Molecular profiles of Trypanosoma brucei, T. evansi and T. equiperdum stocks revealed by the random amplified polymorphic DNA method

PAG3 promotes the differentiation of bloodstream forms in Trypanosoma brucei and reveals the evolutionary relationship among the Trypanozoon trypanosomes

Introduction

Trypanosoma brucei, T. evansi and T. equiperdum are members of the subgenus Trypanozoon and are highly similar morphologically and genetically. The main differences between these three species are their differentiation patterns in the hosts and the role of vectors in their life cycles. However, the mechanisms causing these differences are still controversial.

Methods

PAG3 gene was accessed by PCR amplification in 26 strains of Trypanozoon and sequences were then analyzed by BLAST accompanied with T. evansitype B group. RNA interference and CRISPR/Cas9 were used for revealing possible role of PAG3 in slender to stumpy transformation.

Results

The procyclin associated gene 3 (PAG3) can be found in the pleomorphicspecies, T.brucei, which undergoes differentiation of slender forms to the stumpy form. This differentiation process is crucial for transmission to the tsetse fly vector. However, a homologue of PAG3 was not detected in either T. evansi or in the majority of T. equiperdum strains which are allmonomorphic. Furthere xperiments in T. brucei demonstrated that, when PAG3 was down-regulated or absent, there was a significant reduction in the differentiation from slender to stumpy forms.

Conclusion

Therefore, we conclude that PAG3 is a key nuclear gene involved in the slender to stumpy differentiation pathway of T.brucei in the mammalian host. Loss of this gene might also offer a simple evolutionary mechanism explaining why T. evansi and some T. equiperdum have lost the ability to differentiate and have been driven to adapt to transmission cycles that by pass the tsetse vector or mechanical contact.

A novel metabarcoded deep amplicon sequencing tool for disease surveillance and determining the species composition of Trypanosoma in cattle and other farm animals

The World Health Organization (WHO) and the Food and Agriculture Organization (FAO) have developed strategies to control trypanosomiasis in humans and livestock in endemic areas. These require a better understanding of the distribution of different Trypanosoma species and improved predictions of where they might appear in the future, based on accurate diagnosis and robust surveillance systems. Here, we describe a metabarcoding deep amplicon sequencing method to identify and determine the Trypanosoma species in co-infecting communities. First, four morphological verified Trypanosoma species (T. brucei, T. congolense, T. vivax and T. theileri) were used to prepare test DNA pools derived from different numbers of parasites to evaluate the method's detection threshold for each of the four species and to assess the accuracy of their proportional quantification. Having demonstrated the accurate determination of species composition in Trypanosoma communities, the method was applied to determine its detection threshold using blood samples collected from cattle with confirmed Trypanosoma infections based on a PCR assay. Each sample showed a different Trypanosoma species composition based on the proportion of MiSeq reads. Finally, we applied the assay to field samples to develop new insight into the species composition of Trypanosoma communities in cattle, camels, buffalo, horses, sheep, and goat in endemically infected regions of Pakistan. We confirmed that Trypanosoma evansi is the major species in Pakistan and for the first time showed the presence of Trypanosoma theileri. The metabarcoding deep amplicon sequencing method and bioinformatics pathway have several potential applications in animal and human research, including evaluation of drug treatment responses, understanding of the emergence and spread of drug resistance, and description of species interactions during co-infections and determination of host and geographic distribution of trypanosomiasis in humans and livestock.

Multidrug resistance protein structure of Trypanosoma evansi isolated from buffaloes in Ngawi District, Indonesia: A bioinformatics analysis

Background and Aim:

Trypanosomiasis, also known as surra, is an infectious disease with a wide host spectrum. In Indonesia, this disease is caused by Trypanosoma evansi. Various trypanocidal drugs have been used to treat this pathogen and subsequent disease. Yet, the long-term trypanocidal administration generates drug-resistant T. evansi. Some have identified genetic alterations in T. evansi transporter protein-coding genes that may be responsible for drug resistance. The Multidrug Resistance Protein E (MRPE) gene is a likely candidate gene responsible for the individual resistance. To date, no research has focused on T. evansi MRPE (TevMRPE) in this context. Hence, this research aimed at analyzing and characterizing the TevMRPE gene and protein using a bioinformatics approach.

