collection. Our results show expansion of the disease to new foci in central Uganda occurred from the northward spread of T. b. rhodesiense. They also confirm the emergence of the human infective strains from non-infective T. b. brucei strains of different genetic backgrounds, and the importance of cattle as Tbr reservoir, as confounders that shape the epidemiology of sleeping sickness in the region.

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.

A spectrum of disease in human African trypanosomiasis: the host and parasite genetics of virulence

For over 50 years it has been known that there are considerable differences in the severity and rate of progression of both Trypanosoma brucei rhodesiense and T. b. gambiense infection between individuals. Yet research into the factors, whether parasite or host, which control virulence in Human African trypanosomiasis is in its infancy. In this paper we review the clinical evidence for virulence variation and the epidemiological and experimental data that give clues as to the mechanisms involved. Evidence will be presented for both asymptomatic forms of T. b. gambiense infection and low virulence forms of T. b. rhodesiense infection in humans. While in both cases the mechanisms remain to be elucidated, the overall infection virulence phenotype is determined by both parasite and host genotype.

Conserved sequence of the TgsGP gene in Group 1 Trypanosoma brucei gambiense

The trypanosome responsible for the majority of cases of human trypanosomiasis in Africa is Group 1 Trypanosoma brucei gambiense. Currently the most reliable test for the parasite is based on a single gene, which encodes a 47kDa receptor-like T. b. gambiense-specific glycoprotein, TgsGP, expressed in the flagellar pocket of bloodstream forms. Although TgsGP has been demonstrated in T. b. gambiense throughout its geographic range, similar genes have been demonstrated in other T. brucei sspp. isolates, and there are no data on the extent of sequence variation in TgsGP. Here we have carried out a comparison of TgsGP sequences in a range of Group 1 T. b. gambiense isolates and compared the gene to homologues in other T. brucei sspp. in order to provide information to support the use of this gene as the key identification target for Group 1 T. b. gambiense. We demonstrate that the sequence of TgsGP is well conserved in Group 1 T. b. gambiense across the endemic range of gambian human trypanosomiasis and confirm that this gene is a suitable target for specific detection of this parasite. The TgsGp-like genes in some isolates of T. b. brucei, T. b. rhodesiense and Group 2 T. b. gambiense are closely similar to VSG Tb10.v4.0178, which may be the ancestral gene from which TgsGP was derived.

Trypanosoma brucei gambiense: study of population genetic structure of Central African stocks using amplified fragment length polymorphism (AFLP)

To understand the maintenance and resurgence of historical Human African Trypanosomiasis (HAT) foci, AFLP was used to genotype 100 Central African Trypanosoma brucei s.l. stocks. This technique confirmed the high genetic stability of T. b. gambiense group 1 stocks and the micro genetic variability within Central African T. b. gambiense stocks. It revealed several T. b. gambiense genotypes and allowed the identification of minor and major genotypes in HAT foci. The coexistence of these genotypes in the same focus suggests that clustering of stocks according to HAT focus does not provide the true genetic picture of trypanosome circulating within the disease focus because the minor genotypes are generally underestimated. The presence of minor and major genotypes in HAT foci may explain the persistence and the resurgence of Central African sleeping sickness foci.

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.

Detection of Trypanosoma brucei rhodesiense in animals from sleeping sickness foci in East Africa using the serum resistance associated (SRA) gene

The human serum resistance associated (SRA) gene has been found exclusively in Trypanosoma brucei rhodesiense, allowing the unequivocal detection of this pathogen in reservoir hosts and the tsetse vector without recourse to laborious strain characterisation procedures. We investigated the presence of the SRA gene in 264 T. brucei ssp. isolates from humans, domestic animals and Glossina pallidipes from foci of human trypanosomiasis in Kenya and Uganda. The SRA gene was present in all isolates that were resistant to human serum, and absent from all serum sensitive isolates tested. Further, the gene was present in all isolates that had previously been shown to be identical to human infective trypanosomes by isoenzyme characterisation. The SRA gene was detected in isolates from cattle, sheep, pigs, dog, reedbuck, hyena and G. pallidipes from sleeping sickness foci, but was not found in Trypanosoma evansi or in Trypanosoma brucei gambiense isolates. The present study indicates that the SRA gene may be invaluable in detecting and differentiating T. brucei rhodesiense from other T. brucei ssp. in reservoir hosts and tsetse.

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.

The population genetics of Trypanosoma brucei and the origin of human infectivity

The African trypanosome, Trypanosoma brucei, is a zoonotic parasite transmitted by tsetse flies. Two of the three subspecies, T. brucei gambiense and T.b. rhodesiense, cause sleeping sickness in humans whereas the third subspecies, T.b. brucei, is not infective to humans. We propose that the key to understanding genetic relationships within this species is the analysis of gene flow to determine the importance of genetic exchange within populations and the relatedness of populations. T.brucei parasites undergo genetic exchange when present in infections of mixed genotypes in tsetse flies in the laboratory, although this is not an obligatory process. Infections of mixed genotype are surprisingly common in field isolates from tsetse flies such that there is opportunity for genetic exchange to occur. Population genetic analyses, taking into account geographical and host species of origin, show that genetic exchange occurs sufficiently frequently in the field to be an important determinant of genetic diversity, except where particular clones have acquired the ability to infect humans. Thus, T. brucei populations have an 'epidemic' genetic structure, but the better-characterized human-infective populations have a 'clonal' structure. Remarkably, the ability to infect humans appears to have arisen on multiple occasions in different geographical locations in sub-Saharan Africa. Our data indicate that the classical subspecies terminology for T. brucei is genetically inappropriate. It is an implicit assumption in most infectious disease biology that when a zoonotic pathogen acquires the capability to infect humans, it does so once and then spreads through the human population from that single-source event. For at least one major pathogen in tropical medicine, T. brucei, this assumption is invalid.

