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Morrison LJ, Barrett MP, Steketee PC, Cecchi G, Kijanga O, Mramba F, Auty HK. What is needed to achieve effective and sustainable control of African animal trypanosomosis? Trends Parasitol 2024; 40:679-686. [PMID: 39048503 DOI: 10.1016/j.pt.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/14/2024] [Accepted: 06/20/2024] [Indexed: 07/27/2024]
Abstract
A welcome resurgence in African animal trypanosomosis (AAT) research has resulted in advances in capabilities, foundational datasets, and understanding. Additionally, there is the prospect of the first new trypanocide in >60 years. However, it is vital to ensure that advances translate to improved and sustainable control in the field. A recent meeting, the Symposium on African Livestock Trypanosomes - Tanzania, convened stakeholders from across the spectrum of AAT research and control to ask how this can be achieved. Current constraints on progress were defined, as were critical gaps and opportunities that need addressing. There is a requirement and opportunity for the AAT research community to communicate, collaborate, and coordinate to maintain momentum and achieve the ultimate goal of sustainable AAT control.
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Affiliation(s)
| | | | | | - Giuliano Cecchi
- Animal Production and Health Division (NSA), Food and Agriculture Organization of the United Nations (FAO), Rome, Italy
| | - Oliver Kijanga
- Vector and Vector-Borne Diseases Institute, Tanga, Tanzania
| | | | - Harriet K Auty
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
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2
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Morrison LJ, Steketee PC, Tettey MD, Matthews KR. Pathogenicity and virulence of African trypanosomes: From laboratory models to clinically relevant hosts. Virulence 2023; 14:2150445. [PMID: 36419235 DOI: 10.1080/21505594.2022.2150445] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
African trypanosomes are vector-borne protozoa, which cause significant human and animal disease across sub-Saharan Africa, and animal disease across Asia and South America. In humans, infection is caused by variants of Trypanosoma brucei, and is characterized by varying rate of progression to neurological disease, caused by parasites exiting the vasculature and entering the brain. Animal disease is caused by multiple species of trypanosome, primarily T. congolense, T. vivax, and T. brucei. These trypanosomes also infect multiple species of mammalian host, and this complexity of trypanosome and host diversity is reflected in the spectrum of severity of disease in animal trypanosomiasis, ranging from hyperacute infections associated with mortality to long-term chronic infections, and is also a main reason why designing interventions for animal trypanosomiasis is so challenging. In this review, we will provide an overview of the current understanding of trypanosome determinants of infection progression and severity, covering laboratory models of disease, as well as human and livestock disease. We will also highlight gaps in knowledge and capabilities, which represent opportunities to both further our fundamental understanding of how trypanosomes cause disease, as well as facilitating the development of the novel interventions that are so badly needed to reduce the burden of disease caused by these important pathogens.
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Affiliation(s)
- Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Pieter C Steketee
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Mabel D Tettey
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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3
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VSGs Expressed during Natural T. b. gambiense Infection Exhibit Extensive Sequence Divergence and a Subspecies-Specific Bias towards Type B N-Terminal Domains. mBio 2022; 13:e0255322. [PMID: 36354333 PMCID: PMC9765701 DOI: 10.1128/mbio.02553-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Trypanosoma brucei gambiense is the primary causative agent of human African trypanosomiasis (HAT), a vector-borne disease endemic to West and Central Africa. The extracellular parasite evades antibody recognition within the host bloodstream by altering its variant surface glycoprotein (VSG) coat through a process of antigenic variation. The serological tests that are widely used to screen for HAT use VSG as one of the target antigens. However, the VSGs expressed during human infection have not been characterized. Here, we use VSG sequencing (VSG-seq) to analyze the VSGs expressed in the blood of patients infected with T. b. gambiense and compared them to VSG expression in Trypanosoma brucei rhodesiense infections in humans as well as Trypanosoma brucei brucei infections in mice. The 44 VSGs expressed during T. b. gambiense infection revealed a striking bias toward expression of type B N termini (82% of detected VSGs). This bias is specific to T. b. gambiense, which is unique among T. brucei subspecies in its chronic clinical presentation and anthroponotic nature. The expressed T. b. gambiense VSGs also share very little similarity to sequences from 36 T. b. gambiense whole-genome sequencing data sets, particularly in areas of the VSG protein exposed to host antibodies, suggesting the antigen repertoire is under strong selective pressure to diversify. Overall, this work demonstrates new features of antigenic variation in T. brucei gambiense and highlights the importance of understanding VSG repertoires in nature. IMPORTANCE Human African trypanosomiasis is a neglected tropical disease primarily caused by the extracellular parasite Trypanosoma brucei gambiense. To avoid elimination by the host, these parasites repeatedly replace their variant surface glycoprotein (VSG) coat. Despite the important role of VSGs in prolonging infection, VSG expression during human infections is poorly understood. A better understanding of natural VSG gene expression dynamics can clarify the mechanisms that T. brucei uses to alter its VSG coat. We analyzed the expressed VSGs detected in the blood of patients with trypanosomiasis. Our findings indicate that there are features of antigenic variation unique to human-infective T. brucei subspecies and that natural VSG repertoires may vary more than previously expected.
