Comparative analysis of a Trypanosoma brucei gambiense antigen gene family and its potential use in epidemiology of sleeping sickness

Identification of sVSG117 as an immunodiagnostic antigen and evaluation of a dual-antigen lateral flow test for the diagnosis of human African trypanosomiasis

BACKGROUND

The diagnosis of human African trypanosomiasis (HAT) caused by Trypanosoma brucei gambiense relies mainly on the Card Agglutination Test for Trypanosomiasis (CATT). There is no immunodiagnostic for HAT caused by T. b. rhodesiense. Our principle aim was to develop a prototype lateral flow test that might be an improvement on CATT.

METHODOLOGY/PRINCIPLE FINDINGS

Pools of infection and control sera were screened against four different soluble form variant surface glycoproteins (sVSGs) by ELISA and one, sVSG117, showed particularly strong immunoreactivity to pooled infection sera. Using individual sera, sVSG117 was shown to be able to discriminate between T. b. gambiense infection and control sera by both ELISA and lateral flow test. The sVSG117 antigen was subsequently used with a previously described recombinant diagnostic antigen, rISG65, to create a dual-antigen lateral flow test prototype. The latter was used blind in a virtual field trial of 431 randomized infection and control sera from the WHO HAT Specimen Biobank.

CONCLUSION/SIGNIFICANCE

In the virtual field trial, using two positive antigen bands as the criterion for infection, the sVSG117 and rISG65 dual-antigen lateral flow test prototype showed a sensitivity of 97.3% (95% CI: 93.3 to 99.2) and a specificity of 83.3% (95% CI: 76.4 to 88.9) for the detection of T. b. gambiense infections. The device was not as good for detecting T. b. rhodesiense infections using two positive antigen bands as the criterion for infection, with a sensitivity of 58.9% (95% CI: 44.9 to 71.9) and specificity of 97.3% (95% CI: 90.7 to 99.7). However, using one or both positive antigen band(s) as the criterion for T. b. rhodesiense infection improved the sensitivity to 83.9% (95% CI: 71.7 to 92.4) with a specificity of 85.3% (95% CI: 75.3 to 92.4). These results encourage further development of the dual-antigen device for clinical use.

Using detergent to enhance detection sensitivity of African trypanosomes in human CSF and blood by loop-mediated isothermal amplification (LAMP)

BACKGROUND

The loop-mediated isothermal amplification (LAMP) assay, with its advantages of simplicity, rapidity and cost effectiveness, has evolved as one of the most sensitive and specific methods for the detection of a broad range of pathogenic microorganisms including African trypanosomes. While many LAMP-based assays are sufficiently sensitive to detect DNA well below the amount present in a single parasite, the detection limit of the assay is restricted by the number of parasites present in the volume of sample assayed; i.e. 1 per µL or 10(3) per mL. We hypothesized that clinical sensitivities that mimic analytical limits based on parasite DNA could be approached or even obtained by simply adding detergent to the samples prior to LAMP assay.

METHODOLOGY/PRINCIPAL FINDINGS

For proof of principle we used two different LAMP assays capable of detecting 0.1 fg genomic DNA (0.001 parasite). The assay was tested on dilution series of intact bloodstream form Trypanosoma brucei rhodesiense in human cerebrospinal fluid (CSF) or blood with or without the addition of the detergent Triton X-100 and 60 min incubation at ambient temperature. With human CSF and in the absence of detergent, the LAMP detection limit for live intact parasites using 1 µL of CSF as the source of template was at best 10(3) parasites/mL. Remarkably, detergent enhanced LAMP assay reaches sensitivity about 100 to 1000-fold lower; i.e. 10 to 1 parasite/mL. Similar detergent-mediated increases in LAMP assay analytical sensitivity were also found using DNA extracted from filter paper cards containing blood pretreated with detergent before card spotting or blood samples spotted on detergent pretreated cards.

CONCLUSIONS/SIGNIFICANCE

This simple procedure for the enhanced detection of live African trypanosomes in biological fluids by LAMP paves the way for the adaptation of LAMP for the economical and sensitive diagnosis of other protozoan parasites and microorganisms that cause diseases that plague the developing world.

The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis

Background

Trypanosoma brucei gambiense is the causative agent of chronic Human African Trypanosomiasis or sleeping sickness, a disease endemic across often poor and rural areas of Western and Central Africa. We have previously published the genome sequence of a T. b. brucei isolate, and have now employed a comparative genomics approach to understand the scale of genomic variation between T. b. gambiense and the reference genome. We sought to identify features that were uniquely associated with T. b. gambiense and its ability to infect humans.

Methods and Findings

An improved high-quality draft genome sequence for the group 1 T. b. gambiense DAL 972 isolate was produced using a whole-genome shotgun strategy. Comparison with T. b. brucei showed that sequence identity averages 99.2% in coding regions, and gene order is largely collinear. However, variation associated with segmental duplications and tandem gene arrays suggests some reduction of functional repertoire in T. b. gambiense DAL 972. A comparison of the variant surface glycoproteins (VSG) in T. b. brucei with all T. b. gambiense sequence reads showed that the essential structural repertoire of VSG domains is conserved across T. brucei.

Conclusions

This study provides the first estimate of intraspecific genomic variation within T. brucei, and so has important consequences for future population genomics studies. We have shown that the T. b. gambiense genome corresponds closely with the reference, which should therefore be an effective scaffold for any T. brucei genome sequence data. As VSG repertoire is also well conserved, it may be feasible to describe the total diversity of variant antigens. While we describe several as yet uncharacterized gene families with predicted cell surface roles that were expanded in number in T. b. brucei, no T. b. gambiense-specific gene was identified outside of the subtelomeres that could explain the ability to infect humans.