Materials and Methods:

T. evansi was isolated from buffalo suffering from surra in Ngawi Regency, Indonesia. Isolated T. evansi was inoculated and cultured in male mice. The T. evansi genome was isolated from mouse blood with a parasitemia degree as high as 10⁵. A polymerase chain reaction procedure was conducted to amplify the putative MRPE coding gene. The amplicon was sequenced and analyzed using MEGA X, BLAST, and I-tasser softwares.

Results:

The putative TevMRPE coding gene showed sequence similarity as high as 99.79% against the MRPE gene from Trypanosoma brucei gambiense. The protein profile and characteristics depicted that the putative TevMRPE protein was related to a family of Adenosine Triphosphate-Binding Cassette (ABC) transporter proteins. This family of transporter proteins plays a crucial role in the resistance toward several medicines.

Conclusion:

The obtained gene sequence in this research was identified as the TevMRPE. This gene is homologous to the T. brucei gambiense MRPE gene and possesses ligand active sites for Adenylyl Imidodiphosphate. In addition, MRPE contains enzyme active sites similar to the cystic fibrosis transmembrane conductance regulator. These data suggest that ABC transport proteins, like MRPE, may be necessary to confer trypanocidal drug resistance in T. evansi.

Characterization and phylogenetic analysis of multidrug-resistant protein - encoding genes in Trypanosoma evansi isolated from buffaloes in Ngawi district, Indonesia

Background and Aim:

Excessive use of trypanocidal drugs can lead to cases of drug resistance. Multiple cases of resistance have been widely reported for drugs such as isometamidium chloride and diminazene aceturate. These cases deserve serious attention, especially in Indonesia, where the first case was recorded and where the molecular basis of trypanocidal drug resistance has never been evaluated. This study aimed to analyze the multidrug resistance protein (MRP) gene in Trypanosoma evansi isolates, sampled from Indonesia, by focusing on the phylogenetic relationship between these isolates and other Trypanosoma spp.

Materials and Methods:

A total of 88 blood samples were drawn from buffaloes in the Ngawi district, Indonesia. Animals infected with T. evansi were detected through the microhematocrit technique and Giemsa blood smear methods. Positive blood samples were used to inoculate in male mice (Mus musculus BALB-C strain) as an animal model for culturing the T. evansi. The genomic DNA of the blood taken from the T. evansi- infected mice was used for polymerase chain reaction amplification, sequencing, and phylogenetic analysis.

Results:

Two genes were analyzed; the first gene detected for T. evansi corresponded to Trypanosomabrucei with a homology of 99% and the second gene to Trypanosoma brucei gambiense, with a homology of 100%. These two genes of the MRP from T. evansi showed clear similarity to the MRPE and MRPA genes of the T. brucei ssp.

Conclusion:

The MRP gene is conserved on the subspecies level of T. brucei. Only few point mutations were found between various sequences, which mean that the proteins have the same structure. This is important to treat the parasite with the appropriate drugs in the future.

First report of the prevalence and genotype of Trypanosoma spp. in bats in Yunnan Province, Southwestern China