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.

Satellites, space, time and the African trypanosomiases

The human and animal trypanosomiases of Africa provide unique challenges to epidemiologists because of the spatial and temporal scales over which variation in transmission takes place. This chapter describes how our descriptions of the different components of transmission, from the parasites to the affected hosts, eventually developed to include geographical dimensions. It then briefly mentions two key analytical techniques used in the application of multi-temporal remotely sensed imagery to the interpretation of field data; temporal Fourier analysis for data reduction, and a variety of discriminant analytical techniques to describe the distribution and abundance of vectors and diseases. Satellite data may be used both for biological, process-based models and for statistical descriptions of vector populations and disease transmission. Examples are given of models for the tsetse Glossina morsitans in the Yankari Game Reserve, Nigeria, and in The Gambia. In both sites the satellite derived index of Land Surface Temperature (LST) is the best correlate of monthly mortality rates and is used to drive tsetse population models. The Gambia model is then supplemented with a disease transmission component; the mean infection rates of the vectors and of local cattle are satisfactorily described by the model, as are the seasonal variations of infection in the cattle. High and low spatial resolution satellite data have been used in a number of statistical studies of land cover types and tsetse habitats. In addition multi-temporal data may be related to both the incidence and prevalence of trypanosomiasis. Analysis of past and recent animal and human trypanosomiasis data from south-east Uganda supports the suggestion of the importance of cattle as a reservoir of the human disease in this area; mean infection prevalences in both human and animal hosts rise and fall in a similar fashion over the same range of increasing vegetation index values. Monthly sleeping sickness case data from the districts and counties of south-east Uganda are analysed and often show significant correlations with local LST. Case numbers increase with LST in areas that are relatively cooler than average for this part of Uganda, but decrease with LST in areas that are on average warmer. This indicates different seasonal cycles of risk across the region, and may be related to the differing vectorial roles of the two local tsetse, G. fuscipes and G. pallidipes. Finally, the increasing pace of change, and the likelihood of new or reemerging vector-borne diseases, highlight the need for accurate and timely information on habitat changes and the impacts these will have on disease transmission. The next generation of satellites will have significantly more spectral and spatial resolution than the current satellites, and will enable us to refine both statistical and biological predictions of trypanosomiasis and other vector-borne diseases within disease early warning systems.

Analysis of ploidy (in megabase chromosomes) in Trypanosoma brucei after genetic exchange

The megabase chromosomes of Trypanosoma brucei are normally diploid, but the extent to which this ploidy is maintained when parasites undergo genetic exchange is not known. To investigate this issue, a panel of 30 recombinant clones resulting from the co-transmission through tsetse flies of three different parental T. brucei lines in all pair-wise combinations (STIB 247, STIB 386 and TREU 927/4) were examined. These clones are products of 28 different mating events; four of them result from self-fertilisation and the others are F1 hybrids. DNA contents of the three parental lines were determined by flow cytometry and shown to differ only slightly with DNA content increasing in the order 927/4 < 247 < 386. Flow cytometry of the recombinant clones indicated DNA contents were similar to the parents in 28 clones and raised approximately 1.5 times the parental values in only two. The two F1 hybrid progeny with raised DNA contents were shown by marker analysis to be trisomic for seven independent loci indicating that they were probably triploid whereas progeny with DNA contents similar to parental values inherited a single allele from each parent for four independent loci indicating that they were diploid.

Genetic exchange in the trypanosomatidae

The only trypanosomatid so far proved to undergo genetic exchange is Trypanosoma brucei, for which hybrid production after co-transmission of different parental strains through the tsetse fly vector has been demonstrated experimentally. Analogous mating experiments have been attempted with other Trypanosoma and Leishmania species, so far without success. However, natural Leishmania hybrids, with a combination of the molecular characters of two sympatric species, have been described amongst both New and Old World isolates. Typical homozygotic and heterozygotic banding patterns for isoenzyme and deoxyribonucleic acid markers have also been demonstrated amongst naturally-occurring T. cruzi isolates. The mechanism of genetic exchange in T. brucei remains unclear, although it appears to be a true sexual process involving meiosis. However, no haploid stage has been observed, and intermediates in the process are still a matter for conjecture. The frequency of sex in trypanosomes in nature is also a matter for speculation and controversy, with conflicting results arising from population genetics analysis. Experimental findings for T. brucei are discussed in the first section of this review, together with laboratory evidence of genetic exchange in other species. The second section covers population genetics analysis of the large body of data from field isolates of Leishmania and Trypanosoma species. The final discussion attempts to put the evidence from experimental and population genetics into its biological context.

History of sleeping sickness in East Africa

The history of human sleeping sickness in East Africa is characterized by the appearance of disease epidemics interspersed by long periods of endemicity. Despite the presence of the tsetse fly in large areas of East Africa, these epidemics tend to occur multiply in specific regions or foci rather than spreading over vast areas. Many theories have been proposed to explain this phenomenon, but recent molecular approaches and detailed analyses of epidemics have highlighted the stability of human-infective trypanosome strains within these foci. The new molecular data, taken alongside the history and biology of human sleeping sickness, are beginning to highlight the important factors involved in the generation of epidemics. Specific, human-infective trypanosome strains may be associated with each focus, which, in the presence of the right conditions, can be responsible for the generation of an epidemic. Changes in agricultural practice, favoring the presence of tsetse flies, and the important contribution of domestic animals as a reservoir for the parasite are key factors in the maintenance of such epidemics. This review examines the contribution of molecular and genetic data to our understanding of the epidemiology and history of human sleeping sickness in East Africa.