Sleeping sickness, or Human African Trypanosomiasis, is a disease affecting the health and productivity of poor people in many rural areas of sub-Saharan Africa. The disease is caused by a single-celled flagellate, Trypanosoma brucei, which evades the immune system by periodically switching the proteins on its surface. We have produced a genome sequence for T. brucei gambiense, which is the particular subspecies causing most disease in humans. We compared this with an existing reference genome for a non-human infecting strain (T. b. brucei 927) to identify genes in T. b. gambiense that might explain its ability to infect humans and to assess how well the reference performs as a universal plan for all T. brucei. The genome sequences differ only due to rare insertions and duplications and homologous genes are over 95% identical on average. The archive of surface antigens that enable the parasite to switch its protein coat is remarkably consistent, even though it evolves very quickly. We identified genes with predicted cell surface functions that are only present in T. b. brucei and have evolved rapidly in recent time. These genes might help to explain variation in disease pathology between different T. brucei strains in different hosts.

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.

Fly transmission and mating of Trypanosoma brucei brucei strain 427

Like yeast, Trypanosoma brucei is a model organism and has a published genome sequence. Although T. b. brucei strain 427 is used for studies of trypanosome molecular biology, particularly antigenic variation, in many labs worldwide, this strain was not selected for the genome sequencing project as it is monomorphic and unable to complete development in the insect vector. Instead, the fly transmissible, mating competent strain TREU 927 was used for the genome project, but is not as easily grown or genetically manipulable as strain 427; furthermore, recent findings have spread concern on the potential human infectivity of TREU 927. Here we show that a 40-year-old cryopreserved line of strain 427, Variant 3, is fly transmissible and also able to undergo genetic exchange with another strain of T. b. brucei. Comparison of Variant 3 with lab isolates of 427 shows that all have variant surface glycoprotein genes 117, 121 and 221, and identical alleles for 3 microsatellite loci. Therefore, despite some differences in molecular karyotype, there is no doubt that Variant 3 is an ancestral line of present day 427 lab isolates. Since Variant 3 grows fast both as bloodstream forms and procyclics and is readily genetically manipulable, it may prove useful where a fly transmissible version of 427 is required.

Variant Surface Glycoprotein gene repertoires in Trypanosoma brucei have diverged to become strain-specific

Background

In a mammalian host, the cell surface of African trypanosomes is protected by a monolayer of a single variant surface glycoprotein (VSG). The VSG is central to antigenic variation; one VSG gene is expressed at any one time and there is a low frequency stochastic switch to expression of a different VSG gene. The genome of Trypanosoma brucei contains a repertoire of > 1000 VSG sequences. The degree of conservation of the genomic VSG repertoire in different strains has not been investigated in detail.

Results

Eighteen expressed VSGs from Ugandan isolates were compared with homologues (> 40 % sequence identity) in the two available T. brucei genome sequences. Fourteen homologues were present in the genome of Trypanosoma brucei brucei TREU927 from Kenya and fourteen in the genome of T. b. gambiense Dal972 from Cote d'Ivoire. The Ugandan VSGs averaged 71% and 73 % identity to homologues in T. b. brucei and T. b. gambiense respectively. The sequence divergence between homologous VSGs from the three different strains was not random but was more prevalent in the parts of the VSG believed to interact with the host immune system on the living trypanosome.

Conclusion

It is probable that the VSG repertoires in the different isolates contain many common VSG genes. The location of divergence between VSGs is consistent with selection for strain-specific VSG repertoires, possibly to allow superinfection of an animal by a second strain. A consequence of strain-specific VSG repertoires is that any vaccine based on large numbers of VSGs from a single strain will only provide partial protection against other strains.

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.

From silent genes to noisy populations-dialogue between the genotype and phenotypes of antigenic variation

African trypanosomes evade humoral immunity through antigenic variation whereby, they switch expression of the variant surface glycoprotein (VSG) gene encoding their glycoprotein surface coat. Switching proceeds by duplication from an archive of silent VSG genes into a transcriptionally active locus, and precedent suggests silent genes can contribute, combinatorially to formation of expressed, functional genes through segmental gene conversion. The genome project has revealed that most of the silent archive consists of hundreds of VSG genes in subtelomeric tandem arrays, and that most of these are not functional genes. The aim of this review is to explore links between the uncovered trypanosome genotype and the phenotype of antigenic variation, stretching from the broad phenotype-transmission in the field and the overcoming of herd immunity-to events within single infections. Highlighting in particular the possible impact of phenotype selection on the evolution of the VSG archive and the mechanisms for its expression leads to a theoretical framework to further our understanding of this complex immune evasion strategy.

Will the real Trypanosoma b. gambiense please stand up

Controversy has surrounded the differentiation of Trypanosoma brucei gambiense from T. b. rhodesiense (causative agents of Gambian and Rhodesian sleeping sickness, respectively) almost from the moment they were named. In the light of recent findings from biochemical and immunological characterization studies, Wendy Gibson reviews the status of T. b. gambiense to see if there is now a consensus concerning its identity.