Trypanosome is considered as one of important parasites in almost all mammalian species, which occurs in Chiroptera throughout the world. Although numerous trypanosome species have been identified in bats in Asia, Africa, South America and Europe, little is known about the genetic diversity and pathogenicity of trypanosomes in Chinese bat. Recently, some human Trypanosoma cruzi infection attributed to a bat-related T. cruzi (TcBat) from the Noctilio spp., Myotis spp. and Artibeus spp was found. Consequently, it is a necessity to know trypanosome species in bats from China. In order to determine the prevalence and genotypes in bat from southwestern China, wehere detected trypanosomes prevalence 227bat brain tissue samples, including 60 Rousettus leschenaultia, 58 Hipposideros Pomona, 69 Rhinolophus pusillus, 40 Myotis daubentonni in Yunnan Province of China using nested PCR based on 18S rRNA. 14 (6.2%) of them were trypanosmes positive including 13 insect-eating bats and 1 fruit bat. The prevalence of trypanosome in R.leschenaultia, H. Pomona, and R.pusillus was 1.67%(1/60), 6.90%(4/58) and 13.0%(9/69), respectively (P < 0.01), suggesting R. pusillus was a main-vector host bat. The positive rate of T.sp, T. dionisii, T.brucei brucei and T.sp ZY-2 was 4.8% (11/227), 0.4%(1/227), 0.4%(1/227), and 0.4% (1/227), resepectively. These results showed that T.sp-Yunnan is the predominant genospecies. To our knowledge, this is the first report about Trypanosome species in bats in Yunnan Province, southwestern China.

Molecular characterization and phylogenetic analysis of Trypanosoma evansi from Northern India based on 18S ribosomal gene

Six Trypanosoma evansi isolates were collected from ponies (PH1 and PK6), camel (CB2), donkeys (DJ3 and DH4) and cattle (CK5) from different States of Northern India (Haryana, Rajasthan, Uttar Pradesh and Gujarat) for molecular characterization based on 18S rRNA gene. The 18S rRNA gene (2251 bp) of different isolates was amplified, cloned and custom sequenced separately. Based on sequence and phylogenetic analysis of all six isolates, collected from different hosts as well as geographical areas, were having high identity among Indian T. evansi strains (99.7%) and with other strains of T. evansi (99.2%) distributed worldwide. There is less genetic diversity among different salivarian strains of T. evansi except few nucleotide changes at significant locations in one Indian isolate of camel origin (CB2). All Indian T. evansi isolates were grouped in salivarian clade with high bootstrap values and remained far away from stercorarian clade having 88-90% nucleotide identity. The study will be helpful in understanding the evolutionary relationship, molecular epidemiology and variation in disease pathogenesis among different T. evansi strains. Further, more studies are required on large number of isolates collected from diverse host and geographical areas to reaffirm the present finding.

Trypanosoma brucei Plimmer & Bradford, 1899 is a synonym of T. evansi (Steel, 1885) according to current knowledge and by application of nomenclature rules

Proper application of the principles of biological nomenclature is fundamental for scientific and technical communication about organisms. As other scientific disciplines, taxonomy inherently is open to change, thus species names cannot be final and immutable. Nevertheless, altering the names of organisms of high economical, medical, or veterinary importance can become a complex challenge between the scientific need to have correct classifications, and the practical ideal of having fixed classifications. Trypanosoma evansi (Steel, 1885), T. brucei Plimmer & Bradford, 1899 and T. equiperdum Doflein, 1901 are important parasites of mammals. According to current knowledge, the three names are synonyms of a single trypanosome species, the valid name of which should be T. evansi by the mandatory application of the Principle of Priority of zoological nomenclature. Subspecies known as T. brucei brucei Plimmer & Bradford, 1899, T. b. gambiense Dutton, 1902 and T. b. rhodesiense Stephens & Fantham, 1910 should be referred to respectively as T. evansi evansi (Steel, 1885), T. e. gambiense and T. e. rhodesiense. The polyphyletic groupings so far known as T. evansi and T. equiperdum should be referred respectively to as surra- and dourine-causing strains of T. e. evansi. Likewise, trypanosomes so far known as T. b. brucei should be referred to as nagana-causing strains of T. e. evansi. Though it modifies the scientific names of flagship human and animal parasites, the amended nomenclature proposed herein should be adopted because it reflects phylogenetic and biological advancements, fixes errors, and is simpler than the existing classificatory system.