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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
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5
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Silva Pereira S, Mathenge K, Masiga D, Jackson A. Transcriptomic profiling of Trypanosoma congolense mouthpart parasites from naturally infected flies. Parasit Vectors 2022; 15:152. [PMID: 35501882 PMCID: PMC9063227 DOI: 10.1186/s13071-022-05258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/29/2022] [Indexed: 11/10/2022] Open
Abstract
Background Animal African trypanosomiasis, or nagana, is a veterinary disease caused by African trypanosomes transmitted by tsetse flies. In Africa, Trypanosoma congolense is one of the most pathogenic and prevalent causes of nagana in livestock, resulting in high animal morbidity and mortality and extensive production losses. In the tsetse fly, parasites colonise the midgut and eventually reach the mouthparts, from where they can be transmitted as the fly feeds on vertebrate hosts such as cattle. Despite the extreme importance of mouthpart-form parasites for disease transmission, very few global expression profile studies have been conducted in these parasite forms. Methods Here, we collected tsetse flies from the Shimba Hills National Reserve, a wildlife area in southeast Kenya, diagnosed T. congolense infections, and sequenced the transcriptomes of the T. congolense parasites colonising the mouthparts of the flies. Results We found little correlation between mouthpart parasites from natural and experimental fly infections. Furthermore, we performed differential gene expression analysis between mouthpart and bloodstream parasite forms and identified several surface-expressed genes and 152 novel hypothetical proteins differentially expressed in mouthpart parasites. Finally, we profiled variant antigen expression and observed that a variant surface glycoprotein (VSG) transcript belonging to T. congolense phylotype 8 (i.e. TcIL3000.A.H_000381200), previously observed to be enriched in metacyclic transcriptomes, was present in all wild-caught mouthpart samples as well as bloodstream-form parasites, suggestive of constitutive expression. Conclusion Our study provides transcriptomes of trypanosome parasites from naturally infected tsetse flies and suggests that a phylotype 8 VSG gene is constitutively expressed in metacyclic- and bloodstream-form parasites at the population level. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05258-y.
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Affiliation(s)
- Sara Silva Pereira
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK. .,Faculdade de Medicina, Instituto de Medicina Molecular - João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.
| | - Kawira Mathenge
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Daniel Masiga
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Andrew Jackson
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK.