Use of mobile genetic elements as tools for molecular epidemiology

Trypanosomiasis is a complex zoonotic disease where human-infective and non-human-infective strains of Trypanosoma brucei interact in the same transmission cycles. Differentiating these strains is paramount to understanding disease epidemiology. Restriction fragment length polymorphism analysis of repetitive DNA has provided such a method for distinguishing human and non-human isolates. Unfortunately, this approach requires large amounts of material and a more rapid approach is required. We have developed a novel technique, mobile genetic element-PCR, for assaying for positional variation of the mobile genetic element, RIME. The trypanosome genome contains up to 400 copies of RIME. Using this approach we have observed considerable variation between strains of T. brucei. Such a technique may offer potential as a method for differentiating non-human- and human-infective trypanosomes and shows promise as a rapid sensitive tool for investigating the epidemiology of sleeping sickness.

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.

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.

Expression of a variant surface glycoprotein of Trypanosoma gambiense in procyclic forms of Trypanosoma brucei shows that the cell type dictates the nature of the glycosylphosphatidylinositol membrane anchor attached to the glycoprotein

Procyclic forms of Trypanosoma brucei have been genetically modified to express the major metacyclic variant surface glycoprotein (VSG variant AnTat 11.17) of Trypanosoma gambiense. The VSG is expressed in an intact membrane-bound form that can be detected over the entire plasma membrane, together with procyclin, and as a series of lower-molecular-mass fragments that are mostly soluble degradation products. The presence of degraded VSG in the cells and the culture medium suggests that VSG is not efficiently processed and/or efficiently folded when expressed in procyclic cells. The level of procyclin expressed on the surface of these cells is slightly reduced, although there is no difference in procyclin mRNA levels. The intact membrane-bound form of the VSG is N-glycosylated with oligomannose structures and contains a glycosylphosphatidylinositol (GPI) membrane anchor that can be biosynthetically labelled with [3H]ethanolamine. The anchor is sensitive to mammalian GPI-specific phospholipase D but, like the anchor of procyclin, it is resistant to the action of bacterial phosphatidylinositol-specific phospholipase C. This pattern of phospholipase sensitivity suggests that the GPI anchor acquired by VSG when expressed in procyclics is acylated on the inositol ring and therefore resembles a procyclic procyclin-type anchor rather than a trypomastigote VSG-type anchor with respect to the lipid structure. The VSG expressed in procyclics was sensitive to the action of a mixture of sialidase, beta-galactosidase and beta-hexosaminidase, suggesting that the VSG GPI anchor also contains a sialylated polylactosamine side-chain modification similar to that described for procyclin. These results indicate that the nature of the protein expressed has little influence on the post-translational modifications performed in the secretory pathway of procyclic trypanosomes.

Wide variation in DNA content among isolates of Trypanosoma brucei ssp

The DNA contents of 18 Trypanosoma brucei ssp. stocks were compared using flow cytometry, karyotype analysis and quantitation of repetitive DNA by Southern blotting and hybridisation. The DNA contents of Type 1 T. b. gambiense stocks were lower than those of non-gambiense stocks, but both groups showed a wide range of variation in DNA content. Amongst T. b. gambiense stocks. Mabia at the lower end of the range had 14% less DNA than Dal 972 at the top of the range. Similarly, amongst non-gambiense stocks. 117R at the lower end of the range had 14% less DNA than LM55 at the top of the range. The T. b. gambiense stock Mabia had 29% less DNA than non-gambiense stock LM55. The DNA content of Type II T. b. gambiense stocks had minichromosomes albeit fewer than non-gambiense stocks. This result was verified by hybridisation with probes for satellite DNA and a telomere-specific repeat. Hybridisation with the probe for the beta-tubulin genes also revealed an apparent reduction of gene copy number T. b. gambiense relative to non-gambiense stocks. In conclusion, there is a wide range of variation in genome size in T. brucei ssp., with T. b. gambiense stocks at the lower end of the range. The reduction in genome size correlates with loss of repeated genes and non-coding sequences in T. b. gambiense stocks, and is not continued to chromosomes of a particular size.

Characterization of Trypanosoma brucei gambiense isolates using restriction fragment length polymorphisms in 5 variant surface glycoprotein genes

Fifty-eight Type I Trypanosoma brucei gambiense (G) stocks, including 16 from 3 sleeping sickness foci in Cameroon, were compared by Restriction Fragment Length Polymorphism (RFLP) analysis with 14 T.b. brucei and T.b. rhodesiense stocks from various endemic areas of Africa. Loci examined were for 5 variant surface glycoprotein (VSG) genes: the LiTat 1.3, AnTat 11.17 and 2K genes were present as single copy genes, while the VSG 117 and U2 gene probes hybridised with a family of related genes. The RFLP data were subjected to cluster analysis to produce a dendrogram constructed from similarity coefficients. The LiTat 1.3 and AnTat 11.17 genes are considered to be characteristic of G stocks, and neither gene was found in the non-G stocks; however, the LiTat 1.3 gene was absent from 6 of the 58 G stocks, while the AnTat 11.17 gene was absent from 8. Supplementation of the LiTat 1.3 antigen in the Card Agglutination Test for Trypanosomiasis with the AnTat 11.17 antigen might thus improve performance of the test, particularly in Cameroon. The U2 VSG gene probe gave a characteristic RFLP pattern for G stocks, as did the VSG 117 gene; the latter is an isogene of AnTat 1.8 previously used extensively to characterise G stocks by other workers. The 2K gene was absent in some G stocks, while present in some non-G stocks, and was not therefore useful for characterisation of G stocks. In cluster analysis, the T.b. gambiense stocks formed a large homogeneous group, subdivided into 5 subgroups, with the non-gambiense stocks as a heterogeneous outgroup.