Dourine: a neglected disease of equids

Dourine is a venereal transmitted trypanosomosis causing a major health problem threatening equines worldwide. The origin and identification of Trypanosoma equiperdum within the subgenus Trypanozoon is still a subject of debate. Unlike other trypanosomal infections, dourine is transmitted almost exclusively by coitus. Diagnosis of dourine has continued to be a challenge, due to limited knowledge about the parasite and host-parasite interaction following infection. The pathological lesions caused by the diseases are poorly described and are observed mainly in the reproductive organs, in the nervous system, and on the skin. Dourine has been neglected by research and current knowledge on the disease, and the parasite is very deficient despite its considerably high burden. This paper looks in to the challenges in identification of T. equiperdum and diagnosis techniques with the aim to update our current knowledge of the disease.

Phylogeny of Trypanosoma brucei and Trypanosoma evansi in naturally infected cattle in Nigeria by analysis of repetitive and ribosomal DNA sequences

In continuing efforts to better understand the genetics of bovine trypanosomosis, we assessed genetic diversity of Trypanosoma brucei and Trypanosoma evansi in naturally infected Nigerian cattle using repetitive DNA and internal transcribed spacer 1 of rDNA sequences and compared these sequences to species from other countries. The length of repetitive DNA sequences in both species ranged from 161 to 244 bp and 239 to 240 bp for T. brucei and T. evansi, respectively, while the ITS1 rDNA sequences length range from 299 to 364 bp. The mean GC content of ITS1 rDNA sequences was 33.57 %, and that of repetitive sequences were 39.9 and 31.1 % for T. brucei and T. evansi, respectively. Result from sequence alignment revealed both T. brucei and T. evansi repetitive DNA sequences to be more polymorphic than ITS1 rDNA sequences, with moderate points of deletion and insertions. T. brucei separated into two clades when subjected to phylogenetic analysis. T. evansi repetitive DNA sequences clustered tightly within the T. brucei clade while the ITS1 rDNA sequences of T. brucei were clearly separated from T. theileri and T. vivax individually used as outgroups. This study suggest that ITS1 rDNA sequences may not be suitable for phylogenetic differentiation of the Trypanozoon group and also suggest that T. evansi may be a phenotypic variant of T. brucei which may have potential implications in designing prevention and therapeutic strategies.

Further evidence from SSCP and ITS DNA sequencing support Trypanosoma evansi and Trypanosoma equiperdum as subspecies or even strains of Trypanosoma brucei

The subgenus Trypanozoon includes three species Trypanosoma brucei, Trypanosoma evansi and Trypanosoma equiperdum, which are morphologically identical and indistinguishable even using some molecular methods. In this study, PCR-based single strand conformation polymorphism (PCR-SSCP) was used to analyze the ribosomal DNA of the Trypanozoon species. Data indicate different patterns of ITS2 fragments between T. brucei, T. evansi and T. equiperdum by SSCP. Furthermore, analysis of total ITS sequences within these three members of the subgenus Trypanozoon showed a high degree of homology using phylogenetic analysis but were polyphyletic in haplotype networks. These data provide novel nuclear evidence to further support the notion that T. evansi and T. equiperdum should be subspecies or even strains of T. brucei.

The internal transcribed spacer 1 (ITS-1), a controversial marker for the genetic diversity of Trypanosoma evansi

Seven Trypanosoma evansi isolates from China and a Trypanosoma congolense sp. gifted from Kenya were characterized genetically by the internal transcribed spacer 1 (ITS-1) of nuclear ribosomal DNA (rDNA). The ITS-1 rDNA with the length of 338-342 bp was amplified by polymerase chain reaction (PCR) and sequenced from individual isolates of T. evansi. Although sequence variation between T. evansi isolates from China only was 0.3-3.8%, the constructed phylogenetic tree based on the ITS-1 rDNA sequence by the method of neighbor-joining and maximum parsimony revealed the genetic diversity among T. evansi isolates from China. For T. congolense sp., the most phylogenetically related species was T. congolense IL1180. Although the sequence variation ranged 0.8-14.5% between T. congolense isolates, the phylogenetic tree can not reflected the genetic diversity among T. congolense isolates perhaps because of the fewer number of isolates and sequences. The data could be applicable for the survey of parasite dynamics, epidemiological studies as well as prevention and control of the disease.