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6
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Contreras Garcia M, Walshe E, Steketee PC, Paxton E, Lopez-Vidal J, Pearce MC, Matthews KR, Ezzahra-Akki F, Evans A, Fairlie-Clark K, Matthews JB, Grey F, Morrison LJ. Comparative Sensitivity and Specificity of the 7SL sRNA Diagnostic Test for Animal Trypanosomiasis. Front Vet Sci 2022; 9:868912. [PMID: 35450136 PMCID: PMC9017285 DOI: 10.3389/fvets.2022.868912] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Animal trypanosomiasis (AT) is a significant livestock disease, affecting millions of animals across Sub-Saharan Africa, Central and South America, and Asia, and is caused by the protozoan parasites Trypanosoma brucei, Trypanosoma vivax, and Trypanosoma congolense, with the largest economic impact in cattle. There is over-reliance on presumptive chemotherapy due to inadequate existing diagnostic tests, highlighting the need for improved AT diagnostics. A small RNA species, the 7SL sRNA, is excreted/secreted by trypanosomes in infected animals, and has been previously shown to reliably diagnose active infection. We sought to explore key properties of 7SL sRNA RT-qPCR assays; namely, assessing the potential for cross-reaction with the widespread and benign Trypanosoma theileri, directly comparing assay performance against currently available diagnostic methods, quantitatively assessing specificity and sensitivity, and assessing the rate of decay of 7SL sRNA post-treatment. Results showed that the 7SL sRNA RT-qPCR assays specific for T. brucei, T. vivax, and T. congolense performed better than microscopy and DNA PCR in detecting infection. The 7SL sRNA signal was undetectable or significantly reduced by 96-h post treatment; at 1 × curative dose there was no detectable signal in 5/5 cattle infected with T. congolense, and in 3/5 cattle infected with T. vivax, with the signal being reduced 14,630-fold in the remaining two T. vivax cattle. Additionally, the assays did not cross-react with T. theileri. Finally, by using a large panel of validated infected and uninfected samples, the species-specific assays are shown to be highly sensitive and specific by receiver operating characteristic (ROC) analysis, with 100% sensitivity (95% CI, 96.44-100%) and 100% specificity (95% CI, 96.53-100%), 96.73% (95% CI, 95.54-99.96%) and 99.19% specificity (95% CI, 92.58-99.60%), and 93.42% (95% CI, 85.51-97.16% %) and 82.43% specificity (95% CI, 72.23-89.44% %) for the T brucei, T. congolense and T. vivax assays, respectively, under the conditions used. These findings indicate that the 7SL sRNA has many attributes that would be required for a potential diagnostic marker of AT: no cross-reaction with T. theileri, high specificity and sensitivity, early infection detection, continued signal even in the absence of detectable parasitaemia in blood, and clear discrimination between infected and treated animals.
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Affiliation(s)
- Maria Contreras Garcia
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Emily Walshe
- Roslin Technologies Limited, Roslin Innovation Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Pieter C Steketee
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Edith Paxton
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Javier Lopez-Vidal
- Ashworth Laboratories, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael C Pearce
- Global Alliance for Livestock Veterinary Medicines, Edinburgh, United Kingdom
| | - Keith R Matthews
- Ashworth Laboratories, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Karen Fairlie-Clark
- Roslin Technologies Limited, Roslin Innovation Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Jacqueline B Matthews
- Roslin Technologies Limited, Roslin Innovation Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Finn Grey
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
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7
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Silva Pereira S, Jackson AP, Figueiredo LM. Evolution of the variant surface glycoprotein family in African trypanosomes. Trends Parasitol 2021; 38:23-36. [PMID: 34376326 DOI: 10.1016/j.pt.2021.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 01/22/2023]
Abstract
An intriguing and remarkable feature of African trypanosomes is their antigenic variation system, mediated by the variant surface glycoprotein (VSG) family and fundamental to both immune evasion and disease epidemiology within host populations. Recent studies have revealed that the VSG repertoire has a complex evolutionary history. Sequence diversity, genomic organization, and expression patterns are species-specific, which may explain other variations in parasite virulence and disease pathology. Evidence also shows that we may be underestimating the extent to what VSGs are repurposed beyond their roles as variant antigens, establishing a need to examine VSG functionality more deeply. Here, we review sequence variation within the VSG gene family, and highlight the many opportunities to explore their likely diverse contributions to parasite survival.