Evaluation of variant specific trypanolysis tests for serodiagnosis of human infections with Trypanosoma brucei gambiense

Twelve T.b. gambiense clone populations of distinct Variable Antigen Type (VAT) were combined in immune lysis tests with 340 sera of trypanosome infected patients from 8 different African countries and 267 non trypanosomiasis control sera. The diagnostic specificity of the test was 100%. At a serum dilution of 1:4 the overall test sensitivity with single VATs varied from 39.1 to 98.2% and from 12.1 to 86.8% at 1:32. At a serum dilution of 1:32 some combination tests with 2 VATs still scored above 96%. The VAT recognition patterns were clearly correlated with the geographical origin of the sera, reflecting a diversity in variable antigen repertoires.

The isolation and genetic heterogeneity of Trypanosoma brucei gambiense from north-west Uganda

Fifty-two samples of blood were taken from sleeping sickness patients in north-west Uganda. All samples failed to infect immunosuppressed mice. Ten cryopreserved blood samples were fed to laboratory bred Glossina morsitans morsitans; eight flies developed midgut infections from which procyclic cultures were established in vitro. Isoenzyme electrophoretic analysis of 9 enzymes revealed that 7 of the 8 trypanosome isolates had a combination of enzyme patterns already described for Trypanosoma brucei gambiense. The eighth isolate had a different aspartate aminotransferase polymorphism which placed it in a new zymodeme. Analysis of polymorphisms in genes for 3 variant surface glycoproteins (VSGs) confirmed that the 8 Ugandan trypanosome isolates were T.b.gambiense and revealed further heterogeneity. The VSG 117 gene was present in all the isolates in a pattern of fragments (equivalent to AnTat 1.8) characteristic for T.b.gambiense. For two other VSG genes characteristic of T.b.gambiense, the LiTat 1.3 gene was present in all the isolates, while the AnTat 11.17 gene was present in only 2 of the 8 isolates.

Identification of Trypanosoma brucei gambiense by PCR amplification of variant surface glycoprotein genes

We have developed a sensitive and specific method to identify Trypanosoma brucei gambiense using the polymerase chain reaction (PCR) to amplify the gene encoding variant surface glycoprotein (VSG) Antat 11.17. The test was capable of distinguishing T. b. gambiense from T. b. brucei in most foci of gambian sleeping sickness and gave positive results with previously well-characterised Type I T. b. gambiense stocks from Ivory Coast, Nigeria, Cameroon, Congo, Zaire and Sudan. The test gave negative results with T. b. rhodesiense from Zambia, Kenya and Uganda, virulent or Type II T. b. gambiense from Ivory Coast and T. b. brucei stocks from East and West Africa. The test was modified for colorimetric detection in dot blot format by using nested biotinylated primers in a two-step reaction. Comparison of DNA sequences of VSG genes from T. b. gambiense and other T. brucei ssp. stocks showed a high level of homology, suggesting recent gene flow.

Genomic organization and context of a trypanosome variant surface glycoprotein gene family

We have defined the genomic organization and genomic context of a Trypanosoma brucei brucei gene family encoding variant surface glycoproteins (VSGs). This gene family is neither tandemly repeated nor closely linked in the genome, and is not located on small or intermediate size chromosomes. Two dispersed repeated sequence elements, RIME-ingi and the upstream repeat sequence, are linked to members of this gene family; however, the upstream repeat sequences are closely linked only to the basic copy. In other isolates of T.b. brucei this gene family appears conserved with some variation; a restriction fragment length polymorphism found among these isolates suggests the hypothesis that VSG genes may occasionally be diploid. A model accounting for both the generation of dispersed families of VSG genes, and for the interstrain variability of VSG genes, is proposed.

Absence of the LiTat 1.3 (CATT antigen) gene in Trypanosoma brucei gambiense stocks from Cameroon

Antibodies to the variable antigen type (VAT) designated LiTat 1.3 are common in sera from parasitologically confirmed patients with gambian sleeping sickness. For this reason, LiTat 1.3 has been considered a suitable antigen for detecting Trypanosoma brucei gambiense in the Card Agglutination Test for Trypanosomiasis (CATT; Testryp-CATT, Smith Kline-RIT). However, surveys in the T.b. gambiense endemic focus of Fontem in Cameroon have suggested that expression of LiTat 1.3 might be rare or absent. We show here that the gene for LiTat 1.3 was indeed absent from some T.b. gambiense stocks isolated from this focus, and a LiTat 1.3-like gene was present in others. The divergent gene differed from the cloned version of LiTat 1.3. In addition, antibodies to LiTat 1.3 could not be detected in rabbits infected with either of the two kinds of T.b. gambiense from the Fontem area. We suggest that the absence of LiTat 1.3 expression in this focus may have important implications for the epidemiology and control of sleeping sickness, especially if heavy reliance is placed on the CATT.

High homology between variant surface glycoprotein gene expression sites of Trypanosoma brucei and Trypanosoma gambiense

The AnTat 11.17 variant surface glycoprotein (VSG) is synthesized in both metacyclic and bloodstream forms of Trypanosoma gambiense. We have characterized the AnTat 11.17 gene, and analyzed its expression site (ES) in the bloodstream form by Southern and Northern blotting with probes from the Trypanosoma brucei AnTat 1.3A VSG ES, and by run-on transcription. The AnTat 11.17 ES is located at the end of a 700-kb chromosome. It appears to contain all the genes (ESAGs, for Expression Site-Associated Genes) present in the AnTat 1.3A VSG ES, with the possible exception of ESAG 1. Limited nucleotide sequence analysis of ESAG cDNAs from the AnTat 11.17 ES shows considerable conservation with ESAGs of T. brucei. The transcription promoter of the AnTat 11.17 VSG ES, localized by virtue of the specific accumulation of promoter-proximal transcripts which occurs following UV irradiation, was found to be at the same relative position to the first ESAG (ESAG 7) as in AnTat 1.3A.