Molecular genetic profiles among individual Clonorchis sinensis adults collected from cats in two geographic regions of China revealed by RAPD and MGE-PCR methods

Clonorchis sinensis causes the important food-borne zoonosis, clonorchiasis, which is endemic in East Asia, especially in China mainly in Guangdong, Guangxi and Heilongjiang provinces and Korea. Although comparisons on isoenzymes and some molecular profiles of C. sinensis collected from different parts of China and Korea have been studied, few works on the genetic variation among the individuals from different regions of China has been reported. In the present study, individual adults of C. sinensis were collected from cats in two geographic locations (Guangdong province in the South and Heilongjiang province in the North) of China and 44 of them were examined by using random amplified polymorphic DNA (RAPD)-PCR and mobile genetic elements (MGEs)-PCR techniques to assess the individual genetic variability within and between the two groups of this parasite. Six arbitrary primers and two pairs of MGE primers were employed in the genomic DNA amplification. The molecular patterns showed significant polymorphism among the individuals. The RAPD data displayed that the similarity coefficient (SC) of the individuals within Heilongjiang group was much higher than that of the Guangdong group, which was further confirmed by MGE-PCR results. Individuals from Heilongjiang were found genetically closer with lesser polymorphisms than those collected from Guangdong province. These results demonstrated that RAPD and MGE-PCR techniques, particularly RAPD method, could be useful for investigating genetic variations among C. sinensis individuals. They may also indicate that the genetic variation of C. sinensis occurs in the subtropical region--Guangdong--faster than that in the cold-region--Heilongjiang province--due to more generations (life cycle) occurred.

Establishment of a panel of reference Trypanosoma evansi and Trypanosoma equiperdum strains for drug screening

The animal pathogenic protozoan, Trypanosoma evansi, leads to a wasting disease in equines, cattle and camels, commonly known as Surra. It is extensively distributed geographically with a wide range of mammalian hosts and causes great economical loss. Trypanosoma equiperdum causes a venereal disease called Dourine in horses and donkeys. Chemotherapy appears to be the most effective form of control for T. evansi, whereas infections caused by T. equiperdum are considered incurable. Due to emerging drug resistance, efficient control of T. evansi is severely threatened, emphasising the urgent need to find new alternative drugs. A drug profile for a panel of T. evansi and T. equiperdum strains has been established for the four standard drugs currently used in treatment. The (3)H-hypoxanthine incorporation assay was used to obtain 50% inhibitory concentration (IC(50)) values for each standard drug against the various strains. The results indicate the presence (and in some cases, the emergence) of drug resistance in several strains. This panel of characterised strains with known drug sensitivities and resistances will be of great value for the screening of new active compounds, in comparison with the four standard drugs currently available.

Genetic variability of Trypanosoma evansi isolates detected by inter-simple sequence repeat anchored-PCR and microsatellite

Studies on genetic variability in Trypanosoma evansi have been limited by a lack of high-resolution techniques. In this study, we have investigated the use of inter-simple sequence repeats (ISSR) and microsatellites in revealing polymorphism among T. evansi isolates. Twelve ISSR primers and five microsatellite loci were used to generate polymorphic bands and alleles, respectively, to investigate the genetic variability among T. evansi isolates from Africa and Asia. Seven of the twelve ISSR primers showed variability between isolates with a total of 71 fragments of which 49(69%) were polymorphic. Microsatellite analysis revealed a total of 60 alleles. On average the ISSR markers revealed a higher genetic diversity (23%) than microsatellites (21.1%). The two techniques showed a strong agreement of r=0.95 for Dice and r=0.91 for Jaccard indices in estimating the genetic distances between isolates. The distance UPGMA tree revealed two major clusters of T. evansi which correlate with the minicircle classification of subtype A and B. The cophenetic correlation coefficient between Dice and Jaccard based matrices were r=0.79 for microsatellites and r=0.73 for ISSR indicating a strong agreement between dendrograms. The results suggest that both ISSR and microsatellites markers are useful in detecting genetic variability within T. evansi.