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Affiliation(s)
- Sara Silva Pereira
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Andrew P Jackson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK
| | - Luísa M Figueiredo
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
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8
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Steketee PC, Dickie EA, Iremonger J, Crouch K, Paxton E, Jayaraman S, Alfituri OA, Awuah-Mensah G, Ritchie R, Schnaufer A, Rowan T, de Koning HP, Gadelha C, Wickstead B, Barrett MP, Morrison LJ. Divergent metabolism between Trypanosoma congolense and Trypanosoma brucei results in differential sensitivity to metabolic inhibition. PLoS Pathog 2021; 17:e1009734. [PMID: 34310651 PMCID: PMC8384185 DOI: 10.1371/journal.ppat.1009734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/24/2021] [Accepted: 06/21/2021] [Indexed: 11/18/2022] Open
Abstract
Animal African Trypanosomiasis (AAT) is a debilitating livestock disease prevalent across sub-Saharan Africa, a main cause of which is the protozoan parasite Trypanosoma congolense. In comparison to the well-studied T. brucei, there is a major paucity of knowledge regarding the biology of T. congolense. Here, we use a combination of omics technologies and novel genetic tools to characterise core metabolism in T. congolense mammalian-infective bloodstream-form parasites, and test whether metabolic differences compared to T. brucei impact upon sensitivity to metabolic inhibition. Like the bloodstream stage of T. brucei, glycolysis plays a major part in T. congolense energy metabolism. However, the rate of glucose uptake is significantly lower in bloodstream stage T. congolense, with cells remaining viable when cultured in concentrations as low as 2 mM. Instead of pyruvate, the primary glycolytic endpoints are succinate, malate and acetate. Transcriptomics analysis showed higher levels of transcripts associated with the mitochondrial pyruvate dehydrogenase complex, acetate generation, and the glycosomal succinate shunt in T. congolense, compared to T. brucei. Stable-isotope labelling of glucose enabled the comparison of carbon usage between T. brucei and T. congolense, highlighting differences in nucleotide and saturated fatty acid metabolism. To validate the metabolic similarities and differences, both species were treated with metabolic inhibitors, confirming that electron transport chain activity is not essential in T. congolense. However, the parasite exhibits increased sensitivity to inhibition of mitochondrial pyruvate import, compared to T. brucei. Strikingly, T. congolense exhibited significant resistance to inhibitors of fatty acid synthesis, including a 780-fold higher EC50 for the lipase and fatty acid synthase inhibitor Orlistat, compared to T. brucei. These data highlight that bloodstream form T. congolense diverges from T. brucei in key areas of metabolism, with several features that are intermediate between bloodstream- and insect-stage T. brucei. These results have implications for drug development, mechanisms of drug resistance and host-pathogen interactions.
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Affiliation(s)
- Pieter C Steketee
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Emily A Dickie
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - James Iremonger
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn Crouch
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Edith Paxton
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Siddharth Jayaraman
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Omar A Alfituri
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ryan Ritchie
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Rowan
- Global Alliance for Livestock Veterinary Medicines, Edinburgh, United Kingdom
| | - Harry P de Koning
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Catarina Gadelha
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Michael P Barrett
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.,Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - Liam J Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
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9
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Awuah-Mensah G, McDonald J, Steketee PC, Autheman D, Whipple S, D'Archivio S, Brandt C, Clare S, Harcourt K, Wright GJ, Morrison LJ, Gadelha C, Wickstead B. Reliable, scalable functional genetics in bloodstream-form Trypanosoma congolense in vitro and in vivo. PLoS Pathog 2021; 17:e1009224. [PMID: 33481935 PMCID: PMC7870057 DOI: 10.1371/journal.ppat.1009224] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/08/2021] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Animal African trypanosomiasis (AAT) is a severe, wasting disease of domestic livestock and diverse wildlife species. The disease in cattle kills millions of animals each year and inflicts a major economic cost on agriculture in sub-Saharan Africa. Cattle AAT is caused predominantly by the protozoan parasites Trypanosoma congolense and T. vivax, but laboratory research on the pathogenic stages of these organisms is severely inhibited by difficulties in making even minor genetic modifications. As a result, many of the important basic questions about the biology of these parasites cannot be addressed. Here we demonstrate that an in vitro culture of the T. congolense genomic reference strain can be modified directly in the bloodstream form reliably and at high efficiency. We describe a parental single marker line that expresses T. congolense-optimized T7 RNA polymerase and Tet repressor and show that minichromosome loci can be used as sites for stable, regulatable transgene expression with low background in non-induced cells. Using these tools, we describe organism-specific constructs for inducible RNA-interference (RNAi) and demonstrate knockdown of multiple essential and non-essential genes. We also show that a minichromosomal site can be exploited to create a stable bloodstream-form line that robustly provides >40,000 independent stable clones per transfection-enabling the production of high-complexity libraries of genome-scale. Finally, we show that modified forms of T. congolense are still infectious, create stable high-bioluminescence lines that can be used in models of AAT, and follow the course of infections in mice by in vivo imaging. These experiments establish a base set of tools to change T. congolense from a technically challenging organism to a routine model for functional genetics and allow us to begin to address some of the fundamental questions about the biology of this important parasite.