The molecular epidemiology of parasites

The explosion of new techniques, made available by the rapid advance in molecular biology, has provided a battery of novel approaches and technology which can be applied to more practical issues such as the epidemiology of parasites. In this review, we discuss the ways in which this new field of molecular epidemiology has contributed to and corroborated our existing knowledge of parasite epidemiology. Similar epidemiological questions can be asked about many different types of parasites and, using detailed examples such as the African trypanosomes and the Leishmania parasites, we discuss the techniques and the methodologies that have been or could be employed to solve many of these epidemiological problems.

An expression-site-associated gene family of trypanosomes is expressed in vivo and shows homology to a variant surface glycoprotein gene

Utilizing first-strand cDNA from different stages, a gene family was identified that is expressed in bloodstream form trypanosomes but not in cultured procyclic forms. This family of 50-100 genes, termed bloodstream-specific 1 (BS1), shares a chromosomal distribution pattern similar to the variant surface glycoprotein (VSG) genes and the expression-site-associated genes (ESAGs). The BS1 genes are expressed in several variants of Trypanosoma brucei brucei and in Trypanosoma brucei gambiense. Sequence analysis of five members of this gene family reveals the recently described ESAG 6 and ESAG 7 genes as well as the ESAG X gene to be members of this family. We have been unable to localize the BS1 gene product in the cell but show that chronically infected rabbit serum recognizes recombinant BS1 protein arguing for expression in vivo. Finally we note that the derived protein sequence for the BS1 genes suggests an evolutionary relationship with at least one variant surface glycoprotein gene, and hence these studies may provide clues to understanding the molecular origins of antigenic variation in trypanosomes.

A new method for isolating Trypanosoma brucei gambiense from sleeping sickness patients

Low infectivity to laboratory mammals and low virulence make Trypanosoma brucei gambiense difficult to isolate and grow in amounts sufficient for biochemical characterization. We report the isolation of T.b. gambiense by feeding cryopreserved primary isolates to laboratory-reared Glossina morsitans morsitans, followed by rapid cultivation in vitro of procyclic forms dissected from infected tsetse fly midguts. This technique allows the characterization of hitherto unsampled populations and avoids selection due to long-term subpassage. Of 16 primary isolates from trypanosomiasis patients of the Fontem focus in Cameroon, 12 (75%) produced infections in tsetse whereas only 4 (25%) infected rats. Ten isolates were subsequently cultivated as procyclic forms in vitro; 2 failed to grow owing to bacterial contamination. In addition, 2 primary isolates from Côte d'Ivoire patients and a stock of low virulence from the Congo Republic were similarly grown. Only one primary isolate produced tsetse salivary gland infections, an observation consistent with the hypothesis that some populations of T.b. gambiense are intrinsically incompatible with G.m. morsitans.

Characterization of West African Trypanosoma (Trypanozoon) brucei isolates from man and animals using isoenzyme analysis and DNA hybridization

A total of 18 West African Trypanosoma (Trypanozoon) brucei stocks isolated from man and animals were characterized using isoenzyme analysis with isoelectric focusing (IEF) and DNA hybridization. They were compared with four T. (T.) brucei isolates from East and West Africa that had previously been analysed and well defined. All experiments were carried out with cell lysates of procyclic trypanosomes produced in vitro. The different stocks could be separated into two distinct groups according to their isoenzyme and DNA patterns. The homogeneous group of T. b. gambiense was characterized by zymodeme A and highly specific DNA-banding patterns (type G) always associated with stable human serum resistance. The non-gambiense group (consisting of T.b. rhodesiense and T.b. brucei) was determined by a great variation in these markers. Our results clearly indicate the existence, of T.b. rhodesiense-like parasites in West African patients. Due to their lack of human serum resistance, the four characterized animal isolates can be referred to as T. b. brucei.

Different allele frequencies in Trypanosoma brucei brucei and Trypanosoma brucei gambiense populations

Restriction fragment length polymorphism (RFLP) has been analysed in Trypanosoma brucei DNA following hybridization with different DNA probes. This polymorphism seems to be due to allelic variation, and not to variation between sequence duplicates, since the genomic environment of the probed polymorphic fragments is conserved over considerable distances. In an analysis of 35 non-gambiense stocks, we found different combinations of homozygotes and heterozygotes for the four RFLP probes used, in keeping with previous observations that genetic reassortment occurs in T. b. brucei. Moreover, the non-gambiense populations from West and East Africa can be differentiated according to their characteristic allele frequencies. In sharp contrast, we found that the 49 T. b. gambiense stocks, analysed with the same probes, share the same single allelic combination and are all homozygous for each one of the four markers. This characteristic gambiense allele combination is very common among Western non-gambiense isolates, but rare or absent among Eastern ones. Two stocks isolated from man in West Africa turned out to be non-gambiense by all molecular criteria examined, including total nuclear DNA content. Taken together, these observations suggest that human serum-resistant variants may appear among the West African T. b. brucei population, and that T. b. gambiense evolved from one of these resistant variants as a man-adapted subspecies that became genetically isolated from the rest of the West African trypanosome population.