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.

PCR approach for the detection of Trypanosoma brucei and T. equiperdum and their differentiation from T. evansi based on maxicircle kinetoplast DNA

The goal of this study was to develop a PCR approach based on the sequence of maxicircle kinetoplast DNA (kDNA) of Trypanosoma brucei to distinguish T. brucei/T. equiperdum from T. evansi and to evaluate its diagnostic use for their detection in blood samples. Primers derived from the sequence of the maxicircle kDNA of T. brucei, encoding the NADH dehydrogenase subunit 5 (nad5) gene, were used to test the PCR-amplification from T. brucei (including T. b. brucei and T. b. rhodesiense), T. equiperdum, T. evansi, T. vivax and T. congolense. A primer pair to a nuclear DNA region incorporated into a separate PCR was employed to control for the presence of amplifiable genomic DNA (representing the subgenus Trypanozoon) in each sample subjected to the PCR. Products of approximately 395bp were amplified from all T. brucei and T. equiperdum samples tested using the nad5-PCR, but not from T. evansi DNA samples or any of the control samples representing T. vivax, T. congolense, or host. The current PCR approach allows the rapid differentiation of T. brucei/T.equiperdum from T. evansi and can detect the equivalent of 20-25 cells of T. brucei or T. equiperdum in purified genomic DNA or infected blood samples.

The detection of non-RoTat 1.2 Trypanosoma evansi

The majority of Trypanosoma evansi can be detected using diagnostic tests based on the variant surface glycoprotein (VSG) of Trypanosoma evansi Rode Trypanozoon antigen type (RoTat) 1.2. Exceptions are a number of T. evansi isolated in Kenya. To characterize T. evansi that are undetected by RoTat 1.2, we cloned and sequenced the VSG cDNA from T. evansi JN 2118Hu, an isolate devoid of the RoTat 1.2 VSG gene. A 273 bp DNA segment of the VSG gene was targeted in PCR amplification for the detection of non-RoTat 1.2 T. evansi. Genomic DNA samples from different trypanosomes were tested including 32 T. evansi, 10 Trypanosoma brucei, three Trypanosoma congolense, and one Trypanosoma vivax. Comparison was by PCR amplification of a 488 bp fragment of RoTat1.2 VSG gene. Results showed that the expected 273 bp amplification product was present in all five non-RoTat 1.2 T. evansi tested and was absent in all 27 RoTat 1.2-positive T. evansi tested. It was also absent in all other trypanosomes tested. The PCR test developed in this study is specific for non-RoTat 1.2 T. evansi.

Genetic variability in ESAG6 genes among Trypanosoma evansi isolates and in comparison to other Trypanozoon members

Bloodstream trypanosomes take up iron needed for their propagation through the transferrin receptor that, in Trypanosoma brucei, is encoded by expression-site-associated genes (ESAGs), ESAG6 and 7 genes located in variant surface glycoprotein expression sites. ESAG6 and 7 genes in different expression sites have been shown to encode transferrin receptors with varying affinities for polymorphic transferrins. T. brucei could cope with the different host transferrins by switching between expression sites. ESAG6- and 7-encoded transferrin receptor appear to be present in Trypanosoma evansi but the genes have not yet been characterized. In this study, we cloned and sequenced different members of ESAG6 genes in seven isolates of T. evansi from geographically distinct localities in Thailand. We assessed the intra- and inter-species genetic variability in the transferrin receptor gene regions involved in transferrin binding and established that T. evansi, like T. brucei, has widely diverse ESAG6 genes. In addition, T. evansi possess a clade of ESAG6 variants not observed in T. brucei and different T. evansi strains share at least two conserved variants. We further noted that T. evansi possesses all the reported T. equiperdum ESAG6 variants as a subset. Our findings depict a correlation between the genetic diversity in the transferrin-binding regions of ESAG6 genes with the broad host range of T. evansi and T. brucei compared to the narrow host range of Trypanosoma equiperdum.