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Affiliation(s)
| | - Jennifer McDonald
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Pieter C. Steketee
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Delphine Autheman
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Sarah Whipple
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Simon D'Archivio
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Cordelia Brandt
- Pathogen Support Team, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Simon Clare
- Pathogen Support Team, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Katherine Harcourt
- Pathogen Support Team, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Gavin J. Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Liam J. Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Catarina Gadelha
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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10
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Silva Pereira S, Heap J, Jones AR, Jackson AP. VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock. Gigascience 2020; 8:5556439. [PMID: 31494667 PMCID: PMC6735694 DOI: 10.1093/gigascience/giz091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 06/17/2019] [Accepted: 07/09/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Analysing variant antigen gene families on a population scale is a difficult challenge for conventional methods of read mapping and variant calling due to the great variability in sequence, copy number, and genomic loci. In African trypanosomes, hemoparasites of humans and animals, this is complicated by variant antigen repertoires containing hundreds of genes subject to various degrees of sequence recombination. FINDINGS We introduce Variant Antigen Profiler (VAPPER), a tool that allows automated analysis of the variant surface glycoprotein repertoires of the most prevalent livestock African trypanosomes. VAPPER produces variant antigen profiles for any isolate of the veterinary pathogens Trypanosoma congolense and Trypanosoma vivax from genomic and transcriptomic sequencing data and delivers publication-ready figures that show how the queried isolate compares with a database of existing strains. VAPPER is implemented in Python. It can be installed to a local Galaxy instance from the ToolShed (https://toolshed.g2.bx.psu.edu/) or locally on a Linux platform via the command line (https://github.com/PGB-LIV/VAPPER). The documentation, requirements, examples, and test data are provided in the Github repository. CONCLUSION By establishing two different, yet comparable methodologies, our approach is the first to allow large-scale analysis of African trypanosome variant antigens, large multi-copy gene families that are otherwise refractory to high-throughput analysis.
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Affiliation(s)
- Sara Silva Pereira
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool Science Park Ic2, 146 Brownlow Hill, Liverpool L3 5RF, UK
- Correspondence addres. Sara Silva Pereira, E-mail:
| | - John Heap
- Computational Biology Facility, University of Liverpool, Liverpool L69 7ZB, UK
| | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Andrew P Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool Science Park Ic2, 146 Brownlow Hill, Liverpool L3 5RF, UK
- Correspondence addres. Andrew P. Jackson, E-mail:
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11
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Silva Pereira S, de Almeida Castilho Neto KJG, Duffy CW, Richards P, Noyes H, Ogugo M, Rogério André M, Bengaly Z, Kemp S, Teixeira MMG, Machado RZ, Jackson AP. Variant antigen diversity in Trypanosoma vivax is not driven by recombination. Nat Commun 2020; 11:844. [PMID: 32051413 PMCID: PMC7015903 DOI: 10.1038/s41467-020-14575-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/18/2020] [Indexed: 11/09/2022] Open
Abstract
African trypanosomes (Trypanosoma) are vector-borne haemoparasites that survive in the vertebrate bloodstream through antigenic variation of their Variant Surface Glycoprotein (VSG). Recombination, or rather segmented gene conversion, is fundamental in Trypanosoma brucei for both VSG gene switching and for generating antigenic diversity during infections. Trypanosoma vivax is a related, livestock pathogen whose VSG lack structures that facilitate gene conversion in T. brucei and mechanisms underlying its antigenic diversity are poorly understood. Here we show that species-wide VSG repertoire is broadly conserved across diverse T. vivax clinical strains and has limited antigenic repertoire. We use variant antigen profiling, coalescent approaches and experimental infections to show that recombination plays little role in diversifying T. vivax VSG sequences. These results have immediate consequences for both the current mechanistic model of antigenic variation in African trypanosomes and species differences in virulence and transmission, requiring reconsideration of the wider epidemiology of animal African trypanosomiasis.