The genome and the antigen gene repertoire of Trypanosoma brucei gambiense are smaller than those of T. b. brucei

The amount of nuclear DNA of Trypanosoma brucei gambiense is only 70% of that of T. b. brucei. The difference is partially due to depletion of 50-150 kb mini-chromosomes in T. b. gambiense, as well as a reduction in the content of some repetitive DNA families. Quantitation of 'barren' DNA regions characteristic of the 5' environment of telomeric antigen genes confirms that the T. b. gambiense genome contains fewer chromosome ends, and thus most probably fewer telomeric antigen genes, than T. b. brucei. The extent of the antigen gene repertoire of the two subspecies has been estimated by hybridization with probes specific for the conserved 3' region of antigen genes. It appears that the repertoire of the gambiense subspecies is only about 50% of that of T. b. brucei. These observations are discussed with regard to the stability of the T. b. gambiense repertoire.

Enzyme polymorphism and the identity of Trypanosoma brucei gambiense

Thirty-two isolates from man in known areas of Gambian trypanosomiasis, in the Sudan, Kenya, Zaire, Nigeria, Ivory Coast, Burkina Faso, Liberia and Senegal, were examined by isoenzyme electrophoresis of 11 enzymes. Comparisons were also made with our previously published results on 23 other stocks of similar origins, which had been examined in the same manner. All those stocks of low initial virulence to laboratory rodents, which thus conform to the accepted view of the behaviour of Trypanosoma brucei gambiense can be identified by characteristic combinations of enzyme patterns, especially certain aminotransferase markers. A limited study of superoxide dismutase polymorphism suggested a further marker of value. The isolates of high initial virulence to rodents, which are thus behaviourally akin to T. b. rhodesiense, did not share these characteristics. We conclude that there exists a homogeneous group of trypanosomes of wide dispersion throughout tropical Africa, characterized by certain isoenzyme combinations and low initial virulence to rodents, which corresponds to the classical concept of T. b. gambiense. The features of limited antigenic repertoire, high resistance to normal human serum and restriction fragment length polymorphisms of the genes for certain variant surface glycoproteins also appear to be characteristic of this group.

Isoenzyme characterization of trypanosomes of the subgenus Herpetosoma

Isoenzyme analysis was used to characterize 6 species of trypanosomes of the subgenus Herpetosoma using 13 different enzyme systems. The species studied were Trypanosoma lewisi, T. musculi, T. grosi, T. microti, T. evotomys and T. nabiasi which cannot be distinguished on morphological grounds. Extracts for thin-layer starch-gel electrophoresis were prepared from cultures of insect forms in either Schneider's Drosophila or Grace's insect tissue culture media with foetal calf serum or a nutrient agar medium. Extracts of T. lewisi and T. musculi bloodstream forms were also run for comparison. All parasites gave distinct patterns which enabled them to be differentiated on one or more enzyme systems. Two types of computer analysis were used to group the parasites; using these techniques the murine parasites T. lewisi, T. musculi and T. grosi fell into one broad group, and T. microti and T. evotomys of microtine rodents formed another. These findings are in accord with earlier observations on the behavioural characteristics of these parasites in their mammalian host and their vector (fleas). The clear differences observed provide the basis for the application of other biochemical and immunological techniques for differentiation within this subgenus of trypanosomes.

Nucleic acid probes in clinical microbiology

The infectious disease applications of nucleic acid probe have been described. In addition, the basic procedures of nucleic acid probe technology have been discussed, as have the factors affecting implementation of probe technology in diagnostic laboratories. Despite the questions raised, nucleic acid probes will become part of the diagnostic laboratory in the near future. Commercial interests are developing and marketing new probes, reagents, and kits which will expedite the employment of this technology. High-volume reference laboratories will first use probes as part of a battery of tests which will include ELISA and monoclonal antibody methods. In all probability, probes will replace methods: that have proven to be ineffective, difficult, or costly such as culturing for some enteric pathogens and Legionella, that require long incubation periods, such as mycobacteria, or that have high costs and low yields, such as virology.

Evolutionary aspects of trypanosomes: analysis of genes

The genes for four glycolytic enzymes of Trypanosoma brucei have been analyzed. The proteins encoded by these genes show 38-57% identity with their counterparts in other organisms, whether pro- or eukaryotic. These data are consistent with a phylogenetic tree in which trypanosomes diverged very early from the main branch of the eukaryotic lineage. No definite conclusion can be drawn yet about the evolutionary origin of glycosomes, the microbodies of trypanosomes which contain most enzymes of the glycolytic pathway. A bias could be observed in the codon usage of the glycolytic genes and genes for other housekeeping proteins, indicating that trypanosomes may have selected a nucleotide sequence that enables efficient translation. However, the genes for variant surface glycoproteins (VSGs) do not show such a bias. This lack of preference for special codons is explained by the high evolutionary rate that could be observed for VSG genes.

Rapid change of the repertoire of variant surface glycoprotein genes in trypanosomes by gene duplication and deletion

To study the evolution of the variant surface glycoprotein (VSG) repertoire of trypanosomes we have analysed the DNA region surrounding the VSG 118 gene in different trypanosome strains. We find a remarkable degree of variation in this area. Downstream from the 118 gene a 5.7 X 10(3) base-pair DNA segment containing a potential VSG gene has been quadruplicated in strain 427 of Trypanosoma brucei, but not in most other strains analysed. The VSG 1.1000 gene, located immediately upstream from the 118 gene in one trypanosome strain, has been cleanly deleted in another. Our results are most easily explained by multiple unequal cross-overs between sister chromatids and are the first indication that sister chromatid exchange occurs in trypanosomes.

The use of DNA hybridization and numerical taxonomy in determining relationships between Trypanosoma brucei stocks and subspecies

The nuclear DNAs of 71 trypanosome stocks from different African countries, representative of the three Trypanosoma brucei subspecies, and one T. evansi stock, have been analysed by the combined use of restriction endonuclease digestion, gel electrophoresis and molecular hybridization with both trypanosome surface-antigen-specific and undefined genomic DNA probes. In contrast with T. brucei brucei and T. brucei rhodesiense stocks, all the T. b. gambiense stocks are characterized by a conserved, specific DNA band pattern, regardless of the probe. This allows T. b. gambiense to be non-ambiguously identified. On the contrary, T.b. brucei and T. b. rhodesiense, which could not be discriminated by the same criteria, both yield highly variable DNA band patterns. Our data confirm that domestic animals like pig, dog and sheep constitute a potential reservoir for T.b. gambiense. Using a numerical analysis of the DNA hybridization patterns we have measured the degree of similarity between the 72 trypanosome stocks. This investigation shows that all T.b. gambiense stocks are included in the same homogeneous population, while the stocks from the two other subspecies seem to be distributed in several heterogeneous groups, some of these showing correlation with the geographical origin of the trypanosomes. It is concluded that (i) T.b. gambiense stands out as a real subspecies that has undergone a distinct evolution relative to the 'non-gambiense' group, (ii) the alleged T.b. rhodesiense subspecies does not fit with any of the groups evidenced by our cladistic analysis and hence does not appear as a distinct subspecies and (iii) 'non-gambiense' trypanosomes are probably evolving much more rapidly than T.b. gambiense. Different aspects of trypanosome relationships and evolution are discussed.

Trypanosoma brucei: the extent of conversion in antigen genes may be related to the DNA coding specificity

The boundaries of gene conversion in variant-specific antigen genes have been determined in six clones of Trypanosoma brucei. In each clone, antigenic switching involved interaction between two telomeric members of the AnTat 1.1 multigene family, which share extensive homology throughout their coding regions. All conversion events occurred by substitution of faithful copies of donor sequences. Conversion endpoints were nonrandomly distributed. In four clones, the 5' conversion limit was near the antigen translation initiation codon, while in three clones, the 3' conversion limit was located at the "hinge" between the two major antigen domains. In one case, two segmental conversions were involved in antigen switching. These observations reveal that antigen gene conversion can occur without generating point mutations, and suggest that postrecombinational selection may impose a limit on the number of possible rearrangements within antigen genes.

Comparison of African trypanosomes of different antigenic phenotypes, subspecies and life cycle stages by two-dimensional gel electrophoresis

High resolution two-dimensional polyacrylamide gel (2D gel) electrophoresis and autoradiography were used to analyze the protein gene products of African trypanosomes biosynthetically labelled with [35S]methionine. Using cloned populations of parasites it was found that: antigenically different bloodstream trypanosomes from the same serodeme differed only in their variant surface glycoproteins; Trypanosoma brucei, T.b. rhodesiense and T.b. gambiense subspecies could be distinguished on the basis of differences in expressed proteins; transformation from bloodstream trypomastigotes to procyclic epimastigote culture forms was accompanied by loss of variant surface glycoproteins and several other qualitative and quantitative changes in minor proteins. The results indicate that 2D gel analysis may allow improved classification of African trypanosomes (based on the observation of hundreds of protein markers) and may also provide a general technique for the identification of lifecycle stage specific markers.

Trypanosomes of subgenus Trypanozoon are diploid for housekeeping genes

The ploidy of trypanosomes has until now remained undetermined, although isoenzyme studies and direct measurements of DNA content and complexity suggest diploidy. Direct cytogenetic analysis is not possible, because the chromosomes do not condense at any stage of the cell cycle. We now present evidence from analysis of restriction site polymorphisms in and around three glycolytic enzyme genes (phosphoglycerate kinase, triosephosphate isomerase, glyceraldehyde phosphate dehydrogenase) and the tubulin gene cluster, that trypanosomes of subgenus Trypanozoon are diploid for these housekeeping genes. This result is still compatible with the single copy nature of variant surface glycoprotein (VSG) genes in Trypanozoon, if different VSG genes are present in corresponding positions on paired chromosomes. Using pulse field gradient gel electrophoresis, we show that the genes for the three glycolytic enzymes are all located in very large DNA molecules, but the gene for triosephosphate isomerase is in another fraction from the genes for the other two enzymes. Since all three enzymes are located in glycosomes, which are trypanosome microbodies, the genes for glycosomal enzymes are not all clustered in one chromosomal segment of the trypanosome genome.