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Affiliation(s)
- Sara Silva Pereira
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Kayo J G de Almeida Castilho Neto
- Department of Veterinary Pathology, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Craig W Duffy
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Peter Richards
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Harry Noyes
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Moses Ogugo
- Livestock Genetic Programme, International Livestock Research Institute, 30709 Naivasha Road, Nairobi, Kenya
| | - Marcos Rogério André
- Department of Veterinary Pathology, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Zakaria Bengaly
- International Research Centre for Livestock Development in the Sub-humid Zone (CIRDES), No. 559, rue 5-31 angle, Avenue du Gouverneur Louveau, Bobo-Dioulasso, Burkina Faso
| | - Steve Kemp
- Livestock Genetic Programme, International Livestock Research Institute, 30709 Naivasha Road, Nairobi, Kenya
| | - Marta M G Teixeira
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Avenue Professor Lineu Prestes, 1374 Cidade Universitaria, Sao Paulo, SP, 05508-000, Brazil
| | - Rosangela Z Machado
- Department of Veterinary Pathology, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Andrew P Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK.
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Abbas AH, Silva Pereira S, D'Archivio S, Wickstead B, Morrison LJ, Hall N, Hertz-Fowler C, Darby AC, Jackson AP. The Structure of a Conserved Telomeric Region Associated with Variant Antigen Loci in the Blood Parasite Trypanosoma congolense. Genome Biol Evol 2018; 10:2458-2473. [PMID: 30165630 PMCID: PMC6152948 DOI: 10.1093/gbe/evy186] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2018] [Indexed: 11/13/2022] Open
Abstract
African trypanosomiasis is a vector-borne disease of humans and livestock caused by African trypanosomes (Trypanosoma spp.). Survival in the vertebrate bloodstream depends on antigenic variation of Variant Surface Glycoproteins (VSGs) coating the parasite surface. In T. brucei, a model for antigenic variation, monoallelic VSG expression originates from dedicated VSG expression sites (VES). Trypanosoma brucei VES have a conserved structure consisting of a telomeric VSG locus downstream of unique, repeat sequences, and an independent promoter. Additional protein-coding sequences, known as “Expression Site Associated Genes (ESAGs)”, are also often present and are implicated in diverse, bloodstream-stage functions. Trypanosoma congolense is a related veterinary pathogen, also displaying VSG-mediated antigenic variation. A T. congolense VES has not been described, making it unclear if regulation of VSG expression is conserved between species. Here, we describe a conserved telomeric region associated with VSG loci from long-read DNA sequencing of two T. congolense strains, which consists of a distal repeat, conserved noncoding elements and other genes besides the VSG; although these are not orthologous to T. brucei ESAGs. Most conserved telomeric regions are associated with accessory minichromosomes, but the same structure may also be associated with megabase chromosomes. We propose that this region represents the T. congolense VES, and through comparison with T. brucei, we discuss the parallel evolution of antigenic switching mechanisms, and unique adaptation of the T. brucei VES for developmental regulation of bloodstream-stage genes. Hence, we provide a basis for understanding antigenic switching in T. congolense and the origins of the African trypanosome VES.
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Affiliation(s)
- Ali Hadi Abbas
- Centre for Genomic Research, Biosciences Building, Liverpool, United Kingdom.,Department of Pathology, Faculty of Veterinary Medicine, University of Kufa, Najaf, Iraq
| | - Sara Silva Pereira
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Simon D'Archivio
- School of Life Sciences, University of Nottingham, United Kingdom
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, United Kingdom
| | - Liam J Morrison
- Department of Infection and Immunity, The Roslin Institute, Easter Bush, Edinburgh, United Kingdom
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Alistair C Darby
- Centre for Genomic Research, Biosciences Building, Liverpool, United Kingdom
| | - Andrew P Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, United Kingdom
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