Molecular biology of trypanosome antigenic variation

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Further analysis of intraspecific variation in Trypanosoma brucei using restriction site polymorphisms in the maxi-circle of kinetoplast DNA

We have compared the maxi-circle kinetoplast DNA of 21 Trypanosoma brucei sp. stocks by analysis of restriction sites for nine restriction endonucleases. The analysis shows most of these stocks to have a maxi-circle sequence similar to that of 11 previously analysed stocks, with a difference of less than 3% between any two stocks. However, seven stocks stand out from the rest with at least two sites lost or gained for six of the nine restriction enzymes used. These seven distinctive stocks fall into two groups with some shared and some unique polymorphisms. One group had already been designated the kiboko group on the basis of isoenzyme patterns, but the relationship between nuclear markers and maxi-circle type is less clear-cut for the other group, designated sindo. Both groups seem to be in a wild animal-tsetse fly transmission cycle, with occasional infections in domestic stock, and may be reproductively isolated from the main T. brucei sp. population. The existence of the kiboko and sindo sub-groups shows that the maxi-circle is not shielded from evolutionary change. The lack of difference observed between the maxi-circles of the majority of T. brucei sp. stocks, including the gambiense and rhodesiense variants, must therefore reflect their close homology. Two geographical trends occur in T. brucei as a whole: (a) a trend in maxi-circle size, with increasing length of the variable region from West to East Africa, and (b) a greater frequency of certain restriction enzyme polymorphisms in East African stocks as compared to West African stocks.

Structure of the variant glycoproteins and surface coat of Trypanosoma brucei

The pathogenic African trypanosomes have a unique mechanism for antigenic variation. Each cell is covered by a surface coat consisting of about seven million essentially identical glycoprotein molecules drawn from a large repertoire of variants, each encoded by an individual gene. Amino acid sequence variation extends throughout the molecule but reduces from the amino terminus to the carboxy terminus, where certain features, especially the grouping of cysteine residues, are quite conserved. The range of diversity within the thousand or so variant glycoprotein genes that exist in each cell is large. New variants may arise instantaneously by segmental gene conversion. Variant surface glycoproteins are synthesized with amino terminal signal sequences and hydrophobic carboxy terminal tails. The tails are extraordinarily conserved. After synthesis, they are replaced by a complex glycolipid structure in which myristic (dodecanoic) acid serves to anchor the polypeptide to the surface membrane. Enzymic cleavage of myristic acid releases variant glycoproteins from the surface coat.

Enzyme variation in Trypanosoma brucei spp. I. Evidence for the sub-speciation of Trypanosoma brucei gambiense

Three groups of stocks of Trypanosoma brucei ssp, defined by the criteria of host, human serum resistance and place of isolation as T. b. gambiense, T. b. brucei (Nigeria) and T. b. brucei/rhodesiense (non-gambiense, Uganda) were screened for electrophoretic variation at 20 enzyme loci. One enzyme (Peptidase C) was found to differentiate all T. b. gambiense stocks from the other T. brucei stocks and, taken together with specific variants of 5 other enzymes, could be used to unambiguously define T. b. gambiense stocks. Using a population genetics approach, the frequencies of the different variants in the three groups of stocks were estimated and from them the average similarity and difference between groups were measured using the statistics of genetic identity (I) and genetic distance (D). These results show firstly, that T. b. gambiense is more different from the other two groups than they are from each other and, secondly, that the values of I and D obtained are consistent with T. b. gambiense constituting a sub- or sibling species of T. brucei. Three domestic animal isolates from Zaire and Cameroun were also screened for enzyme variation and two of these identified as T. b. gambiense, thereby establishing the existence of an animal reservoir host. In parallel, these stocks were tested for human serum resistance resulting in the same identification. Studies of the antigen repertoires and antigen gene structure were carried out by other workers on all the T. b. gambiense stocks reported here and the same conclusions reached as to the identification and ability to discriminate this subspecies from other groups of T. brucei stocks. The results presented here are discussed in relation to other published data on enzyme variation in T. brucei.

Distinction of African trypanosome species using nucleic acid hybridization

We have performed restriction endonuclease digestion of nuclear DNAs, combined with gel electrophoresis and molecular hybridization to characterize different Trypanosoma brucei brucei stocks and to identify trypanosome species. Cloned DNA complementary to the messenger RNAs (mRNAs) for different variable surface glycoproteins (VSGs) of T. b. brucei stock LUMP 227 was used to examine differences in genomic DNAs from T. b. brucei stocks and from various other trypanosome species. These cDNA reagents differentiated the stocks of T. b. brucei and also distinguished the trypanosome species. Our data also show that a T. b. brucei nuclear DNA fragment used as a probe in molecular hybridization analysis provides an appropriate marker in determining trypanosome species. We have extended our analysis of trypanosome nuclear DNA by developing a simple and rapid spot test, for the identification of trypanosome species, which can be carried out using crude materials such as isolated parasites, infected whole blood and tsetse saliva. The procedure is species-specific, sensitive to the level of 10(4) organisms and is suitable for use under field conditions. Thus, with appropriate sequences for hybridization, the procedure has obvious applications for the diagnosis of African trypanosomiasis.

At least two transposed sequences are associated in the expression site of a surface antigen gene in different trypanosome clones

The expression of several trypanosome surface antigen genes proceeds by duplication of a basic copy (BC) of the gene and transposition of the expression-linked copy (ELC) into an expression site. This site, which seems to be the same for different genes of the same repertoire, is located near a chromosome end. In the AnTat 1.1 antigen gene expression site, the ELC is found associated with another sequence that we have called the "companion." We found that this companion is the transposed copy of another sequence also located in an unstable DNA terminus, and that it is conserved in the expression site of AnTat 1.10 and AnTat 1.1B, two clones successively derived from AnTat 1.1. The companion sequence is not part of the surface antigen gene, but we may infer from extensive homologies with another ELC sequence (IoTat 1.3, J. E. Donelson, personal communication) that it represents a 5' residual fragment of a former ELC. In three other AnTat 1.1-like clones, the companion sequence was not found associated with the ELC. It is concluded that the expression-linked duplicative transposition of variable antigen genes is a flexible mechanism, which can apply to variably sized stretches of the same BC.